Sat Oct 7 17:21:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0051026 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0051026 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-609 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: 65993848 57862780 8131068 1750584 0 53103008 -/+ buffers/cache: 4759772 61234076 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:27-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-609 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: 2017/10/07-15:21:28-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-609 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: 2017/10/07-15:21:28-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-609 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: 2017/10/07-15:21:28-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-609 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: 2017/10/07-15:21:28-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-609 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: 2017/10/07-15:21:28-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-609 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: 2017/10/07-15:21:28-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-609 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: 2017/10/07-15:21:28-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-609 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-6.0.0/0051026 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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/NYU/0051026/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-6.0.0/0051026/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 17:21:30 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/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-6.0.0/0051026/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 17:21:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/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-609 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 17:21:37 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.30553 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30553/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30553/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.30553/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:21:40 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.30553/nu0.mnc ./tmp.mri_nu_correct.mni.30553/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30553/0/ -iterations 1000 -distance 50 [ntraut@tars-609:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/] [2017-10-07 17:21:40] 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.30553/0/ ./tmp.mri_nu_correct.mni.30553/nu0.mnc ./tmp.mri_nu_correct.mni.30553/nu1.imp 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./tmp.mri_nu_correct.mni.30553/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.30553/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 17:22:49 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 17:22:49 CEST 2017 Ended at Sat Oct 7 17:23:20 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 17:23:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5735, pval=0.2115 >= 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-6.0.0/0051026/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach_avi.log TalAviQA: 0.97279 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 17:23:22 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-6.0.0/0051026/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-609 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 17:23:22 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.31388 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31388/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.31388/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.31388/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:23:24 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.31388/nu0.mnc ./tmp.mri_nu_correct.mni.31388/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31388/0/ [ntraut@tars-609:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/] [2017-10-07 17:23:24] 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.31388/0/ ./tmp.mri_nu_correct.mni.31388/nu0.mnc ./tmp.mri_nu_correct.mni.31388/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.000995075 -------------------------------------------------------- Iteration 2 Sat Oct 7 17:24:15 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.31388/nu1.mnc ./tmp.mri_nu_correct.mni.31388/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.31388/1/ [ntraut@tars-609:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/] [2017-10-07 17:24:15] 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.31388/1/ ./tmp.mri_nu_correct.mni.31388/nu1.mnc ./tmp.mri_nu_correct.mni.31388/nu2.imp Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000973775 mri_binarize --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31388/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-6.0.0/0051026/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31388/ones.mgz sysname Linux hostname tars-609 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.31388/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.31388/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.31388/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/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.31388/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/input.mean.dat sysname Linux hostname tars-609 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.31388/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.31388/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31388/ones.mgz --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/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.31388/ones.mgz --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/output.mean.dat sysname Linux hostname tars-609 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.31388/ones.mgz Loading ./tmp.mri_nu_correct.mni.31388/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.31388/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.31388/nu2.mnc ./tmp.mri_nu_correct.mni.31388/nu2.mnc mul .86439789201991015873 Saving result to './tmp.mri_nu_correct.mni.31388/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.31388/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.31388/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.31388/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 8 seconds. mapping ( 8, 173) to ( 3, 110) Sat Oct 7 17:25:29 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 17:25:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.02441 0.03458 -0.08275 0.58626; 0.00769 0.91669 0.39890 -7.25849; 0.07091 -0.37779 1.05571 4.98672; 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 = 20 Starting OpenSpline(): npoints = 20 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 110 gm peak at 60 (60), valley at 37 (37) csf peak at 31, setting threshold to 50 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 60 (60), valley at 37 (37) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 50 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 17:27:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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=7.0 skull bounding box = (44, 52, 23) --> (211, 208, 224) using (100, 104, 124) as brain centroid... mean wm in atlas = 108, using box (79,85,99) --> (120, 123,148) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 4.7 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.358 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.284202 @ (-9.091, -9.091, -9.091) max log p = -4.102880 @ (4.545, -4.545, -4.545) max log p = -4.082741 @ (2.273, -2.273, -2.273) max log p = -4.058860 @ (-1.136, 1.136, 1.136) max log p = -4.054829 @ (1.705, -0.568, 1.705) max log p = -4.054829 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -15.3, -13.1): log p = -4.055 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.794, old_max_log_p =-4.055 (thresh=-4.1) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.14215 0.47309 -80.40340; 0.00000 -0.40708 0.98278 54.99955; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.753, old_max_log_p =-3.794 (thresh=-3.8) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.05649 0.43761 -71.21009; 0.00000 -0.37655 0.90907 51.69382; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.753, old_max_log_p =-3.753 (thresh=-3.7) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.05649 0.43761 -71.21009; 0.00000 -0.37655 0.90907 51.69382; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.668, old_max_log_p =-3.753 (thresh=-3.7) 1.01812 -0.03807 -0.01095 3.08835; 0.03070 1.03394 0.43357 -69.09100; -0.00404 -0.37801 0.92734 53.77422; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.668 (thresh=-3.7) 1.03563 -0.07362 -0.02459 5.97219; 0.06411 1.04395 0.40243 -70.98071; -0.00303 -0.34398 0.94103 45.01742; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.654 (thresh=-3.6) 1.03563 -0.07362 -0.02459 5.97219; 0.06411 1.04395 0.40243 -70.98071; -0.00303 -0.34398 0.94103 45.01742; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.626, old_max_log_p =-3.654 (thresh=-3.6) 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.626, old_max_log_p =-3.626 (thresh=-3.6) 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 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 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.626 (old=-4.358) transform before final EM align: 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 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 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.1 tol 0.000000 final transform: 1.03290 -0.05625 -0.01819 3.88486; 0.04725 1.05173 0.38778 -69.08199; -0.00198 -0.32647 0.94638 42.55876; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1384.151576 mri_em_register stimesec 1.391788 mri_em_register ru_maxrss 609824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157571 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 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 80 mri_em_register ru_nivcsw 4715 registration took 11 minutes and 59 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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=127 y=124 z=118 r=70 first estimation of the main basin volume: 1493199 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=148, y=110, z=85, Imax=255 CSF=12, 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=9594846747 voxels, voxel volume =1.000 = 9594846747 mmm3 = 9594847.232 cm3 done. PostAnalyze...Basin Prior 134 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=127,y=134, z=109, r=10060 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=34 , nb = 43803 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = -1029705146 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=17 , nb = -1048463709 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 1043219685 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 1073891898 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=19 , nb = 1078015446 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 34, 35, 36, 56 after analyzing : 34, 35, 36, 40 RIGHT_CER before analyzing : 18, 24, 34, 56 after analyzing : 18, 30, 34, 36 LEFT_CER before analyzing : 17, 22, 31, 57 after analyzing : 17, 28, 31, 35 RIGHT_BRAIN before analyzing : 35, 35, 36, 56 after analyzing : 27, 35, 36, 40 LEFT_BRAIN before analyzing : 37, 36, 36, 56 after analyzing : 27, 36, 36, 41 OTHER before analyzing : 19, 52, 80, 88 after analyzing : 19, 70, 80, 74 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 71.621, std = 8.811 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.79, sigma = 7.35 after rotation: sse = 4.79, sigma = 7.35 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.30, its var is 10.43 before Erosion-Dilatation 3.92% of inacurate vertices after Erosion-Dilatation 4.46% 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...42 iterations mri_strip_skull: done peeling brain Brain Size = 1832135 voxels, voxel volume = 1.000 mm3 = 1832135 mmm3 = 1832.135 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 24.026347 mri_watershed stimesec 0.417936 mri_watershed ru_maxrss 831496 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 215214 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 6016 mri_watershed ru_oublock 2896 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1658 mri_watershed ru_nivcsw 89 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 17:39:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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=25.0 skull bounding box = (58, 70, 38) --> (196, 208, 198) using (104, 116, 118) as brain centroid... mean wm in atlas = 107, using box (87,99,98) --> (120, 132,137) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 5.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.075 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.088684 @ (0.000, 0.000, 0.000) max log p = -3.928316 @ (-4.545, -13.636, -13.636) max log p = -3.842317 @ (2.273, 2.273, 2.273) max log p = -3.830234 @ (1.136, -1.136, -1.136) max log p = -3.820868 @ (0.568, 1.705, 1.705) max log p = -3.814574 @ (0.284, -0.284, 2.557) Found translation: (-0.3, -11.1, -8.2): log p = -3.815 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.416, old_max_log_p =-3.815 (thresh=-3.8) 0.99144 -0.12059 -0.04995 22.20240; 0.14032 0.98467 0.40787 -73.27188; 0.00000 -0.35398 0.85459 61.94067; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.416, old_max_log_p =-3.416 (thresh=-3.4) 0.99144 -0.12059 -0.04995 22.20240; 0.14032 0.98467 0.40787 -73.27188; 0.00000 -0.35398 0.85459 61.94067; 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=-3.181, old_max_log_p =-3.416 (thresh=-3.4) 1.03594 -0.05803 -0.02404 5.44814; 0.07658 1.00902 0.41795 -69.49731; 0.00000 -0.36726 0.88664 56.55929; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.177, old_max_log_p =-3.181 (thresh=-3.2) 1.01652 -0.05694 -0.02359 7.72231; 0.07802 1.02794 0.42579 -73.03706; 0.00000 -0.36726 0.88664 56.55929; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.176, old_max_log_p =-3.177 (thresh=-3.2) 1.03558 -0.05801 -0.02403 5.49079; 0.07655 1.00867 0.41780 -69.43092; 0.00000 -0.36726 0.88664 56.55929; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.147, old_max_log_p =-3.176 (thresh=-3.2) 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.147, old_max_log_p =-3.147 (thresh=-3.1) 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.147 (old=-4.075) transform before final EM align: 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.7 tol 0.000000 final transform: 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1036.565418 mri_em_register stimesec 1.215815 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 158955 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 76 mri_em_register ru_nivcsw 3129 registration took 8 minutes and 55 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 17:48:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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=25.0 skull bounding box = (58, 70, 38) --> (196, 208, 198) using (104, 116, 118) as brain centroid... mean wm in atlas = 107, using box (87,99,98) --> (120, 132,137) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 5.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88005; 0.00846 -0.36699 0.88428 55.23253; 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 (126, 69, 34) --> (192, 188, 202) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 555 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 70, 35) --> (128, 183, 202) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 372 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 161, 68) --> (178, 199, 124) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 161, 67) --> (130, 201, 125) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 2 of 13 (15.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 143, 102) --> (148, 207, 135) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 12 (0.0%) samples deleted using 960 total control points for intensity normalization... bias field = 0.960 +- 0.050 6 of 958 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 69, 34) --> (192, 188, 202) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 758 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 70, 35) --> (128, 183, 202) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 1 of 559 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 161, 68) --> (178, 199, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 79 (17.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 161, 67) --> (130, 201, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 60 (21.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 143, 102) --> (148, 207, 135) Brain_Stem: limiting intensities to 88.0 --> 132.0 16 of 91 (17.6%) samples deleted using 1547 total control points for intensity normalization... bias field = 1.006 +- 0.063 11 of 1494 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 69, 34) --> (192, 188, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 842 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 70, 35) --> (128, 183, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 618 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 161, 68) --> (178, 199, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 30 of 67 (44.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 161, 67) --> (130, 201, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 55 of 79 (69.