Sat Oct 7 23:29:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0051311 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0051311 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-904 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: 66074760 59175832 6898928 1758252 0 54158228 -/+ buffers/cache: 5017604 61057156 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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: 2017/10/07-21:29:49-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-904 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-6.0.0/0051311 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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/UCLA_2/0051311/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-6.0.0/0051311/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 23:29:52 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 23:30:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-904 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 23:30:04 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.17659 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17659/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.17659/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.17659/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 23:30:08 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.17659/nu0.mnc ./tmp.mri_nu_correct.mni.17659/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17659/0/ -iterations 1000 -distance 50 [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/] [2017-10-07 23:30:08] 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.17659/0/ ./tmp.mri_nu_correct.mni.17659/nu0.mnc ./tmp.mri_nu_correct.mni.17659/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 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: 43 CV of field change: 0.000994193 mri_convert ./tmp.mri_nu_correct.mni.17659/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.17659/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.17659/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 23:31:23 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 23:31:23 CEST 2017 Ended at Sat Oct 7 23:32:13 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 23:32:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7533, 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-6.0.0/0051311/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/talairach_avi.log TalAviQA: 0.97768 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 23:32:15 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-6.0.0/0051311/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-904 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 23:32:15 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.18752 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18752/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.18752/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.18752/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 23:32:18 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.18752/nu0.mnc ./tmp.mri_nu_correct.mni.18752/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18752/0/ [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/] [2017-10-07 23:32:18] 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.18752/0/ ./tmp.mri_nu_correct.mni.18752/nu0.mnc ./tmp.mri_nu_correct.mni.18752/nu1.imp Processing:.................................................................Done 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./tmp.mri_nu_correct.mni.18752/1/ [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/] [2017-10-07 23:33:13] 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.18752/1/ ./tmp.mri_nu_correct.mni.18752/nu1.mnc ./tmp.mri_nu_correct.mni.18752/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 Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 16 CV of field change: 0.00098563 mri_binarize --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18752/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-6.0.0/0051311/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18752/ones.mgz sysname Linux hostname tars-904 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.18752/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.18752/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.18752/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/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.18752/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/input.mean.dat sysname Linux hostname tars-904 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.18752/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.18752/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18752/ones.mgz --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/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.18752/ones.mgz --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/output.mean.dat sysname Linux hostname tars-904 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.18752/ones.mgz Loading ./tmp.mri_nu_correct.mni.18752/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.18752/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.18752/nu2.mnc ./tmp.mri_nu_correct.mni.18752/nu2.mnc mul 1.04259041581368729225 Saving result to './tmp.mri_nu_correct.mni.18752/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.18752/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.18752/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.18752/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 10 seconds. mapping (13, 111) to ( 3, 110) Sat Oct 7 23:34:44 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 23:34:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0.99551 -0.00649 -0.09109 2.72523; 0.06088 1.15020 0.24347 -5.52109; 0.08437 -0.28685 1.20325 -5.76160; 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 = 19 Starting OpenSpline(): npoints = 19 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 109 gm peak at 55 (55), valley at 25 (25) csf peak at 28, setting threshold to 46 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 110 gm peak at 55 (55), valley at 25 (25) csf peak at 28, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 12 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 23:36:59 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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=6.0 skull bounding box = (45, 55, 35) --> (216, 200, 211) using (102, 103, 123) as brain centroid... mean wm in atlas = 108, using box (81,85,101) --> (123, 120,144) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 6.1 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.577 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.470880 @ (-9.091, -9.091, -9.091) max log p = -4.352172 @ (4.545, -4.545, -4.545) max log p = -4.330606 @ (-2.273, 6.818, -2.273) max log p = -4.305599 @ (1.136, -1.136, 1.136) max log p = -4.289562 @ (-1.705, -0.568, 0.568) max log p = -4.289562 @ (0.000, 0.000, 0.000) Found translation: (-7.4, -8.5, -14.2): log p = -4.290 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.848, old_max_log_p =-4.290 (thresh=-4.3) 0.99144 -0.14882 -0.01959 18.62359; 0.14032 1.21519 0.15998 -79.52754; 0.00000 -0.15011 1.14016 -9.12227; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.823, old_max_log_p =-3.848 (thresh=-3.8) 0.91709 -0.13766 -0.01812 26.59247; 0.14955 1.27409 0.33049 -103.46049; -0.01969 -0.33049 1.19274 14.08657; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.813, old_max_log_p =-3.823 (thresh=-3.8) 0.98587 -0.14798 -0.01948 19.22125; 0.15084 1.30633 0.17198 -88.71935; 0.00000 -0.14926 1.13375 -7.54151; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.813, old_max_log_p =-3.813 (thresh=-3.8) 0.98587 -0.14798 -0.01948 19.22125; 0.15084 1.30633 0.17198 -88.71935; 0.00000 -0.14926 1.13375 -7.54151; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.731, old_max_log_p =-3.813 (thresh=-3.8) 0.97427 -0.06182 -0.00330 8.10079; 0.08319 1.25644 0.31863 -92.64512; -0.01532 -0.31844 1.12262 18.79496; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.719, old_max_log_p =-3.731 (thresh=-3.7) 0.99254 -0.06298 -0.00336 5.91127; 0.08364 1.26619 0.28173 -89.50504; -0.01235 -0.27196 1.11121 13.03175; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.719, old_max_log_p =-3.719 (thresh=-3.7) 1.00703 -0.11309 0.02718 5.66892; 0.11449 1.25435 0.20550 -84.08475; -0.03933 -0.18641 1.12676 3.91661; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.696, old_max_log_p =-3.719 (thresh=-3.7) 1.01070 -0.08697 0.00342 4.74484; 0.09650 1.24972 0.26105 -87.46809; -0.01955 -0.24966 1.11309 11.43538; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.690, old_max_log_p =-3.696 (thresh=-3.7) 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26096 1.10952 11.48164; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.689, old_max_log_p =-3.690 (thresh=-3.7) 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 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 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.689 (old=-4.577) transform before final EM align: 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 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 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 014: -log(p) = 4.2 tol 0.000000 final transform: 1.00889 -0.09280 -0.01695 7.91514; 0.10448 1.24545 0.26970 -88.96503; -0.00379 -0.26065 1.10822 11.59817; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 3121.175509 mri_em_register stimesec 7.953790 mri_em_register ru_maxrss 611708 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157528 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 330534 mri_em_register ru_nivcsw 7029 registration took 32 minutes and 59 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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=131 y=126 z=120 r=66 first estimation of the main basin volume: 1220453 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=108, y=116, z=89, Imax=255 CSF=20, 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=7610560721 voxels, voxel volume =1.000 = 7610560721 mmm3 = 7610560.512 cm3 done. PostAnalyze...Basin Prior 70 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=130,y=130, z=115, r=9258 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=47 , nb = 45657 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=40 , nb = -1034762496 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=27 , nb = -1049397912 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=50 , nb = -1078243316 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=46 , nb = 1074495890 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 1076229100 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 47, 35, 30, 50 after analyzing : 24, 35, 35, 38 RIGHT_CER before analyzing : 40, 33, 28, 56 after analyzing : 21, 33, 33, 38 LEFT_CER before analyzing : 27, 27, 29, 57 after analyzing : 27, 28, 29, 35 RIGHT_BRAIN before analyzing : 50, 35, 31, 48 after analyzing : 26, 35, 35, 38 LEFT_BRAIN before analyzing : 46, 35, 30, 50 after analyzing : 22, 35, 35, 38 OTHER before analyzing : 32, 59, 79, 95 after analyzing : 32, 72, 79, 77 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 67.912, std = 7.762 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.11, sigma = 7.13 after rotation: sse = 5.11, sigma = 7.13 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.64, its var is 7.68 before Erosion-Dilatation 3.85% of inacurate vertices after Erosion-Dilatation 6.52% 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...43 iterations mri_strip_skull: done peeling brain Brain Size = 1498102 voxels, voxel volume = 1.000 mm3 = 1498102 mmm3 = 1498.102 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 31.956141 mri_watershed stimesec 0.456930 mri_watershed ru_maxrss 818376 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211924 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2456 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 2115 mri_watershed ru_nivcsw 1291 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Oct 8 00:10:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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=21.0 skull bounding box = (56, 75, 51) --> (205, 186, 197) using (106, 112, 124) as brain centroid... mean wm in atlas = 107, using box (88,98,106) --> (124, 125,141) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 107 +- 6.0 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.185 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.904794 @ (-9.091, -9.091, -9.091) max log p = -3.764544 @ (4.545, -4.545, -4.545) max log p = -3.764544 @ (0.000, 0.000, 0.000) max log p = -3.759517 @ (1.136, 1.136, 1.136) max log p = -3.723667 @ (-1.705, 0.568, -0.568) max log p = -3.723667 @ (0.000, 0.000, 0.000) Found translation: (-5.1, -11.9, -13.1): log p = -3.724 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.393, old_max_log_p =-3.724 (thresh=-3.7) 0.99144 -0.14882 -0.01959 17.86489; 0.14032 1.21519 0.15998 -77.62984; 0.00000 -0.13885 1.05465 -1.32504; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.393, old_max_log_p =-3.393 (thresh=-3.4) 0.99144 -0.14882 -0.01959 17.86489; 0.14032 1.21519 0.15998 -77.62984; 0.00000 -0.13885 1.05465 -1.32504; 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=-3.231, old_max_log_p =-3.393 (thresh=-3.4) 0.95751 -0.11111 0.02399 12.46966; 0.10671 1.18514 0.22368 -73.13071; -0.04150 -0.22555 1.10131 13.81259; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.231, old_max_log_p =-3.231 (thresh=-3.2) 0.95751 -0.11111 0.02399 12.46966; 0.10671 1.18514 0.22368 -73.13071; -0.04150 -0.22555 1.10131 13.81259; 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=-3.206, old_max_log_p =-3.231 (thresh=-3.2) 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.206, old_max_log_p =-3.206 (thresh=-3.2) 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 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 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.206 (old=-4.185) transform before final EM align: 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 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 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000 final transform: 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1264.877709 mri_em_register stimesec 2.041689 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 158990 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 143 mri_em_register ru_nivcsw 2284 registration took 10 minutes and 52 seconds. #-------------------------------------- #@# CA Normalize Sun Oct 8 00:21:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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=21.0 skull bounding box = (56, 75, 51) --> (205, 186, 197) using (106, 112, 124) as brain centroid... mean wm in atlas = 107, using box (88,98,106) --> (124, 125,141) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 107 +- 6.0 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 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 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 (129, 73, 46) --> (201, 168, 193) Left_Cerebral_White_Matter: limiting intensities to 101.0 --> 132.0 0 of 68 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 77, 45) --> (132, 173, 194) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 50 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 150, 71) --> (187, 182, 119) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 150, 69) --> (135, 187, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 138, 103) --> (154, 197, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 13 (0.0%) samples deleted using 156 total control points for intensity normalization... bias field = 0.934 +- 0.058 0 of 156 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 73, 46) --> (201, 168, 193) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 145 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 77, 45) --> (132, 173, 194) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 7 of 136 (5.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 150, 71) --> (187, 182, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 79 (8.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 150, 69) --> (135, 187, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 39 of 56 (69.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 138, 103) --> (154, 197, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 59 of 97 (60.8%) samples deleted using 513 total control points for intensity normalization... bias field = 1.000 +- 0.061 0 of 395 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 73, 46) --> (201, 168, 193) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 243 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 77, 45) --> (132, 173, 194) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 223 (2.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 150, 71) --> (187, 182, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 28 of 92 (30.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 150, 69) --> (135, 187, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 65 of 95 (68.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 138, 103) --> (154, 197, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 126 of 198 (63.6%) samples deleted using 851 total control points for intensity normalization... bias field = 0.993 +- 0.050 0 of 625 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 45 seconds. #-------------------------------------- #@# CA Reg Sun Oct 8 00:23:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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) = 1.31 (predicted orig area = 6.1) 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=0.843, neg=0, invalid=762 0001: dt=186.891676, rms=0.786 (6.672%), neg=0, invalid=762 0002: dt=221.952000, rms=0.774 (1.504%), neg=0, invalid=762 0003: dt=295.936000, rms=0.763 (1.440%), neg=0, invalid=762 0004: dt=154.613861, rms=0.758 (0.678%), neg=0, invalid=762 0005: dt=517.888000, rms=0.747 (1.531%), neg=0, invalid=762 0006: dt=129.472000, rms=0.743 (0.480%), neg=0, invalid=762 0007: dt=1183.744000, rms=0.731 (1.590%), neg=0, invalid=762 0008: dt=110.976000, rms=0.727 (0.511%), neg=0, invalid=762 0009: dt=1479.680000, rms=0.721 (0.890%), neg=0, invalid=762 0010: dt=221.952000, rms=0.717 (0.571%), neg=0, invalid=762 0011: dt=295.936000, rms=0.716 (0.175%), neg=0, invalid=762 0012: dt=295.936000, rms=0.715 (0.149%), neg=0, invalid=762 0013: dt=295.936000, rms=0.712 (0.353%), neg=0, invalid=762 0014: dt=295.936000, rms=0.710 (0.263%), neg=0, invalid=762 0015: dt=295.936000, rms=0.707 (0.468%), neg=0, invalid=762 0016: dt=295.936000, rms=0.703 (0.475%), neg=0, invalid=762 0017: dt=295.936000, rms=0.701 (0.296%), neg=0, invalid=762 0018: dt=295.936000, rms=0.698 (0.417%), neg=0, invalid=762 0019: dt=295.936000, rms=0.696 (0.383%), neg=0, invalid=762 0020: dt=295.936000, rms=0.694 (0.204%), neg=0, invalid=762 0021: dt=295.936000, rms=0.692 (0.359%), neg=0, invalid=762 0022: dt=295.936000, rms=0.690 (0.238%), neg=0, invalid=762 0023: dt=295.936000, rms=0.689 (0.151%), neg=0, invalid=762 0024: dt=295.936000, rms=0.688 (0.238%), neg=0, invalid=762 0025: dt=295.936000, rms=0.686 (0.215%), neg=0, invalid=762 0026: dt=295.936000, rms=0.685 (0.164%), neg=0, invalid=762 0027: dt=295.936000, rms=0.684 (0.195%), neg=0, invalid=762 0028: dt=295.936000, rms=0.682 (0.178%), neg=0, invalid=762 0029: dt=295.936000, rms=0.681 (0.126%), neg=0, invalid=762 0030: dt=295.936000, rms=0.680 (0.173%), neg=0, invalid=762 0031: dt=295.936000, rms=0.679 (0.184%), neg=0, invalid=762 0032: dt=295.936000, rms=0.678 (0.126%), neg=0, invalid=762 0033: dt=295.936000, rms=0.677 (0.116%), neg=0, invalid=762 0034: dt=295.936000, rms=0.676 (0.154%), neg=0, invalid=762 0035: dt=295.936000, rms=0.676 (0.095%), neg=0, invalid=762 0036: dt=295.936000, rms=0.675 (0.088%), neg=0, invalid=762 0037: dt=129.472000, rms=0.675 (0.026%), neg=0, invalid=762 0038: dt=129.472000, rms=0.675 (0.001%), neg=0, invalid=762 0039: dt=129.472000, rms=0.675 (0.006%), neg=0, invalid=762 0040: dt=129.472000, rms=0.675 (0.015%), neg=0, invalid=762 0041: dt=129.472000, rms=0.675 (0.015%), neg=0, invalid=762 0042: dt=129.472000, rms=0.675 (0.019%), neg=0, invalid=762 0043: dt=129.472000, rms=0.674 (0.017%), neg=0, invalid=762 0044: dt=129.472000, rms=0.674 (0.020%), neg=0, invalid=762 0045: dt=129.472000, rms=0.674 (0.021%), neg=0, invalid=762 0046: dt=129.472000, rms=0.674 (0.023%), neg=0, invalid=762 0047: dt=129.472000, rms=0.674 (0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=762 0048: dt=110.976000, rms=0.674 (0.150%), neg=0, invalid=762 0049: dt=295.936000, rms=0.673 (0.044%), neg=0, invalid=762 0050: dt=295.936000, rms=0.673 (0.070%), neg=0, invalid=762 0051: dt=295.936000, rms=0.672 (0.087%), neg=0, invalid=762 0052: dt=295.936000, rms=0.672 (0.069%), neg=0, invalid=762 0053: dt=295.936000, rms=0.671 (0.071%), neg=0, invalid=762 0054: dt=295.936000, rms=0.671 (0.085%), neg=0, invalid=762 0055: dt=295.936000, rms=0.670 (0.070%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0056: dt=144.941176, rms=0.674 (0.697%), neg=0, invalid=762 0057: dt=248.832000, rms=0.668 (0.923%), neg=0, invalid=762 0058: dt=69.304813, rms=0.664 (0.622%), neg=0, invalid=762 0059: dt=145.152000, rms=0.661 (0.380%), neg=0, invalid=762 0060: dt=121.081081, rms=0.659 (0.424%), neg=0, invalid=762 0061: dt=36.288000, rms=0.658 (0.175%), neg=0, invalid=762 0062: dt=36.288000, rms=0.657 (0.108%), neg=0, invalid=762 0063: dt=36.288000, rms=0.656 (0.162%), neg=0, invalid=762 0064: dt=36.288000, rms=0.654 (0.233%), neg=0, invalid=762 0065: dt=36.288000, rms=0.652 (0.310%), neg=0, invalid=762 0066: dt=36.288000, rms=0.650 (0.343%), neg=0, invalid=762 0067: dt=36.288000, rms=0.648 (0.332%), neg=0, invalid=762 0068: dt=36.288000, rms=0.646 (0.326%), neg=0, invalid=762 0069: dt=36.288000, rms=0.644 (0.331%), neg=0, invalid=762 0070: dt=36.288000, rms=0.642 (0.318%), neg=0, invalid=762 0071: dt=36.288000, rms=0.640 (0.305%), neg=0, invalid=762 0072: dt=36.288000, rms=0.638 (0.279%), neg=0, invalid=762 0073: dt=36.288000, rms=0.636 (0.255%), neg=0, invalid=762 0074: dt=36.288000, rms=0.635 (0.223%), neg=0, invalid=762 0075: dt=36.288000, rms=0.633 (0.198%), neg=0, invalid=762 0076: dt=36.288000, rms=0.632 (0.192%), neg=0, invalid=762 0077: dt=36.288000, rms=0.631 (0.189%), neg=0, invalid=762 0078: dt=36.288000, rms=0.630 (0.170%), neg=0, invalid=762 0079: dt=36.288000, rms=0.629 (0.150%), neg=0, invalid=762 0080: dt=36.288000, rms=0.628 (0.138%), neg=0, invalid=762 0081: dt=36.288000, rms=0.627 (0.118%), neg=0, invalid=762 0082: dt=36.288000, rms=0.627 (0.109%), neg=0, invalid=762 0083: dt=145.152000, rms=0.626 (0.048%), neg=0, invalid=762 0084: dt=145.152000, rms=0.626 (-0.059%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=762 0085: dt=82.944000, rms=0.626 (0.242%), neg=0, invalid=762 0086: dt=103.680000, rms=0.625 (0.104%), neg=0, invalid=762 0087: dt=103.680000, rms=0.625 (-0.121%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0088: dt=0.700000, rms=0.650 (0.114%), neg=0, invalid=762 0089: dt=0.700000, rms=0.650 (0.003%), neg=0, invalid=762 0090: dt=0.700000, rms=0.650 (0.000%), neg=0, invalid=762 0091: dt=0.700000, rms=0.650 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0092: dt=0.000000, rms=0.650 (0.113%), neg=0, invalid=762 0093: dt=0.000000, rms=0.650 (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=0.725, neg=0, invalid=762 0094: dt=5.647416, rms=0.704 (2.859%), neg=0, invalid=762 0095: dt=3.178571, rms=0.703 (0.143%), neg=0, invalid=762 0096: dt=3.178571, rms=0.703 (-0.048%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=762 0097: dt=0.000000, rms=0.703 (0.083%), neg=0, invalid=762 0098: dt=0.000000, rms=0.703 (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=0.779, neg=0, invalid=762 0099: dt=1.280000, rms=0.776 (0.430%), neg=0, invalid=762 0100: dt=2.431655, rms=0.768 (0.975%), neg=0, invalid=762 0101: dt=0.320000, rms=0.768 (0.024%), neg=0, invalid=762 0102: dt=0.320000, rms=0.768 (0.024%), neg=0, invalid=762 0103: dt=0.320000, rms=0.767 (0.030%), neg=0, invalid=762 0104: dt=0.320000, rms=0.767 (0.045%), neg=0, invalid=762 0105: dt=0.320000, rms=0.766 (0.082%), neg=0, invalid=762 0106: dt=0.320000, rms=0.766 (0.110%), neg=0, invalid=762 0107: dt=0.320000, rms=0.765 (0.091%), neg=0, invalid=762 0108: dt=0.320000, rms=0.765 (0.027%), neg=0, invalid=762 0109: dt=1.024000, rms=0.765 (0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0110: dt=1.820896, rms=0.762 (0.395%), neg=0, invalid=762 0111: dt=0.000000, rms=0.762 (-0.001%), neg=0, invalid=762 0112: dt=0.100000, rms=0.762 (-0.003%), 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=0.718, neg=0, invalid=762 0113: dt=0.975596, rms=0.694 (3.456%), neg=0, invalid=762 0114: dt=0.096000, rms=0.692 (0.167%), neg=0, invalid=762 0115: dt=0.096000, rms=0.692 (-0.134%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.693, neg=0, invalid=762 0116: dt=0.028000, rms=0.692 (0.103%), neg=0, invalid=762 0117: dt=0.001750, rms=0.692 (0.000%), neg=0, invalid=762 0118: dt=0.001750, rms=0.692 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.21687 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (985 voxels, overlap=0.019) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (985 voxels, peak = 7), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.14998 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (800 voxels, overlap=0.148) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (800 voxels, peak = 7), gca=7.0 gca peak = 0.26829 (96) mri peak = 0.07790 (88) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (664 voxels, overlap=0.718) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (664 voxels, peak = 91), gca=90.7 gca peak = 0.20183 (93) mri peak = 0.08094 (89) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (578 voxels, overlap=1.005) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (578 voxels, peak = 88), gca=87.9 gca peak = 0.21683 (55) mri peak = 0.08208 (56) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.11605 