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 143, 102) --> (148, 207, 135) Brain_Stem: limiting intensities to 88.0 --> 132.0 70 of 165 (42.4%) samples deleted using 1771 total control points for intensity normalization... bias field = 1.012 +- 0.051 7 of 1569 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 40 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 17:50:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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) = 1.08 (predicted orig area = 7.4) 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=0.804, neg=0, invalid=762 0001: dt=219.132394, rms=0.742 (7.741%), neg=0, invalid=762 0002: dt=229.788396, rms=0.720 (2.873%), neg=0, invalid=762 0003: dt=205.538462, rms=0.711 (1.292%), neg=0, invalid=762 0004: dt=221.952000, rms=0.705 (0.912%), neg=0, invalid=762 0005: dt=129.472000, rms=0.701 (0.502%), neg=0, invalid=762 0006: dt=1183.744000, rms=0.691 (1.499%), neg=0, invalid=762 0007: dt=129.472000, rms=0.687 (0.582%), neg=0, invalid=762 0008: dt=221.952000, rms=0.686 (0.142%), neg=0, invalid=762 0009: dt=221.952000, rms=0.684 (0.201%), neg=0, invalid=762 0010: dt=221.952000, rms=0.682 (0.283%), neg=0, invalid=762 0011: dt=221.952000, rms=0.681 (0.248%), neg=0, invalid=762 0012: dt=221.952000, rms=0.678 (0.417%), neg=0, invalid=762 0013: dt=221.952000, rms=0.675 (0.356%), neg=0, invalid=762 0014: dt=221.952000, rms=0.673 (0.327%), neg=0, invalid=762 0015: dt=221.952000, rms=0.671 (0.282%), neg=0, invalid=762 0016: dt=221.952000, rms=0.669 (0.362%), neg=0, invalid=762 0017: dt=221.952000, rms=0.667 (0.251%), neg=0, invalid=762 0018: dt=221.952000, rms=0.666 (0.168%), neg=0, invalid=762 0019: dt=221.952000, rms=0.665 (0.220%), neg=0, invalid=762 0020: dt=221.952000, rms=0.663 (0.189%), neg=0, invalid=762 0021: dt=221.952000, rms=0.662 (0.181%), neg=0, invalid=762 0022: dt=221.952000, rms=0.661 (0.159%), neg=0, invalid=762 0023: dt=221.952000, rms=0.660 (0.209%), neg=0, invalid=762 0024: dt=221.952000, rms=0.659 (0.157%), neg=0, invalid=762 0025: dt=221.952000, rms=0.658 (0.136%), neg=0, invalid=762 0026: dt=221.952000, rms=0.657 (0.155%), neg=0, invalid=762 0027: dt=221.952000, rms=0.656 (0.140%), neg=0, invalid=762 0028: dt=221.952000, rms=0.655 (0.136%), neg=0, invalid=762 0029: dt=221.952000, rms=0.654 (0.099%), neg=0, invalid=762 0030: dt=221.952000, rms=0.653 (0.118%), neg=0, invalid=762 0031: dt=221.952000, rms=0.653 (0.113%), neg=0, invalid=762 0032: dt=110.976000, rms=0.653 (0.006%), neg=0, invalid=762 0033: dt=110.976000, rms=0.653 (0.008%), neg=0, invalid=762 0034: dt=110.976000, rms=0.653 (0.015%), neg=0, invalid=762 0035: dt=110.976000, rms=0.652 (0.020%), neg=0, invalid=762 0036: dt=110.976000, rms=0.652 (0.024%), neg=0, invalid=762 0037: dt=110.976000, rms=0.652 (0.029%), neg=0, invalid=762 0038: dt=110.976000, rms=0.652 (0.033%), neg=0, invalid=762 0039: dt=110.976000, rms=0.652 (0.029%), neg=0, invalid=762 0040: dt=110.976000, rms=0.651 (0.027%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0041: dt=295.936000, rms=0.651 (0.176%), neg=0, invalid=762 0042: dt=369.920000, rms=0.651 (0.074%), neg=0, invalid=762 0043: dt=369.920000, rms=0.651 (-0.174%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.658, neg=0, invalid=762 0044: dt=207.820225, rms=0.650 (1.155%), neg=0, invalid=762 0045: dt=82.944000, rms=0.645 (0.860%), neg=0, invalid=762 0046: dt=103.680000, rms=0.642 (0.500%), neg=0, invalid=762 0047: dt=88.918768, rms=0.639 (0.454%), neg=0, invalid=762 0048: dt=90.536585, rms=0.637 (0.331%), neg=0, invalid=762 0049: dt=110.545455, rms=0.634 (0.384%), neg=0, invalid=762 0050: dt=70.974359, rms=0.632 (0.268%), neg=0, invalid=762 0051: dt=145.152000, rms=0.630 (0.376%), neg=0, invalid=762 0052: dt=64.920863, rms=0.629 (0.212%), neg=0, invalid=762 0053: dt=64.920863, rms=0.628 (0.189%), neg=0, invalid=762 0054: dt=64.920863, rms=0.626 (0.267%), neg=0, invalid=762 0055: dt=64.920863, rms=0.624 (0.355%), neg=0, invalid=762 0056: dt=64.920863, rms=0.621 (0.395%), neg=0, invalid=762 0057: dt=64.920863, rms=0.618 (0.433%), neg=0, invalid=762 0058: dt=64.920863, rms=0.616 (0.418%), neg=0, invalid=762 0059: dt=64.920863, rms=0.613 (0.390%), neg=0, invalid=762 0060: dt=64.920863, rms=0.611 (0.361%), neg=0, invalid=762 0061: dt=64.920863, rms=0.609 (0.335%), neg=0, invalid=762 0062: dt=64.920863, rms=0.607 (0.320%), neg=0, invalid=762 0063: dt=64.920863, rms=0.606 (0.275%), neg=0, invalid=762 0064: dt=64.920863, rms=0.604 (0.246%), neg=0, invalid=762 0065: dt=64.920863, rms=0.603 (0.214%), neg=0, invalid=762 0066: dt=64.920863, rms=0.602 (0.189%), neg=0, invalid=762 0067: dt=64.920863, rms=0.601 (0.161%), neg=0, invalid=762 0068: dt=64.920863, rms=0.600 (0.127%), neg=0, invalid=762 0069: dt=64.920863, rms=0.599 (0.102%), neg=0, invalid=762 0070: dt=64.920863, rms=0.599 (0.104%), neg=0, invalid=762 0071: dt=64.920863, rms=0.598 (0.114%), neg=0, invalid=762 0072: dt=64.920863, rms=0.597 (0.093%), neg=0, invalid=762 0073: dt=82.944000, rms=0.597 (0.011%), neg=0, invalid=762 0074: dt=82.944000, rms=0.597 (0.028%), neg=0, invalid=762 0075: dt=82.944000, rms=0.597 (0.028%), neg=0, invalid=762 0076: dt=82.944000, rms=0.597 (0.021%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=762 0077: dt=82.944000, rms=0.596 (0.223%), neg=0, invalid=762 0078: dt=103.680000, rms=0.596 (0.044%), neg=0, invalid=762 0079: dt=103.680000, rms=0.596 (0.016%), neg=0, invalid=762 0080: dt=103.680000, rms=0.596 (0.006%), neg=0, invalid=762 0081: dt=103.680000, rms=0.596 (-0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.620, neg=0, invalid=762 0082: dt=0.000000, rms=0.619 (0.102%), neg=0, invalid=762 0083: dt=0.000000, rms=0.619 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.620, neg=0, invalid=762 0084: dt=0.000000, rms=0.619 (0.102%), neg=0, invalid=762 0085: dt=0.000000, rms=0.619 (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=0.690, neg=0, invalid=762 0086: dt=5.674286, rms=0.668 (3.209%), neg=0, invalid=762 0087: dt=2.724138, rms=0.667 (0.117%), neg=0, invalid=762 0088: dt=2.724138, rms=0.667 (-0.041%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=762 0089: dt=0.000000, rms=0.667 (0.093%), neg=0, invalid=762 0090: dt=0.000000, rms=0.667 (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=0.733, neg=0, invalid=762 0091: dt=1.280000, rms=0.728 (0.660%), neg=0, invalid=762 0092: dt=2.214815, rms=0.722 (0.842%), neg=0, invalid=762 0093: dt=0.448000, rms=0.721 (0.037%), neg=0, invalid=762 0094: dt=0.448000, rms=0.721 (0.040%), neg=0, invalid=762 0095: dt=0.448000, rms=0.721 (0.051%), neg=0, invalid=762 0096: dt=0.448000, rms=0.720 (0.043%), neg=0, invalid=762 0097: dt=0.448000, rms=0.720 (0.036%), neg=0, invalid=762 0098: dt=3.072000, rms=0.718 (0.234%), neg=0, invalid=762 0099: dt=0.096000, rms=0.718 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=762 0100: dt=0.448000, rms=0.718 (0.146%), neg=0, invalid=762 0101: dt=0.448000, rms=0.718 (0.011%), neg=0, invalid=762 0102: dt=0.448000, rms=0.718 (0.005%), neg=0, invalid=762 0103: dt=0.448000, rms=0.718 (0.001%), neg=0, invalid=762 0104: dt=0.448000, rms=0.718 (-0.011%), 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=0.684, neg=0, invalid=762 0105: dt=0.838641, rms=0.666 (2.673%), neg=0, invalid=762 0106: dt=0.080000, rms=0.665 (0.143%), neg=0, invalid=762 0107: dt=0.080000, rms=0.665 (-0.077%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0108: dt=0.028000, rms=0.664 (0.128%), neg=0, invalid=762 0109: dt=0.007000, rms=0.664 (0.001%), neg=0, invalid=762 0110: dt=0.007000, rms=0.664 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.07098 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (744 voxels, overlap=0.278) Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (744 voxels, peak = 10), gca=10.1 gca peak = 0.15565 (16) mri peak = 0.13221 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (800 voxels, overlap=0.300) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (800 voxels, peak = 8), gca=8.2 gca peak = 0.26829 (96) mri peak = 0.07232 (90) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (828 voxels, overlap=0.497) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (828 voxels, peak = 89), gca=88.8 gca peak = 0.20183 (93) mri peak = 0.06522 (86) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (747 voxels, overlap=0.442) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (747 voxels, peak = 85), gca=85.1 gca peak = 0.21683 (55) mri peak = 0.08094 (51) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (530 voxels, overlap=0.985) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (530 voxels, peak = 50), gca=50.3 gca peak = 0.30730 (58) mri peak = 0.07838 (56) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (396 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (396 voxels, peak = 55), gca=54.8 gca peak = 0.11430 (101) mri peak = 0.09702 (105) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (67387 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (67387 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.10198 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (71559 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (71559 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04064 (56) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (27293 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (27293 voxels, peak = 56), gca=55.8 gca peak = 0.15082 (58) mri peak = 0.03966 (54) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (24730 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (24730 voxels, peak = 55), gca=54.8 gca peak = 0.14161 (67) mri peak = 0.12764 (67) Right_Caudate (50): linear fit = 0.99 x + 0.0 (567 voxels, overlap=0.938) Right_Caudate (50): linear fit = 0.99 x + 0.0 (567 voxels, peak = 66), gca=66.0 gca peak = 0.15243 (71) mri peak = 0.08142 (67) Left_Caudate (11): linear fit = 0.94 x + 0.0 (960 voxels, overlap=0.747) Left_Caudate (11): linear fit = 0.94 x + 0.0 (960 voxels, peak = 66), gca=66.4 gca peak = 0.13336 (57) mri peak = 0.03619 (46) Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (23404 voxels, overlap=0.450) Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (23404 voxels, peak = 49), gca=48.7 gca peak = 0.13252 (56) mri peak = 0.02993 (41) Right_Cerebellum_Cortex (47): linear fit = 0.77 x + 0.0 (24388 voxels, overlap=0.028) Right_Cerebellum_Cortex (47): linear fit = 0.77 x + 0.0 (24388 voxels, peak = 43), gca=43.4 gca peak = 0.18181 (84) mri peak = 0.06782 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8100 voxels, overlap=0.929) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8100 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.05792 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7549 voxels, overlap=0.978) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7549 voxels, peak = 85), gca=85.1 gca peak = 0.21969 (57) mri peak = 0.05251 (61) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (469 voxels, overlap=1.006) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (469 voxels, peak = 58), gca=58.4 gca peak = 0.39313 (56) mri peak = 0.07993 (61) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05315 (91) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6055 voxels, overlap=0.911) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6055 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.06127 (87) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4945 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4945 voxels, peak = 88), gca=88.4 gca peak = 0.13399 (79) mri peak = 0.04933 (76) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2433 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2433 voxels, peak = 79), gca=78.6 gca peak = 0.14159 (79) mri peak = 0.06141 (77) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2426 voxels, overlap=0.959) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2426 voxels, peak = 77), gca=77.0 gca peak = 0.10025 (80) mri peak = 0.08348 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12482 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12482 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06858 (91) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1202 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1202 voxels, peak = 90), gca=89.9 gca peak = 0.12801 (89) mri peak = 0.07554 (88) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1287 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1287 voxels, peak = 90), gca=90.3 gca peak = 0.20494 (23) mri peak = 0.16031 (52) gca peak = 0.15061 (21) mri peak = 0.17251 ( 8) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (403 voxels, overlap=0.110) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (403 voxels, peak = 8), gca=8.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.97 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.51 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=0.690, neg=0, invalid=762 0111: dt=140.571429, rms=0.682 (1.119%), neg=0, invalid=762 0112: dt=157.333333, rms=0.678 (0.575%), neg=0, invalid=762 0113: dt=129.472000, rms=0.676 (0.214%), neg=0, invalid=762 0114: dt=295.936000, rms=0.674 (0.294%), neg=0, invalid=762 0115: dt=92.480000, rms=0.673 (0.187%), neg=0, invalid=762 0116: dt=517.888000, rms=0.671 (0.277%), neg=0, invalid=762 0117: dt=73.984000, rms=0.670 (0.121%), neg=0, invalid=762 0118: dt=1479.680000, rms=0.668 (0.353%), neg=0, invalid=762 0119: dt=110.976000, rms=0.667 (0.236%), neg=0, invalid=762 0120: dt=110.976000, rms=0.666 (0.031%), neg=0, invalid=762 0121: dt=110.976000, rms=0.666 (0.035%), neg=0, invalid=762 0122: dt=110.976000, rms=0.666 (0.058%), neg=0, invalid=762 0123: dt=110.976000, rms=0.665 (0.071%), neg=0, invalid=762 0124: dt=110.976000, rms=0.665 (0.081%), neg=0, invalid=762 0125: dt=110.976000, rms=0.664 (0.091%), neg=0, invalid=762 0126: dt=110.976000, rms=0.663 (0.098%), neg=0, invalid=762 0127: dt=110.976000, rms=0.663 (0.095%), neg=0, invalid=762 0128: dt=110.976000, rms=0.662 (0.088%), neg=0, invalid=762 0129: dt=110.976000, rms=0.662 (0.089%), neg=0, invalid=762 0130: dt=110.976000, rms=0.661 (0.092%), neg=0, invalid=762 0131: dt=110.976000, rms=0.660 (0.093%), neg=0, invalid=762 0132: dt=110.976000, rms=0.660 (0.084%), neg=0, invalid=762 0133: dt=110.976000, rms=0.659 (0.073%), neg=0, invalid=762 0134: dt=110.976000, rms=0.659 (0.067%), neg=0, invalid=762 0135: dt=110.976000, rms=0.659 (0.067%), neg=0, invalid=762 0136: dt=110.976000, rms=0.658 (0.066%), neg=0, invalid=762 0137: dt=110.976000, rms=0.658 (0.062%), neg=0, invalid=762 0138: dt=110.976000, rms=0.657 (0.061%), neg=0, invalid=762 0139: dt=110.976000, rms=0.657 (0.057%), neg=0, invalid=762 0140: dt=110.976000, rms=0.657 (0.058%), neg=0, invalid=762 0141: dt=110.976000, rms=0.656 (0.059%), neg=0, invalid=762 0142: dt=110.976000, rms=0.656 (0.056%), neg=0, invalid=762 0143: dt=110.976000, rms=0.655 (0.051%), neg=0, invalid=762 0144: dt=110.976000, rms=0.655 (0.052%), neg=0, invalid=762 0145: dt=110.976000, rms=0.655 (0.051%), neg=0, invalid=762 0146: dt=110.976000, rms=0.654 (0.051%), neg=0, invalid=762 0147: dt=110.976000, rms=0.654 (0.049%), neg=0, invalid=762 0148: dt=110.976000, rms=0.654 (0.046%), neg=0, invalid=762 0149: dt=110.976000, rms=0.654 (0.044%), neg=0, invalid=762 0150: dt=110.976000, rms=0.653 (0.044%), neg=0, invalid=762 0151: dt=110.976000, rms=0.653 (0.042%), neg=0, invalid=762 0152: dt=110.976000, rms=0.653 (0.042%), neg=0, invalid=762 0153: dt=110.976000, rms=0.652 (0.041%), neg=0, invalid=762 0154: dt=110.976000, rms=0.652 (0.040%), neg=0, invalid=762 0155: dt=110.976000, rms=0.652 (0.040%), neg=0, invalid=762 0156: dt=110.976000, rms=0.652 (0.039%), neg=0, invalid=762 0157: dt=110.976000, rms=0.651 (0.037%), neg=0, invalid=762 0158: dt=110.976000, rms=0.651 (0.036%), neg=0, invalid=762 0159: dt=110.976000, rms=0.651 (0.035%), neg=0, invalid=762 0160: dt=110.976000, rms=0.651 (0.033%), neg=0, invalid=762 0161: dt=110.976000, rms=0.650 (0.032%), neg=0, invalid=762 0162: dt=110.976000, rms=0.650 (0.028%), neg=0, invalid=762 0163: dt=110.976000, rms=0.650 (0.027%), neg=0, invalid=762 0164: dt=110.976000, rms=0.650 (0.029%), neg=0, invalid=762 0165: dt=110.976000, rms=0.650 (0.028%), neg=0, invalid=762 0166: dt=110.976000, rms=0.650 (0.027%), neg=0, invalid=762 0167: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762 0168: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762 0169: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762 0170: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762 0171: dt=110.976000, rms=0.649 (0.025%), neg=0, invalid=762 0172: dt=110.976000, rms=0.649 (0.025%), neg=0, invalid=762 0173: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762 0174: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762 0175: dt=110.976000, rms=0.648 (0.025%), neg=0, invalid=762 0176: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762 0177: dt=5918.720000, rms=0.648 (0.061%), neg=0, invalid=762 0178: dt=129.472000, rms=0.647 (0.066%), neg=0, invalid=762 0179: dt=23.120000, rms=0.647 (0.005%), neg=0, invalid=762 0180: dt=23.120000, rms=0.647 (0.000%), neg=0, invalid=762 0181: dt=23.120000, rms=0.647 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0182: dt=129.472000, rms=0.647 (0.146%), neg=0, invalid=762 0183: dt=517.888000, rms=0.646 (0.073%), neg=0, invalid=762 0184: dt=517.888000, rms=0.646 (0.081%), neg=0, invalid=762 0185: dt=110.976000, rms=0.646 (0.032%), neg=0, invalid=762 0186: dt=110.976000, rms=0.646 (0.004%), neg=0, invalid=762 0187: dt=110.976000, rms=0.646 (0.009%), neg=0, invalid=762 0188: dt=110.976000, rms=0.645 (0.020%), neg=0, invalid=762 0189: dt=110.976000, rms=0.645 (0.030%), neg=0, invalid=762 0190: dt=110.976000, rms=0.645 (0.037%), neg=0, invalid=762 0191: dt=110.976000, rms=0.645 (0.036%), neg=0, invalid=762 0192: dt=110.976000, rms=0.645 (0.033%), neg=0, invalid=762 0193: dt=110.976000, rms=0.644 (0.032%), neg=0, invalid=762 0194: dt=110.976000, rms=0.644 (0.028%), neg=0, invalid=762 0195: dt=110.976000, rms=0.644 (0.022%), neg=0, invalid=762 0196: dt=110.976000, rms=0.644 (0.024%), neg=0, invalid=762 0197: dt=110.976000, rms=0.644 (0.024%), neg=0, invalid=762 0198: dt=110.976000, rms=0.644 (0.027%), neg=0, invalid=762 0199: dt=110.976000, rms=0.643 (0.026%), neg=0, invalid=762 0200: dt=110.976000, rms=0.643 (0.022%), neg=0, invalid=762 0201: dt=110.976000, rms=0.643 (0.018%), neg=0, invalid=762 0202: dt=443.904000, rms=0.643 (0.004%), neg=0, invalid=762 0203: dt=443.904000, rms=0.643 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0204: dt=134.935961, rms=0.640 (0.672%), neg=0, invalid=762 0205: dt=96.502618, rms=0.637 (0.557%), neg=0, invalid=762 0206: dt=62.352475, rms=0.634 (0.417%), neg=0, invalid=762 0207: dt=103.680000, rms=0.632 (0.346%), neg=0, invalid=762 0208: dt=62.208000, rms=0.630 (0.351%), neg=0, invalid=762 0209: dt=88.553459, rms=0.628 (0.264%), neg=0, invalid=762 0210: dt=63.152318, rms=0.626 (0.272%), neg=0, invalid=762 0211: dt=84.087591, rms=0.625 (0.220%), neg=0, invalid=762 0212: dt=66.666667, rms=0.624 (0.229%), neg=0, invalid=762 0213: dt=82.944000, rms=0.623 (0.183%), neg=0, invalid=762 0214: dt=62.208000, rms=0.621 (0.206%), neg=0, invalid=762 0215: dt=82.944000, rms=0.620 (0.161%), neg=0, invalid=762 0216: dt=64.964824, rms=0.619 (0.182%), neg=0, invalid=762 0217: dt=82.944000, rms=0.618 (0.138%), neg=0, invalid=762 0218: dt=62.208000, rms=0.617 (0.170%), neg=0, invalid=762 0219: dt=82.944000, rms=0.616 (0.121%), neg=0, invalid=762 0220: dt=62.306878, rms=0.616 (0.157%), neg=0, invalid=762 0221: dt=82.944000, rms=0.615 (0.109%), neg=0, invalid=762 0222: dt=36.288000, rms=0.614 (0.118%), neg=0, invalid=762 0223: dt=580.608000, rms=0.609 (0.847%), neg=0, invalid=762 0224: dt=62.208000, rms=0.608 (0.104%), neg=0, invalid=762 0225: dt=62.208000, rms=0.608 (0.066%), neg=0, invalid=762 0226: dt=103.680000, rms=0.607 (0.093%), neg=0, invalid=762 0227: dt=36.288000, rms=0.607 (0.082%), neg=0, invalid=762 0228: dt=580.608000, rms=0.604 (0.484%), neg=0, invalid=762 0229: dt=36.288000, rms=0.603 (0.134%), neg=0, invalid=762 0230: dt=248.832000, rms=0.602 (0.160%), neg=0, invalid=762 0231: dt=36.288000, rms=0.602 (0.075%), neg=0, invalid=762 0232: dt=82.944000, rms=0.601 (0.045%), neg=0, invalid=762 0233: dt=82.944000, rms=0.601 (0.083%), neg=0, invalid=762 0234: dt=82.944000, rms=0.600 (0.123%), neg=0, invalid=762 0235: dt=82.944000, rms=0.599 (0.134%), neg=0, invalid=762 0236: dt=82.944000, rms=0.598 (0.202%), neg=0, invalid=762 0237: dt=82.944000, rms=0.597 (0.205%), neg=0, invalid=762 0238: dt=82.944000, rms=0.596 (0.216%), neg=0, invalid=762 0239: dt=82.944000, rms=0.594 (0.261%), neg=0, invalid=762 0240: dt=82.944000, rms=0.593 (0.248%), neg=0, invalid=762 0241: dt=82.944000, rms=0.591 (0.226%), neg=0, invalid=762 0242: dt=82.944000, rms=0.590 (0.220%), neg=0, invalid=762 0243: dt=82.944000, rms=0.589 (0.232%), neg=0, invalid=762 0244: dt=82.944000, rms=0.588 (0.016%), neg=0, invalid=762 0245: dt=82.944000, rms=0.588 (0.046%), neg=0, invalid=762 0246: dt=82.944000, rms=0.588 (0.061%), neg=0, invalid=762 0247: dt=82.944000, rms=0.587 (0.078%), neg=0, invalid=762 0248: dt=82.944000, rms=0.587 (0.081%), neg=0, invalid=762 0249: dt=82.944000, rms=0.586 (0.100%), neg=0, invalid=762 0250: dt=82.944000, rms=0.586 (0.099%), neg=0, invalid=762 0251: dt=82.944000, rms=0.585 (0.107%), neg=0, invalid=762 0252: dt=82.944000, rms=0.584 (0.127%), neg=0, invalid=762 0253: dt=82.944000, rms=0.584 (0.107%), neg=0, invalid=762 0254: dt=82.944000, rms=0.583 (0.120%), neg=0, invalid=762 0255: dt=82.944000, rms=0.582 (0.125%), neg=0, invalid=762 0256: dt=82.944000, rms=0.582 (0.112%), neg=0, invalid=762 0257: dt=82.944000, rms=0.582 (0.008%), neg=0, invalid=762 0258: dt=82.944000, rms=0.581 (0.025%), neg=0, invalid=762 0259: dt=82.944000, rms=0.581 (0.013%), neg=0, invalid=762 0260: dt=36.288000, rms=0.581 (0.010%), neg=0, invalid=762 0261: dt=18.144000, rms=0.581 (0.002%), neg=0, invalid=762 0262: dt=0.567000, rms=0.581 (0.001%), neg=0, invalid=762 0263: dt=0.283500, 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 0264: dt=110.412214, rms=0.580 (0.409%), neg=0, invalid=762 0265: dt=103.680000, rms=0.579 (0.201%), neg=0, invalid=762 0266: dt=36.288000, rms=0.578 (0.063%), neg=0, invalid=762 0267: dt=145.152000, rms=0.578 (0.087%), neg=0, invalid=762 0268: dt=124.416000, rms=0.577 (0.105%), neg=0, invalid=762 0269: dt=36.288000, rms=0.577 (0.026%), neg=0, invalid=762 0270: dt=36.288000, rms=0.577 (0.015%), neg=0, invalid=762 0271: dt=36.288000, rms=0.577 (0.031%), neg=0, invalid=762 0272: dt=36.288000, rms=0.576 (0.046%), neg=0, invalid=762 0273: dt=36.288000, rms=0.576 (0.058%), neg=0, invalid=762 0274: dt=36.288000, rms=0.576 (0.065%), neg=0, invalid=762 0275: dt=36.288000, rms=0.575 (0.065%), neg=0, invalid=762 0276: dt=36.288000, rms=0.575 (0.067%), neg=0, invalid=762 0277: dt=36.288000, rms=0.575 (0.065%), neg=0, invalid=762 0278: dt=36.288000, rms=0.574 (0.063%), neg=0, invalid=762 0279: dt=36.288000, rms=0.574 (0.067%), neg=0, invalid=762 0280: dt=36.288000, rms=0.573 (0.068%), neg=0, invalid=762 0281: dt=36.288000, rms=0.573 (0.062%), neg=0, invalid=762 0282: dt=36.288000, rms=0.573 (0.056%), neg=0, invalid=762 0283: dt=36.288000, rms=0.572 (0.057%), neg=0, invalid=762 0284: dt=36.288000, rms=0.572 (0.054%), neg=0, invalid=762 0285: dt=36.288000, rms=0.572 (0.056%), neg=0, invalid=762 0286: dt=36.288000, rms=0.572 (0.058%), neg=0, invalid=762 0287: dt=36.288000, rms=0.571 (0.056%), neg=0, invalid=762 0288: dt=36.288000, rms=0.571 (0.053%), neg=0, invalid=762 0289: dt=36.288000, rms=0.571 (0.052%), neg=0, invalid=762 0290: dt=36.288000, rms=0.570 (0.055%), neg=0, invalid=762 0291: dt=36.288000, rms=0.570 (0.054%), neg=0, invalid=762 0292: dt=36.288000, rms=0.570 (0.053%), neg=0, invalid=762 0293: dt=36.288000, rms=0.569 (0.051%), neg=0, invalid=762 0294: dt=36.288000, rms=0.569 (0.049%), neg=0, invalid=762 0295: dt=36.288000, rms=0.569 (0.047%), neg=0, invalid=762 0296: dt=36.288000, rms=0.569 (0.047%), neg=0, invalid=762 0297: dt=36.288000, rms=0.568 (0.047%), neg=0, invalid=762 0298: dt=36.288000, rms=0.568 (0.045%), neg=0, invalid=762 0299: dt=36.288000, rms=0.568 (0.044%), neg=0, invalid=762 0300: dt=36.288000, rms=0.568 (0.042%), neg=0, invalid=762 0301: dt=36.288000, rms=0.567 (0.038%), neg=0, invalid=762 0302: dt=36.288000, rms=0.567 (0.042%), neg=0, invalid=762 0303: dt=36.288000, rms=0.567 (0.040%), neg=0, invalid=762 0304: dt=36.288000, rms=0.567 (0.038%), neg=0, invalid=762 0305: dt=36.288000, rms=0.566 (0.036%), neg=0, invalid=762 0306: dt=36.288000, rms=0.566 (0.036%), neg=0, invalid=762 0307: dt=36.288000, rms=0.566 (0.034%), neg=0, invalid=762 0308: dt=36.288000, rms=0.566 (0.037%), neg=0, invalid=762 0309: dt=36.288000, rms=0.566 (0.034%), neg=0, invalid=762 0310: dt=36.288000, rms=0.565 (0.033%), neg=0, invalid=762 0311: dt=36.288000, rms=0.565 (0.032%), neg=0, invalid=762 0312: dt=36.288000, rms=0.565 (0.031%), neg=0, invalid=762 0313: dt=36.288000, rms=0.565 (0.031%), neg=0, invalid=762 0314: dt=36.288000, rms=0.565 (0.033%), neg=0, invalid=762 0315: dt=36.288000, rms=0.565 (0.029%), neg=0, invalid=762 0316: dt=36.288000, rms=0.564 (0.029%), neg=0, invalid=762 0317: dt=36.288000, rms=0.564 (0.032%), neg=0, invalid=762 0318: dt=36.288000, rms=0.564 (0.027%), neg=0, invalid=762 0319: dt=36.288000, rms=0.564 (0.027%), neg=0, invalid=762 0320: dt=36.288000, rms=0.564 (0.028%), neg=0, invalid=762 0321: dt=36.288000, rms=0.564 (0.026%), neg=0, invalid=762 0322: dt=36.288000, rms=0.563 (0.027%), neg=0, invalid=762 0323: dt=36.288000, rms=0.563 (0.026%), neg=0, invalid=762 0324: dt=36.288000, rms=0.563 (0.025%), neg=0, invalid=762 0325: dt=36.288000, rms=0.563 (0.025%), neg=0, invalid=762 0326: dt=36.288000, rms=0.563 (0.025%), neg=0, invalid=762 0327: dt=36.288000, rms=0.563 (0.027%), neg=0, invalid=762 0328: dt=36.288000, rms=0.563 (0.026%), neg=0, invalid=762 0329: dt=36.288000, rms=0.562 (0.024%), neg=0, invalid=762 0330: dt=36.288000, rms=0.562 (0.022%), neg=0, invalid=762 0331: dt=145.152000, rms=0.562 (0.005%), neg=0, invalid=762 0332: dt=145.152000, rms=0.562 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.571, neg=0, invalid=762 0333: dt=32.000000, rms=0.569 (0.442%), neg=0, invalid=762 0334: dt=70.736842, rms=0.566 (0.516%), neg=0, invalid=762 0335: dt=25.600000, rms=0.563 (0.436%), neg=0, invalid=762 0336: dt=72.000000, rms=0.560 (0.645%), neg=0, invalid=762 0337: dt=23.201401, rms=0.557 (0.427%), neg=0, invalid=762 0338: dt=76.800000, rms=0.554 (0.493%), neg=0, invalid=762 0339: dt=25.600000, rms=0.553 (0.354%), neg=0, invalid=762 0340: dt=44.800000, rms=0.551 (0.322%), neg=0, invalid=762 0341: dt=25.600000, rms=0.550 (0.184%), neg=0, invalid=762 0342: dt=44.800000, rms=0.548 (0.275%), neg=0, invalid=762 0343: dt=25.043478, rms=0.548 (0.120%), neg=0, invalid=762 0344: dt=44.800000, rms=0.546 (0.223%), neg=0, invalid=762 0345: dt=22.237288, rms=0.546 (0.111%), neg=0, invalid=762 0346: dt=76.800000, rms=0.544 (0.267%), neg=0, invalid=762 0347: dt=23.004016, rms=0.543 (0.152%), neg=0, invalid=762 0348: dt=128.000000, rms=0.541 (0.361%), neg=0, invalid=762 0349: dt=11.200000, rms=0.541 (0.136%), neg=0, invalid=762 0350: dt=11.200000, rms=0.540 (0.083%), neg=0, invalid=762 0351: dt=2.000000, rms=0.540 (0.019%), neg=0, invalid=762 0352: dt=0.250000, rms=0.540 (0.002%), neg=0, invalid=762 0353: dt=0.031250, rms=0.540 (0.000%), neg=0, invalid=762 0354: dt=0.007812, rms=0.540 (0.000%), neg=0, invalid=762 0355: dt=0.002734, rms=0.540 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=762 0356: dt=32.000000, rms=0.538 (0.495%), neg=0, invalid=762 0357: dt=44.800000, rms=0.536 (0.329%), neg=0, invalid=762 0358: dt=11.200000, rms=0.536 (0.072%), neg=0, invalid=762 0359: dt=44.800000, rms=0.536 (0.104%), neg=0, invalid=762 0360: dt=32.000000, rms=0.535 (0.164%), neg=0, invalid=762 0361: dt=11.200000, rms=0.534 (0.047%), neg=0, invalid=762 0362: dt=11.200000, rms=0.534 (0.031%), neg=0, invalid=762 0363: dt=11.200000, rms=0.534 (0.043%), neg=0, invalid=762 0364: dt=11.200000, rms=0.534 (0.070%), neg=0, invalid=762 0365: dt=11.200000, rms=0.533 (0.104%), neg=0, invalid=762 0366: dt=11.200000, rms=0.533 (0.107%), neg=0, invalid=762 0367: dt=11.200000, rms=0.532 (0.105%), neg=0, invalid=762 0368: dt=11.200000, rms=0.531 (0.096%), neg=0, invalid=762 0369: dt=11.200000, rms=0.531 (0.107%), neg=0, invalid=762 0370: dt=11.200000, rms=0.530 (0.114%), neg=0, invalid=762 0371: dt=11.200000, rms=0.530 (0.129%), neg=0, invalid=762 0372: dt=11.200000, rms=0.529 (0.140%), neg=0, invalid=762 0373: dt=11.200000, rms=0.528 (0.136%), neg=0, invalid=762 0374: dt=11.200000, rms=0.527 (0.134%), neg=0, invalid=762 0375: dt=11.200000, rms=0.527 (0.025%), neg=0, invalid=762 0376: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=762 0377: dt=11.200000, rms=0.527 (0.052%), neg=0, invalid=762 0378: dt=11.200000, rms=0.526 (0.057%), neg=0, invalid=762 0379: dt=11.200000, rms=0.526 (0.070%), neg=0, invalid=762 0380: dt=11.200000, rms=0.526 (0.072%), neg=0, invalid=762 0381: dt=11.200000, rms=0.525 (0.079%), neg=0, invalid=762 0382: dt=11.200000, rms=0.525 (0.075%), neg=0, invalid=762 0383: dt=11.200000, rms=0.525 (0.074%), neg=0, invalid=762 0384: dt=11.200000, rms=0.524 (0.084%), neg=0, invalid=762 0385: dt=11.200000, rms=0.524 (0.085%), neg=0, invalid=762 0386: dt=11.200000, rms=0.523 (0.079%), neg=0, invalid=762 0387: dt=11.200000, rms=0.523 (0.082%), neg=0, invalid=762 0388: dt=11.200000, rms=0.522 (0.078%), neg=0, invalid=762 0389: dt=11.200000, rms=0.522 (0.078%), neg=0, invalid=762 0390: dt=11.200000, rms=0.522 (0.081%), neg=0, invalid=762 0391: dt=11.200000, rms=0.521 (0.078%), neg=0, invalid=762 0392: dt=11.200000, rms=0.521 (0.076%), neg=0, invalid=762 0393: dt=11.200000, rms=0.520 (0.073%), neg=0, invalid=762 0394: dt=11.200000, rms=0.520 (0.075%), neg=0, invalid=762 0395: dt=11.200000, rms=0.520 (0.070%), neg=0, invalid=762 0396: dt=11.200000, rms=0.519 (0.067%), neg=0, invalid=762 0397: dt=11.200000, rms=0.519 (0.067%), neg=0, invalid=762 0398: dt=11.200000, rms=0.519 (0.001%), neg=0, invalid=762 0399: dt=11.200000, rms=0.519 (0.011%), neg=0, invalid=762 0400: dt=11.200000, rms=0.519 (0.012%), neg=0, invalid=762 0401: dt=11.200000, rms=0.519 (0.018%), neg=0, invalid=762 0402: dt=11.200000, rms=0.519 (0.026%), neg=0, invalid=762 0403: dt=11.200000, rms=0.518 (0.020%), neg=0, invalid=762 0404: dt=11.200000, rms=0.518 (0.001%), neg=0, invalid=762 0405: dt=44.800000, rms=0.518 (0.020%), neg=0, invalid=762 0406: dt=11.200000, rms=0.518 (0.004%), neg=0, invalid=762 0407: dt=2.800000, rms=0.518 (0.004%), neg=0, invalid=762 0408: dt=1.400000, rms=0.518 (-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=0.539, neg=0, invalid=762 0409: dt=0.000000, rms=0.538 (0.148%), neg=0, invalid=762 0410: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 0411: dt=0.150000, rms=0.538 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0412: dt=0.000000, rms=0.538 (0.148%), neg=0, invalid=762 0413: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 0414: dt=0.150000, rms=0.538 (-0.021%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0415: dt=1.024000, rms=0.577 (0.432%), neg=0, invalid=762 0416: dt=0.112000, rms=0.577 (0.005%), neg=0, invalid=762 0417: dt=0.112000, rms=0.577 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0418: dt=0.448000, rms=0.576 (0.192%), neg=0, invalid=762 0419: dt=0.256000, rms=0.576 (0.010%), neg=0, invalid=762 0420: dt=0.256000, rms=0.576 (-0.005%), 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=0.526, neg=0, invalid=762 0421: dt=0.448000, rms=0.511 (2.844%), neg=0, invalid=762 0422: dt=0.448000, rms=0.508 (0.643%), neg=0, invalid=762 0423: dt=0.448000, rms=0.506 (0.343%), neg=0, invalid=762 0424: dt=0.448000, rms=0.505 (0.208%), neg=0, invalid=762 0425: dt=0.461538, rms=0.504 (0.150%), neg=0, invalid=762 0426: dt=0.448000, rms=0.504 (0.109%), neg=0, invalid=762 0427: dt=0.448000, rms=0.503 (0.086%), neg=0, invalid=762 0428: dt=0.448000, rms=0.503 (0.065%), neg=0, invalid=762 0429: dt=0.448000, rms=0.503 (0.058%), neg=0, invalid=762 0430: dt=0.448000, rms=0.503 (0.039%), neg=0, invalid=762 0431: dt=0.448000, rms=0.502 (0.042%), neg=0, invalid=762 0432: dt=0.448000, rms=0.502 (0.062%), neg=0, invalid=762 0433: dt=0.448000, rms=0.502 (0.076%), neg=0, invalid=762 0434: dt=0.448000, rms=0.501 (0.081%), neg=0, invalid=762 0435: dt=0.448000, rms=0.501 (0.065%), neg=0, invalid=762 0436: dt=0.448000, rms=0.501 (0.047%), neg=0, invalid=762 0437: dt=0.448000, rms=0.501 (-0.007%), neg=0, invalid=762 0438: dt=0.000000, rms=0.501 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=762 0439: dt=0.448000, rms=0.496 (1.181%), neg=0, invalid=762 0440: dt=0.448000, rms=0.495 (0.118%), neg=0, invalid=762 0441: dt=0.448000, rms=0.495 (0.041%), neg=0, invalid=762 0442: dt=0.448000, rms=0.495 (0.007%), neg=0, invalid=762 0443: dt=0.448000, rms=0.495 (0.006%), neg=0, invalid=762 0444: dt=0.448000, rms=0.495 (-0.012%), 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=0.493, neg=0, invalid=762 0445: dt=0.000000, rms=0.492 (0.178%), neg=0, invalid=762 0446: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0447: dt=129.472000, rms=0.492 (0.205%), neg=0, invalid=762 0448: dt=129.472000, rms=0.492 (0.024%), neg=0, invalid=762 0449: dt=129.472000, rms=0.492 (-0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0450: dt=9.072000, rms=0.492 (0.200%), neg=0, invalid=762 0451: dt=9.072000, rms=0.492 (0.005%), neg=0, invalid=762 0452: dt=9.072000, rms=0.492 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0453: dt=124.416000, rms=0.491 (0.448%), neg=0, invalid=762 0454: dt=36.288000, rms=0.490 (0.129%), neg=0, invalid=762 0455: dt=36.288000, rms=0.490 (0.046%), neg=0, invalid=762 0456: dt=36.288000, rms=0.490 (0.071%), neg=0, invalid=762 0457: dt=36.288000, rms=0.489 (0.097%), neg=0, invalid=762 0458: dt=36.288000, rms=0.489 (0.101%), neg=0, invalid=762 0459: dt=36.288000, rms=0.488 (0.097%), neg=0, invalid=762 0460: dt=36.288000, rms=0.488 (0.091%), neg=0, invalid=762 0461: dt=62.208000, rms=0.488 (0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0462: dt=23.866221, rms=0.486 (0.469%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0463: dt=32.000000, rms=0.485 (0.209%), neg=0, invalid=762 0464: dt=32.000000, rms=0.485 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0465: dt=32.000000, rms=0.483 (0.356%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0466: dt=32.000000, rms=0.483 (-0.016%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0467: dt=19.200000, rms=0.482 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0468: dt=32.000000, rms=0.481 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0469: dt=11.200000, rms=0.481 (0.055%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0470: dt=38.400000, rms=0.477 (1.069%), neg=0, invalid=762 0471: dt=25.600000, rms=0.475 (0.423%), neg=0, invalid=762 0472: dt=11.200000, rms=0.474 (0.110%), neg=0, invalid=762 0473: dt=11.200000, rms=0.474 (0.089%), neg=0, invalid=762 0474: dt=11.200000, rms=0.473 (0.134%), neg=0, invalid=762 0475: dt=11.200000, rms=0.472 (0.163%), neg=0, invalid=762 0476: dt=11.200000, rms=0.471 (0.178%), neg=0, invalid=762 0477: dt=11.200000, rms=0.471 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0478: dt=11.200000, rms=0.470 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0479: dt=11.200000, rms=0.469 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0480: dt=11.200000, rms=0.468 (0.151%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 12 iterations, nbhd size=1, neg = 0 0481: dt=11.200000, rms=0.468 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0482: dt=11.200000, rms=0.467 (0.144%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0483: dt=11.200000, rms=0.466 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0484: dt=11.200000, rms=0.466 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0485: dt=11.200000, rms=0.465 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0486: dt=11.200000, rms=0.465 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0487: dt=44.800000, rms=0.464 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0488: dt=44.800000, rms=0.464 (-0.101%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0489: dt=2.880000, rms=0.468 (0.209%), neg=0, invalid=762 0490: dt=0.864000, rms=0.468 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0491: dt=0.864000, rms=0.468 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0492: dt=8.000000, rms=0.468 (0.249%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0493: dt=12.081633, rms=0.467 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0494: dt=12.081633, rms=0.467 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0495: dt=12.081633, rms=0.465 (0.333%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0496: dt=12.081633, rms=0.463 (0.387%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 0497: dt=12.081633, rms=0.461 (0.544%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=0, neg = 0 0498: dt=12.081633, rms=0.458 (0.566%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 0499: dt=12.081633, rms=0.456 (0.477%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=0, neg = 0 0500: dt=12.081633, rms=0.455 (0.206%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0501: dt=12.081633, rms=0.455 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 10 iterations, nbhd size=0, neg = 0 0502: dt=12.081633, rms=0.455 (-0.088%), neg=0, invalid=762 0503: dt=0.000984, rms=0.455 (0.000%), neg=0, invalid=762 0504: dt=0.000211, rms=0.455 (0.000%), neg=0, invalid=762 0505: dt=0.000006, rms=0.455 (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=0.462, neg=0, invalid=762 0506: dt=0.000000, rms=0.461 (0.204%), neg=0, invalid=762 0507: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=762 0508: dt=0.000000, rms=0.461 (0.204%), neg=0, invalid=762 0509: dt=0.000000, rms=0.461 (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=0.451, neg=0, invalid=762 iter 0, gcam->neg = 794 after 17 iterations, nbhd size=1, neg = 0 0510: dt=1.921735, rms=0.424 (5.995%), neg=0, invalid=762 0511: dt=0.000013, rms=0.424 (0.001%), neg=0, invalid=762 0512: dt=0.000013, rms=0.424 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0513: dt=0.080000, rms=0.424 (0.315%), neg=0, invalid=762 0514: dt=0.007000, rms=0.424 (0.003%), neg=0, invalid=762 0515: dt=0.007000, rms=0.424 (-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=0.413, neg=0, invalid=762 0516: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0517: dt=27.744000, rms=0.413 (0.005%), neg=0, invalid=762 0518: dt=8.092000, rms=0.413 (0.000%), neg=0, invalid=762 0519: dt=8.092000, rms=0.413 (-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=0.413, neg=0, invalid=762 0520: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0521: dt=36.288000, rms=0.413 (0.034%), neg=0, invalid=762 0522: dt=103.680000, rms=0.412 (0.037%), neg=0, invalid=762 0523: dt=145.152000, rms=0.412 (0.037%), neg=0, invalid=762 0524: dt=145.152000, rms=0.412 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0525: dt=2.800000, rms=0.413 (0.013%), neg=0, invalid=762 0526: dt=2.800000, rms=0.413 (0.004%), neg=0, invalid=762 0527: dt=2.800000, rms=0.413 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 0528: dt=88.510638, rms=0.411 (0.446%), neg=0, invalid=762 0529: dt=24.329588, rms=0.410 (0.300%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0530: dt=44.800000, rms=0.409 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0531: dt=44.800000, rms=0.409 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0532: dt=44.800000, rms=0.408 (0.246%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0533: dt=44.800000, rms=0.408 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 1 iterations, nbhd size=0, neg = 0 0534: dt=44.800000, rms=0.407 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0535: dt=44.800000, rms=0.406 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0536: dt=44.800000, rms=0.406 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 2 iterations, nbhd size=0, neg = 0 0537: dt=44.800000, rms=0.405 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0538: dt=44.800000, rms=0.405 (0.144%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 4 iterations, nbhd size=0, neg = 0 0539: dt=44.800000, rms=0.404 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 7 iterations, nbhd size=0, neg = 0 0540: dt=44.800000, rms=0.404 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 19 iterations, nbhd size=1, neg = 0 0541: dt=44.800000, rms=0.404 (0.008%), neg=0, invalid=762 0542: dt=19.200000, rms=0.404 (0.028%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0543: dt=44.800000, rms=0.404 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0544: dt=44.800000, rms=0.404 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0545: dt=44.800000, rms=0.404 (0.014%), neg=0, invalid=762 0546: dt=44.800000, rms=0.404 (0.006%), neg=0, invalid=762 0547: dt=44.800000, rms=0.404 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0548: dt=0.000158, rms=0.408 (0.000%), neg=0, invalid=762 0549: dt=0.000113, rms=0.408 (0.000%), neg=0, invalid=762 0550: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0551: dt=4.032000, rms=0.407 (0.041%), neg=0, invalid=762 0552: dt=4.032000, rms=0.407 (0.017%), neg=0, invalid=762 0553: dt=4.032000, rms=0.407 (0.008%), neg=0, invalid=762 0554: dt=4.032000, rms=0.407 (-0.021%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0555: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0556: dt=0.000000, rms=0.414 (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=0.403, neg=0, invalid=762 iter 0, gcam->neg = 546 after 16 iterations, nbhd size=1, neg = 0 0557: dt=1.144243, rms=0.394 (2.104%), neg=0, invalid=762 0558: dt=0.000023, rms=0.394 (0.000%), neg=0, invalid=762 0559: dt=0.000023, rms=0.394 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 0560: dt=0.112000, rms=0.394 (0.080%), neg=0, invalid=762 0561: dt=0.112000, rms=0.394 (0.034%), neg=0, invalid=762 0562: dt=0.112000, rms=0.394 (0.028%), neg=0, invalid=762 0563: dt=0.112000, rms=0.394 (-0.001%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 18 minutes and 55 seconds. mri_ca_register utimesec 9206.880341 mri_ca_register stimesec 8.049776 mri_ca_register ru_maxrss 1346376 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4284527 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63224 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4254 mri_ca_register ru_nivcsw 14049 FSRUNTIME@ mri_ca_register 2.3154 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 20:09:13 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-609 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-6.0.0/0051026/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 7.38 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 = 0.12777 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (236 voxels, overlap=0.274) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (236 voxels, peak = 9), gca=8.9 gca peak = 0.17677 (13) mri peak = 0.11596 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (809 voxels, overlap=0.650) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (809 voxels, peak = 8), gca=7.6 gca peak = 0.28129 (95) mri peak = 0.08869 (90) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (653 voxels, overlap=0.480) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (653 voxels, peak = 89), gca=88.8 gca peak = 0.16930 (96) mri peak = 0.09128 (92) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (728 voxels, overlap=0.839) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (728 voxels, peak = 91), gca=90.7 gca peak = 0.24553 (55) mri peak = 0.08646 (55) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, peak = 54), gca=54.2 gca peak = 0.30264 (59) mri peak = 0.09387 (56) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (683 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (683 voxels, peak = 58), gca=58.1 gca peak = 0.07580 (103) mri peak = 0.10501 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (50629 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (50629 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.10932 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (54747 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (54747 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04631 (56) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (37176 voxels, overlap=0.948) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (37176 voxels, peak = 55), gca=54.8 gca peak = 0.11620 (58) mri peak = 0.04428 (52) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (34228 voxels, overlap=0.967) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (34228 voxels, peak = 53), gca=53.1 gca peak = 0.30970 (66) mri peak = 0.12527 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, peak = 66), gca=66.0 gca peak = 0.15280 (69) mri peak = 0.11513 (69) Left_Caudate (11): linear fit = 0.93 x + 0.0 (735 voxels, overlap=0.590) Left_Caudate (11): linear fit = 0.93 x + 0.0 (735 voxels, peak = 64), gca=63.8 gca peak = 0.13902 (56) mri peak = 0.04322 (51) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (21214 voxels, overlap=0.782) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (21214 voxels, peak = 50), gca=50.1 gca peak = 0.14777 (55) mri peak = 0.03979 (45) Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (21478 voxels, overlap=0.680) Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (21478 voxels, peak = 46), gca=45.9 gca peak = 0.16765 (84) mri peak = 0.07523 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6641 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6641 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.06973 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6517 voxels, overlap=0.968) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6517 voxels, peak = 85), gca=85.3 gca peak = 0.29869 (57) mri peak = 0.07809 (56) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (474 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (474 voxels, peak = 55), gca=55.0 gca peak = 0.33601 (57) mri peak = 0.08585 (56) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (548 voxels, overlap=1.028) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (548 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.06187 (91) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4898 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4898 voxels, peak = 90), gca=89.6 gca peak = 0.11793 (83) mri peak = 0.07494 (87) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4844 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4844 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.07322 (75) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1901 voxels, overlap=0.847) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1901 voxels, peak = 78), gca=78.2 gca peak = 0.10360 (77) mri peak = 0.06990 (79) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1949 voxels, overlap=0.771) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1949 voxels, peak = 74), gca=74.3 gca peak = 0.08424 (78) mri peak = 0.08412 (85) Brain_Stem (16): linear fit = 1.05 x + 0.0 (14342 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.05 x + 0.0 (14342 voxels, peak = 82), gca=82.3 gca peak = 0.12631 (89) mri peak = 0.07196 (91) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1692 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1692 voxels, peak = 91), gca=91.2 gca peak = 0.14500 (87) mri peak = 0.07553 (92) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1771 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1771 voxels, peak = 88), gca=88.3 gca peak = 0.14975 (24) mri peak = 0.03440 (20) gca peak = 0.19357 (14) mri peak = 0.12752 ( 8) Fourth_Ventricle (15): linear fit = 0.50 x + 0.0 (293 voxels, overlap=0.230) Fourth_Ventricle (15): linear fit = 0.50 x + 0.0 (293 voxels, peak = 7), gca=6.9 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 Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.97 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.51 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.29483 ( 9) mri peak = 0.12777 ( 9) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (236 voxels, overlap=0.999) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (236 voxels, peak = 9), gca=9.5 gca peak = 0.23941 ( 8) mri peak = 0.11596 ( 9) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (809 voxels, overlap=0.968) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (809 voxels, peak = 8), gca=8.4 gca peak = 0.27103 (88) mri peak = 0.08869 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (653 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (653 voxels, peak = 88), gca=87.6 gca peak = 0.17605 (89) mri peak = 0.09128 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (728 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (728 voxels, peak = 89), gca=88.6 gca peak = 0.28560 (55) mri peak = 0.08646 (55) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, peak = 54), gca=54.2 gca peak = 0.30921 (58) mri peak = 0.09387 (56) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (683 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (683 voxels, peak = 57), gca=56.6 gca peak = 0.07610 (105) mri peak = 0.10501 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50629 voxels, overlap=0.749) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50629 voxels, peak = 105), gca=105.0 gca peak = 0.07820 (106) mri peak = 0.10932 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54747 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54747 voxels, peak = 106), gca=106.0 gca peak = 0.10325 (55) mri peak = 0.04631 (56) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37176 voxels, overlap=0.996) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37176 voxels, peak = 54), gca=54.2 gca peak = 0.12642 (53) mri peak = 0.04428 (52) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (34228 voxels, overlap=0.977) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (34228 voxels, peak = 55), gca=55.4 gca peak = 0.30221 (66) mri peak = 0.12527 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, peak = 66), gca=66.0 gca peak = 0.13199 (64) mri peak = 0.11513 (69) Left_Caudate (11): linear fit = 1.00 x + 0.0 (735 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.00 x + 0.0 (735 voxels, peak = 64), gca=64.0 gca peak = 0.15841 (49) mri peak = 0.04322 (51) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (21214 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (21214 voxels, peak = 48), gca=47.8 gca peak = 0.17082 (46) mri peak = 0.03979 (45) Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (21478 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (21478 voxels, peak = 49), gca=48.5 gca peak = 0.15784 (86) mri peak = 0.07523 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6641 voxels, overlap=0.985) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6641 voxels, peak = 86), gca=85.6 gca peak = 0.15488 (85) mri peak = 0.06973 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6517 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6517 voxels, peak = 85), gca=84.6 gca peak = 0.31099 (56) mri peak = 0.07809 (56) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (474 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (474 voxels, peak = 59), gca=58.5 gca peak = 0.28860 (60) mri peak = 0.08585 (56) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (548 voxels, overlap=1.021) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (548 voxels, peak = 62), gca=61.5 gca peak = 0.10627 (89) mri peak = 0.06187 (91) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4898 voxels, overlap=1.001) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4898 voxels, peak = 90), gca=90.3 gca peak = 0.09747 (90) mri peak = 0.07494 (87) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4844 voxels, overlap=0.983) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4844 voxels, peak = 89), gca=88.7 gca peak = 0.08891 (78) mri peak = 0.07322 (75) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1901 voxels, overlap=0.966) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1901 voxels, peak = 78), gca=78.0 gca peak = 0.09182 (72) mri peak = 0.06990 (79) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1949 voxels, overlap=0.942) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1949 voxels, peak = 72), gca=72.0 gca peak = 0.07773 (85) mri peak = 0.08412 (85) Brain_Stem (16): linear fit = 1.02 x + 0.0 (14342 voxels, overlap=0.714) Brain_Stem (16): linear fit = 1.02 x + 0.0 (14342 voxels, peak = 87), gca=87.1 gca peak = 0.11601 (91) mri peak = 0.07196 (91) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1692 voxels, overlap=0.861) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1692 voxels, peak = 91), gca=90.5 gca peak = 0.16257 (87) mri peak = 0.07553 (92) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1771 voxels, overlap=0.932) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1771 voxels, peak = 87), gca=86.6 gca peak = 0.26228 (13) mri peak = 0.03440 (20) gca peak = 0.31432 ( 8) mri peak = 0.12752 ( 8) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (293 voxels, overlap=0.845) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (293 voxels, peak = 9), gca=8.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18140 (33) gca peak Left_Thalamus = 0.72551 (92) gca peak Third_Ventricle = 0.26228 (13) gca peak CSF = 0.26789 (19) gca peak Left_Accumbens_area = 0.54630 (57) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.26998 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82280 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.51764 (17) gca peak WM_hypointensities = 0.07134 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70942 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.06 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 65881 voxels changed in iteration 0 of unlikely voxel relabeling 174 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 33092 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 374 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 73377 changed. image ll: -2.137, PF=0.500 pass 2: 20498 changed. image ll: -2.137, PF=0.500 pass 3: 6951 changed. pass 4: 2666 changed. 35503 voxels changed in iteration 0 of unlikely voxel relabeling 245 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6082 voxels changed in iteration 0 of unlikely voxel relabeling 70 voxels changed in iteration 1 of unlikely voxel relabeling 80 voxels changed in iteration 2 of unlikely voxel relabeling 10 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5706 voxels changed in iteration 0 of unlikely voxel relabeling 50 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5068 voxels changed in iteration 0 of unlikely voxel relabeling 12 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 3357.288614 mri_ca_label stimesec 1.563762 mri_ca_label ru_maxrss 2119452 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 660702 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63216 mri_ca_label ru_oublock 496 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 291 mri_ca_label ru_nivcsw 9996 auto-labeling took 55 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/cc_up.lta 0051026 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-6.0.0/0051026/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/norm.mgz 41778 voxels in left wm, 46425 in right wm, xrange [122, 131] searching rotation angles z=[-3 11], y=[-8 6] searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 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 global minimum found at slice 126.2, rotations (-1.18, 3.68) final transformation (x=126.2, yr=-1.185, zr=3.681): 0.99772 -0.06420 -0.02064 11.75817; 0.06418 0.99794 -0.00133 5.28474; 0.02068 0.00000 0.99979 14.41391; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 115 111 eigenvectors: -0.00045 -0.00520 0.99999; -0.27178 -0.96234 -0.00512; 0.96236 -0.27178 -0.00098; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 21:05:14 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 21:05:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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... 1819 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 110 gm peak at 56 (56), valley at 22 (22) csf peak at 11, setting threshold to 41 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 59 (59), valley at 22 (22) csf peak at 11, setting threshold to 43 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 50 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 21:08:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1794232 voxels in mask (pct= 10.69) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 21:08:07 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 (106.0): 106.5 +- 5.1 [79.0 --> 125.0] GM (68.0) : 66.8 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 76.4 setting top of gray matter range to 85.9 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... 6652 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5139 filled 2669 bright non-wm voxels segmented. 2973 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 0.44 minutes reading wm segmentation from wm.seg.mgz... 37 voxels added to wm to prevent paths from MTL structures to cortex 2550 additional wm voxels added 0 additional wm voxels added SEG EDIT: 39715 voxels turned on, 38126 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 24 found - 24 modified | TOTAL: 24 pass 2 (xy+): 0 found - 24 modified | TOTAL: 24 pass 1 (xy-): 19 found - 19 modified | TOTAL: 43 pass 2 (xy-): 0 found - 19 modified | TOTAL: 43 pass 1 (yz+): 30 found - 30 modified | TOTAL: 73 pass 2 (yz+): 0 found - 30 modified | TOTAL: 73 pass 1 (yz-): 17 found - 17 modified | TOTAL: 90 pass 2 (yz-): 0 found - 17 modified | TOTAL: 90 pass 1 (xz+): 18 found - 18 modified | TOTAL: 108 pass 2 (xz+): 0 found - 18 modified | TOTAL: 108 pass 1 (xz-): 20 found - 20 modified | TOTAL: 128 pass 2 (xz-): 0 found - 20 modified | TOTAL: 128 Iteration Number : 1 pass 1 (+++): 44 found - 44 modified | TOTAL: 44 pass 2 (+++): 0 found - 44 modified | TOTAL: 44 pass 1 (+++): 24 found - 24 modified | TOTAL: 68 pass 2 (+++): 0 found - 24 modified | TOTAL: 68 pass 1 (+++): 32 found - 32 modified | TOTAL: 100 pass 2 (+++): 0 found - 32 modified | TOTAL: 100 pass 1 (+++): 18 found - 18 modified | TOTAL: 118 pass 2 (+++): 0 found - 18 modified | TOTAL: 118 Iteration Number : 1 pass 1 (++): 115 found - 115 modified | TOTAL: 115 pass 2 (++): 0 found - 115 modified | TOTAL: 115 pass 1 (+-): 102 found - 102 modified | TOTAL: 217 pass 2 (+-): 0 found - 102 modified | TOTAL: 217 pass 1 (--): 110 found - 110 modified | TOTAL: 327 pass 2 (--): 0 found - 110 modified | TOTAL: 327 pass 1 (-+): 93 found - 93 modified | TOTAL: 420 pass 2 (-+): 0 found - 93 modified | TOTAL: 420 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 8 found - 8 modified | TOTAL: 13 pass 2 (yz+): 0 found - 8 modified | TOTAL: 13 pass 1 (yz-): 4 found - 4 modified | TOTAL: 17 pass 2 (yz-): 0 found - 4 modified | TOTAL: 17 pass 1 (xz+): 7 found - 7 modified | TOTAL: 24 pass 2 (xz+): 0 found - 7 modified | TOTAL: 24 pass 1 (xz-): 5 found - 5 modified | TOTAL: 29 pass 2 (xz-): 0 found - 5 modified | TOTAL: 29 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 3 found - 3 modified | TOTAL: 3 pass 2 (+-): 0 found - 3 modified | TOTAL: 3 pass 1 (--): 3 found - 3 modified | TOTAL: 6 pass 2 (--): 0 found - 3 modified | TOTAL: 6 pass 1 (-+): 4 found - 4 modified | TOTAL: 10 pass 2 (-+): 0 found - 4 modified | TOTAL: 10 Iteration Number : 3 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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xz-): 0 found - 2 modified | TOTAL: 2 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 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 = 711 (out of 625633: 0.113645) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 21:10:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88007; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03415 -0.07150 -0.03810 8.52905; 0.09327 1.00522 0.41638 -71.88007; 0.00846 -0.36699 0.88428 55.23253; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2872 (min = 350, max = 1400), aspect = 1.25 (min = 0.10, max = 0.75) need search nearby using seed (124, 121, 145), TAL = (4.0, 17.0, 7.0) talairach voxel to voxel transform 0.96049 0.07119 0.00786 -3.50887; -0.07280 0.84348 -0.40030 83.36012; -0.03940 0.34938 0.96466 -27.83098; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 121, 145) --> (4.0, 17.0, 7.