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (475 voxels, overlap=0.963) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (475 voxels, peak = 54), gca=54.2 gca peak = 0.11430 (101) mri peak = 0.07889 (105) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (46529 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (46529 voxels, peak = 108), gca=107.6 gca peak = 0.12076 (102) mri peak = 0.07761 (106) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (46020 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (46020 voxels, peak = 109), gca=108.6 gca peak = 0.14995 (59) mri peak = 0.05668 (50) Left_Cerebral_Cortex (3): linear fit = 0.87 x + 0.0 (13708 voxels, overlap=0.316) Left_Cerebral_Cortex (3): linear fit = 0.87 x + 0.0 (13708 voxels, peak = 51), gca=51.0 gca peak = 0.15082 (58) mri peak = 0.05744 (50) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (13402 voxels, overlap=0.615) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (13402 voxels, peak = 52), gca=51.9 gca peak = 0.14161 (67) mri peak = 0.10451 (64) Right_Caudate (50): linear fit = 0.93 x + 0.0 (540 voxels, overlap=0.525) Right_Caudate (50): linear fit = 0.93 x + 0.0 (540 voxels, peak = 62), gca=62.0 gca peak = 0.15243 (71) mri peak = 0.09446 (67) Left_Caudate (11): linear fit = 0.90 x + 0.0 (604 voxels, overlap=0.540) Left_Caudate (11): linear fit = 0.90 x + 0.0 (604 voxels, peak = 64), gca=64.3 gca peak = 0.13336 (57) mri peak = 0.04103 (50) Left_Cerebellum_Cortex (8): linear fit = 0.93 x + 0.0 (12771 voxels, overlap=0.813) Left_Cerebellum_Cortex (8): linear fit = 0.93 x + 0.0 (12771 voxels, peak = 53), gca=52.7 gca peak = 0.13252 (56) mri peak = 0.04318 (55) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13347 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13347 voxels, peak = 53), gca=52.9 gca peak = 0.18181 (84) mri peak = 0.07788 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5369 voxels, overlap=0.633) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5369 voxels, peak = 90), gca=90.3 gca peak = 0.20573 (83) mri peak = 0.06807 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4956 voxels, overlap=0.872) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4956 voxels, peak = 85), gca=85.1 gca peak = 0.21969 (57) mri peak = 0.11021 (54) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (267 voxels, overlap=0.992) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (267 voxels, peak = 54), gca=53.9 gca peak = 0.39313 (56) mri peak = 0.10429 (56) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (372 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (372 voxels, peak = 55), gca=55.2 gca peak = 0.14181 (85) mri peak = 0.06244 (82) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4412 voxels, overlap=0.969) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4412 voxels, peak = 81), gca=81.2 gca peak = 0.11978 (83) mri peak = 0.06269 (81) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3664 voxels, overlap=0.923) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3664 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.06625 (73) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1887 voxels, overlap=0.752) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1887 voxels, peak = 74), gca=73.9 gca peak = 0.14159 (79) mri peak = 0.07276 (73) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2031 voxels, overlap=0.888) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2031 voxels, peak = 74), gca=73.9 gca peak = 0.10025 (80) mri peak = 0.09548 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9084 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9084 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06018 (90) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (780 voxels, overlap=0.728) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (780 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.07684 (91) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1151 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1151 voxels, peak = 93), gca=93.0 gca peak = 0.20494 (23) mri peak = 0.19780 (13) gca peak = 0.15061 (21) mri peak = 0.17648 (12) Fourth_Ventricle (15): linear fit = 0.61 x + 0.0 (326 voxels, overlap=0.293) Fourth_Ventricle (15): linear fit = 0.61 x + 0.0 (326 voxels, peak = 13), gca=12.7 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 0.94 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 0.42 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=0.730, neg=0, invalid=762 0119: dt=129.472000, rms=0.723 (0.985%), neg=0, invalid=762 0120: dt=134.826667, rms=0.720 (0.409%), neg=0, invalid=762 0121: dt=129.472000, rms=0.719 (0.188%), neg=0, invalid=762 0122: dt=129.472000, rms=0.717 (0.199%), neg=0, invalid=762 0123: dt=129.472000, rms=0.716 (0.126%), neg=0, invalid=762 0124: dt=369.920000, rms=0.715 (0.236%), neg=0, invalid=762 0125: dt=73.984000, rms=0.714 (0.126%), neg=0, invalid=762 0126: dt=1775.616000, rms=0.710 (0.510%), neg=0, invalid=762 0127: dt=92.480000, rms=0.710 (0.055%), neg=0, invalid=762 0128: dt=517.888000, rms=0.708 (0.208%), neg=0, invalid=762 0129: dt=73.984000, rms=0.708 (0.045%), neg=0, invalid=762 0130: dt=73.984000, rms=0.708 (0.024%), neg=0, invalid=762 0131: dt=73.984000, rms=0.707 (0.040%), neg=0, invalid=762 0132: dt=73.984000, rms=0.707 (0.055%), neg=0, invalid=762 0133: dt=73.984000, rms=0.706 (0.069%), neg=0, invalid=762 0134: dt=73.984000, rms=0.706 (0.079%), neg=0, invalid=762 0135: dt=73.984000, rms=0.705 (0.083%), neg=0, invalid=762 0136: dt=73.984000, rms=0.705 (0.079%), neg=0, invalid=762 0137: dt=73.984000, rms=0.704 (0.075%), neg=0, invalid=762 0138: dt=73.984000, rms=0.704 (0.072%), neg=0, invalid=762 0139: dt=73.984000, rms=0.703 (0.068%), neg=0, invalid=762 0140: dt=73.984000, rms=0.703 (0.068%), neg=0, invalid=762 0141: dt=73.984000, rms=0.702 (0.073%), neg=0, invalid=762 0142: dt=73.984000, rms=0.702 (0.080%), neg=0, invalid=762 0143: dt=73.984000, rms=0.701 (0.074%), neg=0, invalid=762 0144: dt=73.984000, rms=0.701 (0.073%), neg=0, invalid=762 0145: dt=73.984000, rms=0.700 (0.069%), neg=0, invalid=762 0146: dt=73.984000, rms=0.700 (0.062%), neg=0, invalid=762 0147: dt=73.984000, rms=0.699 (0.065%), neg=0, invalid=762 0148: dt=73.984000, rms=0.699 (0.062%), neg=0, invalid=762 0149: dt=73.984000, rms=0.698 (0.062%), neg=0, invalid=762 0150: dt=73.984000, rms=0.698 (0.061%), neg=0, invalid=762 0151: dt=73.984000, rms=0.698 (0.062%), neg=0, invalid=762 0152: dt=73.984000, rms=0.697 (0.063%), neg=0, invalid=762 0153: dt=73.984000, rms=0.697 (0.065%), neg=0, invalid=762 0154: dt=73.984000, rms=0.696 (0.062%), neg=0, invalid=762 0155: dt=73.984000, rms=0.696 (0.058%), neg=0, invalid=762 0156: dt=73.984000, rms=0.695 (0.053%), neg=0, invalid=762 0157: dt=73.984000, rms=0.695 (0.048%), neg=0, invalid=762 0158: dt=73.984000, rms=0.695 (0.047%), neg=0, invalid=762 0159: dt=73.984000, rms=0.694 (0.049%), neg=0, invalid=762 0160: dt=73.984000, rms=0.694 (0.046%), neg=0, invalid=762 0161: dt=73.984000, rms=0.694 (0.041%), neg=0, invalid=762 0162: dt=73.984000, rms=0.694 (0.038%), neg=0, invalid=762 0163: dt=73.984000, rms=0.693 (0.038%), neg=0, invalid=762 0164: dt=73.984000, rms=0.693 (0.037%), neg=0, invalid=762 0165: dt=73.984000, rms=0.693 (0.035%), neg=0, invalid=762 0166: dt=73.984000, rms=0.693 (0.032%), neg=0, invalid=762 0167: dt=73.984000, rms=0.692 (0.029%), neg=0, invalid=762 0168: dt=73.984000, rms=0.692 (0.029%), neg=0, invalid=762 0169: dt=73.984000, rms=0.692 (0.031%), neg=0, invalid=762 0170: dt=73.984000, rms=0.692 (0.032%), neg=0, invalid=762 0171: dt=73.984000, rms=0.692 (0.031%), neg=0, invalid=762 0172: dt=73.984000, rms=0.691 (0.030%), neg=0, invalid=762 0173: dt=73.984000, rms=0.691 (0.029%), neg=0, invalid=762 0174: dt=73.984000, rms=0.691 (0.028%), neg=0, invalid=762 0175: dt=73.984000, rms=0.691 (0.028%), neg=0, invalid=762 0176: dt=73.984000, rms=0.691 (0.029%), neg=0, invalid=762 0177: dt=73.984000, rms=0.690 (0.031%), neg=0, invalid=762 0178: dt=73.984000, rms=0.690 (0.032%), neg=0, invalid=762 0179: dt=73.984000, rms=0.690 (0.030%), neg=0, invalid=762 0180: dt=73.984000, rms=0.690 (0.029%), neg=0, invalid=762 0181: dt=73.984000, rms=0.690 (0.028%), neg=0, invalid=762 0182: dt=73.984000, rms=0.689 (0.029%), neg=0, invalid=762 0183: dt=73.984000, rms=0.689 (0.030%), neg=0, invalid=762 0184: dt=73.984000, rms=0.689 (0.029%), neg=0, invalid=762 0185: dt=73.984000, rms=0.689 (0.026%), neg=0, invalid=762 0186: dt=73.984000, rms=0.689 (0.023%), neg=0, invalid=762 0187: dt=73.984000, rms=0.688 (0.022%), neg=0, invalid=762 0188: dt=8286.208000, rms=0.687 (0.214%), neg=0, invalid=762 0189: dt=55.488000, rms=0.687 (0.034%), neg=0, invalid=762 0190: dt=55.488000, rms=0.687 (0.002%), neg=0, invalid=762 0191: dt=55.488000, rms=0.687 (-0.016%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=762 0192: dt=129.472000, rms=0.686 (0.234%), neg=0, invalid=762 0193: dt=369.920000, rms=0.685 (0.099%), neg=0, invalid=762 0194: dt=129.472000, rms=0.685 (0.084%), neg=0, invalid=762 0195: dt=129.472000, rms=0.685 (0.028%), neg=0, invalid=762 0196: dt=129.472000, rms=0.684 (0.031%), neg=0, invalid=762 0197: dt=129.472000, rms=0.684 (0.038%), neg=0, invalid=762 0198: dt=129.472000, rms=0.684 (0.052%), neg=0, invalid=762 0199: dt=129.472000, rms=0.683 (0.051%), neg=0, invalid=762 0200: dt=129.472000, rms=0.683 (0.061%), neg=0, invalid=762 0201: dt=129.472000, rms=0.683 (0.059%), neg=0, invalid=762 0202: dt=129.472000, rms=0.682 (0.053%), neg=0, invalid=762 0203: dt=129.472000, rms=0.682 (0.047%), neg=0, invalid=762 0204: dt=129.472000, rms=0.682 (0.038%), neg=0, invalid=762 0205: dt=129.472000, rms=0.681 (0.040%), neg=0, invalid=762 0206: dt=129.472000, rms=0.681 (0.038%), neg=0, invalid=762 0207: dt=129.472000, rms=0.681 (0.031%), neg=0, invalid=762 0208: dt=129.472000, rms=0.681 (0.024%), neg=0, invalid=762 0209: dt=129.472000, rms=0.680 (0.027%), neg=0, invalid=762 0210: dt=129.472000, rms=0.680 (0.028%), neg=0, invalid=762 0211: dt=129.472000, rms=0.680 (0.027%), neg=0, invalid=762 0212: dt=129.472000, rms=0.680 (0.025%), neg=0, invalid=762 0213: dt=129.472000, rms=0.680 (0.024%), neg=0, invalid=762 0214: dt=517.888000, rms=0.680 (0.014%), neg=0, invalid=762 0215: dt=517.888000, rms=0.680 (-0.246%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.682, neg=0, invalid=762 0216: dt=107.354839, rms=0.677 (0.662%), neg=0, invalid=762 0217: dt=116.822535, rms=0.672 (0.685%), neg=0, invalid=762 0218: dt=36.288000, rms=0.670 (0.411%), neg=0, invalid=762 0219: dt=497.664000, rms=0.661 (1.318%), neg=0, invalid=762 0220: dt=70.268041, rms=0.655 (0.904%), neg=0, invalid=762 0221: dt=36.288000, rms=0.653 (0.234%), neg=0, invalid=762 0222: dt=580.608000, rms=0.647 (1.005%), neg=0, invalid=762 0223: dt=69.041575, rms=0.642 (0.659%), neg=0, invalid=762 0224: dt=36.288000, rms=0.642 (0.064%), neg=0, invalid=762 0225: dt=580.608000, rms=0.639 (0.431%), neg=0, invalid=762 0226: dt=70.479574, rms=0.636 (0.451%), neg=0, invalid=762 0227: dt=36.288000, rms=0.636 (0.065%), neg=0, invalid=762 0228: dt=580.608000, rms=0.633 (0.424%), neg=0, invalid=762 0229: dt=65.647525, rms=0.631 (0.361%), neg=0, invalid=762 0230: dt=36.288000, rms=0.631 (0.029%), neg=0, invalid=762 0231: dt=36.288000, rms=0.631 (0.029%), neg=0, invalid=762 0232: dt=36.288000, rms=0.630 (0.053%), neg=0, invalid=762 0233: dt=36.288000, rms=0.630 (0.075%), neg=0, invalid=762 0234: dt=36.288000, rms=0.629 (0.095%), neg=0, invalid=762 0235: dt=36.288000, rms=0.628 (0.118%), neg=0, invalid=762 0236: dt=36.288000, rms=0.628 (0.132%), neg=0, invalid=762 0237: dt=36.288000, rms=0.627 (0.146%), neg=0, invalid=762 0238: dt=36.288000, rms=0.626 (0.155%), neg=0, invalid=762 0239: dt=36.288000, rms=0.625 (0.164%), neg=0, invalid=762 0240: dt=36.288000, rms=0.625 (0.030%), neg=0, invalid=762 0241: dt=36.288000, rms=0.624 (0.050%), neg=0, invalid=762 0242: dt=36.288000, rms=0.624 (0.062%), neg=0, invalid=762 0243: dt=36.288000, rms=0.624 (0.017%), neg=0, invalid=762 0244: dt=36.288000, rms=0.624 (0.020%), neg=0, invalid=762 0245: dt=1.134000, rms=0.624 (0.001%), neg=0, invalid=762 0246: dt=0.141750, rms=0.624 (0.000%), neg=0, invalid=762 0247: dt=0.035437, rms=0.624 (0.000%), neg=0, invalid=762 0248: dt=0.017719, rms=0.624 (0.000%), neg=0, invalid=762 0249: dt=0.000069, rms=0.624 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.625, neg=0, invalid=762 0250: dt=145.152000, rms=0.620 (0.751%), neg=0, invalid=762 0251: dt=36.288000, rms=0.619 (0.119%), neg=0, invalid=762 0252: dt=331.776000, rms=0.618 (0.239%), neg=0, invalid=762 0253: dt=36.288000, rms=0.617 (0.162%), neg=0, invalid=762 0254: dt=145.152000, rms=0.616 (0.125%), neg=0, invalid=762 0255: dt=82.944000, rms=0.616 (0.053%), neg=0, invalid=762 0256: dt=145.152000, rms=0.615 (0.106%), neg=0, invalid=762 0257: dt=36.288000, rms=0.615 (0.030%), neg=0, invalid=762 0258: dt=36.288000, rms=0.615 (0.022%), neg=0, invalid=762 0259: dt=36.288000, rms=0.615 (0.040%), neg=0, invalid=762 0260: dt=36.288000, rms=0.614 (0.059%), neg=0, invalid=762 0261: dt=36.288000, rms=0.614 (0.074%), neg=0, invalid=762 0262: dt=36.288000, rms=0.613 (0.086%), neg=0, invalid=762 0263: dt=36.288000, rms=0.613 (0.091%), neg=0, invalid=762 0264: dt=36.288000, rms=0.612 (0.094%), neg=0, invalid=762 0265: dt=36.288000, rms=0.612 (0.094%), neg=0, invalid=762 0266: dt=36.288000, rms=0.611 (0.095%), neg=0, invalid=762 0267: dt=36.288000, rms=0.610 (0.099%), neg=0, invalid=762 0268: dt=36.288000, rms=0.610 (0.016%), neg=0, invalid=762 0269: dt=36.288000, rms=0.610 (0.027%), neg=0, invalid=762 0270: dt=36.288000, rms=0.610 (0.038%), neg=0, invalid=762 0271: dt=36.288000, rms=0.610 (0.048%), neg=0, invalid=762 0272: dt=36.288000, rms=0.609 (0.053%), neg=0, invalid=762 0273: dt=36.288000, rms=0.609 (0.061%), neg=0, invalid=762 0274: dt=36.288000, rms=0.608 (0.066%), neg=0, invalid=762 0275: dt=36.288000, rms=0.608 (0.068%), neg=0, invalid=762 0276: dt=36.288000, rms=0.608 (0.072%), neg=0, invalid=762 0277: dt=36.288000, rms=0.607 (0.078%), neg=0, invalid=762 0278: dt=36.288000, rms=0.607 (0.080%), neg=0, invalid=762 0279: dt=36.288000, rms=0.606 (0.082%), neg=0, invalid=762 0280: dt=36.288000, rms=0.606 (0.010%), neg=0, invalid=762 0281: dt=18.144000, rms=0.606 (0.005%), neg=0, invalid=762 0282: dt=2.268000, rms=0.606 (0.001%), neg=0, invalid=762 0283: dt=0.283500, rms=0.606 (0.000%), neg=0, invalid=762 0284: dt=0.141750, rms=0.606 (0.000%), neg=0, invalid=762 0285: dt=0.070875, rms=0.606 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.614, neg=0, invalid=762 0286: dt=87.183673, rms=0.602 (1.826%), neg=0, invalid=762 0287: dt=2.800000, rms=0.602 (0.154%), neg=0, invalid=762 0288: dt=2.800000, rms=0.601 (0.145%), neg=0, invalid=762 0289: dt=0.010937, rms=0.601 (0.002%), neg=0, invalid=762 0290: dt=0.010937, rms=0.601 (0.001%), neg=0, invalid=762 0291: dt=0.002734, rms=0.601 (0.000%), neg=0, invalid=762 0292: dt=0.001367, rms=0.601 (0.000%), neg=0, invalid=762 0293: dt=0.000684, rms=0.601 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0294: dt=44.800000, rms=0.589 (2.188%), neg=0, invalid=762 0295: dt=58.140845, rms=0.584 (0.849%), neg=0, invalid=762 0296: dt=31.888889, rms=0.579 (0.714%), neg=0, invalid=762 0297: dt=38.400000, rms=0.577 (0.485%), neg=0, invalid=762 0298: dt=32.000000, rms=0.574 (0.415%), neg=0, invalid=762 0299: dt=32.000000, rms=0.572 (0.363%), neg=0, invalid=762 0300: dt=11.200000, rms=0.571 (0.196%), neg=0, invalid=762 0301: dt=11.200000, rms=0.570 (0.125%), neg=0, invalid=762 0302: dt=2.800000, rms=0.570 (0.031%), neg=0, invalid=762 0303: dt=2.800000, rms=0.570 (0.026%), neg=0, invalid=762 0304: dt=1.400000, rms=0.570 (0.013%), neg=0, invalid=762 0305: dt=0.700000, rms=0.570 (0.006%), neg=0, invalid=762 0306: dt=0.043750, rms=0.570 (0.000%), neg=0, invalid=762 0307: dt=0.005469, rms=0.570 (0.000%), neg=0, invalid=762 0308: dt=0.000684, rms=0.570 (0.000%), neg=0, invalid=762 0309: dt=0.000342, rms=0.570 (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=0.589, neg=0, invalid=762 0310: dt=7.144033, rms=0.586 (0.455%), neg=0, invalid=762 0311: dt=12.571429, rms=0.584 (0.261%), neg=0, invalid=762 0312: dt=16.128000, rms=0.582 (0.459%), neg=0, invalid=762 0313: dt=4.032000, rms=0.581 (0.088%), neg=0, invalid=762 0314: dt=1.008000, rms=0.581 (0.018%), neg=0, invalid=762 0315: dt=0.252000, rms=0.581 (0.005%), neg=0, invalid=762 0316: dt=0.063000, rms=0.581 (0.001%), neg=0, invalid=762 0317: dt=0.003938, rms=0.581 (0.000%), neg=0, invalid=762 0318: dt=0.002813, rms=0.581 (0.000%), neg=0, invalid=762 0319: dt=0.000246, rms=0.581 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.582, neg=0, invalid=762 0320: dt=11.520000, rms=0.580 (0.368%), neg=0, invalid=762 0321: dt=16.128000, rms=0.579 (0.090%), neg=0, invalid=762 0322: dt=16.128000, rms=0.578 (0.211%), neg=0, invalid=762 0323: dt=10.514286, rms=0.578 (0.042%), neg=0, invalid=762 0324: dt=10.514286, rms=0.577 (0.137%), neg=0, invalid=762 0325: dt=10.514286, rms=0.577 (0.060%), neg=0, invalid=762 0326: dt=10.514286, rms=0.576 (0.159%), neg=0, invalid=762 0327: dt=10.514286, rms=0.575 (0.084%), neg=0, invalid=762 0328: dt=10.514286, rms=0.575 (0.128%), neg=0, invalid=762 0329: dt=10.514286, rms=0.574 (0.034%), neg=0, invalid=762 0330: dt=10.514286, rms=0.574 (0.110%), neg=0, invalid=762 0331: dt=10.514286, rms=0.573 (0.149%), neg=0, invalid=762 0332: dt=10.514286, rms=0.572 (0.162%), neg=0, invalid=762 0333: dt=10.514286, rms=0.571 (0.168%), neg=0, invalid=762 0334: dt=10.514286, rms=0.570 (0.189%), neg=0, invalid=762 0335: dt=10.514286, rms=0.569 (0.155%), neg=0, invalid=762 0336: dt=10.514286, rms=0.568 (0.131%), neg=0, invalid=762 0337: dt=10.514286, rms=0.568 (0.015%), neg=0, invalid=762 0338: dt=10.514286, rms=0.568 (-0.012%), neg=0, invalid=762 0339: dt=4.032000, rms=0.568 (0.005%), neg=0, invalid=762 0340: dt=8.000000, rms=0.568 (0.007%), neg=0, invalid=762 0341: dt=16.128000, rms=0.568 (0.009%), neg=0, invalid=762 0342: dt=3.456000, rms=0.568 (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=0.587, neg=0, invalid=762 0343: dt=0.000000, rms=0.586 (0.164%), neg=0, invalid=762 0344: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762 0345: dt=0.100000, rms=0.586 (-0.180%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.587, neg=0, invalid=762 0346: dt=0.000000, rms=0.586 (0.164%), neg=0, invalid=762 0347: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762 0348: dt=0.100000, rms=0.586 (-0.164%), 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=0.557, neg=0, invalid=762 0349: dt=0.384000, rms=0.540 (2.990%), neg=0, invalid=762 0350: dt=0.448000, rms=0.534 (1.223%), neg=0, invalid=762 0351: dt=0.448000, rms=0.531 (0.516%), neg=0, invalid=762 0352: dt=0.448000, rms=0.529 (0.320%), neg=0, invalid=762 0353: dt=0.448000, rms=0.528 (0.246%), neg=0, invalid=762 0354: dt=0.448000, rms=0.527 (0.170%), neg=0, invalid=762 0355: dt=0.448000, rms=0.526 (0.155%), neg=0, invalid=762 0356: dt=0.448000, rms=0.526 (0.101%), neg=0, invalid=762 0357: dt=0.448000, rms=0.525 (0.111%), neg=0, invalid=762 0358: dt=0.448000, rms=0.525 (0.068%), neg=0, invalid=762 0359: dt=0.448000, rms=0.524 (0.084%), neg=0, invalid=762 0360: dt=0.448000, rms=0.524 (0.045%), neg=0, invalid=762 0361: dt=0.448000, rms=0.524 (0.067%), neg=0, invalid=762 0362: dt=0.448000, rms=0.523 (0.091%), neg=0, invalid=762 0363: dt=0.224000, rms=0.523 (0.019%), neg=0, invalid=762 0364: dt=0.224000, rms=0.523 (0.045%), neg=0, invalid=762 0365: dt=0.224000, rms=0.523 (0.020%), neg=0, invalid=762 0366: dt=0.224000, rms=0.523 (0.028%), neg=0, invalid=762 0367: dt=0.224000, rms=0.523 (0.035%), neg=0, invalid=762 0368: dt=0.224000, rms=0.522 (0.049%), neg=0, invalid=762 0369: dt=0.224000, rms=0.522 (0.056%), neg=0, invalid=762 0370: dt=0.224000, rms=0.522 (0.007%), neg=0, invalid=762 0371: dt=0.224000, rms=0.522 (0.012%), neg=0, invalid=762 0372: dt=0.224000, rms=0.522 (0.020%), neg=0, invalid=762 0373: dt=0.224000, rms=0.522 (0.022%), neg=0, invalid=762 0374: dt=0.224000, rms=0.522 (0.027%), neg=0, invalid=762 0375: dt=0.224000, rms=0.521 (0.026%), neg=0, invalid=762 0376: dt=0.224000, rms=0.521 (0.028%), neg=0, invalid=762 0377: dt=0.224000, rms=0.521 (0.024%), neg=0, invalid=762 0378: dt=0.224000, rms=0.521 (0.024%), neg=0, invalid=762 0379: dt=0.320000, rms=0.521 (0.003%), neg=0, invalid=762 0380: dt=0.320000, rms=0.521 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0381: dt=0.384000, rms=0.516 (1.232%), neg=0, invalid=762 0382: dt=0.384000, rms=0.515 (0.214%), neg=0, invalid=762 0383: dt=0.384000, rms=0.514 (0.043%), neg=0, invalid=762 0384: dt=0.384000, rms=0.514 (0.007%), neg=0, invalid=762 0385: dt=0.384000, rms=0.514 (-0.001%), 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=0.513, neg=0, invalid=762 0386: dt=0.000000, rms=0.512 (0.219%), neg=0, invalid=762 0387: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=762 0388: dt=221.952000, rms=0.511 (0.291%), neg=0, invalid=762 0389: dt=129.472000, rms=0.511 (0.021%), neg=0, invalid=762 0390: dt=129.472000, rms=0.511 (0.021%), neg=0, invalid=762 0391: dt=129.472000, rms=0.511 (0.035%), neg=0, invalid=762 0392: dt=129.472000, rms=0.511 (0.027%), neg=0, invalid=762 0393: dt=129.472000, rms=0.510 (0.030%), neg=0, invalid=762 0394: dt=129.472000, rms=0.510 (0.021%), neg=0, invalid=762 0395: dt=92.480000, rms=0.510 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0396: dt=15.552000, rms=0.510 (0.248%), neg=0, invalid=762 0397: dt=9.072000, rms=0.510 (0.008%), neg=0, invalid=762 0398: dt=9.072000, rms=0.510 (0.002%), neg=0, invalid=762 0399: dt=9.072000, rms=0.510 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0400: dt=145.152000, rms=0.508 (0.671%), neg=0, invalid=762 0401: dt=25.920000, rms=0.507 (0.141%), neg=0, invalid=762 0402: dt=25.920000, rms=0.507 (0.047%), neg=0, invalid=762 0403: dt=25.920000, rms=0.507 (0.050%), neg=0, invalid=762 0404: dt=25.920000, rms=0.506 (0.062%), neg=0, invalid=762 0405: dt=25.920000, rms=0.506 (0.095%), neg=0, invalid=762 0406: dt=25.920000, rms=0.505 (0.114%), neg=0, invalid=762 0407: dt=25.920000, rms=0.505 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0408: dt=25.920000, rms=0.504 (0.096%), neg=0, invalid=762 0409: dt=36.288000, rms=0.504 (0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0410: dt=38.020906, rms=0.501 (0.801%), neg=0, invalid=762 iter 0, gcam->neg = 33 after 10 iterations, nbhd size=1, neg = 0 0411: dt=82.800000, rms=0.498 (0.676%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0412: dt=24.356688, rms=0.497 (0.285%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 12 iterations, nbhd size=1, neg = 0 0413: dt=38.400000, rms=0.495 (0.234%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0414: dt=38.400000, rms=0.495 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0415: dt=38.400000, rms=0.490 (1.342%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0416: dt=21.960784, rms=0.488 (0.553%), neg=0, invalid=762 0417: dt=38.400000, rms=0.486 (0.310%), neg=0, invalid=762 0418: dt=11.200000, rms=0.485 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0419: dt=11.200000, rms=0.485 (0.089%), neg=0, invalid=762 0420: dt=11.200000, rms=0.484 (0.117%), neg=0, invalid=762 0421: dt=11.200000, rms=0.483 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0422: dt=11.200000, rms=0.482 (0.180%), neg=0, invalid=762 0423: dt=11.200000, rms=0.481 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0424: dt=11.200000, rms=0.481 (0.193%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0425: dt=11.200000, rms=0.480 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0426: dt=11.200000, rms=0.479 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0427: dt=11.200000, rms=0.478 (0.176%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0428: dt=11.200000, rms=0.477 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0429: dt=11.200000, rms=0.476 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0430: dt=11.200000, rms=0.476 (0.151%), neg=0, invalid=762 0431: dt=11.200000, rms=0.475 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0432: dt=11.200000, rms=0.474 (0.137%), neg=0, invalid=762 0433: dt=11.200000, rms=0.474 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0434: dt=11.200000, rms=0.473 (0.103%), neg=0, invalid=762 0435: dt=38.400000, rms=0.473 (0.024%), neg=0, invalid=762 0436: dt=38.400000, rms=0.473 (-0.056%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0437: dt=1.008000, rms=0.478 (0.260%), neg=0, invalid=762 0438: dt=0.252000, rms=0.478 (-0.002%), neg=0, invalid=762 0439: dt=0.252000, rms=0.478 (0.000%), neg=0, invalid=762 0440: dt=0.252000, rms=0.478 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0441: dt=0.864000, rms=0.478 (0.252%), neg=0, invalid=762 0442: dt=0.432000, rms=0.478 (0.001%), neg=0, invalid=762 0443: dt=0.432000, rms=0.478 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0444: dt=0.448000, rms=0.488 (0.289%), neg=0, invalid=762 0445: dt=0.320000, rms=0.488 (0.013%), neg=0, invalid=762 0446: dt=0.320000, rms=0.488 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0447: dt=1.280000, rms=0.487 (0.402%), neg=0, invalid=762 0448: dt=0.448000, rms=0.487 (0.017%), neg=0, invalid=762 0449: dt=0.448000, rms=0.487 (0.007%), neg=0, invalid=762 0450: dt=0.448000, rms=0.487 (-0.028%), 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=0.478, neg=0, invalid=762 iter 0, gcam->neg = 1463 after 16 iterations, nbhd size=1, neg = 0 0451: dt=2.219166, rms=0.442 (7.514%), neg=0, invalid=762 0452: dt=0.080000, rms=0.442 (0.051%), neg=0, invalid=762 0453: dt=0.080000, rms=0.442 (-0.060%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 0454: dt=0.080000, rms=0.442 (0.353%), neg=0, invalid=762 0455: dt=0.003000, rms=0.441 (0.003%), neg=0, invalid=762 0456: dt=0.003000, rms=0.441 (-0.000%), 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=0.427, neg=0, invalid=762 0457: dt=0.000000, rms=0.427 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0458: dt=-0.009615, rms=0.427 (0.000%), neg=0, invalid=762 0459: dt=0.000000, rms=0.427 (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=0.427, neg=0, invalid=762 0460: dt=0.001420, rms=0.427 (0.000%), neg=0, invalid=762 0461: dt=0.000000, rms=0.427 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0462: dt=25.920000, rms=0.427 (0.019%), neg=0, invalid=762 0463: dt=36.288000, rms=0.427 (0.008%), neg=0, invalid=762 0464: dt=36.288000, rms=0.427 (0.009%), neg=0, invalid=762 0465: dt=36.288000, rms=0.427 (0.006%), neg=0, invalid=762 0466: dt=36.288000, rms=0.427 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0467: dt=11.200000, rms=0.427 (0.068%), neg=0, invalid=762 0468: dt=2.800000, rms=0.427 (0.004%), neg=0, invalid=762 0469: dt=2.800000, rms=0.427 (0.000%), neg=0, invalid=762 0470: dt=2.800000, rms=0.427 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0471: dt=78.800000, rms=0.424 (0.734%), neg=0, invalid=762 0472: dt=24.615385, rms=0.423 (0.297%), neg=0, invalid=762 0473: dt=44.800000, rms=0.422 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0474: dt=44.800000, rms=0.422 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0475: dt=44.800000, rms=0.421 (0.300%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0476: dt=44.800000, rms=0.420 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0477: dt=44.800000, rms=0.419 (0.202%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0478: dt=44.800000, rms=0.418 (0.248%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 13 iterations, nbhd size=1, neg = 0 0479: dt=44.800000, rms=0.417 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 14 iterations, nbhd size=1, neg = 0 0480: dt=44.800000, rms=0.417 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 15 iterations, nbhd size=1, neg = 0 0481: dt=44.800000, rms=0.416 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 2 iterations, nbhd size=0, neg = 0 0482: dt=44.800000, rms=0.416 (0.124%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 0483: dt=44.800000, rms=0.416 (0.025%), neg=0, invalid=762 0484: dt=11.200000, rms=0.416 (0.051%), neg=0, invalid=762 0485: dt=38.400000, rms=0.415 (0.031%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0486: dt=38.400000, rms=0.415 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0487: dt=38.400000, rms=0.415 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0488: dt=38.400000, rms=0.415 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0489: dt=38.400000, rms=0.415 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0490: dt=38.400000, rms=0.415 (0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0491: dt=0.000211, rms=0.420 (0.000%), neg=0, invalid=762 0492: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0493: dt=2.304000, rms=0.420 (0.010%), neg=0, invalid=762 0494: dt=1.008000, rms=0.420 (0.002%), neg=0, invalid=762 0495: dt=1.008000, rms=0.420 (0.001%), neg=0, invalid=762 0496: dt=1.008000, rms=0.420 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0497: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0498: dt=0.000000, rms=0.429 (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=0.414, neg=0, invalid=762 iter 0, gcam->neg = 830 after 19 iterations, nbhd size=1, neg = 0 0499: dt=1.195958, rms=0.403 (2.471%), neg=0, invalid=762 0500: dt=0.000023, rms=0.403 (0.000%), neg=0, invalid=762 0501: dt=0.000023, rms=0.403 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=762 0502: dt=0.112000, rms=0.403 (0.062%), neg=0, invalid=762 0503: dt=0.080000, rms=0.403 (0.016%), neg=0, invalid=762 0504: dt=0.080000, rms=0.403 (0.011%), neg=0, invalid=762 0505: dt=0.080000, rms=0.403 (-0.019%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 38 minutes and 21 seconds. mri_ca_register utimesec 10647.572322 mri_ca_register stimesec 9.580543 mri_ca_register ru_maxrss 1337888 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5317668 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62944 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 6758 mri_ca_register ru_nivcsw 15682 FSRUNTIME@ mri_ca_register 2.6391 hours 2 threads #-------------------------------------- #@# SubCort Seg Sun Oct 8 03:01:29 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-904 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-6.0.0/0051311/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 6.09 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 = 0.14817 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (1828 voxels, overlap=0.015) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1828 voxels, peak = 7), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.14591 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (1289 voxels, overlap=0.424) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (1289 voxels, peak = 7), gca=6.7 gca peak = 0.28129 (95) mri peak = 0.08311 (92) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (561 voxels, overlap=1.016) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (561 voxels, peak = 91), gca=90.7 gca peak = 0.16930 (96) mri peak = 0.08997 (92) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (577 voxels, overlap=0.978) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (577 voxels, peak = 92), gca=91.7 gca peak = 0.24553 (55) mri peak = 0.08241 (61) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (517 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (517 voxels, peak = 56), gca=56.4 gca peak = 0.30264 (59) mri peak = 0.10548 (54) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (551 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (551 voxels, peak = 55), gca=55.2 gca peak = 0.07580 (103) mri peak = 0.08118 (105) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31077 voxels, overlap=0.597) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31077 voxels, peak = 108), gca=107.6 gca peak = 0.07714 (104) mri peak = 0.07867 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (30677 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (30677 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.06003 (50) Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (17820 voxels, overlap=0.456) Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (17820 voxels, peak = 50), gca=49.6 gca peak = 0.11620 (58) mri peak = 0.05601 (52) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (16657 voxels, overlap=0.679) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (16657 voxels, peak = 52), gca=51.9 gca peak = 0.30970 (66) mri peak = 0.10903 (67) Right_Caudate (50): linear fit = 0.95 x + 0.0 (960 voxels, overlap=1.010) Right_Caudate (50): linear fit = 0.95 x + 0.0 (960 voxels, peak = 63), gca=63.0 gca peak = 0.15280 (69) mri peak = 0.09378 (63) Left_Caudate (11): linear fit = 0.88 x + 0.0 (979 voxels, overlap=0.343) Left_Caudate (11): linear fit = 0.88 x + 0.0 (979 voxels, peak = 61), gca=61.1 gca peak = 0.13902 (56) mri peak = 0.05154 (50) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (11705 voxels, overlap=0.987) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (11705 voxels, peak = 53), gca=52.9 gca peak = 0.14777 (55) mri peak = 0.05120 (53) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13724 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13724 voxels, peak = 53), gca=53.1 gca peak = 0.16765 (84) mri peak = 0.09098 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4588 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4588 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.08287 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4881 voxels, overlap=0.911) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4881 voxels, peak = 88), gca=87.8 gca peak = 0.29869 (57) mri peak = 0.09573 (56) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (426 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (426 voxels, peak = 53), gca=52.7 gca peak = 0.33601 (57) mri peak = 0.12093 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (223 voxels, overlap=1.025) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (223 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.07111 (82) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3991 voxels, overlap=0.915) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3991 voxels, peak = 86), gca=85.9 gca peak = 0.11793 (83) mri peak = 0.06214 (80) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4116 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4116 voxels, peak = 83), gca=82.6 gca peak = 0.08324 (81) mri peak = 0.07414 (75) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2162 voxels, overlap=0.654) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2162 voxels, peak = 75), gca=74.9 gca peak = 0.10360 (77) mri peak = 0.07462 (74) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2329 voxels, overlap=0.771) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2329 voxels, peak = 72), gca=72.0 gca peak = 0.08424 (78) mri peak = 0.09689 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9447 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9447 voxels, peak = 82), gca=82.3 gca peak = 0.12631 (89) mri peak = 0.06168 (96) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1008 voxels, overlap=0.814) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1008 voxels, peak = 97), gca=96.6 gca peak = 0.14500 (87) mri peak = 0.07095 (91) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1092 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1092 voxels, peak = 90), gca=90.0 gca peak = 0.14975 (24) mri peak = 0.12230 ( 9) Third_Ventricle (14): linear fit = 0.38 x + 0.0 (139 voxels, overlap=0.048) Third_Ventricle (14): linear fit = 0.38 x + 0.0 (139 voxels, peak = 9), gca=9.0 gca peak = 0.19357 (14) mri peak = 0.13376 (14) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (157 voxels, overlap=0.486) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (157 voxels, peak = 10), gca=9.9 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 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 0.95 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.54 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30836 ( 7) mri peak = 0.14817 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (1828 voxels, overlap=0.999) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (1828 voxels, peak = 6), gca=6.3 gca peak = 0.29638 ( 7) mri peak = 0.14591 ( 8) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (1289 voxels, overlap=0.965) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (1289 voxels, peak = 8), gca=7.5 gca peak = 0.25679 (90) mri peak = 0.08311 (92) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (561 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (561 voxels, peak = 91), gca=91.3 gca peak = 0.18583 (92) mri peak = 0.08997 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (577 voxels, overlap=1.006) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (577 voxels, peak = 92), gca=91.5 gca peak = 0.29045 (57) mri peak = 0.08241 (61) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (517 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (517 voxels, peak = 57), gca=57.0 gca peak = 0.27564 (53) mri peak = 0.10548 (54) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (551 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (551 voxels, peak = 53), gca=53.0 gca peak = 0.07601 (108) mri peak = 0.08118 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31077 voxels, overlap=0.784) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31077 voxels, peak = 107), gca=107.5 gca peak = 0.07787 (109) mri peak = 0.07867 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30677 voxels, overlap=0.788) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30677 voxels, peak = 108), gca=108.5 gca peak = 0.11313 (50) mri peak = 0.06003 (50) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (17820 voxels, overlap=0.998) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (17820 voxels, peak = 49), gca=48.8 gca peak = 0.12882 (52) mri peak = 0.05601 (52) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16657 voxels, overlap=0.999) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16657 voxels, peak = 51), gca=51.2 gca peak = 0.34160 (63) mri peak = 0.10903 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (960 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (960 voxels, peak = 63), gca=63.0 gca peak = 0.13671 (61) mri peak = 0.09378 (63) Left_Caudate (11): linear fit = 1.00 x + 0.0 (979 voxels, overlap=0.972) Left_Caudate (11): linear fit = 1.00 x + 0.0 (979 voxels, peak = 61), gca=61.0 gca peak = 0.14834 (52) mri peak = 0.05154 (50) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (11705 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (11705 voxels, peak = 51), gca=50.7 gca peak = 0.15622 (53) mri peak = 0.05120 (53) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (13724 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (13724 voxels, peak = 53), gca=53.0 gca peak = 0.15873 (90) mri peak = 0.09098 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4588 voxels, overlap=0.975) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4588 voxels, peak = 90), gca=89.6 gca peak = 0.16966 (88) mri peak = 0.08287 (86) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4881 voxels, overlap=0.985) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4881 voxels, peak = 87), gca=86.7 gca peak = 0.35242 (54) mri peak = 0.09573 (56) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (426 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (426 voxels, peak = 55), gca=54.8 gca peak = 0.28990 (60) mri peak = 0.12093 (59) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (223 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (223 voxels, peak = 60), gca=60.0 gca peak = 0.11465 (86) mri peak = 0.07111 (82) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3991 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3991 voxels, peak = 86), gca=85.6 gca peak = 0.09952 (80) mri peak = 0.06214 (80) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4116 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4116 voxels, peak = 81), gca=81.2 gca peak = 0.09421 (70) mri peak = 0.07414 (75) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2162 voxels, overlap=0.999) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2162 voxels, peak = 69), gca=69.0 gca peak = 0.09691 (72) mri peak = 0.07462 (74) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2329 voxels, overlap=0.958) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2329 voxels, peak = 73), gca=73.1 gca peak = 0.07599 (83) mri peak = 0.09689 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9447 voxels, overlap=0.714) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9447 voxels, peak = 83), gca=82.6 gca peak = 0.10974 (96) mri peak = 0.06168 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1008 voxels, overlap=0.911) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1008 voxels, peak = 96), gca=95.5 gca peak = 0.15222 (88) mri peak = 0.07095 (91) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1092 voxels, overlap=0.952) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1092 voxels, peak = 88), gca=87.6 gca peak = 0.28896 (14) mri peak = 0.12230 ( 9) Third_Ventricle (14): linear fit = 0.86 x + 0.0 (139 voxels, overlap=0.962) Third_Ventricle (14): linear fit = 0.86 x + 0.0 (139 voxels, peak = 12), gca=12.0 gca peak = 0.26059 (10) mri peak = 0.13376 (14) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (157 voxels, overlap=0.834) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (157 voxels, peak = 10), gca=10.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17854 (25) gca peak Left_Thalamus = 1.00000 (89) gca peak CSF = 0.26466 (20) gca peak Left_Accumbens_area = 0.81130 (55) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.70074 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.18913 (24) gca peak Right_Accumbens_area = 0.34583 (62) gca peak Right_vessel = 0.81794 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.89470 (17) gca peak WM_hypointensities = 0.06869 (81) gca peak non_WM_hypointensities = 0.08561 (45) gca peak Optic_Chiasm = 0.70906 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 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 60115 voxels changed in iteration 0 of unlikely voxel relabeling 172 voxels changed in iteration 1 of unlikely voxel relabeling 15 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 22493 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 527 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 64681 changed. image ll: -2.105, PF=0.500 pass 2: 18839 changed. image ll: -2.105, PF=0.500 pass 3: 5774 changed. pass 4: 2131 changed. 33775 voxels changed in iteration 0 of unlikely voxel relabeling 159 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 4737 voxels changed in iteration 0 of unlikely voxel relabeling 32 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5200 voxels changed in iteration 0 of unlikely voxel relabeling 37 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4667 voxels changed in iteration 0 of unlikely voxel relabeling 29 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 3540.188809 mri_ca_label stimesec 1.728737 mri_ca_label ru_maxrss 2130748 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 765133 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 62936 mri_ca_label ru_oublock 448 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 267 mri_ca_label ru_nivcsw 7961 auto-labeling took 58 minutes and 18 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/cc_up.lta 0051311 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-6.0.0/0051311/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/norm.mgz 31420 voxels in left wm, 27692 in right wm, xrange [125, 134] searching rotation angles z=[-2 12], y=[-7 7] searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.7 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.7 global minimum found at slice 129.2, rotations (0.47, 4.92) final transformation (x=129.2, yr=0.469, zr=4.923): 0.99628 -0.08581 0.00815 8.44840; 0.08581 0.99631 0.00070 0.26983; -0.00818 -0.00000 0.99997 20.06056; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 117 109 eigenvectors: 0.00082 0.00225 1.00000; -0.03438 -0.99941 0.00228; 0.99941 -0.03438 -0.00074; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Sun Oct 8 04:00:32 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Oct 8 04:00:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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... 1597 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 109 gm peak at 54 (54), valley at 20 (20) 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 110 gm peak at 55 (55), valley at 19 (19) csf peak at 28, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 20 seconds. #-------------------------------------------- #@# Mask BFS Sun Oct 8 04:03:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1443268 voxels in mask (pct= 8.60) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Oct 8 04:03:56 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 (108.0): 107.7 +- 5.3 [79.0 --> 125.0] GM (63.0) : 63.3 +- 10.0 [30.0 --> 95.0] setting bottom of white matter range to 73.3 setting top of gray matter range to 83.3 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... 9148 sparsely connected voxels removed... thickening thin strands.... 20 segments, 7763 filled 88 bright non-wm voxels segmented. 4646 diagonally connected voxels added... white matter segmentation took 1.4 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 0.61 minutes reading wm segmentation from wm.seg.mgz... 405 voxels added to wm to prevent paths from MTL structures to cortex 1961 additional wm voxels added 0 additional wm voxels added SEG EDIT: 48316 voxels turned on, 39597 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 102 new 102 115,126,128 old 102 new 102 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 12 found - 12 modified | TOTAL: 24 pass 2 (xy-): 0 found - 12 modified | TOTAL: 24 pass 1 (yz+): 17 found - 17 modified | TOTAL: 41 pass 2 (yz+): 0 found - 17 modified | TOTAL: 41 pass 1 (yz-): 29 found - 29 modified | TOTAL: 70 pass 2 (yz-): 0 found - 29 modified | TOTAL: 70 pass 1 (xz+): 13 found - 13 modified | TOTAL: 83 pass 2 (xz+): 0 found - 13 modified | TOTAL: 83 pass 1 (xz-): 15 found - 15 modified | TOTAL: 98 pass 2 (xz-): 0 found - 15 modified | TOTAL: 98 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 14 found - 14 modified | TOTAL: 32 pass 2 (+++): 0 found - 14 modified | TOTAL: 32 pass 1 (+++): 6 found - 6 modified | TOTAL: 38 pass 2 (+++): 0 found - 6 modified | TOTAL: 38 pass 1 (+++): 11 found - 11 modified | TOTAL: 49 pass 2 (+++): 0 found - 11 modified | TOTAL: 49 Iteration Number : 1 pass 1 (++): 235 found - 235 modified | TOTAL: 235 pass 2 (++): 0 found - 235 modified | TOTAL: 235 pass 1 (+-): 281 found - 281 modified | TOTAL: 516 pass 2 (+-): 0 found - 281 modified | TOTAL: 516 pass 1 (--): 243 found - 243 modified | TOTAL: 759 pass 2 (--): 0 found - 243 modified | TOTAL: 759 pass 1 (-+): 247 found - 247 modified | TOTAL: 1006 pass 2 (-+): 0 found - 247 modified | TOTAL: 1006 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 6 found - 6 modified | TOTAL: 11 pass 2 (xy-): 0 found - 6 modified | TOTAL: 11 pass 1 (yz+): 4 found - 4 modified | TOTAL: 15 pass 2 (yz+): 0 found - 4 modified | TOTAL: 15 pass 1 (yz-): 2 found - 2 modified | TOTAL: 17 pass 2 (yz-): 0 found - 2 modified | TOTAL: 17 pass 1 (xz+): 4 found - 4 modified | TOTAL: 21 pass 2 (xz+): 0 found - 4 modified | TOTAL: 21 pass 1 (xz-): 5 found - 5 modified | TOTAL: 26 pass 2 (xz-): 0 found - 5 modified | TOTAL: 26 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 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 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 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 : 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 Total Number of Modified Voxels = 1195 (out of 485218: 0.246281) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Oct 8 04:06:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.95970 -0.11366 -0.01385 17.30839; 0.11444 1.18235 0.23256 -75.74860; -0.01114 -0.23848 1.09834 12.30527; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1597 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max = 0.75) need search nearby using seed (124, 121, 151), TAL = (4.0, 23.0, 7.0) talairach voxel to voxel transform 1.03028 0.09750 -0.00766 -10.35275; -0.09761 0.80190 -0.17102 64.53651; -0.01074 0.17510 0.87325 2.70390; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 121, 151) --> (4.0, 23.0, 7.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (4.00, 23.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 23.00, 7.00) SRC: (109.50, 125.40, 154.61) search lh wm seed point around talairach space (-14.00, 23.00, 7.00), SRC: (146.59, 121.88, 154.23) 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 Sun Oct 8 04:06:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 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 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 2 found - 2 modified | TOTAL: 10 pass 2 (xz-): 0 found - 2 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 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 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 = 12 (out of 233604: 0.005137) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 370 vertices, 429 faces slice 60: 5508 vertices, 5711 faces slice 70: 14280 vertices, 14668 faces slice 80: 26295 vertices, 26722 faces slice 90: 38280 vertices, 38683 faces slice 100: 50218 vertices, 50664 faces slice 110: 62727 vertices, 63162 faces slice 120: 75916 vertices, 76394 faces slice 130: 88153 vertices, 88603 faces slice 140: 100213 vertices, 100639 faces slice 150: 110733 vertices, 111100 faces slice 160: 119768 vertices, 120068 faces slice 170: 128046 vertices, 128334 faces slice 180: 134337 vertices, 134536 faces slice 190: 138336 vertices, 138462 faces slice 200: 139346 vertices, 139388 faces slice 210: 139346 vertices, 139388 faces slice 220: 139346 vertices, 139388 faces slice 230: 139346 vertices, 139388 faces slice 240: 139346 vertices, 139388 faces slice 250: 139346 vertices, 139388 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... 139346 voxel in cpt #1: X=-42 [v=139346,e=418164,f=278776] located at (-32.566956, -12.473964, 6.639351) For the whole surface: X=-42 [v=139346,e=418164,f=278776] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Oct 8 04:06:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 3 found - 3 modified | TOTAL: 5 pass 2 (yz-): 0 found - 3 modified | TOTAL: 5 pass 1 (xz+): 2 found - 2 modified | TOTAL: 7 pass 2 (xz+): 0 found - 2 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 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 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 232816: 0.003866) 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 50: 562 vertices, 618 faces slice 60: 6543 vertices, 6823 faces slice 70: 16841 vertices, 17262 faces slice 80: 29602 vertices, 29994 faces slice 90: 42492 vertices, 42932 faces slice 100: 54817 vertices, 55264 faces slice 110: 67460 vertices, 67890 faces slice 120: 79936 vertices, 80370 faces slice 130: 91495 vertices, 91909 faces slice 140: 103196 vertices, 103616 faces slice 150: 113148 vertices, 113498 faces slice 160: 122368 vertices, 122671 faces slice 170: 129723 vertices, 130012 faces slice 180: 135976 vertices, 136187 faces slice 190: 139987 vertices, 140140 faces slice 200: 140834 vertices, 140884 faces slice 210: 140834 vertices, 140884 faces slice 220: 140834 vertices, 140884 faces slice 230: 140834 vertices, 140884 faces slice 240: 140834 vertices, 140884 faces slice 250: 140834 vertices, 140884 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... 140834 voxel in cpt #1: X=-50 [v=140834,e=422652,f=281768] located at (28.968601, -14.518121, 1.524312) For the whole surface: X=-50 [v=140834,e=422652,f=281768] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Oct 8 04:07:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun Oct 8 04:07:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 10126 of (10126 10129) to complete... Waiting for PID 10129 of (10126 10129) 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 (10126 10129) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun Oct 8 04:07:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun Oct 8 04:07:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 10182 of (10182 10186) to complete... Waiting for PID 10186 of (10182 10186) 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 = 44.1 mm, total surface area = 72260 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.032 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 60.537796 mris_inflate stimesec 0.128980 mris_inflate ru_maxrss 203972 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29467 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9824 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3898 mris_inflate ru_nivcsw 4125 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.5 mm, total surface area = 73001 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.035 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 48.431637 mris_inflate stimesec 0.120981 mris_inflate ru_maxrss 206112 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29490 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9928 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2724 mris_inflate ru_nivcsw 4442 PIDs (10182 10186) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun Oct 8 04:08:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun Oct 8 04:08:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 10252 of (10252 10256) to complete... Waiting for PID 10256 of (10252 10256) 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 0.99 +- 0.53 (0.00-->7.66) (max @ vno 52576 --> 53865) face area 0.03 +- 0.03 (-0.12-->1.03) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.332... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.518, avgs=0 005/300: dt: 0.9000, rms radial error=175.260, avgs=0 010/300: dt: 0.9000, rms radial error=174.707, avgs=0 015/300: dt: 0.9000, rms radial error=173.981, avgs=0 020/300: dt: 0.9000, rms radial error=173.155, avgs=0 025/300: dt: 0.9000, rms radial error=172.272, avgs=0 030/300: dt: 0.9000, rms radial error=171.357, avgs=0 035/300: dt: 0.9000, rms radial error=170.427, avgs=0 040/300: dt: 0.9000, rms radial error=169.488, avgs=0 045/300: dt: 0.9000, rms radial error=168.546, avgs=0 050/300: dt: 0.9000, rms radial error=167.604, avgs=0 055/300: dt: 0.9000, rms radial error=166.666, avgs=0 060/300: dt: 0.9000, rms radial error=165.730, avgs=0 065/300: dt: 0.9000, rms radial error=164.799, avgs=0 070/300: dt: 0.9000, rms radial error=163.872, avgs=0 075/300: dt: 0.9000, rms radial error=162.950, avgs=0 080/300: dt: 0.9000, rms radial error=162.033, avgs=0 085/300: dt: 0.9000, rms radial error=161.120, avgs=0 090/300: dt: 0.9000, rms radial error=160.213, avgs=0 095/300: dt: 0.9000, rms radial error=159.310, avgs=0 100/300: dt: 0.9000, rms radial error=158.413, avgs=0 105/300: dt: 0.9000, rms radial error=157.520, avgs=0 110/300: dt: 0.9000, rms radial error=156.632, avgs=0 115/300: dt: 0.9000, rms radial error=155.749, avgs=0 120/300: dt: 0.9000, rms radial error=154.871, avgs=0 125/300: dt: 0.9000, rms radial error=153.998, avgs=0 130/300: dt: 0.9000, rms radial error=153.130, avgs=0 135/300: dt: 0.9000, rms radial error=152.266, avgs=0 140/300: dt: 0.9000, rms radial error=151.408, avgs=0 145/300: dt: 0.9000, rms radial error=150.554, avgs=0 150/300: dt: 0.9000, rms radial error=149.705, avgs=0 155/300: dt: 0.9000, rms radial error=148.861, avgs=0 160/300: dt: 0.9000, rms radial error=148.021, avgs=0 165/300: dt: 0.9000, rms radial error=147.186, avgs=0 170/300: dt: 0.9000, rms radial error=146.356, avgs=0 175/300: dt: 0.9000, rms radial error=145.530, avgs=0 180/300: dt: 0.9000, rms radial error=144.709, avgs=0 185/300: dt: 0.9000, rms radial error=143.892, avgs=0 190/300: dt: 0.9000, rms radial error=143.080, avgs=0 195/300: dt: 0.9000, rms radial error=142.272, avgs=0 200/300: dt: 0.9000, rms radial error=141.468, avgs=0 205/300: dt: 0.9000, rms radial error=140.670, avgs=0 210/300: dt: 0.9000, rms radial error=139.875, avgs=0 215/300: dt: 0.9000, rms radial error=139.085, avgs=0 220/300: dt: 0.9000, rms radial error=138.300, avgs=0 225/300: dt: 0.9000, rms radial error=137.519, avgs=0 230/300: dt: 0.9000, rms radial error=136.742, avgs=0 235/300: dt: 0.9000, rms radial error=135.970, avgs=0 240/300: dt: 0.9000, rms radial error=135.202, avgs=0 245/300: dt: 0.9000, rms radial error=134.438, avgs=0 250/300: dt: 0.9000, rms radial error=133.679, avgs=0 255/300: dt: 0.9000, rms radial error=132.924, avgs=0 260/300: dt: 0.9000, rms radial error=132.173, avgs=0 265/300: dt: 0.9000, rms radial error=131.427, avgs=0 270/300: dt: 0.9000, rms radial error=130.685, avgs=0 275/300: dt: 0.9000, rms radial error=129.946, avgs=0 280/300: dt: 0.9000, rms radial error=129.212, avgs=0 285/300: dt: 0.9000, rms radial error=128.483, avgs=0 290/300: dt: 0.9000, rms radial error=127.757, avgs=0 295/300: dt: 0.9000, rms radial error=127.035, avgs=0 300/300: dt: 0.9000, rms radial error=126.318, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15939.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2504.53 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 228.13 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/12 = 0.00974 epoch 4 (K=640.0), pass 1, starting sse = 11.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/17 = 0.00894 final distance error %23.18 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 294.522225 mris_sphere stimesec 0.233964 mris_sphere ru_maxrss 204184 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 29518 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 9808 mris_sphere ru_oublock 9848 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 9029 mris_sphere ru_nivcsw 22293 FSRUNTIME@ mris_sphere 0.0823 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 0.98 +- 0.54 (0.00-->7.50) (max @ vno 67255 --> 68430) face area 0.03 +- 0.03 (-0.17-->0.80) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.326... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.727, avgs=0 005/300: dt: 0.9000, rms radial error=175.469, avgs=0 010/300: dt: 0.9000, rms radial error=174.916, avgs=0 015/300: dt: 0.9000, rms radial error=174.191, avgs=0 020/300: dt: 0.9000, rms radial error=173.365, avgs=0 025/300: dt: 0.9000, rms radial error=172.482, avgs=0 030/300: dt: 0.9000, rms radial error=171.568, avgs=0 035/300: dt: 0.9000, rms radial error=170.637, avgs=0 040/300: dt: 0.9000, rms radial error=169.697, avgs=0 045/300: dt: 0.9000, rms radial error=168.756, avgs=0 050/300: dt: 0.9000, rms radial error=167.815, avgs=0 055/300: dt: 0.9000, rms radial error=166.876, avgs=0 060/300: dt: 0.9000, rms radial error=165.941, avgs=0 065/300: dt: 0.9000, rms radial error=165.010, avgs=0 070/300: dt: 0.9000, rms radial error=164.084, avgs=0 075/300: dt: 0.9000, rms radial error=163.162, avgs=0 080/300: dt: 0.9000, rms radial error=162.245, avgs=0 085/300: dt: 0.9000, rms radial error=161.333, avgs=0 090/300: dt: 0.9000, rms radial error=160.426, avgs=0 095/300: dt: 0.9000, rms radial error=159.524, avgs=0 100/300: dt: 0.9000, rms radial error=158.626, avgs=0 105/300: dt: 0.9000, rms radial error=157.734, avgs=0 110/300: dt: 0.9000, rms radial error=156.847, avgs=0 115/300: dt: 0.9000, rms radial error=155.964, avgs=0 120/300: dt: 0.9000, rms radial error=155.086, avgs=0 125/300: dt: 0.9000, rms radial error=154.213, avgs=0 130/300: dt: 0.9000, rms radial error=153.345, avgs=0 135/300: dt: 0.9000, rms radial error=152.481, avgs=0 140/300: dt: 0.9000, rms radial error=151.623, avgs=0 145/300: dt: 0.9000, rms radial error=150.768, avgs=0 150/300: dt: 0.9000, rms radial error=149.919, avgs=0 155/300: dt: 0.9000, rms radial error=149.074, avgs=0 160/300: dt: 0.9000, rms radial error=148.234, avgs=0 165/300: dt: 0.9000, rms radial error=147.399, avgs=0 170/300: dt: 0.9000, rms radial error=146.568, avgs=0 175/300: dt: 0.9000, rms radial error=145.742, avgs=0 180/300: dt: 0.9000, rms radial error=144.921, avgs=0 185/300: dt: 0.9000, rms radial error=144.104, avgs=0 190/300: dt: 0.9000, rms radial error=143.292, avgs=0 195/300: dt: 0.9000, rms radial error=142.485, avgs=0 200/300: dt: 0.9000, rms radial error=141.681, avgs=0 205/300: dt: 0.9000, rms radial error=140.883, avgs=0 210/300: dt: 0.9000, rms radial error=140.089, avgs=0 215/300: dt: 0.9000, rms radial error=139.299, avgs=0 220/300: dt: 0.9000, rms radial error=138.514, avgs=0 225/300: dt: 0.9000, rms radial error=137.733, avgs=0 230/300: dt: 0.9000, rms radial error=136.956, avgs=0 235/300: dt: 0.9000, rms radial error=136.184, avgs=0 240/300: dt: 0.9000, rms radial error=135.416, avgs=0 245/300: dt: 0.9000, rms radial error=134.653, avgs=0 250/300: dt: 0.9000, rms radial error=133.893, avgs=0 255/300: dt: 0.9000, rms radial error=133.138, avgs=0 260/300: dt: 0.9000, rms radial error=132.387, avgs=0 265/300: dt: 0.9000, rms radial error=131.641, avgs=0 270/300: dt: 0.9000, rms radial error=130.898, avgs=0 275/300: dt: 0.9000, rms radial error=130.160, avgs=0 280/300: dt: 0.9000, rms radial error=129.426, avgs=0 285/300: dt: 0.9000, rms radial error=128.696, avgs=0 290/300: dt: 0.9000, rms radial error=127.970, avgs=0 295/300: dt: 0.9000, rms radial error=127.248, avgs=0 300/300: dt: 0.9000, rms radial error=126.530, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16228.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2598.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 248.79 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/10 = 0.00720 epoch 4 (K=640.0), pass 1, starting sse = 15.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00749 final distance error %25.01 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 317.713700 mris_sphere stimesec 0.273958 mris_sphere ru_maxrss 206308 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 29537 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 9912 mris_sphere ru_oublock 9952 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8825 mris_sphere ru_nivcsw 20885 FSRUNTIME@ mris_sphere 0.0864 hours 1 threads PIDs (10252 10256) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sun Oct 8 04:13:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Oct 8 04:13:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Oct 8 04:13:19 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 lh #@# Fix Topology rh Sun Oct 8 04:13:19 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 rh Waiting for PID 10482 of (10482 10485) to complete... Waiting for PID 10485 of (10482 10485) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 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=-42 (nv=139346, nf=278776, ne=418164, g=22) 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... 2737 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 27 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7890 (-4.8945) -vertex loglikelihood: -6.8951 (-3.4475) -normal dot loglikelihood: -3.5819 (-3.5819) -quad curv loglikelihood: -6.5129 (-3.2565) Total Loglikelihood : -26.7789 CORRECTING DEFECT 0 (vertices=17, convex hull=32, v0=58) After retessellation of defect 0 (v0=58), euler #=-24 (137664,412243,274555) : difference with theory (-24) = 0 CORRECTING DEFECT 1 (vertices=5, convex hull=22, v0=9693) After retessellation of defect 1 (v0=9693), euler #=-23 (137664,412248,274561) : difference with theory (-23) = 0 CORRECTING DEFECT 2 (vertices=82, convex hull=67, v0=16434) After retessellation of defect 2 (v0=16434), euler #=-22 (137678,412318,274618) : difference with theory (-22) = 0 CORRECTING DEFECT 3 (vertices=40, convex hull=63, v0=23247) After retessellation of defect 3 (v0=23247), euler #=-21 (137701,412413,274691) : difference with theory (-21) = 0 CORRECTING DEFECT 4 (vertices=22, convex hull=38, v0=26254) After retessellation of defect 4 (v0=26254), euler #=-20 (137710,412452,274722) : difference with theory (-20) = 0 CORRECTING DEFECT 5 (vertices=107, convex hull=112, v0=31553) After retessellation of defect 5 (v0=31553), euler #=-19 (137755,412633,274859) : difference with theory (-19) = 0 CORRECTING DEFECT 6 (vertices=43, convex hull=83, v0=52726) After retessellation of defect 6 (v0=52726), euler #=-18 (137767,412703,274918) : difference with theory (-18) = 0 CORRECTING DEFECT 7 (vertices=329, convex hull=195, v0=56138) After retessellation of defect 7 (v0=56138), euler #=-17 (137874,413113,275222) : difference with theory (-17) = 0 CORRECTING DEFECT 8 (vertices=36, convex hull=42, v0=57150) After retessellation of defect 8 (v0=57150), euler #=-16 (137886,413162,275260) : difference with theory (-16) = 0 CORRECTING DEFECT 9 (vertices=31, convex hull=47, v0=69006) After retessellation of defect 9 (v0=69006), euler #=-15 (137900,413223,275308) : difference with theory (-15) = 0 CORRECTING DEFECT 10 (vertices=35, convex hull=69, v0=69199) After retessellation of defect 10 (v0=69199), euler #=-14 (137917,413308,275377) : difference with theory (-14) = 0 CORRECTING DEFECT 11 (vertices=31, convex hull=35, v0=72507) After retessellation of defect 11 (v0=72507), euler #=-13 (137928,413353,275412) : difference with theory (-13) = 0 CORRECTING DEFECT 12 (vertices=122, convex hull=59, v0=74238) After retessellation of defect 12 (v0=74238), euler #=-12 (137945,413428,275471) : difference with theory (-12) = 0 CORRECTING DEFECT 13 (vertices=69, convex hull=137, v0=81626) After retessellation of defect 13 (v0=81626), euler #=-11 (137959,413528,275558) : difference with theory (-11) = 0 CORRECTING DEFECT 14 (vertices=171, convex hull=144, v0=85529) After retessellation of defect 14 (v0=85529), euler #=-10 (138033,413816,275773) : difference with theory (-10) = 0 CORRECTING DEFECT 15 (vertices=49, convex hull=106, v0=87337) After retessellation of defect 15 (v0=87337), euler #=-9 (138055,413926,275862) : difference with theory (-9) = 0 CORRECTING DEFECT 16 (vertices=39, convex hull=52, v0=92564) After retessellation of defect 16 (v0=92564), euler #=-8 (138077,414016,275931) : difference with theory (-8) = 0 CORRECTING DEFECT 17 (vertices=23, convex hull=33, v0=93729) After retessellation of defect 17 (v0=93729), euler #=-7 (138083,414046,275956) : difference with theory (-7) = 0 CORRECTING DEFECT 18 (vertices=24, convex hull=59, v0=93887) After retessellation of defect 18 (v0=93887), euler #=-6 (138095,414107,276006) : difference with theory (-6) = 0 CORRECTING DEFECT 19 (vertices=69, convex hull=38, v0=95322) After retessellation of defect 19 (v0=95322), euler #=-5 (138105,414154,276044) : difference with theory (-5) = 0 CORRECTING DEFECT 20 (vertices=56, convex hull=53, v0=99762) After retessellation of defect 20 (v0=99762), euler #=-4 (138117,414212,276091) : difference with theory (-4) = 0 CORRECTING DEFECT 21 (vertices=13, convex hull=25, v0=101051) After retessellation of defect 21 (v0=101051), euler #=-3 (138119,414225,276103) : difference with theory (-3) = 0 CORRECTING DEFECT 22 (vertices=106, convex hull=41, v0=102169) After retessellation of defect 22 (v0=102169), euler #=-2 (138128,414265,276135) : difference with theory (-2) = 0 CORRECTING DEFECT 23 (vertices=7, convex hull=20, v0=111208) After retessellation of defect 23 (v0=111208), euler #=-1 (138130,414278,276147) : difference with theory (-1) = 0 CORRECTING DEFECT 24 (vertices=23, convex hull=66, v0=130383) After retessellation of defect 24 (v0=130383), euler #=0 (138142,414343,276201) : difference with theory (0) = 0 CORRECTING DEFECT 25 (vertices=95, convex hull=100, v0=132130) After retessellation of defect 25 (v0=132130), euler #=1 (138169,414470,276302) : difference with theory (1) = 0 CORRECTING DEFECT 26 (vertices=37, convex hull=73, v0=135282) After retessellation of defect 26 (v0=135282), euler #=2 (138191,414567,276378) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->8.79) (max @ vno 131208 --> 134668) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->8.79) (max @ vno 131208 --> 134668) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 94 mutations (37.0%), 160 crossovers (63.0%), 100 vertices were eliminated building final representation... 1155 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138191, nf=276378, ne=414567, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 16.8 minutes 0 defective edges removing intersecting faces 000: 193 intersecting mris_fix_topology utimesec 1010.039450 mris_fix_topology stimesec 0.220966 mris_fix_topology ru_maxrss 431784 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 54447 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 19616 mris_fix_topology ru_oublock 13168 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 568 mris_fix_topology ru_nivcsw 2139 FSRUNTIME@ mris_fix_topology lh 0.2806 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 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=-50 (nv=140834, nf=281768, ne=422652, g=26) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 3420 ambiguous faces found in tessellation segmenting defects... 36 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 36 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7348 (-4.8674) -vertex loglikelihood: -6.8606 (-3.4303) -normal dot loglikelihood: -3.6111 (-3.6111) -quad curv loglikelihood: -6.5602 (-3.2801) Total Loglikelihood : -26.7668 CORRECTING DEFECT 0 (vertices=21, convex hull=41, v0=430) After retessellation of defect 0 (v0=430), euler #=-33 (138759,415426,276634) : difference with theory (-33) = 0 CORRECTING DEFECT 1 (vertices=27, convex hull=54, v0=993) After retessellation of defect 1 (v0=993), euler #=-32 (138768,415474,276674) : difference with theory (-32) = 0 CORRECTING DEFECT 2 (vertices=33, convex hull=78, v0=6713) After retessellation of defect 2 (v0=6713), euler #=-31 (138782,415551,276738) : difference with theory (-31) = 0 CORRECTING DEFECT 3 (vertices=12, convex hull=25, v0=9798) After retessellation of defect 3 (v0=9798), euler #=-30 (138782,415557,276745) : difference with theory (-30) = 0 CORRECTING DEFECT 4 (vertices=32, convex hull=69, v0=14733) After retessellation of defect 4 (v0=14733), euler #=-29 (138800,415637,276808) : difference with theory (-29) = 0 CORRECTING DEFECT 5 (vertices=37, convex hull=67, v0=21556) After retessellation of defect 5 (v0=21556), euler #=-28 (138814,415706,276864) : difference with theory (-28) = 0 CORRECTING DEFECT 6 (vertices=46, convex hull=56, v0=22998) After retessellation of defect 6 (v0=22998), euler #=-27 (138824,415756,276905) : difference with theory (-27) = 0 CORRECTING DEFECT 7 (vertices=39, convex hull=79, v0=24789) After retessellation of defect 7 (v0=24789), euler #=-26 (138842,415843,276975) : difference with theory (-26) = 0 CORRECTING DEFECT 8 (vertices=23, convex hull=58, v0=28469) After retessellation of defect 8 (v0=28469), euler #=-25 (138855,415906,277026) : difference with theory (-25) = 0 CORRECTING DEFECT 9 (vertices=29, convex hull=72, v0=44609) After retessellation of defect 9 (v0=44609), euler #=-24 (138870,415978,277084) : difference with theory (-24) = 0 CORRECTING DEFECT 10 (vertices=14, convex hull=61, v0=46348) After retessellation of defect 10 (v0=46348), euler #=-23 (138877,416020,277120) : difference with theory (-23) = 0 CORRECTING DEFECT 11 (vertices=533, convex hull=230, v0=54413) After retessellation of defect 11 (v0=54413), euler #=-22 (139078,416742,277642) : difference with theory (-22) = 0 CORRECTING DEFECT 12 (vertices=75, convex hull=114, v0=57254) After retessellation of defect 12 (v0=57254), euler #=-21 (139111,416891,277759) : difference with theory (-21) = 0 CORRECTING DEFECT 13 (vertices=6, convex hull=29, v0=60947) After retessellation of defect 13 (v0=60947), euler #=-20 (139114,416907,277773) : difference with theory (-20) = 0 CORRECTING DEFECT 14 (vertices=13, convex hull=23, v0=61982) After retessellation of defect 14 (v0=61982), euler #=-19 (139117,416923,277787) : difference with theory (-19) = 0 CORRECTING DEFECT 15 (vertices=34, convex hull=56, v0=72095) After retessellation of defect 15 (v0=72095), euler #=-18 (139128,416977,277831) : difference with theory (-18) = 0 CORRECTING DEFECT 16 (vertices=29, convex hull=74, v0=86194) After retessellation of defect 16 (v0=86194), euler #=-17 (139145,417060,277898) : difference with theory (-17) = 0 CORRECTING DEFECT 17 (vertices=83, convex hull=35, v0=88125) After retessellation of defect 17 (v0=88125), euler #=-16 (139154,417101,277931) : difference with theory (-16) = 0 CORRECTING DEFECT 18 (vertices=6, convex hull=31, v0=91299) After retessellation of defect 18 (v0=91299), euler #=-15 (139157,417119,277947) : difference with theory (-15) = 0 CORRECTING DEFECT 19 (vertices=6, convex hull=18, v0=93459) After retessellation of defect 19 (v0=93459), euler #=-14 (139159,417131,277958) : difference with theory (-14) = 0 CORRECTING DEFECT 20 (vertices=52, convex hull=63, v0=94693) After retessellation of defect 20 (v0=94693), euler #=-13 (139179,417218,278026) : difference with theory (-13) = 0 CORRECTING DEFECT 21 (vertices=74, convex hull=29, v0=94740) After retessellation of defect 21 (v0=94740), euler #=-12 (139187,417255,278056) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=51, convex hull=60, v0=96926) After retessellation of defect 22 (v0=96926), euler #=-11 (139205,417331,278115) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=28, convex hull=64, v0=99171) After retessellation of defect 23 (v0=99171), euler #=-10 (139223,417407,278174) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=25, convex hull=31, v0=99326) After retessellation of defect 24 (v0=99326), euler #=-9 (139229,417435,278197) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=32, convex hull=25, v0=100457) After retessellation of defect 25 (v0=100457), euler #=-8 (139232,417455,278215) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=269, convex hull=67, v0=102839) After retessellation of defect 26 (v0=102839), euler #=-7 (139249,417533,278277) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=12, convex hull=27, v0=108088) After retessellation of defect 27 (v0=108088), euler #=-6 (139253,417554,278295) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=22, convex hull=47, v0=108235) After retessellation of defect 28 (v0=108235), euler #=-5 (139266,417607,278336) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=45, convex hull=92, v0=114956) After retessellation of defect 29 (v0=114956), euler #=-4 (139289,417714,278421) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=21, convex hull=29, v0=115595) After retessellation of defect 30 (v0=115595), euler #=-3 (139293,417733,278437) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=76, convex hull=76, v0=118470) After retessellation of defect 31 (v0=118470), euler #=-2 (139317,417840,278521) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=37, convex hull=68, v0=124542) After retessellation of defect 32 (v0=124542), euler #=-1 (139327,417897,278569) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=152, convex hull=41, v0=127554) After retessellation of defect 33 (v0=127554), euler #=0 (139339,417948,278609) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=46, convex hull=88, v0=129681) After retessellation of defect 34 (v0=129681), euler #=1 (139354,418029,278676) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=43, convex hull=75, v0=135169) After retessellation of defect 35 (v0=135169), euler #=2 (139374,418116,278744) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.09-->6.59) (max @ vno 60282 --> 139396) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.09-->6.59) (max @ vno 60282 --> 139396) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 112 mutations (33.9%), 218 crossovers (66.1%), 81 vertices were eliminated building final representation... 1460 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139374, nf=278744, ne=418116, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 19.2 minutes 0 defective edges removing intersecting faces 000: 201 intersecting 001: 2 intersecting mris_fix_topology utimesec 1150.230138 mris_fix_topology stimesec 0.253961 mris_fix_topology ru_maxrss 435940 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55422 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13296 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 673 mris_fix_topology ru_nivcsw 3223 FSRUNTIME@ mris_fix_topology rh 0.3195 hours 1 threads PIDs (10482 10485) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 138191 - 414567 + 276378 = 2 --> 0 holes F =2V-4: 276378 = 276382-4 (0) 2E=3F: 829134 = 829134 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 139374 - 418116 + 278744 = 2 --> 0 holes F =2V-4: 278744 = 278748-4 (0) 2E=3F: 836232 = 836232 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 66 intersecting 001: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 04:32:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 04:32:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 rh Waiting for PID 11131 of (11131 11134) to complete... Waiting for PID 11134 of (11131 11134) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... 35848 bright wm thresholded. 156 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.orig... computing class statistics... border white: 240312 voxels (1.43%) border gray 287731 voxels (1.72%) WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0] GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 45.3 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 34.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 45.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.03-->2.90) (max @ vno 130587 --> 138144) face area 0.27 +- 0.12 (0.00-->2.04) mean absolute distance = 0.58 +- 0.65 3585 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=105+-7.0, GM=56+-7.0 mean inside = 91.9, mean outside = 65.