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (4.00, 17.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 17.00, 7.00) SRC: (108.06, 119.66, 150.14) search lh wm seed point around talairach space (-14.00, 17.00, 7.00), SRC: (142.63, 117.04, 148.72) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Oct 7 21:10:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 4 found - 4 modified | TOTAL: 12 pass 2 (xz+): 0 found - 4 modified | TOTAL: 12 pass 1 (xz-): 0 found - 0 modified | TOTAL: 12 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 (+-): 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 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 16 (out of 301317: 0.005310) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 455 vertices, 512 faces slice 50: 6527 vertices, 6789 faces slice 60: 17670 vertices, 18173 faces slice 70: 31184 vertices, 31623 faces slice 80: 43810 vertices, 44301 faces slice 90: 56963 vertices, 57396 faces slice 100: 69489 vertices, 69975 faces slice 110: 82002 vertices, 82475 faces slice 120: 93775 vertices, 94260 faces slice 130: 105416 vertices, 105880 faces slice 140: 117248 vertices, 117737 faces slice 150: 127597 vertices, 127998 faces slice 160: 137191 vertices, 137568 faces slice 170: 144700 vertices, 145018 faces slice 180: 151345 vertices, 151621 faces slice 190: 156060 vertices, 156303 faces slice 200: 158460 vertices, 158552 faces slice 210: 158460 vertices, 158552 faces slice 220: 158460 vertices, 158552 faces slice 230: 158460 vertices, 158552 faces slice 240: 158460 vertices, 158552 faces slice 250: 158460 vertices, 158552 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... 158460 voxel in cpt #1: X=-92 [v=158460,e=475656,f=317104] located at (-27.342358, -18.675875, 3.579446) For the whole surface: X=-92 [v=158460,e=475656,f=317104] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 21:10:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.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+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 3 found - 3 modified | TOTAL: 7 pass 2 (yz-): 0 found - 3 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 2 found - 2 modified | TOTAL: 4 pass 2 (-+): 0 found - 2 modified | TOTAL: 4 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 = 15 (out of 299486: 0.005009) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 464 vertices, 547 faces slice 50: 6638 vertices, 6919 faces slice 60: 17456 vertices, 17904 faces slice 70: 30814 vertices, 31277 faces slice 80: 43547 vertices, 44011 faces slice 90: 56485 vertices, 56910 faces slice 100: 68926 vertices, 69418 faces slice 110: 81186 vertices, 81660 faces slice 120: 92576 vertices, 93033 faces slice 130: 103729 vertices, 104187 faces slice 140: 114844 vertices, 115291 faces slice 150: 125370 vertices, 125773 faces slice 160: 134664 vertices, 135052 faces slice 170: 142422 vertices, 142750 faces slice 180: 149147 vertices, 149443 faces slice 190: 154020 vertices, 154249 faces slice 200: 156741 vertices, 156836 faces slice 210: 156808 vertices, 156880 faces slice 220: 156808 vertices, 156880 faces slice 230: 156808 vertices, 156880 faces slice 240: 156808 vertices, 156880 faces slice 250: 156808 vertices, 156880 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... 156808 voxel in cpt #1: X=-72 [v=156808,e=470640,f=313760] located at (29.297466, -18.371065, -0.228923) For the whole surface: X=-72 [v=156808,e=470640,f=313760] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 21:10:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 21:10:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 10884 of (10884 10887) to complete... Waiting for PID 10887 of (10884 10887) 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 (10884 10887) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 21:10:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 21:10:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 10929 of (10929 10932) to complete... Waiting for PID 10932 of (10929 10932) 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 = 49.1 mm, total surface area = 83230 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.055 (target=0.015) step 035: RMS=0.050 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.043 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 49.681447 mris_inflate stimesec 0.101984 mris_inflate ru_maxrss 231260 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 33224 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11152 mris_inflate ru_oublock 11168 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2369 mris_inflate ru_nivcsw 3501 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.6 mm, total surface area = 82072 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=0.119 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.043 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 49.010549 mris_inflate stimesec 0.111982 mris_inflate ru_maxrss 228780 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 33114 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11048 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2057 mris_inflate ru_nivcsw 3632 PIDs (10929 10932) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 21:11:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 21:11:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 11004 of (11004 11008) to complete... Waiting for PID 11008 of (11004 11008) 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 0.92 +- 0.56 (0.00-->7.92) (max @ vno 111050 --> 111068) face area 0.02 +- 0.03 (-0.21-->0.69) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.305... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.795, avgs=0 005/300: dt: 0.9000, rms radial error=175.539, avgs=0 010/300: dt: 0.9000, rms radial error=174.988, avgs=0 015/300: dt: 0.9000, rms radial error=174.265, avgs=0 020/300: dt: 0.9000, rms radial error=173.443, avgs=0 025/300: dt: 0.9000, rms radial error=172.563, avgs=0 030/300: dt: 0.9000, rms radial error=171.651, avgs=0 035/300: dt: 0.9000, rms radial error=170.723, avgs=0 040/300: dt: 0.9000, rms radial error=169.786, avgs=0 045/300: dt: 0.9000, rms radial error=168.847, avgs=0 050/300: dt: 0.9000, rms radial error=167.907, avgs=0 055/300: dt: 0.9000, rms radial error=166.970, avgs=0 060/300: dt: 0.9000, rms radial error=166.036, avgs=0 065/300: dt: 0.9000, rms radial error=165.105, avgs=0 070/300: dt: 0.9000, rms radial error=164.178, avgs=0 075/300: dt: 0.9000, rms radial error=163.257, avgs=0 080/300: dt: 0.9000, rms radial error=162.339, avgs=0 085/300: dt: 0.9000, rms radial error=161.425, avgs=0 090/300: dt: 0.9000, rms radial error=160.516, avgs=0 095/300: dt: 0.9000, rms radial error=159.611, avgs=0 100/300: dt: 0.9000, rms radial error=158.710, avgs=0 105/300: dt: 0.9000, rms radial error=157.813, avgs=0 110/300: dt: 0.9000, rms radial error=156.921, avgs=0 115/300: dt: 0.9000, rms radial error=156.033, avgs=0 120/300: dt: 0.9000, rms radial error=155.150, avgs=0 125/300: dt: 0.9000, rms radial error=154.271, avgs=0 130/300: dt: 0.9000, rms radial error=153.398, avgs=0 135/300: dt: 0.9000, rms radial error=152.531, avgs=0 140/300: dt: 0.9000, rms radial error=151.669, avgs=0 145/300: dt: 0.9000, rms radial error=150.813, avgs=0 150/300: dt: 0.9000, rms radial error=149.960, avgs=0 155/300: dt: 0.9000, rms radial error=149.113, avgs=0 160/300: dt: 0.9000, rms radial error=148.271, avgs=0 165/300: dt: 0.9000, rms radial error=147.433, avgs=0 170/300: dt: 0.9000, rms radial error=146.599, avgs=0 175/300: dt: 0.9000, rms radial error=145.771, avgs=0 180/300: dt: 0.9000, rms radial error=144.948, avgs=0 185/300: dt: 0.9000, rms radial error=144.130, avgs=0 190/300: dt: 0.9000, rms radial error=143.316, avgs=0 195/300: dt: 0.9000, rms radial error=142.507, avgs=0 200/300: dt: 0.9000, rms radial error=141.702, avgs=0 205/300: dt: 0.9000, rms radial error=140.902, avgs=0 210/300: dt: 0.9000, rms radial error=140.106, avgs=0 215/300: dt: 0.9000, rms radial error=139.314, avgs=0 220/300: dt: 0.9000, rms radial error=138.527, avgs=0 225/300: dt: 0.9000, rms radial error=137.744, avgs=0 230/300: dt: 0.9000, rms radial error=136.966, avgs=0 235/300: dt: 0.9000, rms radial error=136.192, avgs=0 240/300: dt: 0.9000, rms radial error=135.422, avgs=0 245/300: dt: 0.9000, rms radial error=134.657, avgs=0 250/300: dt: 0.9000, rms radial error=133.896, avgs=0 255/300: dt: 0.9000, rms radial error=133.139, avgs=0 260/300: dt: 0.9000, rms radial error=132.387, avgs=0 265/300: dt: 0.9000, rms radial error=131.639, avgs=0 270/300: dt: 0.9000, rms radial error=130.895, avgs=0 275/300: dt: 0.9000, rms radial error=130.155, avgs=0 280/300: dt: 0.9000, rms radial error=129.419, avgs=0 285/300: dt: 0.9000, rms radial error=128.689, avgs=0 290/300: dt: 0.9000, rms radial error=127.963, avgs=0 295/300: dt: 0.9000, rms radial error=127.241, avgs=0 300/300: dt: 0.9000, rms radial error=126.523, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18704.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 3214.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 345.02 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00355 epoch 4 (K=640.0), pass 1, starting sse = 26.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00762 final distance error %29.41 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 283.492902 mris_sphere stimesec 0.132979 mris_sphere ru_maxrss 231456 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33781 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11192 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8381 mris_sphere ru_nivcsw 19937 FSRUNTIME@ mris_sphere 0.0787 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 0.92 +- 0.56 (0.00-->6.92) (max @ vno 66136 --> 67326) face area 0.02 +- 0.03 (-0.32-->0.76) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.304... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.704, avgs=0 005/300: dt: 0.9000, rms radial error=175.448, avgs=0 010/300: dt: 0.9000, rms radial error=174.898, avgs=0 015/300: dt: 0.9000, rms radial error=174.175, avgs=0 020/300: dt: 0.9000, rms radial error=173.351, avgs=0 025/300: dt: 0.9000, rms radial error=172.469, avgs=0 030/300: dt: 0.9000, rms radial error=171.555, avgs=0 035/300: dt: 0.9000, rms radial error=170.623, avgs=0 040/300: dt: 0.9000, rms radial error=169.684, avgs=0 045/300: dt: 0.9000, rms radial error=168.743, avgs=0 050/300: dt: 0.9000, rms radial error=167.802, avgs=0 055/300: dt: 0.9000, rms radial error=166.863, avgs=0 060/300: dt: 0.9000, rms radial error=165.927, avgs=0 065/300: dt: 0.9000, rms radial error=164.995, avgs=0 070/300: dt: 0.9000, rms radial error=164.067, avgs=0 075/300: dt: 0.9000, rms radial error=163.143, avgs=0 080/300: dt: 0.9000, rms radial error=162.223, avgs=0 085/300: dt: 0.9000, rms radial error=161.307, avgs=0 090/300: dt: 0.9000, rms radial error=160.396, avgs=0 095/300: dt: 0.9000, rms radial error=159.489, avgs=0 100/300: dt: 0.9000, rms radial error=158.587, avgs=0 105/300: dt: 0.9000, rms radial error=157.689, avgs=0 110/300: dt: 0.9000, rms radial error=156.796, avgs=0 115/300: dt: 0.9000, rms radial error=155.907, avgs=0 120/300: dt: 0.9000, rms radial error=155.023, avgs=0 125/300: dt: 0.9000, rms radial error=154.148, avgs=0 130/300: dt: 0.9000, rms radial error=153.278, avgs=0 135/300: dt: 0.9000, rms radial error=152.413, avgs=0 140/300: dt: 0.9000, rms radial error=151.552, avgs=0 145/300: dt: 0.9000, rms radial error=150.697, avgs=0 150/300: dt: 0.9000, rms radial error=149.845, avgs=0 155/300: dt: 0.9000, rms radial error=148.999, avgs=0 160/300: dt: 0.9000, rms radial error=148.157, avgs=0 165/300: dt: 0.9000, rms radial error=147.321, avgs=0 170/300: dt: 0.9000, rms radial error=146.490, avgs=0 175/300: dt: 0.9000, rms radial error=145.663, avgs=0 180/300: dt: 0.9000, rms radial error=144.841, avgs=0 185/300: dt: 0.9000, rms radial error=144.023, avgs=0 190/300: dt: 0.9000, rms radial error=143.210, avgs=0 195/300: dt: 0.9000, rms radial error=142.402, avgs=0 200/300: dt: 0.9000, rms radial error=141.599, avgs=0 205/300: dt: 0.9000, rms radial error=140.800, avgs=0 210/300: dt: 0.9000, rms radial error=140.006, avgs=0 215/300: dt: 0.9000, rms radial error=139.216, avgs=0 220/300: dt: 0.9000, rms radial error=138.432, avgs=0 225/300: dt: 0.9000, rms radial error=137.651, avgs=0 230/300: dt: 0.9000, rms radial error=136.875, avgs=0 235/300: dt: 0.9000, rms radial error=136.103, avgs=0 240/300: dt: 0.9000, rms radial error=135.336, avgs=0 245/300: dt: 0.9000, rms radial error=134.573, avgs=0 250/300: dt: 0.9000, rms radial error=133.814, avgs=0 255/300: dt: 0.9000, rms radial error=133.059, avgs=0 260/300: dt: 0.9000, rms radial error=132.308, avgs=0 265/300: dt: 0.9000, rms radial error=131.562, avgs=0 270/300: dt: 0.9000, rms radial error=130.820, avgs=0 275/300: dt: 0.9000, rms radial error=130.082, avgs=0 280/300: dt: 0.9000, rms radial error=129.348, avgs=0 285/300: dt: 0.9000, rms radial error=128.618, avgs=0 290/300: dt: 0.9000, rms radial error=127.892, avgs=0 295/300: dt: 0.9000, rms radial error=127.171, avgs=0 300/300: dt: 0.9000, rms radial error=126.453, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18527.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 3164.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 3 (K=160.0), pass 1, starting sse = 343.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00598 epoch 4 (K=640.0), pass 1, starting sse = 25.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00869 final distance error %28.86 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 289.765948 mris_sphere stimesec 0.161975 mris_sphere ru_maxrss 228976 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33168 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11032 mris_sphere ru_oublock 11080 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8945 mris_sphere ru_nivcsw 20444 FSRUNTIME@ mris_sphere 0.0799 hours 1 threads PIDs (11004 11008) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 21:16:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 21:16:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 21:16:36 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 lh #@# Fix Topology rh Sat Oct 7 21:16:36 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 rh Waiting for PID 11230 of (11230 11233) to complete... Waiting for PID 11233 of (11230 11233) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 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=-92 (nv=158460, nf=317104, ne=475656, g=47) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 7112 ambiguous faces found in tessellation segmenting defects... 49 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 3 -merging segment 32 into 22 -merging segment 35 into 27 -merging segment 36 into 27 -merging segment 44 into 41 -merging segment 45 into 41 43 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5149 (-4.7575) -vertex loglikelihood: -6.4071 (-3.2036) -normal dot loglikelihood: -3.6311 (-3.6311) -quad curv loglikelihood: -6.4013 (-3.2007) Total Loglikelihood : -25.9545 CORRECTING DEFECT 0 (vertices=59, convex hull=70, v0=5710) After retessellation of defect 0 (v0=5710), euler #=-42 (154062,460300,306196) : difference with theory (-40) = 2 CORRECTING DEFECT 1 (vertices=31, convex hull=23, v0=6517) After retessellation of defect 1 (v0=6517), euler #=-41 (154066,460319,306212) : difference with theory (-39) = 2 CORRECTING DEFECT 2 (vertices=100, convex hull=123, v0=8169) After retessellation of defect 2 (v0=8169), euler #=-40 (154097,460470,306333) : difference with theory (-38) = 2 CORRECTING DEFECT 3 (vertices=133, convex hull=176, v0=9232) After retessellation of defect 3 (v0=9232), euler #=-38 (154136,460683,306509) : difference with theory (-37) = 1 CORRECTING DEFECT 4 (vertices=13, convex hull=21, v0=12496) After retessellation of defect 4 (v0=12496), euler #=-37 (154137,460693,306519) : difference with theory (-36) = 1 CORRECTING DEFECT 5 (vertices=25, convex hull=40, v0=17354) After retessellation of defect 5 (v0=17354), euler #=-36 (154144,460729,306549) : difference with theory (-35) = 1 CORRECTING DEFECT 6 (vertices=76, convex hull=67, v0=21337) After retessellation of defect 6 (v0=21337), euler #=-35 (154155,460789,306599) : difference with theory (-34) = 1 CORRECTING DEFECT 7 (vertices=88, convex hull=112, v0=25494) After retessellation of defect 7 (v0=25494), euler #=-34 (154197,460967,306736) : difference with theory (-33) = 1 CORRECTING DEFECT 8 (vertices=311, convex hull=198, v0=26629) After retessellation of defect 8 (v0=26629), euler #=-33 (154267,461271,306971) : difference with theory (-32) = 1 CORRECTING DEFECT 9 (vertices=14, convex hull=23, v0=34933) After retessellation of defect 9 (v0=34933), euler #=-32 (154268,461280,306980) : difference with theory (-31) = 1 CORRECTING DEFECT 10 (vertices=16, convex hull=34, v0=39537) After retessellation of defect 10 (v0=39537), euler #=-31 (154270,461301,307000) : difference with theory (-30) = 1 CORRECTING DEFECT 11 (vertices=29, convex hull=41, v0=43397) After retessellation of defect 11 (v0=43397), euler #=-30 (154278,461340,307032) : difference with theory (-29) = 1 CORRECTING DEFECT 12 (vertices=1007, convex hull=647, v0=43420) XL defect detected... After retessellation of defect 12 (v0=43420), euler #=-32 (154615,462733,308086) : difference with theory (-28) = 4 CORRECTING DEFECT 13 (vertices=40, convex hull=78, v0=55303) After retessellation of defect 13 (v0=55303), euler #=-31 (154634,462819,308154) : difference with theory (-27) = 4 CORRECTING DEFECT 14 (vertices=31, convex hull=54, v0=58170) After retessellation of defect 14 (v0=58170), euler #=-30 (154643,462868,308195) : difference with theory (-26) = 4 CORRECTING DEFECT 15 (vertices=25, convex hull=48, v0=60856) After retessellation of defect 15 (v0=60856), euler #=-29 (154655,462919,308235) : difference with theory (-25) = 4 CORRECTING DEFECT 16 (vertices=55, convex hull=102, v0=61919) After retessellation of defect 16 (v0=61919), euler #=-28 (154689,463064,308347) : difference with theory (-24) = 4 CORRECTING DEFECT 17 (vertices=13, convex