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=71.0, 116 (116) missing vertices, mean dist 0.3 [0.4 (%33.8)->0.7 (%66.2))] %76 local maxima, %20 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 0.91 +- 0.25 (0.09-->3.17) (max @ vno 72099 --> 72142) face area 0.27 +- 0.13 (0.00-->2.14) mean absolute distance = 0.27 +- 0.39 2967 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5828566.5, rms=14.101 001: dt: 0.5000, sse=3163324.8, rms=9.961 (29.358%) 002: dt: 0.5000, sse=2130821.8, rms=7.776 (21.939%) 003: dt: 0.5000, sse=1630200.8, rms=6.448 (17.076%) 004: dt: 0.5000, sse=1409752.6, rms=5.769 (10.522%) 005: dt: 0.5000, sse=1296108.9, rms=5.376 (6.813%) 006: dt: 0.5000, sse=1256569.2, rms=5.236 (2.610%) 007: dt: 0.5000, sse=1220788.2, rms=5.097 (2.652%) rms = 5.07, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1212928.8, rms=5.068 (0.572%) 009: dt: 0.2500, sse=872511.0, rms=3.516 (30.632%) 010: dt: 0.2500, sse=799205.3, rms=3.094 (11.983%) rms = 3.06, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=795160.0, rms=3.061 (1.065%) 012: dt: 0.1250, sse=708332.5, rms=2.423 (20.857%) 013: dt: 0.1250, sse=692640.4, rms=2.325 (4.057%) rms = 2.31, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=690988.1, rms=2.308 (0.714%) 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 mean border=75.9, 106 (36) missing vertices, mean dist -0.2 [0.3 (%79.7)->0.2 (%20.3))] %86 local maxima, % 9 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 0.90 +- 0.24 (0.11-->3.27) (max @ vno 91467 --> 90257) face area 0.35 +- 0.16 (0.00-->2.79) mean absolute distance = 0.19 +- 0.28 2873 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1799238.1, rms=6.472 015: dt: 0.5000, sse=1271073.2, rms=4.682 (27.666%) rms = 5.10, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=971985.1, rms=3.260 (30.374%) 017: dt: 0.2500, sse=884295.2, rms=2.705 (17.017%) 018: dt: 0.2500, sse=841317.5, rms=2.384 (11.866%) rms = 2.42, time step reduction 2 of 3 to 0.125... 019: dt: 0.1250, sse=815062.8, rms=2.165 (9.189%) 020: dt: 0.1250, sse=779678.9, rms=1.825 (15.679%) 021: dt: 0.1250, sse=773294.4, rms=1.757 (3.747%) rms = 1.75, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=772957.4, rms=1.749 (0.465%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=78.6, 104 (35) missing vertices, mean dist -0.1 [0.2 (%72.0)->0.2 (%28.0))] %90 local maxima, % 5 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 0.90 +- 0.25 (0.09-->3.38) (max @ vno 137832 --> 137848) face area 0.34 +- 0.16 (0.00-->2.80) mean absolute distance = 0.16 +- 0.25 2270 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1043450.6, rms=3.725 rms = 4.70, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=834889.4, rms=2.441 (34.472%) 024: dt: 0.2500, sse=777642.2, rms=1.911 (21.688%) rms = 1.92, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=762493.3, rms=1.766 (7.599%) 026: dt: 0.1250, sse=741858.1, rms=1.547 (12.429%) rms = 1.50, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=737703.9, rms=1.501 (2.935%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=79.4, 109 (34) missing vertices, mean dist -0.0 [0.2 (%55.7)->0.2 (%44.3))] %91 local maxima, % 4 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-6.0.0/0051311/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=758994.1, rms=1.811 rms = 3.12, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=710640.3, rms=1.199 (33.818%) 029: dt: 0.2500, sse=704772.4, rms=1.105 (7.813%) rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.08, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=701658.6, rms=1.080 (2.291%) positioning took 0.5 minutes generating cortex label... 12 non-cortical segments detected only using segment with 7182 vertices erasing segment 1 (vno[0] = 76332) erasing segment 2 (vno[0] = 84616) erasing segment 3 (vno[0] = 88126) erasing segment 4 (vno[0] = 91531) erasing segment 5 (vno[0] = 94153) erasing segment 6 (vno[0] = 98135) erasing segment 7 (vno[0] = 98478) erasing segment 8 (vno[0] = 98489) erasing segment 9 (vno[0] = 104034) erasing segment 10 (vno[0] = 108007) erasing segment 11 (vno[0] = 137881) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->3.35) (max @ vno 90257 --> 91467) face area 0.34 +- 0.15 (0.00-->2.83) refinement took 5.4 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... 35848 bright wm thresholded. 156 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.orig... computing class statistics... border white: 240312 voxels (1.43%) border gray 287731 voxels (1.72%) WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0] GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 58.0 (was 85) setting MAX_CSF to 36.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 26.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.04-->4.58) (max @ vno 138977 --> 139000) face area 0.27 +- 0.12 (0.00-->3.16) mean absolute distance = 0.58 +- 0.67 3762 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=105+-7.0, GM=58+-6.1 mean inside = 92.0, mean outside = 65.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=72.3, 52 (52) missing vertices, mean dist 0.3 [0.4 (%35.8)->0.7 (%64.2))] %74 local maxima, %22 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 0.91 +- 0.25 (0.13-->5.76) (max @ vno 60282 --> 138977) face area 0.27 +- 0.13 (0.00-->5.56) mean absolute distance = 0.27 +- 0.40 2143 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5467821.0, rms=13.538 001: dt: 0.5000, sse=2945513.5, rms=9.482 (29.958%) 002: dt: 0.5000, sse=2017694.5, rms=7.449 (21.441%) 003: dt: 0.5000, sse=1586877.9, rms=6.253 (16.052%) 004: dt: 0.5000, sse=1388094.6, rms=5.630 (9.969%) 005: dt: 0.5000, sse=1274923.0, rms=5.248 (6.785%) 006: dt: 0.5000, sse=1235404.0, rms=5.112 (2.592%) 007: dt: 0.5000, sse=1206988.0, rms=4.978 (2.626%) rms = 4.95, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1192553.5, rms=4.949 (0.578%) 009: dt: 0.2500, sse=855988.6, rms=3.381 (31.691%) 010: dt: 0.2500, sse=785341.0, rms=2.946 (12.850%) rms = 2.90, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=776621.4, rms=2.902 (1.500%) 012: dt: 0.1250, sse=691380.2, rms=2.260 (22.122%) 013: dt: 0.1250, sse=679022.5, rms=2.158 (4.504%) rms = 2.14, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=686921.1, rms=2.137 (0.979%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.0, 57 (8) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))] %85 local maxima, %10 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 0.90 +- 0.25 (0.08-->5.96) (max @ vno 60282 --> 138977) face area 0.34 +- 0.16 (0.00-->7.98) mean absolute distance = 0.18 +- 0.29 2133 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1726784.0, rms=6.185 015: dt: 0.5000, sse=1234674.0, rms=4.496 (27.310%) rms = 4.94, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=946672.4, rms=3.072 (31.683%) 017: dt: 0.2500, sse=868999.9, rms=2.543 (17.223%) 018: dt: 0.2500, sse=829932.0, rms=2.249 (11.534%) rms = 2.28, time step reduction 2 of 3 to 0.125... 019: dt: 0.1250, sse=806890.4, rms=2.041 (9.247%) 020: dt: 0.1250, sse=774507.4, rms=1.719 (15.774%) 021: dt: 0.1250, sse=768998.5, rms=1.659 (3.496%) rms = 1.66, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=768732.5, rms=1.656 (0.205%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 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 3 vertex label from ripped group mean border=79.7, 72 (2) missing vertices, mean dist -0.1 [0.2 (%71.6)->0.2 (%28.4))] %90 local maxima, % 6 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 0.90 +- 0.25 (0.09-->6.06) (max @ vno 60282 --> 138977) face area 0.34 +- 0.16 (0.00-->8.07) mean absolute distance = 0.16 +- 0.25 2187 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1019899.9, rms=3.560 rms = 4.56, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=823222.6, rms=2.297 (35.490%) 024: dt: 0.2500, sse=771493.2, rms=1.811 (21.135%) rms = 1.81, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=758685.1, rms=1.679 (7.281%) 026: dt: 0.1250, sse=741915.2, rms=1.480 (11.875%) rms = 1.44, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=739957.0, rms=1.438 (2.841%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 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 3 vertex label from ripped group mean border=80.4, 87 (2) missing vertices, mean dist -0.0 [0.2 (%54.6)->0.2 (%45.4))] %91 local maxima, % 5 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-6.0.0/0051311/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=758699.2, rms=1.727 rms = 2.97, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=712249.9, rms=1.147 (33.592%) 029: dt: 0.2500, sse=707332.9, rms=1.059 (7.654%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=704595.3, rms=1.037 (2.037%) positioning took 0.5 minutes generating cortex label... 8 non-cortical segments detected only using segment with 7022 vertices erasing segment 1 (vno[0] = 96954) erasing segment 2 (vno[0] = 100245) erasing segment 3 (vno[0] = 100483) erasing segment 4 (vno[0] = 101478) erasing segment 5 (vno[0] = 101683) erasing segment 6 (vno[0] = 102458) erasing segment 7 (vno[0] = 139191) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->6.08) (max @ vno 60282 --> 138977) face area 0.34 +- 0.16 (0.00-->7.95) refinement took 5.7 minutes PIDs (11131 11134) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 04:38:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 04:38:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 11352 of (11352 11355) to complete... Waiting for PID 11355 of (11352 11355) 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 (11352 11355) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 04:38:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 04:38:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 11398 of (11398 11401) to complete... Waiting for PID 11401 of (11398 11401) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.3 mm, total surface area = 83768 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.182 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 61.082714 mris_inflate stimesec 0.108983 mris_inflate ru_maxrss 202404 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29715 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10824 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3526 mris_inflate ru_nivcsw 3846 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.7 mm, total surface area = 84391 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.183 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 47.815730 mris_inflate stimesec 0.094985 mris_inflate ru_maxrss 204116 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29635 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10920 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2309 mris_inflate ru_nivcsw 4203 PIDs (11398 11401) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 04:39:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 04:39:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 11498 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11501 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11504 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11507 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11510 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11513 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11516 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11519 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11522 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11525 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11531 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... Waiting for PID 11534 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 3.249*4pi (40.828) --> -2 handles ICI = 156.9, FI = 2021.3, variation=30512.116 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 145 vertices thresholded to be in k1 ~ [-0.34 0.27], k2 ~ [-0.08 0.10] total integrated curvature = 0.519*4pi (6.527) --> 0 handles ICI = 1.5, FI = 8.2, variation=146.046 104 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 122 vertices thresholded to be in [-0.12 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.021 done. mris_curvature -w rh.white.preaparc total integrated curvature = -2.483*4pi (-31.207) --> 3 handles ICI = 155.6, FI = 2059.7, variation=31019.524 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 206 vertices thresholded to be in k1 ~ [-0.19 0.23], k2 ~ [-0.10 0.07] total integrated curvature = 0.572*4pi (7.182) --> 0 handles ICI = 1.5, FI = 8.7, variation=152.789 120 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 158 vertices thresholded to be in [-0.12 0.11] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.021 done. PIDs (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 04:40:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051311 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 [ 0051311/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 [ 243 ] Gb_filter = 0 WARN: S lookup min: -0.461582 WARN: S explicit min: 0.000000 vertex = 170 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 04:40:59 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051311 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 [ 0051311/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 [ 257 ] Gb_filter = 0 WARN: S lookup min: -0.100520 WARN: S explicit min: 0.000000 vertex = 103 #-------------------------------------------- #@# Sphere lh Sun Oct 8 04:41:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 04:41:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 11695 of (11695 11699) to complete... Waiting for PID 11699 of (11695 11699) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0.307... 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.70 pass 1: epoch 2 of 3 starting distance error %18.70 unfolding complete - removing small folds... starting distance error %18.66 removing remaining folds... final distance error %18.68 MRISunfold() return, current seed 1234 -01: dt=0.0000, 124 negative triangles 199: dt=0.9900, 124 negative triangles 200: dt=0.9900, 39 negative triangles 201: dt=0.9900, 25 negative triangles 202: dt=0.9900, 16 negative triangles 203: dt=0.9900, 15 negative triangles 204: dt=0.9900, 18 negative triangles 205: dt=0.9900, 8 negative triangles 206: dt=0.9900, 7 negative triangles 207: dt=0.9900, 8 negative triangles 208: dt=0.9900, 5 negative triangles 209: dt=0.9900, 4 negative triangles 210: dt=0.9900, 2 negative triangles 211: dt=0.9900, 2 negative triangles 212: dt=0.9900, 1 negative triangles 213: dt=0.9900, 1 negative triangles 214: dt=0.9900, 3 negative triangles 215: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.16 hours mris_sphere utimesec 4172.881625 mris_sphere stimesec 1.909709 mris_sphere ru_maxrss 284624 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50398 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9768 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 122416 mris_sphere ru_nivcsw 347293 FSRUNTIME@ mris_sphere 1.1595 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0.301... 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 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.70 pass 1: epoch 2 of 3 starting distance error %18.69 unfolding complete - removing small folds... starting distance error %18.63 removing remaining folds... final distance error %18.65 MRISunfold() return, current seed 1234 -01: dt=0.0000, 89 negative triangles 220: dt=0.9900, 89 negative triangles 221: dt=0.9900, 23 negative triangles 222: dt=0.9900, 10 negative triangles 223: dt=0.9900, 14 negative triangles 224: dt=0.9900, 6 negative triangles 225: dt=0.9900, 6 negative triangles 226: dt=0.9900, 4 negative triangles 227: dt=0.9900, 4 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, 2 negative triangles 232: dt=0.9900, 1 negative triangles 233: dt=0.9900, 1 negative triangles 234: dt=0.9900, 1 negative triangles 235: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.19 hours mris_sphere utimesec 4384.874397 mris_sphere stimesec 1.973699 mris_sphere ru_maxrss 289184 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50516 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9848 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 137180 mris_sphere ru_nivcsw 340264 FSRUNTIME@ mris_sphere 1.1945 hours 1 threads PIDs (11695 11699) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 05:52:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 05:52:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 15619 of (15619 15622) to complete... Waiting for PID 15622 of (15619 15622) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 5.700 curvature mean = 0.023, std = 0.817 curvature mean = 0.018, std = 0.868 Starting MRISrigidBodyAlignGlobal() d=16.00 min @ (-4.00, -4.00, 0.00) sse = 227802.1, tmin=3.1244 d=8.00 min @ (2.00, 2.00, 0.00) sse = 225854.3, tmin=4.2226 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 223141.5, tmin=5.3361 d=1.00 min @ (0.25, 0.25, 0.00) sse = 223084.5, tmin=7.5552 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 223037.5, tmin=8.6392 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 8.64 min curvature mean = -0.001, std = 0.839 curvature mean = 0.009, std = 0.945 curvature mean = -0.002, std = 0.851 curvature mean = 0.004, std = 0.977 curvature mean = -0.002, std = 0.854 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.026, std = 0.315 curvature mean = 0.039, std = 0.249 curvature mean = 0.072, std = 0.313 curvature mean = 0.035, std = 0.306 curvature mean = 0.041, std = 0.497 curvature mean = 0.034, std = 0.333 curvature mean = 0.023, std = 0.638 curvature mean = 0.034, std = 0.344 curvature mean = 0.008, std = 0.756 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles 111: dt=0.9900, 15 negative triangles expanding nbhd size to 1 112: dt=0.9900, 19 negative triangles 113: dt=0.9900, 13 negative triangles 114: dt=0.9900, 19 negative triangles 115: dt=0.9900, 21 negative triangles 116: dt=0.9900, 20 negative triangles 117: dt=0.9900, 20 negative triangles 118: dt=0.9900, 18 negative triangles 119: dt=0.9900, 15 negative triangles 120: dt=0.9900, 13 negative triangles 121: dt=0.9900, 8 negative triangles 122: dt=0.9900, 9 negative triangles 123: dt=0.9900, 6 negative triangles 124: dt=0.9900, 4 negative triangles 125: dt=0.9900, 2 negative triangles 126: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.56 hours mris_register utimesec 5606.586669 mris_register stimesec 4.234356 mris_register ru_maxrss 256680 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 36015 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 9728 mris_register ru_oublock 9792 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 407330 mris_register ru_nivcsw 269930 FSRUNTIME@ mris_register 1.5585 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 5.713 curvature mean = 0.027, std = 0.813 curvature mean = 0.020, std = 0.866 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 249752.4, tmin=1.0370 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 226703.2, tmin=3.1728 d=4.00 min @ (1.00, 1.00, 1.00) sse = 223628.5, tmin=5.3280 d=2.00 min @ (0.00, 0.00, -0.50) sse = 222983.6, tmin=6.4211 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 222951.1, tmin=7.5114 d=0.50 min @ (0.12, 0.00, 0.12) sse = 222924.3, tmin=8.5917 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 8.59 min curvature mean = -0.005, std = 0.828 curvature mean = 0.009, std = 0.946 curvature mean = -0.009, std = 0.837 curvature mean = 0.004, std = 0.978 curvature mean = -0.011, std = 0.839 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.026, std = 0.319 curvature mean = 0.033, std = 0.240 curvature mean = 0.075, std = 0.318 curvature mean = 0.029, std = 0.297 curvature mean = 0.040, std = 0.500 curvature mean = 0.029, std = 0.322 curvature mean = 0.023, std = 0.639 curvature mean = 0.029, std = 0.334 curvature mean = 0.008, std = 0.758 MRISregister() return, current seed 0 -01: dt=0.0000, 19 negative triangles 115: dt=0.9900, 19 negative triangles expanding nbhd size to 1 116: dt=0.9900, 27 negative triangles 117: dt=0.9900, 18 negative triangles 118: dt=0.9900, 12 negative triangles 119: dt=0.9900, 17 negative triangles 120: dt=0.9900, 18 negative triangles 121: dt=0.9900, 15 negative triangles 122: dt=0.9900, 7 negative triangles 123: dt=0.9900, 7 negative triangles 124: dt=0.9900, 15 negative triangles 125: dt=0.9900, 7 negative triangles 126: dt=0.9900, 9 negative triangles 127: dt=0.9900, 7 negative triangles 128: dt=0.9900, 4 negative triangles 129: dt=0.9900, 4 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 3 negative triangles 132: dt=0.9900, 1 negative triangles 133: dt=0.9900, 4 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.57 hours mris_register utimesec 5649.931079 mris_register stimesec 4.622297 mris_register ru_maxrss 258224 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 36443 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 9880 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 404345 mris_register ru_nivcsw 270991 FSRUNTIME@ mris_register 1.5706 hours 1 threads PIDs (15619 15622) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 07:26:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 07:26:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 23687 of (23687 23690) to complete... Waiting for PID 23690 of (23687 23690) 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 (23687 23690) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 07:27:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 07:27:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 23733 of (23733 23736) to complete... Waiting for PID 23736 of (23733 23736) 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 (23733 23736) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 07:27:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 07:27:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 23783 of (23783 23786) to complete... Waiting for PID 23786 of (23783 23786) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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... 1033 labels changed using aseg relabeling using gibbs priors... 000: 3032 changed, 138191 examined... 001: 716 changed, 12871 examined... 002: 169 changed, 4065 examined... 003: 64 changed, 1012 examined... 004: 24 changed, 393 examined... 005: 11 changed, 156 examined... 006: 6 changed, 65 examined... 007: 0 changed, 36 examined... 241 labels changed using aseg 000: 120 total segments, 78 labels (350 vertices) changed 001: 42 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... 1638 vertices marked for relabeling... 1638 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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... 1353 labels changed using aseg relabeling using gibbs priors... 000: 2925 changed, 139374 examined... 001: 722 changed, 12530 examined... 002: 138 changed, 3960 examined... 003: 47 changed, 832 examined... 004: 26 changed, 286 examined... 005: 9 changed, 154 examined... 006: 3 changed, 54 examined... 007: 3 changed, 18 examined... 008: 1 changed, 18 examined... 009: 1 changed, 7 examined... 010: 0 changed, 7 examined... 122 labels changed using aseg 000: 101 total segments, 64 labels (310 vertices) changed 001: 38 total segments, 1 labels (1 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1320 vertices marked for relabeling... 1320 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. PIDs (23783 23786) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 07:27:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 07:27:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 rh Waiting for PID 23846 of (23846 23849) to complete... Waiting for PID 23849 of (23846 23849) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... 35848 bright wm thresholded. 156 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.orig... computing class statistics... border white: 240312 voxels (1.43%) border gray 287731 voxels (1.72%) WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0] GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 45.3 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 34.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 45.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.0 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-7.0, GM=56+-7.0 mean inside = 91.9, mean outside = 65.1 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 0.90 +- 0.25 (0.03-->3.35) (max @ vno 90257 --> 91467) face area 0.33 +- 0.15 (0.00-->2.81) mean absolute distance = 0.49 +- 0.62 2437 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 83 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown deleting segment 5 with 17 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 166 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 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 8 points - only 0.00% unknown deleting segment 11 with 27 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown deleting segment 18 with 19 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 19 with 2 points - only 0.00% unknown deleting segment 20 with 19 points - only 0.00% unknown mean border=70.5, 113 (112) missing vertices, mean dist 0.4 [0.6 (%10.4)->0.5 (%89.6))] %72 local maxima, %24 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 0.92 +- 0.26 (0.11-->3.58) (max @ vno 137832 --> 137848) face area 0.33 +- 0.16 (0.00-->2.58) mean absolute distance = 0.28 +- 0.40 2414 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3755122.5, rms=10.794 001: dt: 0.5000, sse=1720844.8, rms=6.294 (41.697%) 002: dt: 0.5000, sse=1358764.8, rms=5.124 (18.583%) 003: dt: 0.5000, sse=1314777.1, rms=4.971 (2.987%) 004: dt: 0.5000, sse=1252582.4, rms=4.735 (4.745%) rms = 4.84, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=949344.0, rms=3.266 (31.025%) 006: dt: 0.2500, sse=877987.2, rms=2.809 (13.996%) 007: dt: 0.2500, sse=841022.6, rms=2.544 (9.443%) rms = 2.55, time step reduction 2 of 3 to 0.125... 008: dt: 0.1250, sse=820443.2, rms=2.386 (6.187%) 009: dt: 0.1250, sse=795615.6, rms=2.152 (9.837%) rms = 2.11, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=789494.6, rms=2.105 (2.156%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 64 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 29 points - only 0.00% unknown deleting segment 6 with 47 points - only 0.00% unknown deleting segment 7 with 5 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 5 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=75.6, 127 (45) missing vertices, mean dist -0.2 [0.3 (%81.2)->0.2 (%18.8))] %86 local maxima, %10 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 0.91 +- 0.25 (0.07-->3.74) (max @ vno 103892 --> 102841) face area 0.35 +- 0.17 (0.00-->2.92) mean absolute distance = 0.19 +- 0.28 2959 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1829541.1, rms=6.500 011: dt: 0.5000, sse=1274621.9, rms=4.612 (29.043%) rms = 4.99, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=978680.4, rms=3.181 (31.019%) 013: dt: 0.2500, sse=888229.3, rms=2.577 (19.006%) 014: dt: 0.2500, sse=843763.6, rms=2.248 (12.752%) rms = 2.30, time step reduction 2 of 3 to 0.125... 015: dt: 0.1250, sse=818631.8, rms=2.023 (10.024%) 016: dt: 0.1250, sse=785208.8, rms=1.676 (17.151%) 017: dt: 0.1250, sse=779556.1, rms=1.607 (4.131%) rms = 1.61, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=779488.3, rms=1.606 (0.043%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 63 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 38 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 deleting segment 10 with 6 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 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown deleting segment 16 with 9 points - only 0.00% unknown mean border=78.4, 122 (42) missing vertices, mean dist -0.1 [0.2 (%72.6)->0.2 (%27.4))] %90 local maxima, % 5 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 0.90 +- 0.25 (0.07-->3.84) (max @ vno 103892 --> 102841) face area 0.34 +- 0.16 (0.00-->2.91) mean absolute distance = 0.16 +- 0.25 2168 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1055452.4, rms=3.723 rms = 4.64, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=844207.4, rms=2.417 (35.075%) 020: dt: 0.2500, sse=781465.7, rms=1.848 (23.528%) rms = 1.84, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=781604.3, rms=1.838 (0.528%) 022: dt: 0.1250, sse=745635.4, rms=1.448 (21.246%) 023: dt: 0.1250, sse=741126.8, rms=1.395 (3.653%) rms = 1.40, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=741352.9, rms=1.405 (-0.695%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 69 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 16 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 55 points - only 0.00% unknown deleting segment 6 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 10 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 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 12 points - only 0.00% unknown mean border=79.3, 119 (39) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))] %91 local maxima, % 4 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-6.0.0/0051311/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=765083.0, rms=1.774 rms = 3.17, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=714790.0, rms=1.123 (36.713%) 026: dt: 0.2500, sse=712543.6, rms=1.049 (6.567%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=708560.7, rms=1.023 (2.540%) positioning took 0.5 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7168 vertices erasing segment 1 (vno[0] = 76332) erasing segment 2 (vno[0] = 84616) erasing segment 3 (vno[0] = 91531) erasing segment 4 (vno[0] = 94153) erasing segment 5 (vno[0] = 98442) erasing segment 6 (vno[0] = 98478) erasing segment 7 (vno[0] = 98489) erasing segment 8 (vno[0] = 98786) erasing segment 9 (vno[0] = 104034) erasing segment 10 (vno[0] = 108007) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.area vertex spacing 0.90 +- 0.26 (0.03-->3.82) (max @ vno 102841 --> 103892) face area 0.34 +- 0.16 (0.00-->2.94) 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... removing 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=43.8, 95 (95) missing vertices, mean dist 1.6 [1.1 (%0.0)->2.8 (%100.0))] % 9 local maxima, %45 large gradients and %42 min vals, 220 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=35400876.0, rms=36.216 001: dt: 0.0500, sse=30142642.0, rms=33.361 (7.881%) 002: dt: 0.0500, sse=26413566.0, rms=31.179 (6.541%) 003: dt: 0.0500, sse=23615460.0, rms=29.435 (5.593%) 004: dt: 0.0500, sse=21416034.0, rms=27.989 (4.915%) 005: dt: 0.0500, sse=19622606.0, rms=26.751 (4.422%) 006: dt: 0.0500, sse=18119448.0, rms=25.667 (4.050%) 007: dt: 0.0500, sse=16831526.0, rms=24.701 (3.764%) 008: dt: 0.0500, sse=15711696.0, rms=23.829 (3.530%) 009: dt: 0.0500, sse=14724296.0, rms=23.033 (3.341%) 010: dt: 0.0500, sse=13846595.0, rms=22.301 (3.177%) positioning took 1.0 minutes mean border=43.7, 76 (48) missing vertices, mean dist 1.3 [0.5 (%0.1)->2.3 (%99.9))] %10 local maxima, %45 large gradients and %41 min vals, 218 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=14543182.0, rms=22.888 011: dt: 0.0500, sse=13754083.0, rms=22.227 (2.887%) 012: dt: 0.0500, sse=13043432.0, rms=21.615 (2.756%) 013: dt: 0.0500, sse=12399521.0, rms=21.044 (2.639%) 014: dt: 0.0500, sse=11814524.0, rms=20.512 (2.528%) 015: dt: 0.0500, sse=11282697.0, rms=20.016 (2.418%) 016: dt: 0.0500, sse=10798164.0, rms=19.553 (2.313%) 017: dt: 0.0500, sse=10355857.0, rms=19.121 (2.212%) 018: dt: 0.0500, sse=9950833.0, rms=18.716 (2.118%) 019: dt: 0.0500, sse=9579313.0, rms=18.336 (2.027%) 020: dt: 0.0500, sse=9237729.0, rms=17.980 (1.941%) positioning took 1.0 minutes mean border=43.6, 85 (34) missing vertices, mean dist 1.1 [0.1 (%0.7)->2.0 (%99.3))] %10 local maxima, %44 large gradients and %41 min vals, 208 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=9338763.0, rms=18.093 021: dt: 0.0500, sse=9018147.0, rms=17.755 (1.871%) 022: dt: 0.0500, sse=8721436.0, rms=17.436 (1.798%) 023: dt: 0.0500, sse=8445248.0, rms=17.133 (1.735%) 024: dt: 0.0500, sse=8188415.0, rms=16.847 (1.671%) 025: dt: 0.0500, sse=7948759.5, rms=16.575 (1.613%) 026: dt: 0.0500, sse=7723675.5, rms=16.315 (1.565%) 027: dt: 0.0500, sse=7510516.5, rms=16.066 (1.530%) 028: dt: 0.0500, sse=7307269.5, rms=15.824 (1.505%) 029: dt: 0.0500, sse=7112988.0, rms=15.589 (1.483%) 030: dt: 0.0500, sse=6926479.0, rms=15.360 (1.468%) positioning took 0.9 minutes mean border=43.5, 112 (30) missing vertices, mean dist 0.9 [0.1 (%4.9)->1.7 (%95.1))] %10 local maxima, %44 large gradients and %41 min vals, 166 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=6972207.5, rms=15.419 031: dt: 0.5000, sse=5598785.5, rms=13.625 (11.640%) 032: dt: 0.5000, sse=4584189.0, rms=12.123 (11.021%) 033: dt: 0.5000, sse=3793819.2, rms=10.811 (10.822%) 034: dt: 0.5000, sse=3181480.2, rms=9.667 (10.578%) 035: dt: 0.5000, sse=2730441.5, rms=8.729 (9.705%) 036: dt: 0.5000, sse=2366877.2, rms=7.889 (9.629%) 037: dt: 0.5000, sse=2089727.8, rms=7.184 (8.930%) 038: dt: 0.5000, sse=1870660.0, rms=6.573 (8.510%) 039: dt: 0.5000, sse=1730285.9, rms=6.149 (6.445%) 040: dt: 0.5000, sse=1625369.5, rms=5.812 (5.489%) 041: dt: 0.5000, sse=1570804.9, rms=5.628 (3.152%) 042: dt: 0.5000, sse=1521996.8, rms=5.458 (3.024%) 043: dt: 0.5000, sse=1496413.9, rms=5.368 (1.657%) 044: dt: 0.5000, sse=1465133.0, rms=5.254 (2.122%) rms = 5.23, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1459227.6, rms=5.232 (0.425%) 046: dt: 0.2500, sse=1347008.4, rms=4.757 (9.069%) 047: dt: 0.2500, sse=1311001.9, rms=4.612 (3.048%) rms = 4.62, time step reduction 2 of 3 to 0.125... rms = 4.57, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1302025.4, rms=4.572 (0.879%) positioning took 2.5 minutes mean border=42.2, 2417 (15) missing vertices, mean dist 0.1 [0.2 (%47.2)->0.6 (%52.8))] %20 local maxima, %36 large gradients and %39 min vals, 100 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=1629398.2, rms=5.002 049: dt: 0.5000, sse=1534525.8, rms=4.632 (7.395%) 050: dt: 0.5000, sse=1497675.2, rms=4.513 (2.571%) rms = 4.57, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1371910.9, rms=3.893 (13.723%) 052: dt: 0.2500, sse=1337024.2, rms=3.697 (5.052%) rms = 3.65, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1328096.1, rms=3.649 (1.284%) 054: dt: 0.1250, sse=1298250.0, rms=3.477 (4.719%) rms = 3.44, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1291071.1, rms=3.438 (1.108%) positioning took 1.3 minutes mean border=41.4, 2512 (11) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.4 (%51.9))] %35 local maxima, %21 large gradients and %38 min vals, 99 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=1355480.8, rms=3.741 rms = 4.21, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1316513.9, rms=3.529 (5.675%) 057: dt: 0.2500, sse=1304796.2, rms=3.469 (1.695%) rms = 3.46, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=1302105.6, rms=3.463 (0.171%) 059: dt: 0.1250, sse=1281792.0, rms=3.343 (3.473%) rms = 3.31, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1275961.2, rms=3.312 (0.910%) positioning took 1.0 minutes mean border=40.8, 4618 (10) missing vertices, mean dist 0.0 [0.2 (%50.1)->0.3 (%49.9))] %37 local maxima, %18 large gradients and %37 min vals, 110 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-6.0.0/0051311/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1298095.1, rms=3.415 rms = 3.82, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1279861.1, rms=3.307 (3.139%) rms = 3.26, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1268734.1, rms=3.260 (1.423%) 063: dt: 0.1250, sse=1258230.9, rms=3.193 (2.059%) rms = 3.16, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1252270.2, rms=3.164 (0.930%) positioning took 0.9 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.area.pial vertex spacing 1.04 +- 0.46 (0.09-->6.78) (max @ vno 92738 --> 91562) face area 0.42 +- 0.34 (0.00-->5.97) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 138191 vertices processed 25000 of 138191 vertices processed 50000 of 138191 vertices processed 75000 of 138191 vertices processed 100000 of 138191 vertices processed 125000 of 138191 vertices processed 0 of 138191 vertices processed 25000 of 138191 vertices processed 50000 of 138191 vertices processed 75000 of 138191 vertices processed 100000 of 138191 vertices processed 125000 of 138191 vertices processed thickness calculation complete, 143:745 truncations. 28741 vertices at 0 distance 95024 vertices at 1 distance 87752 vertices at 2 distance 37377 vertices at 3 distance 11270 vertices at 4 distance 3122 vertices at 5 distance 922 vertices at 6 distance 311 vertices at 7 distance 122 vertices at 8 distance 61 vertices at 9 distance 60 vertices at 10 distance 43 vertices at 11 distance 33 vertices at 12 distance 25 vertices at 13 distance 20 vertices at 14 distance 24 vertices at 15 distance 22 vertices at 16 distance 21 vertices at 17 distance 15 vertices at 18 distance 15 vertices at 19 distance 10 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.thickness positioning took 15.8 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... 35848 bright wm thresholded. 156 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.orig... computing class statistics... border white: 240312 voxels (1.43%) border gray 287731 voxels (1.72%) WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0] GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 58.0 (was 85) setting MAX_CSF to 36.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 26.0 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-7.0, GM=58+-6.1 mean inside = 92.0, mean outside = 65.8 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 0.89 +- 0.25 (0.04-->6.08) (max @ vno 60282 --> 138977) face area 0.33 +- 0.16 (0.00-->7.91) mean absolute distance = 0.48 +- 0.63 2484 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 181 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 34 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown mean border=71.9, 71 (71) missing vertices, mean dist 0.3 [0.6 (%11.3)->0.5 (%88.7))] %70 local maxima, %26 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 0.92 +- 0.26 (0.08-->6.18) (max @ vno 60282 --> 138977) face area 0.33 +- 0.16 (0.00-->7.21) mean absolute distance = 0.28 +- 0.39 1995 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3506080.5, rms=10.292 001: dt: 0.5000, sse=1637130.2, rms=5.947 (42.215%) 002: dt: 0.5000, sse=1305644.6, rms=4.883 (17.894%) rms = 4.83, time step reduction 1 of 3 to 0.250... 003: dt: 0.5000, sse=1289566.8, rms=4.833 (1.024%) 004: dt: 0.2500, sse=900513.7, rms=2.920 (39.584%) 005: dt: 0.2500, sse=852226.1, rms=2.594 (11.165%) 006: dt: 0.2500, sse=841431.1, rms=2.505 (3.426%) rms = 2.47, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=838076.6, rms=2.466 (1.569%) 008: dt: 0.1250, sse=788703.8, rms=2.061 (16.399%) 009: dt: 0.1250, sse=783273.6, rms=1.987 (3.614%) rms = 1.97, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=780424.3, rms=1.974 (0.665%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 4 with 48 points - only 0.00% unknown deleting segment 5 with 61 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown mean border=76.8, 70 (13) missing vertices, mean dist -0.2 [0.3 (%80.5)->0.2 (%19.5))] %85 local maxima, %11 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 0.90 +- 0.25 (0.12-->6.34) (max @ vno 60282 --> 138977) face area 0.35 +- 0.17 (0.00-->8.36) mean absolute distance = 0.19 +- 0.29 2215 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1736477.6, rms=6.191 011: dt: 0.5000, sse=1224823.8, rms=4.380 (29.249%) rms = 4.85, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=942636.1, rms=2.937 (32.940%) 013: dt: 0.2500, sse=864538.9, rms=2.383 (18.875%) 014: dt: 0.2500, sse=830967.2, rms=2.099 (11.912%) rms = 2.14, time step reduction 2 of 3 to 0.125... 015: dt: 0.1250, sse=815277.8, rms=1.886 (10.134%) 016: dt: 0.1250, sse=778571.7, rms=1.558 (17.378%) 017: dt: 0.1250, sse=773968.8, rms=1.506 (3.381%) rms = 1.51, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=774367.0, rms=1.514 (-0.546%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 66 points - only 0.00% unknown deleting segment 4 with 64 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 15 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown mean border=79.5, 81 (9) missing vertices, mean dist -0.1 [0.2 (%72.2)->0.2 (%27.8))] %90 local maxima, % 6 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 0.90 +- 0.25 (0.04-->6.49) (max @ vno 60282 --> 138977) face area 0.34 +- 0.17 (0.00-->8.51) mean absolute distance = 0.16 +- 0.25 2171 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1030806.9, rms=3.559 rms = 4.52, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=831310.8, rms=2.276 (36.065%) 020: dt: 0.2500, sse=778198.8, rms=1.744 (23.345%) rms = 1.73, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=773353.0, rms=1.732 (0.710%) 022: dt: 0.1250, sse=744248.8, rms=1.383 (20.166%) rms = 1.33, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=741281.4, rms=1.334 (3.503%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 82 points - only 0.00% unknown deleting segment 4 with 64 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 17 points - only 0.00% unknown deleting segment 7 with 34 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 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=80.2, 75 (6) missing vertices, mean dist -0.0 [0.2 (%55.4)->0.2 (%44.6))] %91 local maxima, % 5 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-6.0.0/0051311/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=762835.1, rms=1.693 rms = 3.04, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=716406.3, rms=1.070 (36.794%) 025: dt: 0.2500, sse=720953.5, rms=1.004 (6.194%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=712810.8, rms=0.979 (2.487%) positioning took 0.5 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6998 vertices erasing segment 1 (vno[0] = 100245) erasing segment 2 (vno[0] = 100483) erasing segment 3 (vno[0] = 101478) erasing segment 4 (vno[0] = 101683) erasing segment 5 (vno[0] = 102458) erasing segment 6 (vno[0] = 106694) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.area vertex spacing 0.90 +- 0.26 (0.02-->6.50) (max @ vno 60282 --> 138977) face area 0.34 +- 0.16 (0.00-->8.45) 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... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=45.7, 68 (68) missing vertices, mean dist 1.6 [0.7 (%0.0)->2.8 (%100.0))] %11 local maxima, %45 large gradients and %40 min vals, 252 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=33686880.0, rms=35.163 001: dt: 0.0500, sse=28598608.0, rms=32.340 (8.029%) 002: dt: 0.0500, sse=24998718.0, rms=30.183 (6.669%) 003: dt: 0.0500, sse=22307940.0, rms=28.464 (5.695%) 004: dt: 0.0500, sse=20196632.0, rms=27.039 (5.007%) 005: dt: 0.0500, sse=18481422.0, rms=25.823 (4.496%) 006: dt: 0.0500, sse=17047234.0, rms=24.761 (4.114%) 007: dt: 0.0500, sse=15822758.0, rms=23.817 (3.815%) 008: dt: 0.0500, sse=14760817.0, rms=22.966 (3.572%) 009: dt: 0.0500, sse=13828668.0, rms=22.192 (3.369%) 010: dt: 0.0500, sse=13001732.0, rms=21.483 (3.198%) positioning took 1.0 minutes mean border=45.6, 62 (30) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.3 (%100.0))] %12 local maxima, %45 large gradients and %40 min vals, 284 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=13753555.0, rms=22.134 011: dt: 0.0500, sse=13011137.0, rms=21.496 (2.881%) 012: dt: 0.0500, sse=12343652.0, rms=20.906 (2.745%) 013: dt: 0.0500, sse=11739548.0, rms=20.357 (2.625%) 014: dt: 0.0500, sse=11190804.0, rms=19.846 (2.514%) 015: dt: 0.0500, sse=10692594.0, rms=19.369 (2.400%) 016: dt: 0.0500, sse=10238159.0, rms=18.924 (2.298%) 017: dt: 0.0500, sse=9823011.0, rms=18.508 (2.198%) 018: dt: 0.0500, sse=9443201.0, rms=18.119 (2.102%) 019: dt: 0.0500, sse=9094914.0, rms=17.755 (2.011%) 020: dt: 0.0500, sse=8774104.0, rms=17.412 (1.929%) positioning took 1.0 minutes mean border=45.5, 70 (22) missing vertices, mean dist 1.1 [0.1 (%0.7)->2.0 (%99.3))] %12 local maxima, %45 large gradients and %39 min vals, 266 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=8848638.0, rms=17.501 021: dt: 0.0500, sse=8547564.0, rms=17.175 (1.863%) 022: dt: 0.0500, sse=8269377.5, rms=16.868 (1.787%) 023: dt: 0.0500, sse=8009411.5, rms=16.576 (1.731%) 024: dt: 0.0500, sse=7767427.0, rms=16.299 (1.669%) 025: dt: 0.0500, sse=7541563.5, rms=16.037 (1.611%) 026: dt: 0.0500, sse=7329277.5, rms=15.786 (1.565%) 027: dt: 0.0500, sse=7127478.5, rms=15.543 (1.535%) 028: dt: 0.0500, sse=6934666.0, rms=15.308 (1.514%) 029: dt: 0.0500, sse=6749800.0, rms=15.079 (1.497%) 030: dt: 0.0500, sse=6571519.5, rms=14.855 (1.488%) positioning took 1.0 minutes mean border=45.4, 94 (17) missing vertices, mean dist 1.0 [0.1 (%5.2)->1.7 (%94.8))] %12 local maxima, %44 large gradients and %39 min vals, 242 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=6635909.0, rms=14.938 031: dt: 0.5000, sse=5311811.5, rms=13.164 (11.876%) 032: dt: 0.5000, sse=4357166.5, rms=11.713 (11.025%) 033: dt: 0.5000, sse=3644997.2, rms=10.501 (10.346%) 034: dt: 0.5000, sse=3093473.2, rms=9.450 (10.012%) 035: dt: 0.5000, sse=2674150.0, rms=8.564 (9.375%) 036: dt: 0.5000, sse=2334165.0, rms=7.769 (9.280%) 037: dt: 0.5000, sse=2068139.1, rms=7.087 (8.785%) 038: dt: 0.5000, sse=1857737.1, rms=6.496 (8.337%) 039: dt: 0.5000, sse=1712160.9, rms=6.055 (6.793%) 040: dt: 0.5000, sse=1605909.4, rms=5.710 (5.696%) 041: dt: 0.5000, sse=1540755.8, rms=5.490 (3.851%) 042: dt: 0.5000, sse=1492366.5, rms=5.318 (3.129%) 043: dt: 0.5000, sse=1463870.8, rms=5.215 (1.941%) 044: dt: 0.5000, sse=1441382.5, rms=5.132 (1.597%) 045: dt: 0.5000, sse=1426086.8, rms=5.075 (1.097%) rms = 5.04, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1416135.0, rms=5.035 (0.785%) 047: dt: 0.2500, sse=1308482.0, rms=4.564 (9.371%) 048: dt: 0.2500, sse=1272248.1, rms=4.411 (3.334%) rms = 4.41, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1273089.4, rms=4.411 (0.010%) 050: dt: 0.1250, sse=1252802.1, rms=4.317 (2.129%) rms = 4.30, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1250073.1, rms=4.305 (0.288%) positioning took 2.9 minutes mean border=44.0, 2227 (5) missing vertices, mean dist 0.1 [0.2 (%45.5)->0.6 (%54.5))] %23 local maxima, %35 large gradients and %36 min vals, 129 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=1593886.6, rms=4.846 052: dt: 0.5000, sse=1497191.9, rms=4.467 (7.823%) 053: dt: 0.5000, sse=1466858.5, rms=4.372 (2.119%) rms = 4.41, time step reduction 1 of 3 to 0.250... 054: dt: 0.2500, sse=1339865.2, rms=3.729 (14.697%) 055: dt: 0.2500, sse=1301667.6, rms=3.508 (5.944%) rms = 3.46, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1294036.9, rms=3.465 (1.222%) 057: dt: 0.1250, sse=1264678.0, rms=3.288 (5.097%) rms = 3.25, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1257964.2, rms=3.251 (1.146%) positioning took 1.3 minutes mean border=43.0, 2351 (5) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))] %38 local maxima, %21 large gradients and %35 min vals, 137 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=1336434.6, rms=3.646 rms = 4.08, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1290467.0, rms=3.389 (7.028%) 060: dt: 0.2500, sse=1274165.2, rms=3.300 (2.648%) rms = 3.29, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1270490.0, rms=3.289 (0.332%) 062: dt: 0.1250, sse=1252317.0, rms=3.175 (3.454%) rms = 3.15, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1247989.9, rms=3.152 (0.728%) positioning took 1.0 minutes mean border=42.4, 4370 (5) missing vertices, mean dist 0.0 [0.2 (%48.3)->0.3 (%51.7))] %40 local maxima, %18 large gradients and %35 min vals, 134 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-6.0.0/0051311/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1269251.2, rms=3.261 rms = 3.71, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1250575.6, rms=3.147 (3.489%) rms = 3.11, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1241583.0, rms=3.110 (1.186%) 066: dt: 0.1250, sse=1231497.6, rms=3.043 (2.143%) rms = 3.02, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1226325.2, rms=3.017 (0.855%) positioning took 0.9 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.area.pial vertex spacing 1.03 +- 0.46 (0.03-->9.26) (max @ vno 139072 --> 65119) face area 0.42 +- 0.34 (0.00-->6.53) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 139374 vertices processed 25000 of 139374 vertices processed 50000 of 139374 vertices processed 75000 of 139374 vertices processed 100000 of 139374 vertices processed 125000 of 139374 vertices processed 0 of 139374 vertices processed 25000 of 139374 vertices processed 50000 of 139374 vertices processed 75000 of 139374 vertices processed 100000 of 139374 vertices processed 125000 of 139374 vertices processed thickness calculation complete, 221:675 truncations. 