hull=37, v0=65754) After retessellation of defect 17 (v0=65754), euler #=-27 (154690,463078,308361) : difference with theory (-23) = 4 CORRECTING DEFECT 18 (vertices=9, convex hull=26, v0=66640) After retessellation of defect 18 (v0=66640), euler #=-26 (154695,463101,308380) : difference with theory (-22) = 4 CORRECTING DEFECT 19 (vertices=44, convex hull=77, v0=67758) After retessellation of defect 19 (v0=67758), euler #=-25 (154713,463191,308453) : difference with theory (-21) = 4 CORRECTING DEFECT 20 (vertices=38, convex hull=73, v0=68151) After retessellation of defect 20 (v0=68151), euler #=-24 (154737,463294,308533) : difference with theory (-20) = 4 CORRECTING DEFECT 21 (vertices=603, convex hull=466, v0=88744) L defect detected... normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces normal vector of length zero at vertex 156729 with 3 faces After retessellation of defect 21 (v0=88744), euler #=-22 (154865,463904,309017) : difference with theory (-19) = 3 CORRECTING DEFECT 22 (vertices=36, convex hull=91, v0=90235) After retessellation of defect 22 (v0=90235), euler #=-21 (154889,464015,309105) : difference with theory (-18) = 3 CORRECTING DEFECT 23 (vertices=45, convex hull=64, v0=98098) After retessellation of defect 23 (v0=98098), euler #=-20 (154910,464104,309174) : difference with theory (-17) = 3 CORRECTING DEFECT 24 (vertices=47, convex hull=41, v0=102803) After retessellation of defect 24 (v0=102803), euler #=-19 (154930,464179,309230) : difference with theory (-16) = 3 CORRECTING DEFECT 25 (vertices=7, convex hull=12, v0=105270) After retessellation of defect 25 (v0=105270), euler #=-18 (154930,464180,309232) : difference with theory (-15) = 3 CORRECTING DEFECT 26 (vertices=361, convex hull=257, v0=106117) After retessellation of defect 26 (v0=106117), euler #=-16 (154975,464465,309474) : difference with theory (-14) = 2 CORRECTING DEFECT 27 (vertices=16, convex hull=36, v0=107444) After retessellation of defect 27 (v0=107444), euler #=-15 (154979,464488,309494) : difference with theory (-13) = 2 CORRECTING DEFECT 28 (vertices=38, convex hull=75, v0=107713) After retessellation of defect 28 (v0=107713), euler #=-14 (155000,464582,309568) : difference with theory (-12) = 2 CORRECTING DEFECT 29 (vertices=22, convex hull=26, v0=109915) After retessellation of defect 29 (v0=109915), euler #=-13 (155004,464601,309584) : difference with theory (-11) = 2 CORRECTING DEFECT 30 (vertices=10, convex hull=14, v0=110941) After retessellation of defect 30 (v0=110941), euler #=-12 (155006,464609,309591) : difference with theory (-10) = 2 CORRECTING DEFECT 31 (vertices=26, convex hull=70, v0=112326) After retessellation of defect 31 (v0=112326), euler #=-11 (155019,464674,309644) : difference with theory (-9) = 2 CORRECTING DEFECT 32 (vertices=34, convex hull=60, v0=113650) After retessellation of defect 32 (v0=113650), euler #=-10 (155035,464746,309701) : difference with theory (-8) = 2 CORRECTING DEFECT 33 (vertices=68, convex hull=45, v0=117904) After retessellation of defect 33 (v0=117904), euler #=-9 (155044,464787,309734) : difference with theory (-7) = 2 CORRECTING DEFECT 34 (vertices=11, convex hull=24, v0=120616) After retessellation of defect 34 (v0=120616), euler #=-8 (155045,464799,309746) : difference with theory (-6) = 2 CORRECTING DEFECT 35 (vertices=23, convex hull=42, v0=121483) After retessellation of defect 35 (v0=121483), euler #=-7 (155051,464833,309775) : difference with theory (-5) = 2 CORRECTING DEFECT 36 (vertices=48, convex hull=31, v0=123033) After retessellation of defect 36 (v0=123033), euler #=-6 (155059,464867,309802) : difference with theory (-4) = 2 CORRECTING DEFECT 37 (vertices=421, convex hull=340, v0=130071) After retessellation of defect 37 (v0=130071), euler #=-3 (155191,465431,310237) : difference with theory (-3) = 0 CORRECTING DEFECT 38 (vertices=180, convex hull=102, v0=132119) After retessellation of defect 38 (v0=132119), euler #=-2 (155241,465626,310383) : difference with theory (-2) = 0 CORRECTING DEFECT 39 (vertices=89, convex hull=39, v0=134913) After retessellation of defect 39 (v0=134913), euler #=-1 (155250,465665,310414) : difference with theory (-1) = 0 CORRECTING DEFECT 40 (vertices=42, convex hull=72, v0=148285) After retessellation of defect 40 (v0=148285), euler #=0 (155272,465760,310488) : difference with theory (0) = 0 CORRECTING DEFECT 41 (vertices=32, convex hull=48, v0=148798) After retessellation of defect 41 (v0=148798), euler #=1 (155282,465808,310527) : difference with theory (1) = 0 CORRECTING DEFECT 42 (vertices=96, convex hull=75, v0=151826) After retessellation of defect 42 (v0=151826), euler #=2 (155300,465894,310596) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.24 (0.02-->12.52) (max @ vno 128501 --> 157949) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.24 (0.02-->12.52) (max @ vno 128501 --> 157949) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 127 mutations (33.0%), 258 crossovers (67.0%), 339 vertices were eliminated building final representation... 3160 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=155300, nf=310596, ne=465894, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 34.2 minutes 0 defective edges removing intersecting faces 000: 430 intersecting 001: 15 intersecting mris_fix_topology utimesec 2054.864613 mris_fix_topology stimesec 0.252961 mris_fix_topology ru_maxrss 500724 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55723 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 22304 mris_fix_topology ru_oublock 14896 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 650 mris_fix_topology ru_nivcsw 7078 FSRUNTIME@ mris_fix_topology lh 0.5705 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 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=-72 (nv=156808, nf=313760, ne=470640, g=37) 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... 6584 ambiguous faces found in tessellation segmenting defects... 59 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 24 into 20 -merging segment 33 into 29 57 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5286 (-4.7643) -vertex loglikelihood: -6.4769 (-3.2384) -normal dot loglikelihood: -3.5897 (-3.5897) -quad curv loglikelihood: -6.5179 (-3.2590) Total Loglikelihood : -26.1131 CORRECTING DEFECT 0 (vertices=33, convex hull=41, v0=1205) After retessellation of defect 0 (v0=1205), euler #=-56 (152809,456929,304064) : difference with theory (-54) = 2 CORRECTING DEFECT 1 (vertices=8, convex hull=32, v0=1674) After retessellation of defect 1 (v0=1674), euler #=-55 (152810,456942,304077) : difference with theory (-53) = 2 CORRECTING DEFECT 2 (vertices=189, convex hull=92, v0=2699) After retessellation of defect 2 (v0=2699), euler #=-54 (152855,457119,304210) : difference with theory (-52) = 2 CORRECTING DEFECT 3 (vertices=178, convex hull=91, v0=3356) After retessellation of defect 3 (v0=3356), euler #=-53 (152871,457212,304288) : difference with theory (-51) = 2 CORRECTING DEFECT 4 (vertices=65, convex hull=46, v0=3973) After retessellation of defect 4 (v0=3973), euler #=-52 (152878,457251,304321) : difference with theory (-50) = 2 CORRECTING DEFECT 5 (vertices=18, convex hull=23, v0=4949) After retessellation of defect 5 (v0=4949), euler #=-51 (152879,457261,304331) : difference with theory (-49) = 2 CORRECTING DEFECT 6 (vertices=60, convex hull=47, v0=6630) After retessellation of defect 6 (v0=6630), euler #=-50 (152886,457304,304368) : difference with theory (-48) = 2 CORRECTING DEFECT 7 (vertices=80, convex hull=77, v0=7155) After retessellation of defect 7 (v0=7155), euler #=-49 (152909,457408,304450) : difference with theory (-47) = 2 CORRECTING DEFECT 8 (vertices=18, convex hull=23, v0=8395) After retessellation of defect 8 (v0=8395), euler #=-48 (152912,457420,304460) : difference with theory (-46) = 2 CORRECTING DEFECT 9 (vertices=223, convex hull=129, v0=8450) After retessellation of defect 9 (v0=8450), euler #=-47 (152969,457653,304637) : difference with theory (-45) = 2 CORRECTING DEFECT 10 (vertices=12, convex hull=38, v0=8895) After retessellation of defect 10 (v0=8895), euler #=-46 (152971,457673,304656) : difference with theory (-44) = 2 CORRECTING DEFECT 11 (vertices=49, convex hull=62, v0=12465) After retessellation of defect 11 (v0=12465), euler #=-45 (152996,457773,304732) : difference with theory (-43) = 2 CORRECTING DEFECT 12 (vertices=33, convex hull=30, v0=13790) After retessellation of defect 12 (v0=13790), euler #=-44 (153003,457805,304758) : difference with theory (-42) = 2 CORRECTING DEFECT 13 (vertices=15, convex hull=31, v0=16243) After retessellation of defect 13 (v0=16243), euler #=-43 (153006,457825,304776) : difference with theory (-41) = 2 CORRECTING DEFECT 14 (vertices=58, convex hull=77, v0=18661) After retessellation of defect 14 (v0=18661), euler #=-42 (153028,457924,304854) : difference with theory (-40) = 2 CORRECTING DEFECT 15 (vertices=89, convex hull=87, v0=19916) After retessellation of defect 15 (v0=19916), euler #=-41 (153050,458028,304937) : difference with theory (-39) = 2 CORRECTING DEFECT 16 (vertices=37, convex hull=83, v0=19962) After retessellation of defect 16 (v0=19962), euler #=-40 (153068,458114,305006) : difference with theory (-38) = 2 CORRECTING DEFECT 17 (vertices=6, convex hull=29, v0=21079) After retessellation of defect 17 (v0=21079), euler #=-39 (153070,458128,305019) : difference with theory (-37) = 2 CORRECTING DEFECT 18 (vertices=19, convex hull=42, v0=25106) After retessellation of defect 18 (v0=25106), euler #=-38 (153076,458159,305045) : difference with theory (-36) = 2 CORRECTING DEFECT 19 (vertices=68, convex hull=66, v0=26338) After retessellation of defect 19 (v0=26338), euler #=-37 (153087,458218,305094) : difference with theory (-35) = 2 CORRECTING DEFECT 20 (vertices=37, convex hull=76, v0=26869) After retessellation of defect 20 (v0=26869), euler #=-35 (153099,458286,305152) : difference with theory (-34) = 1 CORRECTING DEFECT 21 (vertices=101, convex hull=112, v0=27908) After retessellation of defect 21 (v0=27908), euler #=-34 (153120,458406,305252) : difference with theory (-33) = 1 CORRECTING DEFECT 22 (vertices=12, convex hull=20, v0=28273) After retessellation of defect 22 (v0=28273), euler #=-33 (153122,458419,305264) : difference with theory (-32) = 1 CORRECTING DEFECT 23 (vertices=235, convex hull=114, v0=30506) After retessellation of defect 23 (v0=30506), euler #=-32 (153158,458579,305389) : difference with theory (-31) = 1 CORRECTING DEFECT 24 (vertices=146, convex hull=123, v0=37008) After retessellation of defect 24 (v0=37008), euler #=-31 (153203,458762,305528) : difference with theory (-30) = 1 CORRECTING DEFECT 25 (vertices=6, convex hull=19, v0=38210) After retessellation of defect 25 (v0=38210), euler #=-30 (153203,458769,305536) : difference with theory (-29) = 1 CORRECTING DEFECT 26 (vertices=25, convex hull=60, v0=43067) After retessellation of defect 26 (v0=43067), euler #=-29 (153211,458816,305576) : difference with theory (-28) = 1 CORRECTING DEFECT 27 (vertices=60, convex hull=93, v0=43109) After retessellation of defect 27 (v0=43109), euler #=-28 (153238,458939,305673) : difference with theory (-27) = 1 CORRECTING DEFECT 28 (vertices=233, convex hull=155, v0=45713) After retessellation of defect 28 (v0=45713), euler #=-26 (153313,459252,305913) : difference with theory (-26) = 0 CORRECTING DEFECT 29 (vertices=22, convex hull=44, v0=47663) After retessellation of defect 29 (v0=47663), euler #=-25 (153322,459295,305948) : difference with theory (-25) = 0 CORRECTING DEFECT 30 (vertices=29, convex hull=44, v0=47762) After retessellation of defect 30 (v0=47762), euler #=-24 (153331,459338,305983) : difference with theory (-24) = 0 CORRECTING DEFECT 31 (vertices=68, convex hull=81, v0=51368) After retessellation of defect 31 (v0=51368), euler #=-23 (153355,459440,306062) : difference with theory (-23) = 0 CORRECTING DEFECT 32 (vertices=167, convex hull=188, v0=61072) After retessellation of defect 32 (v0=61072), euler #=-22 (153415,459708,306271) : difference with theory (-22) = 0 CORRECTING DEFECT 33 (vertices=44, convex hull=48, v0=61524) After retessellation of defect 33 (v0=61524), euler #=-21 (153428,459765,306316) : difference with theory (-21) = 0 CORRECTING DEFECT 34 (vertices=8, convex hull=18, v0=63835) After retessellation of defect 34 (v0=63835), euler #=-20 (153428,459770,306322) : difference with theory (-20) = 0 CORRECTING DEFECT 35 (vertices=89, convex hull=53, v0=63854) After retessellation of defect 35 (v0=63854), euler #=-19 (153456,459874,306399) : difference with theory (-19) = 0 CORRECTING DEFECT 36 (vertices=36, convex hull=23, v0=68372) After retessellation of defect 36 (v0=68372), euler #=-18 (153462,459899,306419) : difference with theory (-18) = 0 CORRECTING DEFECT 37 (vertices=156, convex hull=89, v0=75863) After retessellation of defect 37 (v0=75863), euler #=-17 (153508,460079,306554) : difference with theory (-17) = 0 CORRECTING DEFECT 38 (vertices=28, convex hull=79, v0=76369) After retessellation of defect 38 (v0=76369), euler #=-16 (153522,460149,306611) : difference with theory (-16) = 0 CORRECTING DEFECT 39 (vertices=311, convex hull=129, v0=84492) After retessellation of defect 39 (v0=84492), euler #=-15 (153579,460388,306794) : difference with theory (-15) = 0 CORRECTING DEFECT 40 (vertices=18, convex hull=29, v0=92476) After retessellation of defect 40 (v0=92476), euler #=-14 (153581,460405,306810) : difference with theory (-14) = 0 CORRECTING DEFECT 41 (vertices=19, convex hull=28, v0=101106) After retessellation of defect 41 (v0=101106), euler #=-13 (153587,460431,306831) : difference with theory (-13) = 0 CORRECTING DEFECT 42 (vertices=55, convex hull=72, v0=102304) After retessellation of defect 42 (v0=102304), euler #=-12 (153608,460527,306907) : difference with theory (-12) = 0 CORRECTING DEFECT 43 (vertices=9, convex hull=19, v0=106950) After retessellation of defect 43 (v0=106950), euler #=-11 (153609,460534,306914) : difference with theory (-11) = 0 CORRECTING DEFECT 44 (vertices=318, convex hull=92, v0=109744) After retessellation of defect 44 (v0=109744), euler #=-10 (153636,460659,307013) : difference with theory (-10) = 0 CORRECTING DEFECT 45 (vertices=54, convex hull=34, v0=111265) After retessellation of defect 45 (v0=111265), euler #=-9 (153647,460705,307049) : difference with theory (-9) = 0 CORRECTING DEFECT 46 (vertices=9, convex hull=26, v0=114576) After retessellation of defect 46 (v0=114576), euler #=-8 (153651,460724,307065) : difference with theory (-8) = 0 CORRECTING DEFECT 47 (vertices=121, convex hull=57, v0=116644) After retessellation of defect 47 (v0=116644), euler #=-7 (153660,460769,307102) : difference with theory (-7) = 0 CORRECTING DEFECT 48 (vertices=22, convex hull=36, v0=116750) After retessellation of defect 48 (v0=116750), euler #=-6 (153663,460790,307121) : difference with theory (-6) = 0 CORRECTING DEFECT 49 (vertices=50, convex hull=83, v0=116903) After retessellation of defect 49 (v0=116903), euler #=-5 (153698,460930,307227) : difference with theory (-5) = 0 CORRECTING DEFECT 50 (vertices=64, convex hull=84, v0=122189) After retessellation of defect 50 (v0=122189), euler #=-4 (153732,461068,307332) : difference with theory (-4) = 0 CORRECTING DEFECT 51 (vertices=56, convex hull=95, v0=122482) After retessellation of defect 51 (v0=122482), euler #=-3 (153766,461211,307442) : difference with theory (-3) = 0 CORRECTING DEFECT 52 (vertices=25, convex hull=76, v0=122577) After retessellation of defect 52 (v0=122577), euler #=-2 (153781,461287,307504) : difference with theory (-2) = 0 CORRECTING DEFECT 53 (vertices=19, convex hull=22, v0=142391) After retessellation of defect 53 (v0=142391), euler #=-1 (153781,461293,307511) : difference with theory (-1) = 0 CORRECTING DEFECT 54 (vertices=16, convex hull=29, v0=150272) After retessellation of defect 54 (v0=150272), euler #=0 (153783,461306,307523) : difference with theory (0) = 0 CORRECTING DEFECT 55 (vertices=39, convex hull=34, v0=155582) After retessellation of defect 55 (v0=155582), euler #=1 (153789,461336,307548) : difference with theory (1) = 0 CORRECTING DEFECT 56 (vertices=37, convex hull=66, v0=156639) After retessellation of defect 56 (v0=156639), euler #=2 (153799,461391,307594) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.03-->7.59) (max @ vno 20310 --> 25806) 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 (0.03-->7.59) (max @ vno 20310 --> 25806) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 180 mutations (34.4%), 344 crossovers (65.6%), 83 vertices were eliminated building final representation... 3009 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=153799, nf=307594, ne=461391, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 28.1 minutes 0 defective edges removing intersecting faces 000: 339 intersecting 001: 11 intersecting 002: 3 intersecting mris_fix_topology utimesec 1684.829866 mris_fix_topology stimesec 0.190970 mris_fix_topology ru_maxrss 480080 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56173 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 22072 mris_fix_topology ru_oublock 14800 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 738 mris_fix_topology ru_nivcsw 4475 FSRUNTIME@ mris_fix_topology rh 0.4678 hours 1 threads PIDs (11230 11233) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 155300 - 465894 + 310596 = 2 --> 0 holes F =2V-4: 310596 = 310600-4 (0) 2E=3F: 931788 = 931788 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 153799 - 461391 + 307594 = 2 --> 0 holes F =2V-4: 307594 = 307598-4 (0) 2E=3F: 922782 = 922782 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 129 intersecting 001: 17 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 21 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Oct 7 21:51:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 lh #-------------------------------------------- #@# Make White Surf rh Sat Oct 7 21:51:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 rh Waiting for PID 12593 of (12593 12596) to complete... Waiting for PID 12596 of (12593 12596) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 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-6.0.0/0051026/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... 26893 bright wm thresholded. 2956 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig... computing class statistics... border white: 289174 voxels (1.72%) border gray 336461 voxels (2.01%) WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0] GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70) setting MAX_BORDER_WHITE to 112.4 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 41.4 (was 40) setting MAX_GRAY to 93.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->6.56) (max @ vno 36261 --> 154244) face area 0.28 +- 0.13 (0.00-->3.54) mean absolute distance = 0.61 +- 0.76 4682 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=103+-7.8, GM=62+-7.8 mean inside = 92.0, mean outside = 71.