28637 vertices at 0 distance 93291 vertices at 1 distance 88975 vertices at 2 distance 38766 vertices at 3 distance 11881 vertices at 4 distance 3540 vertices at 5 distance 1139 vertices at 6 distance 347 vertices at 7 distance 151 vertices at 8 distance 95 vertices at 9 distance 52 vertices at 10 distance 21 vertices at 11 distance 26 vertices at 12 distance 35 vertices at 13 distance 31 vertices at 14 distance 28 vertices at 15 distance 26 vertices at 16 distance 31 vertices at 17 distance 17 vertices at 18 distance 15 vertices at 19 distance 26 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.thickness positioning took 15.9 minutes PIDs (23846 23849) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 07:43:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label Total face volume 271164 Total vertex volume 267919 (mask=0) #@# 0051311 lh 267919 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 07:43:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label Total face volume 271597 Total vertex volume 268028 (mask=0) #@# 0051311 rh 268028 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 07:43:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 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 = 238 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/ribbon.mgz mris_volmask took 17.72 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 08:01:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 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 0051311 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 08:01:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 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 0051311 rh pial Waiting for PID 25410 of (25410 25413 25416 25419) to complete... Waiting for PID 25413 of (25410 25413 25416 25419) to complete... Waiting for PID 25416 of (25410 25413 25416 25419) to complete... Waiting for PID 25419 of (25410 25413 25416 25419) 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 0051311 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164 Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1751 1185 3061 2.548 0.430 0.122 0.032 28 2.5 bankssts 615 414 1115 2.693 0.484 0.100 0.013 5 0.3 caudalanteriorcingulate 3360 2263 6758 2.677 0.425 0.114 0.021 36 2.9 caudalmiddlefrontal 2359 1525 3329 1.972 0.452 0.147 0.038 40 3.4 cuneus 483 317 1829 3.805 0.728 0.106 0.027 4 0.4 entorhinal 4170 2848 9692 2.932 0.572 0.127 0.027 57 4.7 fusiform 7437 5191 16241 2.646 0.535 0.130 0.027 129 9.1 inferiorparietal 3777 2605 9676 2.914 0.662 0.140 0.037 66 5.3 inferiortemporal 1789 1162 3163 2.452 0.941 0.125 0.028 27 1.9 isthmuscingulate 9160 5981 15375 2.353 0.490 0.136 0.029 142 10.6 lateraloccipital 3810 2644 8905 2.923 0.591 0.134 0.033 52 5.1 lateralorbitofrontal 4541 3113 7617 2.283 0.564 0.140 0.032 68 6.1 lingual 2613 1775 5365 2.702 0.607 0.120 0.028 38 3.0 medialorbitofrontal 4473 3129 11900 2.903 0.636 0.134 0.031 84 6.0 middletemporal 998 641 1860 2.523 0.603 0.081 0.015 6 0.5 parahippocampal 2160 1366 4160 2.785 0.450 0.100 0.019 17 1.5 paracentral 2528 1754 5524 2.719 0.444 0.117 0.026 31 2.6 parsopercularis 960 647 2352 2.725 0.542 0.156 0.048 21 1.9 parsorbitalis 1914 1355 4178 2.660 0.427 0.138 0.035 40 2.5 parstriangularis 1921 1319 2059 1.793 0.411 0.140 0.033 28 2.5 pericalcarine 7804 5159 13868 2.319 0.574 0.121 0.024 105 7.5 postcentral 1716 1140 3778 2.886 0.628 0.116 0.023 21 1.7 posteriorcingulate 8302 5589 17097 2.717 0.497 0.101 0.018 73 5.8 precentral 7201 4907 14122 2.569 0.544 0.126 0.026 106 7.5 precuneus 1266 821 2799 2.857 0.525 0.118 0.023 18 1.1 rostralanteriorcingulate 7239 4949 14379 2.504 0.533 0.143 0.039 155 11.6 rostralmiddlefrontal 11100 7625 25452 2.825 0.534 0.124 0.026 139 11.5 superiorfrontal 9031 5916 16043 2.470 0.464 0.124 0.023 123 8.5 superiorparietal 6076 4070 14232 2.905 0.619 0.106 0.021 66 5.4 superiortemporal 4606 3160 9826 2.784 0.532 0.129 0.025 78 5.1 supramarginal 456 293 1112 2.687 0.526 0.155 0.042 13 0.9 frontalpole 669 466 2453 3.637 0.631 0.144 0.040 12 1.1 temporalpole 688 419 1283 2.602 0.343 0.105 0.018 7 0.4 transversetemporal 3465 2333 7241 3.092 0.687 0.126 0.033 55 4.3 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 0051311 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164 Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1751 1188 3061 2.548 0.430 0.135 0.037 38 3.0 bankssts 615 503 1115 2.693 0.484 0.151 0.037 10 1.1 caudalanteriorcingulate 3360 2700 6758 2.677 0.425 0.142 0.033 52 4.9 caudalmiddlefrontal 2359 1919 3329 1.972 0.452 0.146 0.035 35 3.5 cuneus 483 646 1829 3.805 0.728 0.213 0.050 7 1.1 entorhinal 4170 3811 9692 2.932 0.572 0.166 0.043 70 8.2 fusiform 7437 6973 16241 2.646 0.535 0.164 0.038 117 12.9 inferiorparietal 3777 3799 9676 2.914 0.662 0.195 0.056 194 10.2 inferiortemporal 1789 1468 3163 2.452 0.941 0.163 0.045 33 3.7 isthmuscingulate 9160 7264 15375 2.353 0.490 0.140 0.034 140 13.5 lateraloccipital 3810 3364 8905 2.923 0.591 0.169 0.044 72 7.6 lateralorbitofrontal 4541 3764 7617 2.283 0.564 0.151 0.045 84 8.4 lingual 2613 2267 5365 2.702 0.607 0.163 0.040 49 4.7 medialorbitofrontal 4473 4852 11900 2.903 0.636 0.182 0.037 65 8.0 middletemporal 998 867 1860 2.523 0.603 0.138 0.032 7 1.5 parahippocampal 2160 1617 4160 2.785 0.450 0.126 0.027 30 2.5 paracentral 2528 2245 5524 2.719 0.444 0.154 0.032 31 3.7 parsopercularis 960 999 2352 2.725 0.542 0.210 0.048 15 2.1 parsorbitalis 1914 1761 4178 2.660 0.427 0.175 0.038 30 3.5 parstriangularis 1921 1062 2059 1.793 0.411 0.117 0.037 40 3.2 pericalcarine 7804 6627 13868 2.319 0.574 0.139 0.028 92 9.1 postcentral 1716 1467 3778 2.886 0.628 0.164 0.041 55 3.1 posteriorcingulate 8302 6720 17097 2.717 0.497 0.123 0.024 94 8.7 precentral 7201 5943 14122 2.569 0.544 0.149 0.036 111 11.5 precuneus 1266 1155 2799 2.857 0.525 0.156 0.036 18 2.0 rostralanteriorcingulate 7239 6410 14379 2.504 0.533 0.177 0.044 131 14.9 rostralmiddlefrontal 11100 9930 25452 2.825 0.534 0.148 0.033 158 15.7 superiorfrontal 9031 7007 16043 2.470 0.464 0.141 0.033 133 13.0 superiorparietal 6076 5426 14232 2.905 0.619 0.148 0.031 78 8.8 superiortemporal 4606 3730 9826 2.784 0.532 0.148 0.036 66 7.1 supramarginal 456 544 1112 2.687 0.526 0.238 0.050 6 1.3 frontalpole 669 907 2453 3.637 0.631 0.202 0.040 12 1.2 temporalpole 688 579 1283 2.602 0.343 0.127 0.033 4 1.0 transversetemporal 3465 2282 7241 3.092 0.687 0.143 0.044 75 5.6 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 0051311 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597 Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1636 1131 3064 2.684 0.433 0.120 0.022 22 1.3 bankssts 1049 722 2374 2.903 0.544 0.114 0.016 11 0.7 caudalanteriorcingulate 2734 1864 5384 2.678 0.413 0.115 0.021 29 2.2 caudalmiddlefrontal 2752 1773 4203 2.089 0.526 0.146 0.044 48 4.7 cuneus 585 388 1929 3.454 0.684 0.137 0.046 8 1.0 entorhinal 4177 2779 9760 3.018 0.575 0.129 0.028 62 4.9 fusiform 8872 6055 18999 2.727 0.482 0.131 0.026 141 9.5 inferiorparietal 3945 2608 9248 2.929 0.651 0.123 0.030 66 4.9 inferiortemporal 1746 1124 3194 2.434 0.930 0.119 0.028 26 1.9 isthmuscingulate 8556 5549 14547 2.366 0.515 0.132 0.030 130 9.6 lateraloccipital 3538 2426 7704 2.792 0.593 0.138 0.036 60 4.8 lateralorbitofrontal 4594 3070 8635 2.418 0.652 0.141 0.036 75 6.9 lingual 2614 1866 5771 2.629 0.590 0.129 0.032 45 3.2 medialorbitofrontal 4846 3276 12295 3.066 0.594 0.123 0.025 78 4.8 middletemporal 843 583 1743 2.702 0.529 0.097 0.018 7 0.4 parahippocampal 2404 1541 4347 2.609 0.438 0.104 0.020 19 1.9 paracentral 2133 1474 4705 2.777 0.464 0.120 0.024 28 2.1 parsopercularis 1107 775 2733 2.851 0.595 0.153 0.042 22 2.0 parsorbitalis 2620 1814 5349 2.566 0.428 0.139 0.030 60 3.0 parstriangularis 2399 1592 2624 1.864 0.431 0.133 0.031 33 3.0 pericalcarine 5894 3887 9629 2.194 0.550 0.113 0.021 69 4.8 postcentral 2260 1506 4724 2.677 0.850 0.129 0.029 35 2.4 posteriorcingulate 7711 5141 15317 2.678 0.472 0.110 0.020 75 6.3 precentral 6871 4594 13690 2.645 0.520 0.120 0.026 94 7.3 precuneus 996 682 2234 2.911 0.439 0.142 0.038 25 1.4 rostralanteriorcingulate 7823 5334 15522 2.466 0.559 0.139 0.037 161 11.6 rostralmiddlefrontal 11518 7865 25748 2.793 0.539 0.120 0.026 143 11.3 superiorfrontal 9407 6253 16577 2.425 0.420 0.123 0.024 138 8.7 superiorparietal 5854 3968 13019 2.857 0.524 0.110 0.021 69 5.2 superiortemporal 5353 3604 10994 2.743 0.460 0.120 0.023 75 5.0 supramarginal 469 311 1231 2.743 0.521 0.171 0.056 17 1.3 frontalpole 542 384 2482 4.018 0.659 0.143 0.044 11 1.1 temporalpole 567 338 1069 2.611 0.303 0.111 0.018 8 0.3 transversetemporal 3239 2204 7153 3.142 0.707 0.127 0.031 44 4.0 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 0051311 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597 Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1636 1127 3064 2.684 0.433 0.132 0.035 26 2.2 bankssts 1049 918 2374 2.903 0.544 0.152 0.032 24 1.3 caudalanteriorcingulate 2734 2074 5384 2.678 0.413 0.131 0.027 36 3.4 caudalmiddlefrontal 2752 2254 4203 2.089 0.526 0.154 0.041 45 5.0 cuneus 585 691 1929 3.454 0.684 0.174 0.042 7 1.1 entorhinal 4177 3622 9760 3.018 0.575 0.161 0.042 92 8.6 fusiform 8872 7617 18999 2.727 0.482 0.156 0.038 142 14.6 inferiorparietal 3945 3608 9248 2.929 0.651 0.164 0.041 66 7.7 inferiortemporal 1746 1382 3194 2.434 0.930 0.156 0.044 32 3.2 isthmuscingulate 8556 6770 14547 2.366 0.515 0.140 0.036 151 13.4 lateraloccipital 3538 3103 7704 2.792 0.593 0.178 0.073 91 14.6 lateralorbitofrontal 4594 4094 8635 2.418 0.652 0.163 0.044 85 8.9 lingual 2614 2471 5771 2.629 0.590 0.164 0.040 39 4.6 medialorbitofrontal 4846 4711 12295 3.066 0.594 0.161 0.035 64 7.9 middletemporal 843 709 1743 2.702 0.529 0.144 0.034 17 1.4 parahippocampal 2404 1763 4347 2.609 0.438 0.122 0.028 28 2.8 paracentral 2133 1868 4705 2.777 0.464 0.151 0.032 28 3.1 parsopercularis 1107 1142 2733 2.851 0.595 0.203 0.050 24 2.6 parsorbitalis 2620 2348 5349 2.566 0.428 0.165 0.037 36 4.2 parstriangularis 2399 1311 2624 1.864 0.431 0.104 0.027 47 2.5 pericalcarine 5894 4880 9629 2.194 0.550 0.133 0.026 60 6.6 postcentral 2260 1936 4724 2.677 0.850 0.158 0.038 36 4.0 posteriorcingulate 7711 6026 15317 2.678 0.472 0.123 0.024 95 8.1 precentral 6871 5643 13690 2.645 0.520 0.144 0.034 101 10.4 precuneus 996 903 2234 2.911 0.439 0.171 0.046 22 1.9 rostralanteriorcingulate 7823 7057 15522 2.466 0.559 0.184 0.047 144 17.3 rostralmiddlefrontal 11518 10018 25748 2.793 0.539 0.147 0.032 158 16.1 superiorfrontal 9407 7406 16577 2.425 0.420 0.141 0.032 139 12.9 superiorparietal 5854 5090 13019 2.857 0.524 0.140 0.030 76 7.9 superiortemporal 5353 4225 10994 2.743 0.460 0.135 0.031 72 7.0 supramarginal 469 571 1231 2.743 0.521 0.224 0.047 6 1.1 frontalpole 542 832 2482 4.018 0.659 0.208 0.033 7 0.8 temporalpole 567 468 1069 2.611 0.303 0.123 0.024 3 0.6 transversetemporal 3239 2090 7153 3.142 0.707 0.132 0.038 115 5.5 insula PIDs (25410 25413 25416 25419) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 08:02:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 08:02:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 25513 of (25513 25516) to complete... Waiting for PID 25516 of (25513 25516) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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... 34 labels changed using aseg relabeling using gibbs priors... 000: 9319 changed, 138191 examined... 001: 2212 changed, 36062 examined... 002: 623 changed, 11496 examined... 003: 242 changed, 3509 examined... 004: 106 changed, 1341 examined... 005: 64 changed, 632 examined... 006: 37 changed, 335 examined... 007: 19 changed, 220 examined... 008: 12 changed, 101 examined... 009: 1 changed, 57 examined... 010: 0 changed, 6 examined... 10 labels changed using aseg 000: 295 total segments, 206 labels (2377 vertices) changed 001: 101 total segments, 12 labels (94 vertices) changed 002: 92 total segments, 3 labels (18 vertices) changed 003: 89 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... 1044 vertices marked for relabeling... 1044 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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... 6 labels changed using aseg relabeling using gibbs priors... 000: 9217 changed, 139374 examined... 001: 2143 changed, 36317 examined... 002: 624 changed, 11383 examined... 003: 261 changed, 3577 examined... 004: 117 changed, 1456 examined... 005: 65 changed, 695 examined... 006: 27 changed, 356 examined... 007: 10 changed, 159 examined... 008: 3 changed, 60 examined... 009: 2 changed, 20 examined... 010: 2 changed, 14 examined... 011: 3 changed, 10 examined... 012: 3 changed, 13 examined... 013: 0 changed, 9 examined... 0 labels changed using aseg 000: 279 total segments, 194 labels (2874 vertices) changed 001: 93 total segments, 8 labels (59 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 25 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1069 vertices marked for relabeling... 1069 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. PIDs (25513 25516) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 08:02:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 08:02:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh white Waiting for PID 25563 of (25563 25566) to complete... Waiting for PID 25566 of (25563 25566) 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 0051311 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164 Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1263 829 2154 2.276 0.493 0.140 0.040 29 2.0 G&S_frontomargin 2451 1629 4911 2.550 0.561 0.133 0.026 41 2.5 G&S_occipital_inf 1703 1077 3542 2.618 0.523 0.114 0.021 18 1.4 G&S_paracentral 1806 1201 3902 2.692 0.405 0.123 0.023 25 1.7 G&S_subcentral 827 565 2197 2.727 0.485 0.177 0.058 22 2.3 G&S_transv_frontopol 2230 1503 4686 2.865 0.447 0.121 0.024 25 2.2 G&S_cingul-Ant 1145 811 2105 2.653 0.365 0.108 0.013 9 0.7 G&S_cingul-Mid-Ant 1175 790 2489 2.893 0.458 0.106 0.022 9 1.1 G&S_cingul-Mid-Post 785 534 2326 3.263 0.528 0.164 0.040 17 1.3 G_cingul-Post-dorsal 332 216 813 2.826 0.840 0.144 0.039 8 0.4 G_cingul-Post-ventral 2386 1522 3634 1.980 0.576 0.154 0.041 50 3.6 G_cuneus 1523 1022 4137 3.006 0.398 0.122 0.029 28 1.6 G_front_inf-Opercular 477 317 1165 2.691 0.397 0.184 0.067 23 1.1 G_front_inf-Orbital 967 689 2606 2.821 0.418 0.154 0.042 21 1.8 G_front_inf-Triangul 4351 2962 10755 2.756 0.518 0.149 0.040 112 6.8 G_front_middle 7372 4984 19235 2.973 0.537 0.132 0.029 119 8.2 G_front_sup 732 504 1794 3.232 0.757 0.138 0.036 16 0.9 G_Ins_lg&S_cent_ins 763 520 2445 3.518 0.761 0.133 0.040 21 1.1 G_insular_short 2756 1858 6558 2.626 0.518 0.155 0.037 72 4.5 G_occipital_middle 1628 1058 3080 2.484 0.493 0.139 0.032 23 2.0 G_occipital_sup 1899 1246 5199 3.155 0.508 0.140 0.032 35 2.4 G_oc-temp_lat-fusifor 3262 2154 5761 2.217 0.604 0.153 0.040 63 5.3 G_oc-temp_med-Lingual 1159 732 3111 3.115 0.889 0.103 0.025 11 1.2 G_oc-temp_med-Parahip 2427 1682 7066 3.042 0.631 0.148 0.042 47 4.2 G_orbital 2349 1667 6392 2.849 0.601 0.148 0.033 55 3.3 G_pariet_inf-Angular 2375 1595 6397 2.999 0.543 0.142 0.031 55 3.1 G_pariet_inf-Supramar 3074 1976 6207 2.511 0.446 0.116 0.022 48 2.8 G_parietal_sup 3143 2025 6496 2.479 0.564 0.129 0.030 53 3.6 G_postcentral 2897 1955 7482 2.909 0.450 0.108 0.020 34 2.3 G_precentral 3857 2642 8730 2.539 0.554 0.133 0.031 77 4.5 G_precuneus 764 517 1961 2.716 0.591 0.133 0.034 18 1.2 G_rectus 518 305 936 2.963 0.678 0.112 0.042 8 0.7 G_subcallosal 521 304 1104 2.732 0.291 0.106 0.019 6 0.3 G_temp_sup-G_T_transv 1991 1345 6326 3.155 0.603 0.144 0.034 44 2.7 G_temp_sup-Lateral 906 618 2652 3.339 0.658 0.093 0.025 6 1.0 G_temp_sup-Plan_polar 805 566 1781 2.684 0.488 0.074 0.011 3 0.2 G_temp_sup-Plan_tempo 2163 1485 6427 3.014 0.658 0.154 0.044 50 3.7 G_temporal_inf 2385 1688 7733 3.094 0.647 0.146 0.037 60 3.8 G_temporal_middle 430 288 721 2.412 0.383 0.139 0.033 8 0.5 Lat_Fis-ant-Horizont 388 280 593 2.353 0.320 0.099 0.017 2 0.2 Lat_Fis-ant-Vertical 1111 728 1419 2.430 0.315 0.111 0.019 11 0.9 Lat_Fis-post 2084 1325 3106 2.110 0.483 0.141 0.033 37 2.5 Pole_occipital 1390 949 4656 3.317 0.770 0.141 0.037 27 2.0 Pole_temporal 2273 1590 2777 2.138 0.656 0.135 0.029 25 3.0 S_calcarine 3839 2597 4943 2.112 0.521 0.094 0.017 21 2.6 S_central 1377 940 2133 2.505 0.435 0.084 0.011 5 0.6 S_cingul-Marginalis 615 403 1040 3.153 0.561 0.096 0.017 3 0.4 S_circular_insula_ant 1262 840 1809 2.632 0.534 0.082 0.014 4 0.8 S_circular_insula_inf 1710 1157 2590 2.734 0.361 0.104 0.018 8 1.3 S_circular_insula_sup 624 429 1284 2.884 0.653 0.136 0.038 9 0.9 S_collat_transv_ant 444 296 610 2.399 0.483 0.126 0.024 4 0.4 S_collat_transv_post 1730 1215 2755 2.393 0.381 0.114 0.020 12 1.6 S_front_inf 1559 1082 2377 2.313 0.360 0.122 0.026 19 1.7 S_front_middle 2776 1938 4647 2.488 0.379 0.100 0.017 14 2.1 S_front_sup 184 135 401 2.552 0.389 0.086 0.016 1 0.1 S_interm_prim-Jensen 3413 2291 5301 2.442 0.424 0.120 0.020 41 2.9 S_intrapariet&P_trans 1294 873 1673 2.186 0.324 0.108 0.021 7 1.2 S_oc_middle&Lunatus 1878 1277 2795 2.441 0.443 0.127 0.023 19 1.9 S_oc_sup&transversal 938 624 1242 2.545 0.359 0.127 0.022 8 0.9 S_occipital_ant 739 519 1280 2.786 0.450 0.121 0.026 5 0.8 S_oc-temp_lat 2313 1626 3567 2.465 0.423 0.104 0.017 13 1.7 S_oc-temp_med&Lingual 316 219 460 2.455 0.374 0.120 0.022 4 0.3 S_orbital_lateral 570 429 909 2.402 0.405 0.117 0.019 4 0.3 S_orbital_med-olfact 1264 876 2590 2.757 0.542 0.129 0.031 13 1.7 S_orbital-H_Shaped 2553 1704 4399 2.610 0.512 0.122 0.022 29 2.2 S_parieto_occipital 1308 807 1364 1.963 0.778 0.100 0.017 16 0.8 S_pericallosal 3038 2070 4544 2.398 0.448 0.125 0.021 33 2.8 S_postcentral 1794 1221 2961 2.612 0.452 0.093 0.017 10 1.2 S_precentral-inf-part 1700 1122 2661 2.581 0.442 0.099 0.017 11 1.2 S_precentral-sup-part 845 603 1571 2.722 0.693 0.126 0.026 10 0.8 S_suborbital 1207 808 1739 2.481 0.462 0.119 0.022 8 1.1 S_subparietal 1105 778 1801 2.510 0.515 0.116 0.021 8 1.0 S_temporal_inf 6811 4675 12345 2.625 0.474 0.112 0.023 79 6.9 S_temporal_sup 414 289 559 2.346 0.265 0.107 0.014 2 0.3 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 0051311 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597 Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 917 635 1703 2.402 0.576 0.150 0.046 19 1.7 G&S_frontomargin 1511 941 3262 2.752 0.618 0.112 0.021 20 1.2 G&S_occipital_inf 1550 964 2933 2.459 0.423 0.119 0.025 19 1.5 G&S_paracentral 1165 773 2516 2.692 0.452 0.136 0.031 19 1.4 G&S_subcentral 1363 921 3258 2.668 0.461 0.155 0.044 36 2.5 G&S_transv_frontopol 2871 1990 5579 2.619 0.515 0.119 0.027 44 2.9 G&S_cingul-Ant 1311 900 2812 2.826 0.507 0.104 0.017 10 0.8 G&S_cingul-Mid-Ant 1674 1120 3362 2.855 0.493 0.129 0.030 21 1.9 G&S_cingul-Mid-Post 680 443 2062 3.200 0.555 0.157 0.044 16 1.2 G_cingul-Post-dorsal 333 221 936 3.027 0.657 0.161 0.039 8 0.5 G_cingul-Post-ventral 2635 1682 4034 2.020 0.572 0.152 0.049 52 5.0 G_cuneus 1620 1085 4167 2.868 0.442 0.134 0.032 32 2.1 G_front_inf-Opercular 494 335 961 2.535 0.463 0.143 0.033 10 0.6 G_front_inf-Orbital 1081 751 2779 2.750 0.378 0.174 0.047 47 1.9 G_front_inf-Triangul 3519 2386 9083 2.747 0.515 0.150 0.043 98 5.9 G_front_middle 7837 5296 20147 2.933 0.533 0.129 0.031 125 8.8 G_front_sup 646 458 1891 3.495 0.705 0.139 0.037 15 0.8 G_Ins_lg&S_cent_ins 722 480 2230 3.558 0.733 0.139 0.039 15 1.2 G_insular_short 2544 1693 6121 2.679 0.456 0.137 0.032 53 3.1 G_occipital_middle 2006 1306 4029 2.545 0.598 0.142 0.033 36 2.5 G_occipital_sup 2029 1287 5644 3.198 0.573 0.144 0.036 45 2.9 G_oc-temp_lat-fusifor 2950 1926 6419 2.572 0.645 0.151 0.040 56 4.7 G_oc-temp_med-Lingual 1056 694 3060 3.184 0.714 0.127 0.040 14 1.4 G_oc-temp_med-Parahip 2391 1691 6846 2.979 0.535 0.155 0.045 58 4.1 G_orbital 3370 2322 9421 2.896 0.527 0.147 0.033 83 4.4 G_pariet_inf-Angular 2548 1688 6128 2.879 0.474 0.135 0.028 48 3.1 G_pariet_inf-Supramar 3301 2174 6579 2.478 0.369 0.130 0.027 64 3.6 G_parietal_sup 2059 1323 3918 2.268 0.522 0.128 0.024 34 2.1 G_postcentral 2709 1820 7137 2.899 0.413 0.111 0.019 35 2.0 G_precentral 3314 2181 7982 2.729 0.503 0.130 0.031 64 4.0 G_precuneus 811 612 2667 2.930 0.584 0.157 0.053 22 1.6 G_rectus 176 120 400 3.490 0.500 0.131 0.048 3 0.4 G_subcallosal 400 233 891 2.739 0.344 0.117 0.020 7 0.2 G_temp_sup-G_T_transv 2171 1433 5986 3.125 0.530 0.139 0.033 41 2.7 G_temp_sup-Lateral 764 544 1989 2.924 0.880 0.117 0.037 15 1.3 G_temp_sup-Plan_polar 895 602 1867 2.778 0.365 0.082 0.011 4 0.4 G_temp_sup-Plan_tempo 2092 1354 5588 3.068 0.672 0.132 0.033 38 2.9 G_temporal_inf 2925 1969 8926 3.262 0.546 0.140 0.030 61 3.5 G_temporal_middle 509 345 840 2.490 0.403 0.117 0.017 5 0.4 Lat_Fis-ant-Horizont 399 295 620 2.278 0.292 0.092 0.012 2 0.1 Lat_Fis-ant-Vertical 1370 905 1977 2.669 0.321 0.111 0.020 10 1.1 Lat_Fis-post 3703 2366 5215 2.050 0.472 0.146 0.038 64 5.4 Pole_occipital 1509 1041 5095 3.394 0.744 0.139 0.038 33 2.4 Pole_temporal 2654 1808 3332 2.160 0.613 0.136 0.033 38 3.9 S_calcarine 3347 2243 4052 2.074 0.533 0.102 0.017 21 2.5 S_central 1644 1122 2514 2.444 0.528 0.091 0.013 7 0.9 S_cingul-Marginalis 605 396 894 2.786 0.405 0.092 0.017 2 0.4 S_circular_insula_ant 1215 807 1778 2.609 0.496 0.074 0.011 4 0.6 S_circular_insula_inf 1454 989 2386 2.841 0.431 0.112 0.020 9 1.3 S_circular_insula_sup 1033 672 1987 2.858 0.555 0.109 0.024 17 1.1 S_collat_transv_ant 553 375 687 2.127 0.315 0.122 0.018 5 0.4 S_collat_transv_post 1808 1240 2788 2.390 0.439 0.108 0.018 17 1.4 S_front_inf 1834 1273 2823 2.159 0.478 0.123 0.026 19 2.1 S_front_middle 2825 1942 4416 2.435 0.373 0.104 0.018 19 2.1 S_front_sup 616 431 872 2.505 0.309 0.109 0.014 4 0.4 S_interm_prim-Jensen 4130 2781 6022 2.353 0.368 0.101 0.015 31 2.4 S_intrapariet&P_trans 1123 781 1446 2.192 0.310 0.103 0.017 6 0.8 S_oc_middle&Lunatus 1555 1045 2238 2.482 0.392 0.145 0.030 21 1.9 S_oc_sup&transversal 846 569 1201 2.432 0.308 0.093 0.016 5 0.4 S_occipital_ant 740 519 1389 2.743 0.537 0.098 0.017 5 0.4 S_oc-temp_lat 1917 1367 3033 2.548 0.374 0.104 0.016 11 1.3 S_oc-temp_med&Lingual 395 277 674 2.437 0.474 0.126 0.023 3 0.4 S_orbital_lateral 633 447 1008 2.576 0.578 0.112 0.020 5 0.5 S_orbital_med-olfact 1352 916 2742 2.828 0.608 0.134 0.032 15 1.8 S_orbital-H_Shaped 2258 1502 3465 2.563 0.457 0.111 0.022 17 2.1 S_parieto_occipital 1893 1200 1863 1.999 0.842 0.102 0.017 19 1.1 S_pericallosal 2242 1522 3340 2.305 0.398 0.105 0.018 20 1.4 S_postcentral 1776 1223 2961 2.659 0.456 0.107 0.015 12 1.1 S_precentral-inf-part 1406 932 2128 2.576 0.375 0.103 0.016 10 0.9 S_precentral-sup-part 394 268 505 2.342 0.443 0.124 0.020 3 0.3 S_suborbital 1366 960 2474 2.528 0.495 0.112 0.019 12 1.1 S_subparietal 992 700 1533 2.663 0.478 0.123 0.020 8 1.0 S_temporal_inf 6924 4733 12072 2.689 0.447 0.111 0.019 69 5.2 S_temporal_sup 202 148 342 2.751 0.473 0.121 0.016 1 0.2 S_temporal_transverse PIDs (25563 25566) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 08:03:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 08:03:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 25631 of (25631 25634) to complete... Waiting for PID 25634 of (25631 25634) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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... 1170 labels changed using aseg relabeling using gibbs priors... 000: 2023 changed, 138191 examined... 001: 460 changed, 9343 examined... 002: 135 changed, 2654 examined... 003: 56 changed, 802 examined... 004: 39 changed, 336 examined... 005: 28 changed, 221 examined... 006: 16 changed, 160 examined... 007: 16 changed, 108 examined... 008: 11 changed, 86 examined... 009: 12 changed, 74 examined... 010: 10 changed, 66 examined... 011: 7 changed, 68 examined... 012: 3 changed, 41 examined... 013: 3 changed, 24 examined... 014: 1 changed, 20 examined... 015: 1 changed, 7 examined... 016: 0 changed, 7 examined... 306 labels changed using aseg 000: 63 total segments, 30 labels (259 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 764 vertices marked for relabeling... 764 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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... 1004 labels changed using aseg relabeling using gibbs priors... 000: 1989 changed, 139374 examined... 001: 433 changed, 9394 examined... 002: 117 changed, 2511 examined... 003: 37 changed, 721 examined... 004: 14 changed, 206 examined... 005: 7 changed, 90 examined... 006: 3 changed, 45 examined... 007: 3 changed, 18 examined... 008: 1 changed, 20 examined... 009: 1 changed, 7 examined... 010: 1 changed, 7 examined... 011: 0 changed, 7 examined... 107 labels changed using aseg 000: 54 total segments, 21 labels (145 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 961 vertices marked for relabeling... 961 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 18 seconds. PIDs (25631 25634) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 08:03:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 08:03:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh white Waiting for PID 25677 of (25677 25680) to complete... Waiting for PID 25680 of (25677 25680) 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 0051311 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164 Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1253 872 2743 2.864 0.459 0.117 0.019 15 0.9 caudalanteriorcingulate 3505 2366 6926 2.662 0.420 0.114 0.021 37 3.0 caudalmiddlefrontal 3230 2096 5010 2.134 0.551 0.143 0.035 52 4.3 cuneus 443 288 1718 3.869 0.681 0.109 0.029 4 0.5 entorhinal 3966 2710 9141 2.930 0.555 0.127 0.027 54 4.4 fusiform 7263 5067 15800 2.650 0.539 0.129 0.027 121 8.9 inferiorparietal 3798 2615 9795 2.951 0.670 0.138 0.037 64 5.5 inferiortemporal 1793 1166 3224 2.486 0.933 0.127 0.028 27 1.9 isthmuscingulate 9120 5968 15449 2.355 0.485 0.137 0.029 142 10.6 lateraloccipital 4146 2857 9742 2.878 0.638 0.142 0.039 73 6.7 lateralorbitofrontal 4711 3209 7846 2.271 0.563 0.139 0.032 71 6.3 lingual 2229 1520 4827 2.721 0.618 0.125 0.031 38 2.9 medialorbitofrontal 6173 4283 15321 2.851 0.591 0.134 0.032 120 8.3 middletemporal 1036 661 1922 2.509 0.613 0.081 0.015 6 0.6 parahippocampal 2567 1632 5200 2.826 0.460 0.100 0.020 20 1.8 paracentral 2389 1646 5236 2.753 0.425 0.116 0.025 30 2.3 parsopercularis 1110 748 2405 2.759 0.564 0.144 0.037 17 1.6 parsorbitalis 2158 1524 4605 2.617 0.436 0.138 0.034 46 2.9 parstriangularis 1882 1290 1997 1.790 0.419 0.141 0.033 28 2.5 pericalcarine 8692 5775 15560 2.342 0.566 0.121 0.024 115 8.2 postcentral 1861 1239 3914 2.830 0.657 0.116 0.023 22 1.8 posteriorcingulate 8173 5497 16834 2.720 0.495 0.101 0.018 71 5.8 precentral 7188 4905 14299 2.560 0.542 0.128 0.027 112 7.6 precuneus 1650 1084 3616 2.872 0.545 0.118 0.023 22 1.5 rostralanteriorcingulate 5073 3454 10249 2.544 0.546 0.142 0.037 102 7.8 rostralmiddlefrontal 12121 8310 26972 2.742 0.541 0.127 0.028 172 14.1 superiorfrontal 7154 4677 12279 2.442 0.452 0.120 0.022 93 6.6 superiorparietal 7788 5250 18313 2.906 0.656 0.111 0.024 90 7.6 superiortemporal 4346 2961 9175 2.789 0.538 0.131 0.025 75 4.9 supramarginal 705 426 1293 2.583 0.351 0.105 0.018 7 0.4 transversetemporal 2940 2001 6511 3.147 0.667 0.119 0.028 44 3.1 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 0051311 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597 Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1097 759 2521 2.886 0.558 0.116 0.016 12 0.7 caudalanteriorcingulate 2853 1956 5694 2.683 0.413 0.116 0.022 30 2.4 caudalmiddlefrontal 3274 2120 5178 2.147 0.573 0.138 0.040 49 5.0 cuneus 540 353 1791 3.470 0.668 0.134 0.045 7 0.9 entorhinal 3925 2610 9120 3.004 0.573 0.128 0.028 59 4.5 fusiform 8787 6011 18784 2.726 0.487 0.131 0.027 143 9.2 inferiorparietal 4222 2801 9970 2.951 0.649 0.123 0.030 69 5.3 inferiortemporal 1698 1098 3135 2.461 0.911 0.121 0.029 26 1.9 isthmuscingulate 8718 5653 14894 2.367 0.513 0.134 0.030 135 10.1 lateraloccipital 3768 2623 8466 2.802 0.618 0.146 0.040 73 5.8 lateralorbitofrontal 4575 3054 8578 2.413 0.653 0.139 0.036 74 6.8 lingual 1781 1295 4327 2.719 0.616 0.134 0.035 31 2.4 medialorbitofrontal 5964 4050 14540 3.022 0.583 0.124 0.024 95 5.8 middletemporal 883 624 1845 2.688 0.510 0.102 0.018 7 0.4 parahippocampal 2513 1610 4598 2.627 0.444 0.105 0.021 21 2.0 paracentral 2413 1675 5168 2.727 0.471 0.121 0.025 34 2.3 parsopercularis 953 642 2105 2.700 0.596 0.128 0.030 13 1.2 parsorbitalis 2613 1805 5394 2.594 0.421 0.139 0.030 58 3.1 parstriangularis 2322 1532 2546 1.876 0.429 0.134 0.031 32 2.9 pericalcarine 6551 4319 10684 2.204 0.544 0.114 0.021 77 5.5 postcentral 2375 1572 4780 2.648 0.860 0.128 0.029 35 2.7 posteriorcingulate 7359 4890 14722 2.681 0.470 0.110 0.020 72 6.1 precentral 7017 4717 14163 2.640 0.526 0.122 0.026 100 7.6 precuneus 1237 838 2547 2.866 0.475 0.140 0.037 29 1.7 rostralanteriorcingulate 5407 3686 10844 2.458 0.554 0.140 0.037 117 8.3 rostralmiddlefrontal 14618 9968 32009 2.734 0.546 0.123 0.028 205 15.6 superiorfrontal 7884 5244 13745 2.418 0.394 0.122 0.024 116 7.1 superiorparietal 7630 5168 17585 2.881 0.639 0.117 0.024 101 7.9 superiortemporal 5049 3389 10318 2.752 0.437 0.116 0.022 63 4.5 supramarginal 568 335 1072 2.614 0.304 0.112 0.018 8 0.3 transversetemporal 3068 2095 6905 3.181 0.678 0.123 0.029 39 3.5 insula PIDs (25677 25680) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 08:04:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts pctsurfcon --s 0051311 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 08:04:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts pctsurfcon --s 0051311 --rh-only Waiting for PID 25793 of (25793 25804) to complete... Waiting for PID 25804 of (25793 25804) to complete... pctsurfcon --s 0051311 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts/pctsurfcon.log Sun Oct 8 08:04:34 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-6.0.0/0051311/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-904 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-6.0.0/0051311/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.wm.mgh --regheader 0051311 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 69144 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.wm.mgh Dim: 138191 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.gm.mgh --projfrac 0.3 --regheader 0051311 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 85842 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.gm.mgh Dim: 138191 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.w-g.pct.mgh --annot 0051311 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/lh.w-g.pct.mgh --annot 0051311 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-904 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/lh.w-g.pct.mgh Vertex Area is 0.673771 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 0051311 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts/pctsurfcon.log Sun Oct 8 08:04:34 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-6.0.0/0051311/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-904 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-6.0.0/0051311/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.wm.mgh --regheader 0051311 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 69378 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.wm.mgh Dim: 139374 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.gm.mgh --projfrac 0.3 --regheader 0051311 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 86485 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.gm.mgh Dim: 139374 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.w-g.pct.mgh --annot 0051311 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.w-g.pct.mgh --annot 0051311 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-904 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.w-g.pct.mgh Vertex Area is 0.671675 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 (25793 25804) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 08:04:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 806 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 631 voxels changed to hypointensity... 1586 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 08:05:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 mri_aparc2aseg --s 0051311 --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 08:05:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 mri_aparc2aseg --s 0051311 --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 08:05:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 mri_aparc2aseg --s 0051311 --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 25959 of (25959 25962 25965) to complete... Waiting for PID 25962 of (25959 25962 25965) to complete... Waiting for PID 25965 of (25959 25962 25965) to complete... mri_aparc2aseg --s 0051311 --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 0051311 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/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 6.09 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 108 rescaling Left_Cerebral_Cortex from 61 --> 49 rescaling Left_Lateral_Ventricle from 13 --> 6 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 51 rescaling Left_Thalamus from 94 --> 89 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 69 rescaling Left_Pallidum from 98 --> 92 rescaling Third_Ventricle from 25 --> 12 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 53 rescaling Left_Amygdala from 56 --> 55 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 55 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 107 rescaling Right_Cerebral_Cortex from 58 --> 51 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 24 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 81 rescaling Right_Caudate from 62 --> 63 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 57 rescaling Right_Amygdala from 55 --> 60 rescaling Right_Accumbens_area from 65 --> 62 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 16 rescaling WM_hypointensities from 78 --> 81 rescaling non_WM_hypointensities from 40 --> 45 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 = 532369 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 165 changed. pass 2: 6 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc+aseg.mgz mri_aparc2aseg --s 0051311 --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 0051311 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/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 6.09 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 108 rescaling Left_Cerebral_Cortex from 61 --> 49 rescaling Left_Lateral_Ventricle from 13 --> 6 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 51 rescaling Left_Thalamus from 94 --> 89 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 69 rescaling Left_Pallidum from 98 --> 92 rescaling Third_Ventricle from 25 --> 12 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 53 rescaling Left_Amygdala from 56 --> 55 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 55 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 107 rescaling Right_Cerebral_Cortex from 58 --> 51 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 24 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 81 rescaling Right_Caudate from 62 --> 63 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 57 rescaling Right_Amygdala from 55 --> 60 rescaling Right_Accumbens_area from 65 --> 62 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 16 rescaling WM_hypointensities from 78 --> 81 rescaling non_WM_hypointensities from 40 --> 45 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 = 532442 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 165 changed. pass 2: 6 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0051311 --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 0051311 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/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 6.09 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 108 rescaling Left_Cerebral_Cortex from 61 --> 49 rescaling Left_Lateral_Ventricle from 13 --> 6 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 51 rescaling Left_Thalamus from 94 --> 89 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 69 rescaling Left_Pallidum from 98 --> 92 rescaling Third_Ventricle from 25 --> 12 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 53 rescaling Left_Amygdala from 56 --> 55 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 55 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 107 rescaling Right_Cerebral_Cortex from 58 --> 51 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 24 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 81 rescaling Right_Caudate from 62 --> 63 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 57 rescaling Right_Amygdala from 55 --> 60 rescaling Right_Accumbens_area from 65 --> 62 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 16 rescaling WM_hypointensities from 78 --> 81 rescaling non_WM_hypointensities from 40 --> 45 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 = 532442 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 165 changed. pass 2: 6 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (25959 25962 25965) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 08:13:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 08:13:23 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-6.0.0/0051311/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-904 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-6.0.0/0051311/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-904 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 08:13:23 CEST 2017 Ended at Sun Oct 8 08:13:30 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 08:13:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 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 0051311 $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 0051311 sysname Linux hostname tars-904 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1336087 mm^3 (det: 1.458067 ) Computing euler number orig.nofix lheno = -42, rheno = -50 orig.nofix lhholes = 22, rhholes = 26 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 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 08:17:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311 mri_aparc2aseg --s 0051311 --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 0051311 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-6.0.0/0051311/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7753 vertices from left hemi Ripped 7720 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-6.0.0/0051311/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 928308 Used brute-force search on 677 voxels Fixing Parahip LH WM Found 11 clusters 0 k 2.000000 1 k 6.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 6.000000 7 k 1067.000000 8 k 1.000000 9 k 5.000000 10 k 27.000000 Fixing Parahip RH WM Found 10 clusters 0 k 3.000000 1 k 2.000000 2 k 2.000000 3 k 1180.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 1.000000 9 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 0051311 --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 0051311 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-904 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1336087 mm^3 (det: 1.458067 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 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-6.0.0/0051311/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 08:28:06 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 26789 of (26789 26795 26801 26807 26813) to complete... Waiting for PID 26795 of (26789 26795 26801 26807 26813) to complete... Waiting for PID 26801 of (26789 26795 26801 26807 26813) to complete... Waiting for PID 26807 of (26789 26795 26801 26807 26813) to complete... Waiting for PID 26813 of (26789 26795 26801 26807 26813) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 545 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4674 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 763 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8672 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 282 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4359 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 479 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6462 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 404 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6188 mri_label2label: Done PIDs (26789 26795 26801 26807 26813) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 26865 of (26865 26871 26877 26883) to complete... Waiting for PID 26871 of (26865 26871 26877 26883) to complete... Waiting for PID 26877 of (26865 26871 26877 26883) to complete... Waiting for PID 26883 of (26865 26871 26877 26883) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4337 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 1517 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15106 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 425 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4606 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 412 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3834 mri_label2label: Done PIDs (26865 26871 26877 26883) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 26923 of (26923 26929 26935 26941 26947) to complete... Waiting for PID 26929 of (26923 26929 26935 26941 26947) to complete... Waiting for PID 26935 of (26923 26929 26935 26941 26947) to complete... Waiting for PID 26941 of (26923 26929 26935 26941 26947) to complete... Waiting for PID 26947 of (26923 26929 26935 26941 26947) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 1399 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6040 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 3162 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11276 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 790 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2808 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1325 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1232 mri_label2label: Done PIDs (26923 26929 26935 26941 26947) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 27009 of (27009 27015 27020 27024 27032) to complete... Waiting for PID 27015 of (27009 27015 27020 27024 27032) to complete... Waiting for PID 27020 of (27009 27015 27020 27024 27032) to complete... Waiting for PID 27024 of (27009 27015 27020 27024 27032) to complete... Waiting for PID 27032 of (27009 27015 27020 27024 27032) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1138 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 413 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2505 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1596 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2208 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2453 mri_label2label: Done PIDs (27009 27015 27020 27024 27032) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 27072 of (27072 27078 27084 27089) to complete... Waiting for PID 27078 of (27072 27078 27084 27089) to complete... Waiting for PID 27084 of (27072 27078 27084 27089) to complete... Waiting for PID 27089 of (27072 27078 27084 27089) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1648 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 814 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7849 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 200 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2112 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1331 mri_label2label: Done PIDs (27072 27078 27084 27089) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 27147 of (27147 27153 27156 27163 27170) to complete... Waiting for PID 27153 of (27147 27153 27156 27163 27170) to complete... Waiting for PID 27156 of (27147 27153 27156 27163 27170) to complete... Waiting for PID 27163 of (27147 27153 27156 27163 27170) to complete... Waiting for PID 27170 of (27147 27153 27156 27163 27170) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 916 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4321 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 1383 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4717 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 208 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 721 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 480 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 138191 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 464 mri_label2label: Done PIDs (27147 27153 27156 27163 27170) completed and logs appended. mris_label2annot --s 0051311 --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-6.0.0/0051311/label cmdline mris_label2annot --s 0051311 --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-904 machine x86_64 user ntraut subject 0051311 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-6.0.0/0051311/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 93652 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.BA_exvivo.annot mris_label2annot --s 0051311 --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-6.0.0/0051311/label cmdline mris_label2annot --s 0051311 --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-904 machine x86_64 user ntraut subject 0051311 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-6.0.0/0051311/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 111380 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 271164 Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 1359 848 2892 2.519 0.443 0.148 0.035 28 1.9 BA1_exvivo 4436 2954 8118 2.541 0.485 0.127 0.024 62 4.3 BA2_exvivo 1288 849 1347 1.977 0.396 0.114 0.023 9 1.2 BA3a_exvivo 2751 1886 4243 2.003 0.573 0.109 0.020 27 2.2 BA3b_exvivo 1672 1059 3872 2.923 0.437 0.095 0.019 13 1.1 BA4a_exvivo 1417 961 2444 2.607 0.369 0.083 0.014 6 0.8 BA4p_exvivo 10522 7138 24107 2.816 0.528 0.112 0.021 107 8.7 BA6_exvivo 2530 1728 5876 2.849 0.440 0.106 0.023 31 2.1 BA44_exvivo 2611 1857 5691 2.584 0.468 0.144 0.036 56 3.9 BA45_exvivo 3463 2344 4446 1.867 0.467 0.134 0.035 49 4.9 V1_exvivo 8849 5756 14003 2.220 0.532 0.148 0.035 151 12.0 V2_exvivo 2612 1785 4972 2.524 0.462 0.131 0.024 44 2.4 MT_exvivo 497 309 1630 3.451 0.810 0.101 0.026 5 0.4 perirhinal_exvivo 532 373 1288 3.032 0.927 0.099 0.025 4 0.5 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 0051311 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 271164 Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 860 541 1866 2.548 0.468 0.135 0.032 14 1.0 BA1_exvivo 2180 1474 4139 2.533 0.451 0.128 0.026 32 2.3 BA2_exvivo 1081 715 1066 1.925 0.387 0.117 0.024 8 1.0 BA3a_exvivo 1802 1229 2285 1.786 0.384 0.099 0.017 15 1.3 BA3b_exvivo 1650 1063 3791 2.888 0.447 0.087 0.016 10 1.0 BA4a_exvivo 1163 792 1943 2.567 0.382 0.091 0.016 7 0.7 BA4p_exvivo 6044 4117 14226 2.838 0.537 0.112 0.021 62 5.0 BA6_exvivo 1646 1111 3813 2.829 0.430 0.111 0.025 25 1.5 BA44_exvivo 1111 797 2824 2.752 0.444 0.158 0.042 22 2.0 BA45_exvivo 3703 2523 4978 1.892 0.482 0.135 0.035 52 5.2 V1_exvivo 4353 2812 6372 2.099 0.498 0.158 0.039 87 6.7 V2_exvivo 691 485 1469 2.615 0.488 0.141 0.025 11 0.7 MT_exvivo 248 152 941 3.810 0.688 0.101 0.017 2 0.2 perirhinal_exvivo 279 192 680 3.108 0.750 0.082 0.022 1 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 08:31:37 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 27297 of (27297 27303 27309 27315 27321) to complete... Waiting for PID 27303 of (27297 27303 27309 27315 27321) to complete... Waiting for PID 27309 of (27297 27303 27309 27315 27321) to complete... Waiting for PID 27315 of (27297 27303 27309 27315 27321) to complete... Waiting for PID 27321 of (27297 27303 27309 27315 27321) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 252 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4214 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 295 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6982 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 176 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4156 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 297 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4819 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6079 mri_label2label: Done PIDs (27297 27303 27309 27315 27321) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 27368 of (27368 27374 27380 27383) to complete... Waiting for PID 27374 of (27368 27374 27380 27383) to complete... Waiting for PID 27380 of (27368 27374 27380 27383) to complete... Waiting for PID 27383 of (27368 27374 27380 27383) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 172 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4645 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 1174 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13430 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 792 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7704 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 1029 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6384 mri_label2label: Done PIDs (27368 27374 27380 27383) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 27438 of (27438 27444 27449 27456 27461) to complete... Waiting for PID 27444 of (27438 27444 27449 27456 27461) to complete... Waiting for PID 27449 of (27438 27444 27449 27456 27461) to complete... Waiting for PID 27456 of (27438 27444 27449 27456 27461) to complete... Waiting for PID 27461 of (27438 27444 27449 27456 27461) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 1813 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6540 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 3395 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11411 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 511 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2443 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1090 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 766 mri_label2label: Done PIDs (27438 27444 27449 27456 27461) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 27507 of (27507 27513 27519 27524 27531) to complete... Waiting for PID 27513 of (27507 27513 27519 27524 27531) to complete... Waiting for PID 27519 of (27507 27513 27519 27524 27531) to complete... Waiting for PID 27524 of (27507 27513 27519 27524 27531) to complete... Waiting for PID 27531 of (27507 27513 27519 27524 27531) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 938 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2739 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1754 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2348 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1449 mri_label2label: Done PIDs (27507 27513 27519 27524 27531) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 27578 of (27578 27584 27589 27596) to complete... Waiting for PID 27584 of (27578 27584 27589 27596) to complete... Waiting for PID 27589 of (27578 27584 27589 27596) to complete... Waiting for PID 27596 of (27578 27584 27589 27596) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1564 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 585 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7544 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1233 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 239 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1417 mri_label2label: Done PIDs (27578 27584 27589 27596) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 27643 of (27643 27649 27655 27661 27667) to complete... Waiting for PID 27649 of (27643 27649 27655 27661 27667) to complete... Waiting for PID 27655 of (27643 27649 27655 27661 27667) to complete... Waiting for PID 27661 of (27643 27649 27655 27661 27667) to complete... Waiting for PID 27667 of (27643 27649 27655 27661 27667) 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 1183 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4415 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 1457 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4894 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 355 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 722 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 0051311 --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 = 0051311 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-6.0.0/0051311/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374 Number of reverse mapping hits = 1 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 292 mri_label2label: Done PIDs (27643 27649 27655 27661 27667) completed and logs appended. mris_label2annot --s 0051311 --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-6.0.0/0051311/label cmdline mris_label2annot --s 0051311 --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-904 machine x86_64 user ntraut subject 0051311 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-6.0.0/0051311/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 96535 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.BA_exvivo.annot mris_label2annot --s 0051311 --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-6.0.0/0051311/label cmdline mris_label2annot --s 0051311 --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-904 machine x86_64 user ntraut subject 0051311 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-6.0.0/0051311/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 115381 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 271597 Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 943 558 1945 2.454 0.392 0.154 0.029 18 1.2 BA1_exvivo 2810 1918 5068 2.363 0.428 0.110 0.020 34 2.1 BA2_exvivo 1153 777 1142 1.930 0.428 0.130 0.029 11 1.2 BA3a_exvivo 2110 1400 2811 1.852 0.467 0.099 0.017 17 1.4 BA3b_exvivo 1507 971 3285 2.786 0.360 0.094 0.019 11 1.1 BA4a_exvivo 1360 878 2219 2.553 0.382 0.098 0.017 10 1.0 BA4p_exvivo 8745 5947 19970 2.832 0.497 0.114 0.021 94 7.1 BA6_exvivo 3788 2607 7914 2.734 0.467 0.117 0.023 43 3.6 BA44_exvivo 4327 2977 9011 2.582 0.480 0.140 0.032 94 5.6 BA45_exvivo 4179 2726 5777 1.963 0.532 0.134 0.039 64 6.5 V1_exvivo 8928 5820 14519 2.269 0.583 0.149 0.039 159 13.7 V2_exvivo 2198 1478 3590 2.450 0.373 0.099 0.017 17 1.5 MT_exvivo 530 326 1724 3.407 0.653 0.120 0.031 5 0.6 perirhinal_exvivo 261 203 624 2.933 0.607 0.081 0.015 1 0.1 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 0051311 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 271597 Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 ) lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139 rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212 lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148 rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279 SubCortGMVol 58840.000 SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342 SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348 BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221 BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049 BrainSegVolNotVent 1128868.000 CerebellumVol 140022.000 VentChorVol 16624.000 3rd4th5thCSF 3405.000 CSFVol 865.000, OptChiasmVol 128.000 MaskVol 1478177.000 600 346 1191 2.411 0.390 0.142 0.024 10 0.6 BA1_exvivo 1553 1054 2922 2.423 0.406 0.106 0.019 17 1.1 BA2_exvivo 1046 699 953 1.922 0.396 0.129 0.027 9 1.2 BA3a_exvivo 1682 1154 1969 1.710 0.381 0.091 0.013 10 0.9 BA3b_exvivo 920 569 2139 2.859 0.372 0.106 0.026 9 0.8 BA4a_exvivo 1074 740 1773 2.546 0.411 0.092 0.015 6 0.7 BA4p_exvivo 5483 3734 12985 2.850 0.507 0.117 0.022 65 4.6 BA6_exvivo 1039 708 2505 2.836 0.464 0.141 0.032 20 1.4 BA44_exvivo 1200 859 2780 2.597 0.395 0.148 0.037 31 1.6 BA45_exvivo 4009 2600 5260 1.940 0.513 0.132 0.038 58 6.2 V1_exvivo 4560 2997 7329 2.161 0.579 0.159 0.044 89 7.8 V2_exvivo 333 214 672 2.451 0.314 0.110 0.016 5 0.2 MT_exvivo 316 193 1023 3.335 0.650 0.120 0.023 3 0.3 perirhinal_exvivo 178 142 471 3.061 0.564 0.088 0.014 1 0.1 entorhinal_exvivo Started at Sat Oct 7 23:29:49 CEST 2017 Ended at Sun Oct 8 08:35:00 CEST 2017 #@#%# recon-all-run-time-hours 9.086 recon-all -s 0051311 finished without error at Sun Oct 8 08:35:00 CEST 2017