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=76.7, 95 (95) missing vertices, mean dist 0.3 [0.5 (%37.8)->0.7 (%62.2))] %80 local maxima, %15 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 +- 0.25 (0.08-->6.78) (max @ vno 36261 --> 154244) face area 0.28 +- 0.13 (0.00-->3.18) mean absolute distance = 0.31 +- 0.51 4227 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4237459.0, rms=10.978 001: dt: 0.5000, sse=2323469.2, rms=7.582 (30.929%) 002: dt: 0.5000, sse=1608527.0, rms=5.804 (23.458%) 003: dt: 0.5000, sse=1284634.9, rms=4.777 (17.687%) 004: dt: 0.5000, sse=1140978.5, rms=4.242 (11.204%) 005: dt: 0.5000, sse=1085455.5, rms=3.992 (5.901%) 006: dt: 0.5000, sse=1054390.9, rms=3.876 (2.888%) rms = 3.83, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=1043708.2, rms=3.827 (1.286%) 008: dt: 0.2500, sse=793741.1, rms=2.394 (37.429%) 009: dt: 0.2500, sse=741274.1, rms=1.986 (17.073%) 010: dt: 0.2500, sse=727388.1, rms=1.856 (6.499%) 011: dt: 0.2500, sse=719200.0, rms=1.779 (4.186%) rms = 1.74, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=715649.3, rms=1.741 (2.124%) 013: dt: 0.1250, sse=704674.8, rms=1.622 (6.850%) rms = 1.61, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=703162.6, rms=1.608 (0.875%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=79.9, 91 (27) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.2 (%26.5))] %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 (0.11-->6.65) (max @ vno 36261 --> 154244) face area 0.35 +- 0.16 (0.00-->4.35) mean absolute distance = 0.23 +- 0.37 3655 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1467843.6, rms=4.803 015: dt: 0.5000, sse=1102273.4, rms=3.274 (31.842%) rms = 3.62, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=947479.0, rms=2.360 (27.927%) 017: dt: 0.2500, sse=882242.4, rms=1.835 (22.254%) 018: dt: 0.2500, sse=859392.9, rms=1.590 (13.343%) 019: dt: 0.2500, sse=849371.6, rms=1.507 (5.211%) 020: dt: 0.2500, sse=845542.6, rms=1.447 (4.006%) rms = 1.42, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=843350.0, rms=1.419 (1.882%) 022: dt: 0.1250, sse=835869.6, rms=1.341 (5.512%) rms = 1.33, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=835307.7, rms=1.334 (0.500%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... mean border=81.8, 86 (16) missing vertices, mean dist -0.1 [0.3 (%65.1)->0.2 (%34.9))] %89 local maxima, % 7 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 +- 0.24 (0.07-->6.57) (max @ vno 36261 --> 154244) face area 0.34 +- 0.16 (0.00-->4.30) mean absolute distance = 0.21 +- 0.32 3171 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1013774.0, rms=2.919 rms = 2.87, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=1009442.2, rms=2.874 (1.563%) 025: dt: 0.2500, sse=853382.6, rms=1.682 (41.470%) 026: dt: 0.2500, sse=818416.8, rms=1.383 (17.754%) rms = 1.36, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=817121.0, rms=1.365 (1.358%) 028: dt: 0.1250, sse=817001.8, rms=1.202 (11.905%) rms = 1.19, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=802714.8, rms=1.190 (1.021%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=82.5, 85 (12) missing vertices, mean dist -0.0 [0.2 (%54.7)->0.2 (%45.3))] %90 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-6.0.0/0051026/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=823905.6, rms=1.575 rms = 1.93, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=785920.6, rms=1.096 (30.433%) 031: dt: 0.2500, sse=773736.1, rms=0.891 (18.653%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.89, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=773111.1, rms=0.887 (0.540%) positioning took 0.5 minutes generating cortex label... 8 non-cortical segments detected only using segment with 7713 vertices erasing segment 1 (vno[0] = 108007) erasing segment 2 (vno[0] = 109207) erasing segment 3 (vno[0] = 113599) erasing segment 4 (vno[0] = 113687) erasing segment 5 (vno[0] = 114755) erasing segment 6 (vno[0] = 114813) erasing segment 7 (vno[0] = 116914) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.area vertex spacing 0.89 +- 0.25 (0.04-->6.58) (max @ vno 36261 --> 154244) face area 0.33 +- 0.16 (0.00-->4.20) refinement took 5.9 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 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-6.0.0/0051026/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... 26893 bright wm thresholded. 2956 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig... computing class statistics... border white: 289174 voxels (1.72%) border gray 336461 voxels (2.01%) WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0] GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70) setting MAX_BORDER_WHITE to 111.4 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 41.4 (was 40) setting MAX_GRAY to 92.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.78) (max @ vno 153384 --> 153404) face area 0.28 +- 0.12 (0.00-->2.21) mean absolute distance = 0.61 +- 0.73 4484 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=102+-7.0, GM=62+-7.0 mean inside = 91.6, mean outside = 70.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=76.3, 37 (37) missing vertices, mean dist 0.3 [0.5 (%38.2)->0.7 (%61.8))] %79 local maxima, %17 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 +- 0.25 (0.10-->3.59) (max @ vno 7675 --> 8624) face area 0.28 +- 0.13 (0.00-->2.57) mean absolute distance = 0.30 +- 0.51 4050 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4253042.5, rms=11.085 001: dt: 0.5000, sse=2342605.0, rms=7.674 (30.772%) 002: dt: 0.5000, sse=1607994.1, rms=5.849 (23.780%) 003: dt: 0.5000, sse=1275656.0, rms=4.791 (18.092%) 004: dt: 0.5000, sse=1131521.4, rms=4.254 (11.209%) 005: dt: 0.5000, sse=1070876.5, rms=3.997 (6.041%) 006: dt: 0.5000, sse=1048886.5, rms=3.902 (2.378%) 007: dt: 0.5000, sse=1036944.9, rms=3.845 (1.462%) rms = 3.82, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1032159.2, rms=3.821 (0.607%) 009: dt: 0.2500, sse=782325.4, rms=2.380 (37.723%) 010: dt: 0.2500, sse=729933.4, rms=1.959 (17.661%) 011: dt: 0.2500, sse=718221.4, rms=1.849 (5.641%) 012: dt: 0.2500, sse=710742.1, rms=1.776 (3.955%) rms = 1.74, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=708455.8, rms=1.745 (1.742%) 014: dt: 0.1250, sse=696465.6, rms=1.624 (6.931%) rms = 1.61, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=695435.2, rms=1.611 (0.779%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 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 mean border=79.5, 55 (4) missing vertices, mean dist -0.2 [0.3 (%73.4)->0.2 (%26.6))] %84 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 +- 0.24 (0.07-->3.53) (max @ vno 7675 --> 8624) face area 0.35 +- 0.16 (0.00-->3.61) mean absolute distance = 0.23 +- 0.38 3652 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1445717.5, rms=4.762 016: dt: 0.5000, sse=1086688.9, rms=3.250 (31.744%) rms = 3.64, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=937696.7, rms=2.336 (28.130%) 018: dt: 0.2500, sse=875905.9, rms=1.838 (21.333%) 019: dt: 0.2500, sse=853190.2, rms=1.606 (12.625%) 020: dt: 0.2500, sse=845931.8, rms=1.529 (4.758%) 021: dt: 0.2500, sse=840943.7, rms=1.464 (4.291%) rms = 1.43, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=839135.0, rms=1.434 (2.029%) 023: dt: 0.1250, sse=831255.1, rms=1.352 (5.692%) rms = 1.34, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=830365.5, rms=1.343 (0.709%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=81.5, 61 (2) missing vertices, mean dist -0.1 [0.3 (%65.2)->0.2 (%34.8))] %88 local maxima, % 7 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 +- 0.24 (0.10-->3.54) (max @ vno 84062 --> 82939) face area 0.34 +- 0.16 (0.00-->3.65) mean absolute distance = 0.21 +- 0.32 3054 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1003716.2, rms=2.898 rms = 2.90, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=885804.0, rms=2.091 (27.832%) 026: dt: 0.2500, sse=818895.2, rms=1.416 (32.311%) 027: dt: 0.2500, sse=808405.7, rms=1.290 (8.842%) rms = 1.26, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=806505.0, rms=1.261 (2.308%) 029: dt: 0.1250, sse=799436.8, rms=1.195 (5.250%) rms = 1.20, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=799887.6, rms=1.197 (-0.214%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.1, 82 (2) missing vertices, mean dist -0.0 [0.2 (%54.3)->0.2 (%45.7))] %90 local maxima, % 6 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-6.0.0/0051026/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=822026.9, rms=1.592 rms = 1.95, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=784586.8, rms=1.124 (29.395%) 032: dt: 0.2500, sse=775378.9, rms=0.910 (19.038%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=772723.5, rms=0.905 (0.610%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 7531 vertices erasing segment 1 (vno[0] = 108009) erasing segment 2 (vno[0] = 110000) erasing segment 3 (vno[0] = 110055) erasing segment 4 (vno[0] = 110085) erasing segment 5 (vno[0] = 110101) erasing segment 6 (vno[0] = 111126) erasing segment 7 (vno[0] = 112181) erasing segment 8 (vno[0] = 113450) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->3.78) (max @ vno 153384 --> 153404) face area 0.34 +- 0.15 (0.00-->3.66) refinement took 6.1 minutes PIDs (12593 12596) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sat Oct 7 21:57:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Oct 7 21:57:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 12824 of (12824 12827) to complete... Waiting for PID 12827 of (12824 12827) 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 (12824 12827) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Oct 7 21:57:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Oct 7 21:57:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 12871 of (12871 12874) to complete... Waiting for PID 12874 of (12871 12874) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 49.3 mm, total surface area = 94212 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 49.081538 mris_inflate stimesec 0.117982 mris_inflate ru_maxrss 226956 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32786 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10928 mris_inflate ru_oublock 12160 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2320 mris_inflate ru_nivcsw 3616 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.7 mm, total surface area = 93561 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 48.612609 mris_inflate stimesec 0.110983 mris_inflate ru_maxrss 224584 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32192 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12048 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2069 mris_inflate ru_nivcsw 3463 PIDs (12871 12874) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Oct 7 21:58:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 Sat Oct 7 21:58:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 12982 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 12985 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 12988 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 12991 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 12994 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 12997 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 13000 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 13003 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 13006 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 13009 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 13013 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... Waiting for PID 13019 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = -4.936*4pi (-62.025) --> 6 handles ICI = 186.7, FI = 1914.6, variation=30438.390 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 201 vertices thresholded to be in k1 ~ [-0.57 0.65], k2 ~ [-0.15 0.21] total integrated curvature = 0.363*4pi (4.556) --> 1 handles ICI = 1.6, FI = 9.8, variation=170.629 173 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 118 vertices thresholded to be in [-0.20 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = -9.204*4pi (-115.662) --> 10 handles ICI = 184.5, FI = 1900.3, variation=30243.861 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 171 vertices thresholded to be in k1 ~ [-0.24 0.43], k2 ~ [-0.13 0.06] total integrated curvature = 0.570*4pi (7.159) --> 0 handles ICI = 1.5, FI = 10.3, variation=172.318 137 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 150 vertices thresholded to be in [-0.13 0.18] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022 done. PIDs (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sat Oct 7 21:59:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051026 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 [ 0051026/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 [ 311 ] Gb_filter = 0 WARN: S lookup min: -1.058048 WARN: S explicit min: 0.000000 vertex = 26 #----------------------------------------- #@# Curvature Stats rh Sat Oct 7 21:59:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051026 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 [ 0051026/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 [ 309 ] Gb_filter = 0 WARN: S lookup min: -0.592156 WARN: S explicit min: 0.000000 vertex = 213 #-------------------------------------------- #@# Sphere lh Sat Oct 7 21:59:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Oct 7 21:59:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 13181 of (13181 13185) to complete... Waiting for PID 13185 of (13181 13185) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0.285... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.46 pass 1: epoch 2 of 3 starting distance error %21.46 unfolding complete - removing small folds... starting distance error %21.40 removing remaining folds... final distance error %21.42 MRISunfold() return, current seed 1234 -01: dt=0.0000, 203 negative triangles 195: dt=0.9900, 203 negative triangles 196: dt=0.9900, 97 negative triangles 197: dt=0.9900, 77 negative triangles 198: dt=0.9900, 60 negative triangles 199: dt=0.9900, 55 negative triangles 200: dt=0.9900, 53 negative triangles 201: dt=0.9900, 47 negative triangles 202: dt=0.9900, 50 negative triangles 203: dt=0.9900, 50 negative triangles 204: dt=0.9900, 46 negative triangles 205: dt=0.9900, 45 negative triangles 206: dt=0.9900, 37 negative triangles 207: dt=0.9900, 44 negative triangles 208: dt=0.9900, 37 negative triangles 209: dt=0.9900, 31 negative triangles 210: dt=0.9900, 35 negative triangles 211: dt=0.9900, 33 negative triangles 212: dt=0.9900, 28 negative triangles 213: dt=0.9900, 33 negative triangles 214: dt=0.9900, 31 negative triangles 215: dt=0.9900, 25 negative triangles 216: dt=0.9900, 30 negative triangles 217: dt=0.9900, 28 negative triangles 218: dt=0.9900, 28 negative triangles 219: dt=0.9900, 32 negative triangles 220: dt=0.9900, 29 negative triangles 221: dt=0.9900, 24 negative triangles 222: dt=0.9900, 23 negative triangles 223: dt=0.9900, 20 negative triangles 224: dt=0.9900, 19 negative triangles 225: dt=0.9900, 17 negative triangles 226: dt=0.9900, 20 negative triangles 227: dt=0.9900, 18 negative triangles 228: dt=0.9900, 15 negative triangles 229: dt=0.9900, 17 negative triangles 230: dt=0.9900, 17 negative triangles 231: dt=0.9900, 16 negative triangles 232: dt=0.9900, 15 negative triangles 233: dt=0.9900, 18 negative triangles 234: dt=0.9900, 18 negative triangles 235: dt=0.9900, 16 negative triangles 236: dt=0.9900, 17 negative triangles 237: dt=0.9900, 16 negative triangles 238: dt=0.9405, 18 negative triangles 239: dt=0.9405, 17 negative triangles 240: dt=0.9405, 16 negative triangles 241: dt=0.9405, 18 negative triangles 242: dt=0.9405, 20 negative triangles 243: dt=0.9405, 16 negative triangles 244: dt=0.9405, 20 negative triangles 245: dt=0.9405, 16 negative triangles 246: dt=0.9405, 21 negative triangles 247: dt=0.9405, 16 negative triangles 248: dt=0.8935, 17 negative triangles 249: dt=0.8935, 14 negative triangles 250: dt=0.8935, 10 negative triangles 251: dt=0.8935, 15 negative triangles 252: dt=0.8935, 11 negative triangles 253: dt=0.8935, 13 negative triangles 254: dt=0.8935, 17 negative triangles 255: dt=0.8935, 14 negative triangles 256: dt=0.8935, 9 negative triangles 257: dt=0.8935, 13 negative triangles 258: dt=0.8935, 12 negative triangles 259: dt=0.8935, 13 negative triangles 260: dt=0.8935, 17 negative triangles 261: dt=0.8935, 13 negative triangles 262: dt=0.8935, 10 negative triangles 263: dt=0.8935, 12 negative triangles 264: dt=0.8935, 9 negative triangles 265: dt=0.8935, 13 negative triangles 266: dt=0.8488, 13 negative triangles 267: dt=0.8488, 17 negative triangles 268: dt=0.8488, 13 negative triangles 269: dt=0.8488, 9 negative triangles 270: dt=0.8488, 13 negative triangles 271: dt=0.8488, 9 negative triangles 272: dt=0.8488, 13 negative triangles 273: dt=0.8488, 11 negative triangles 274: dt=0.8488, 14 negative triangles 275: dt=0.8488, 17 negative triangles 276: dt=0.8064, 13 negative triangles 277: dt=0.8064, 9 negative triangles 278: dt=0.8064, 11 negative triangles 279: dt=0.8064, 11 negative triangles 280: dt=0.8064, 10 negative triangles 281: dt=0.8064, 13 negative triangles 282: dt=0.8064, 12 negative triangles 283: dt=0.8064, 9 negative triangles 284: dt=0.8064, 12 negative triangles 285: dt=0.8064, 10 negative triangles 286: dt=0.7660, 10 negative triangles 287: dt=0.7660, 9 negative triangles 288: dt=0.7660, 10 negative triangles 289: dt=0.7660, 7 negative triangles 290: dt=0.7660, 11 negative triangles 291: dt=0.7660, 8 negative triangles 292: dt=0.7660, 8 negative triangles 293: dt=0.7660, 10 negative triangles 294: dt=0.7660, 8 negative triangles 295: dt=0.7660, 6 negative triangles 296: dt=0.7660, 10 negative triangles 297: dt=0.7660, 9 negative triangles 298: dt=0.7660, 9 negative triangles 299: dt=0.7660, 12 negative triangles 300: dt=0.7660, 11 negative triangles 301: dt=0.7660, 4 negative triangles 302: dt=0.7660, 5 negative triangles 303: dt=0.7660, 5 negative triangles 304: dt=0.7660, 4 negative triangles 305: dt=0.7660, 3 negative triangles 306: dt=0.7660, 2 negative triangles 307: dt=0.7660, 3 negative triangles 308: dt=0.7660, 2 negative triangles 309: dt=0.7660, 2 negative triangles 310: dt=0.7660, 1 negative triangles 311: dt=0.7660, 1 negative triangles 312: dt=0.7660, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.11 hours mris_sphere utimesec 3981.195766 mris_sphere stimesec 1.239811 mris_sphere ru_maxrss 319176 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 55980 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11040 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 143430 mris_sphere ru_nivcsw 325635 FSRUNTIME@ mris_sphere 1.1054 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0.283... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.14 pass 1: epoch 2 of 3 starting distance error %21.14 unfolding complete - removing small folds... starting distance error %21.08 removing remaining folds... final distance error %21.09 MRISunfold() return, current seed 1234 -01: dt=0.0000, 180 negative triangles 190: dt=0.9900, 180 negative triangles 191: dt=0.9900, 72 negative triangles 192: dt=0.9900, 62 negative triangles 193: dt=0.9900, 51 negative triangles 194: dt=0.9900, 51 negative triangles 195: dt=0.9900, 43 negative triangles 196: dt=0.9900, 38 negative triangles 197: dt=0.9900, 40 negative triangles 198: dt=0.9900, 33 negative triangles 199: dt=0.9900, 40 negative triangles 200: dt=0.9900, 43 negative triangles 201: dt=0.9900, 42 negative triangles 202: dt=0.9900, 41 negative triangles 203: dt=0.9900, 38 negative triangles 204: dt=0.9900, 37 negative triangles 205: dt=0.9900, 39 negative triangles 206: dt=0.9900, 34 negative triangles 207: dt=0.9900, 22 negative triangles 208: dt=0.9900, 26 negative triangles 209: dt=0.9900, 26 negative triangles 210: dt=0.9900, 27 negative triangles 211: dt=0.9900, 28 negative triangles 212: dt=0.9900, 26 negative triangles 213: dt=0.9900, 25 negative triangles 214: dt=0.9900, 29 negative triangles 215: dt=0.9900, 24 negative triangles 216: dt=0.9900, 18 negative triangles 217: dt=0.9900, 20 negative triangles 218: dt=0.9900, 27 negative triangles 219: dt=0.9900, 18 negative triangles 220: dt=0.9900, 15 negative triangles 221: dt=0.9900, 16 negative triangles 222: dt=0.9900, 21 negative triangles 223: dt=0.9900, 26 negative triangles 224: dt=0.9900, 18 negative triangles 225: dt=0.9900, 18 negative triangles 226: dt=0.9900, 22 negative triangles 227: dt=0.9900, 17 negative triangles 228: dt=0.9900, 16 negative triangles 229: dt=0.9900, 14 negative triangles 230: dt=0.9900, 15 negative triangles 231: dt=0.9900, 14 negative triangles 232: dt=0.9900, 12 negative triangles 233: dt=0.9900, 14 negative triangles 234: dt=0.9900, 13 negative triangles 235: dt=0.9900, 14 negative triangles 236: dt=0.9900, 16 negative triangles 237: dt=0.9900, 15 negative triangles 238: dt=0.9900, 12 negative triangles 239: dt=0.9900, 18 negative triangles 240: dt=0.9900, 15 negative triangles 241: dt=0.9900, 16 negative triangles 242: dt=0.9405, 14 negative triangles 243: dt=0.9405, 11 negative triangles 244: dt=0.9405, 14 negative triangles 245: dt=0.9405, 11 negative triangles 246: dt=0.9405, 15 negative triangles 247: dt=0.9405, 12 negative triangles 248: dt=0.9405, 15 negative triangles 249: dt=0.9405, 14 negative triangles 250: dt=0.9405, 11 negative triangles 251: dt=0.9405, 13 negative triangles 252: dt=0.9405, 11 negative triangles 253: dt=0.8935, 15 negative triangles 254: dt=0.8935, 15 negative triangles 255: dt=0.8935, 14 negative triangles 256: dt=0.8935, 14 negative triangles 257: dt=0.8935, 12 negative triangles 258: dt=0.8935, 13 negative triangles 259: dt=0.8935, 11 negative triangles 260: dt=0.8935, 14 negative triangles 261: dt=0.8935, 13 negative triangles 262: dt=0.8935, 14 negative triangles 263: dt=0.8488, 15 negative triangles 264: dt=0.8488, 11 negative triangles 265: dt=0.8488, 10 negative triangles 266: dt=0.8488, 10 negative triangles 267: dt=0.8488, 10 negative triangles 268: dt=0.8488, 10 negative triangles 269: dt=0.8488, 10 negative triangles 270: dt=0.8488, 11 negative triangles 271: dt=0.8488, 9 negative triangles 272: dt=0.8488, 12 negative triangles 273: dt=0.8488, 10 negative triangles 274: dt=0.8488, 15 negative triangles 275: dt=0.8488, 10 negative triangles 276: dt=0.8488, 12 negative triangles 277: dt=0.8488, 8 negative triangles 278: dt=0.8488, 12 negative triangles 279: dt=0.8488, 10 negative triangles 280: dt=0.8488, 9 negative triangles 281: dt=0.8488, 8 negative triangles 282: dt=0.8488, 10 negative triangles 283: dt=0.8488, 9 negative triangles 284: dt=0.8488, 11 negative triangles 285: dt=0.8488, 8 negative triangles 286: dt=0.8488, 9 negative triangles 287: dt=0.8064, 11 negative triangles 288: dt=0.8064, 9 negative triangles 289: dt=0.8064, 10 negative triangles 290: dt=0.8064, 9 negative triangles 291: dt=0.8064, 9 negative triangles 292: dt=0.8064, 11 negative triangles 293: dt=0.8064, 9 negative triangles 294: dt=0.8064, 9 negative triangles 295: dt=0.8064, 9 negative triangles 296: dt=0.8064, 9 negative triangles 297: dt=0.7660, 10 negative triangles 298: dt=0.7660, 8 negative triangles 299: dt=0.7660, 7 negative triangles 300: dt=0.7660, 6 negative triangles 301: dt=0.7660, 6 negative triangles 302: dt=0.7660, 7 negative triangles 303: dt=0.7660, 7 negative triangles 304: dt=0.7660, 6 negative triangles 305: dt=0.7660, 6 negative triangles 306: dt=0.7660, 4 negative triangles 307: dt=0.7660, 6 negative triangles 308: dt=0.7660, 5 negative triangles 309: dt=0.7660, 5 negative triangles 310: dt=0.7660, 5 negative triangles 311: dt=0.7660, 2 negative triangles 312: dt=0.7660, 4 negative triangles 313: dt=0.7660, 1 negative triangles 314: dt=0.7660, 3 negative triangles 315: dt=0.7660, 1 negative triangles 316: dt=0.7660, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.11 hours mris_sphere utimesec 4042.976374 mris_sphere stimesec 1.056839 mris_sphere ru_maxrss 316148 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 55733 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10936 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 143839 mris_sphere ru_nivcsw 320326 FSRUNTIME@ mris_sphere 1.1147 hours 1 threads PIDs (13181 13185) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Oct 7 23:06:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 Sat Oct 7 23:06:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 16072 of (16072 16075) to complete... Waiting for PID 16075 of (16072 16075) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 5.587 curvature mean = 0.026, std = 0.815 curvature mean = 0.020, std = 0.847 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 363448.8, tmin=1.1895 d=32.00 min @ (0.00, -8.00, 8.00) sse = 268727.1, tmin=2.4051 d=16.00 min @ (4.00, 4.00, 0.00) sse = 231352.7, tmin=3.6365 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 215689.5, tmin=4.8891 d=4.00 min @ (1.00, 1.00, 0.00) sse = 213149.1, tmin=6.1524 d=2.00 min @ (-0.50, -0.50, 0.50) sse = 212497.0, tmin=7.4213 d=1.00 min @ (0.25, 0.00, 0.00) sse = 212365.1, tmin=8.6778 d=0.50 min @ (0.00, 0.12, -0.12) sse = 212301.4, tmin=9.9393 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 9.94 min curvature mean = -0.018, std = 0.828 curvature mean = 0.008, std = 0.939 curvature mean = -0.024, std = 0.837 curvature mean = 0.003, std = 0.975 curvature mean = -0.026, std = 0.839 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.029, std = 0.313 curvature mean = 0.034, std = 0.245 curvature mean = 0.067, std = 0.305 curvature mean = 0.030, std = 0.302 curvature mean = 0.038, std = 0.482 curvature mean = 0.030, std = 0.327 curvature mean = 0.023, std = 0.613 curvature mean = 0.030, std = 0.339 curvature mean = 0.008, std = 0.718 MRISregister() return, current seed 0 -01: dt=0.0000, 33 negative triangles 123: dt=0.9900, 33 negative triangles expanding nbhd size to 1 124: dt=0.9900, 47 negative triangles 125: dt=0.9900, 33 negative triangles 126: dt=0.9900, 38 negative triangles 127: dt=0.9900, 39 negative triangles 128: dt=0.9900, 34 negative triangles 129: dt=0.9900, 25 negative triangles 130: dt=0.9900, 27 negative triangles 131: dt=0.9900, 25 negative triangles 132: dt=0.9900, 28 negative triangles 133: dt=0.9900, 24 negative triangles 134: dt=0.9900, 16 negative triangles 135: dt=0.9900, 18 negative triangles 136: dt=0.9900, 15 negative triangles 137: dt=0.9900, 11 negative triangles 138: dt=0.9900, 13 negative triangles 139: dt=0.9900, 11 negative triangles 140: dt=0.9900, 11 negative triangles 141: dt=0.9900, 13 negative triangles 142: dt=0.9900, 11 negative triangles 143: dt=0.9900, 11 negative triangles 144: dt=0.9900, 13 negative triangles 145: dt=0.9900, 11 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 10 negative triangles 148: dt=0.9900, 9 negative triangles 149: dt=0.9900, 9 negative triangles 150: dt=0.9900, 10 negative triangles 151: dt=0.9900, 8 negative triangles 152: dt=0.9900, 8 negative triangles 153: dt=0.9900, 8 negative triangles 154: dt=0.9900, 6 negative triangles 155: dt=0.9900, 6 negative triangles 156: dt=0.9900, 8 negative triangles 157: dt=0.9900, 6 negative triangles 158: dt=0.9900, 6 negative triangles 159: dt=0.9900, 5 negative triangles 160: dt=0.9900, 3 negative triangles 161: dt=0.9900, 3 negative triangles 162: dt=0.9900, 3 negative triangles 163: dt=0.9900, 7 negative triangles 164: dt=0.9900, 5 negative triangles 165: dt=0.9900, 3 negative triangles 166: dt=0.9900, 5 negative triangles 167: dt=0.9900, 2 negative triangles 168: dt=0.9900, 2 negative triangles 169: dt=0.9900, 1 negative triangles 170: dt=0.9900, 4 negative triangles 171: dt=0.9900, 1 negative triangles 172: dt=0.9900, 1 negative triangles 173: dt=0.9900, 1 negative triangles 174: dt=0.9900, 3 negative triangles 175: dt=0.9900, 1 negative triangles 176: dt=0.9900, 1 negative triangles 177: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.16 hours mris_register utimesec 4185.182755 mris_register stimesec 2.024692 mris_register ru_maxrss 280516 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 41627 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 10928 mris_register ru_oublock 11032 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 286530 mris_register ru_nivcsw 200349 FSRUNTIME@ mris_register 1.1627 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 5.609 curvature mean = 0.013, std = 0.813 curvature mean = 0.018, std = 0.852 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 409367.8, tmin=1.1770 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 242232.1, tmin=2.3802 d=8.00 min @ (0.00, 2.00, 2.00) sse = 226017.7, tmin=4.8307 d=2.00 min @ (0.00, 0.00, -0.50) sse = 225757.7, tmin=7.2843 d=1.00 min @ (0.00, -0.25, 0.25) sse = 225598.1, tmin=8.5238 d=0.50 min @ (0.12, 0.12, -0.12) sse = 225553.8, tmin=9.7855 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 9.79 min curvature mean = -0.013, std = 0.819 curvature mean = 0.008, std = 0.943 curvature mean = -0.019, std = 0.825 curvature mean = 0.003, std = 0.977 curvature mean = -0.020, std = 0.826 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.027, std = 0.292 curvature mean = 0.030, std = 0.240 curvature mean = 0.066, std = 0.333 curvature mean = 0.028, std = 0.297 curvature mean = 0.038, std = 0.521 curvature mean = 0.027, std = 0.322 curvature mean = 0.022, std = 0.663 curvature mean = 0.027, std = 0.334 curvature mean = 0.007, std = 0.774 MRISregister() return, current seed 0 -01: dt=0.0000, 51 negative triangles 116: dt=0.9900, 51 negative triangles expanding nbhd size to 1 117: dt=0.9900, 71 negative triangles 118: dt=0.9900, 51 negative triangles 119: dt=0.9900, 55 negative triangles 120: dt=0.9405, 53 negative triangles 121: dt=0.9405, 46 negative triangles 122: dt=0.9405, 49 negative triangles 123: dt=0.9405, 51 negative triangles 124: dt=0.9405, 49 negative triangles 125: dt=0.9405, 42 negative triangles 126: dt=0.9405, 41 negative triangles 127: dt=0.9405, 40 negative triangles 128: dt=0.9405, 36 negative triangles 129: dt=0.9405, 34 negative triangles 130: dt=0.9405, 31 negative triangles 131: dt=0.9405, 32 negative triangles 132: dt=0.9405, 30 negative triangles 133: dt=0.9405, 28 negative triangles 134: dt=0.9405, 25 negative triangles 135: dt=0.9405, 26 negative triangles 136: dt=0.9405, 27 negative triangles 137: dt=0.9405, 21 negative triangles 138: dt=0.9405, 21 negative triangles 139: dt=0.9405, 23 negative triangles 140: dt=0.9405, 20 negative triangles 141: dt=0.9405, 18 negative triangles 142: dt=0.9405, 16 negative triangles 143: dt=0.9405, 20 negative triangles 144: dt=0.9405, 20 negative triangles 145: dt=0.9405, 16 negative triangles 146: dt=0.9405, 17 negative triangles 147: dt=0.9405, 13 negative triangles 148: dt=0.9405, 9 negative triangles 149: dt=0.9405, 7 negative triangles 150: dt=0.9405, 7 negative triangles 151: dt=0.9405, 5 negative triangles 152: dt=0.9405, 8 negative triangles 153: dt=0.9405, 8 negative triangles 154: dt=0.9405, 6 negative triangles 155: dt=0.9405, 3 negative triangles 156: dt=0.9405, 3 negative triangles 157: dt=0.9405, 2 negative triangles 158: dt=0.9405, 2 negative triangles 159: dt=0.9405, 2 negative triangles 160: dt=0.9405, 1 negative triangles 161: dt=0.9405, 1 negative triangles 162: dt=0.9405, 4 negative triangles 163: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.23 hours mris_register utimesec 4573.610705 mris_register stimesec 2.038690 mris_register ru_maxrss 278608 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 39760 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10904 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 316317 mris_register ru_nivcsw 191615 FSRUNTIME@ mris_register 1.2300 hours 1 threads PIDs (16072 16075) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 00:20:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 00:20:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 18883 of (18883 18886) to complete... Waiting for PID 18886 of (18883 18886) 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 (18883 18886) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 00:20:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 00:20:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 18929 of (18929 18932) to complete... Waiting for PID 18932 of (18929 18932) 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 (18929 18932) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 00:20:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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 00:20:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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 18979 of (18979 18982) to complete... Waiting for PID 18982 of (18979 18982) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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... 1292 labels changed using aseg relabeling using gibbs priors... 000: 3268 changed, 155300 examined... 001: 784 changed, 14001 examined... 002: 178 changed, 4325 examined... 003: 61 changed, 1077 examined... 004: 20 changed, 375 examined... 005: 9 changed, 118 examined... 006: 6 changed, 57 examined... 007: 2 changed, 33 examined... 008: 1 changed, 18 examined... 009: 0 changed, 6 examined... 250 labels changed using aseg 000: 142 total segments, 94 labels (323 vertices) changed 001: 52 total segments, 3 labels (13 vertices) changed 002: 48 total segments, 2 labels (3 vertices) changed 003: 46 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2005 vertices marked for relabeling... 2005 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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... 1323 labels changed using aseg relabeling using gibbs priors... 000: 2924 changed, 153799 examined... 001: 690 changed, 12665 examined... 002: 159 changed, 3921 examined... 003: 63 changed, 966 examined... 004: 23 changed, 373 examined... 005: 6 changed, 148 examined... 006: 1 changed, 43 examined... 007: 1 changed, 5 examined... 008: 0 changed, 7 examined... 173 labels changed using aseg 000: 89 total segments, 51 labels (229 vertices) changed 001: 41 total segments, 4 labels (4 vertices) changed 002: 37 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... 1789 vertices marked for relabeling... 1789 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. PIDs (18979 18982) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 00:20:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 00:20:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 rh Waiting for PID 19040 of (19040 19043) to complete... Waiting for PID 19043 of (19040 19043) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 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-6.0.0/0051026/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... 26893 bright wm thresholded. 2956 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig... computing class statistics... border white: 289174 voxels (1.72%) border gray 336461 voxels (2.01%) WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0] GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70) setting MAX_BORDER_WHITE to 112.4 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 41.4 (was 40) setting MAX_GRAY to 93.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=62+-7.8 mean inside = 92.0, mean outside = 71.1 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 0.89 +- 0.25 (0.04-->6.58) (max @ vno 36261 --> 154244) face area 0.33 +- 0.16 (0.00-->4.18) mean absolute distance = 0.51 +- 0.74 3842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 25 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 3 with 51 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 259 points - only 0.00% unknown deleting segment 6 with 29 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 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 mean border=76.1, 95 (95) missing vertices, mean dist 0.3 [0.5 (%16.3)->0.5 (%83.7))] %78 local maxima, %18 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 (0.08-->6.58) (max @ vno 36261 --> 154244) face area 0.33 +- 0.16 (0.00-->4.03) mean absolute distance = 0.32 +- 0.52 3850 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2804627.2, rms=8.317 001: dt: 0.5000, sse=1517290.5, rms=5.087 (38.839%) 002: dt: 0.5000, sse=1222872.0, rms=4.029 (20.802%) 003: dt: 0.5000, sse=1179258.8, rms=3.823 (5.103%) 004: dt: 0.5000, sse=1135155.0, rms=3.632 (4.999%) rms = 3.71, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=930379.7, rms=2.490 (31.437%) 006: dt: 0.2500, sse=859760.2, rms=1.943 (21.956%) 007: dt: 0.2500, sse=839704.8, rms=1.744 (10.262%) 008: dt: 0.2500, sse=833168.4, rms=1.681 (3.604%) rms = 1.64, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=831559.8, rms=1.638 (2.539%) 010: dt: 0.1250, sse=822879.6, rms=1.565 (4.475%) rms = 1.56, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=822383.4, rms=1.555 (0.635%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 112 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown mean border=79.7, 89 (35) missing vertices, mean dist -0.2 [0.3 (%75.5)->0.2 (%24.5))] %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 (0.10-->6.48) (max @ vno 36261 --> 154244) face area 0.36 +- 0.17 (0.00-->4.59) mean absolute distance = 0.24 +- 0.38 3610 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1507966.9, rms=4.872 012: dt: 0.5000, sse=1117570.0, rms=3.239 (33.513%) rms = 3.53, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=964327.4, rms=2.336 (27.895%) 014: dt: 0.2500, sse=895519.9, rms=1.772 (24.145%) 015: dt: 0.2500, sse=870471.1, rms=1.508 (14.860%) 016: dt: 0.2500, sse=862148.3, rms=1.418 (5.975%) 017: dt: 0.2500, sse=857755.9, rms=1.364 (3.796%) rms = 1.34, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=855856.8, rms=1.340 (1.824%) 019: dt: 0.1250, sse=849833.5, rms=1.265 (5.595%) rms = 1.26, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=849464.0, rms=1.262 (0.193%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 41 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 115 points - only 0.00% unknown deleting segment 5 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 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 mean border=81.7, 82 (24) missing vertices, mean dist -0.1 [0.3 (%65.8)->0.2 (%34.2))] %89 local maxima, % 7 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-->6.33) (max @ vno 36261 --> 154244) face area 0.34 +- 0.17 (0.00-->4.36) mean absolute distance = 0.22 +- 0.32 3286 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1025113.4, rms=2.928 021: dt: 0.5000, sse=1018467.2, rms=2.858 (2.403%) rms = 3.32, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=873522.2, rms=1.838 (35.672%) 023: dt: 0.2500, sse=829900.0, rms=1.398 (23.951%) 024: dt: 0.2500, sse=819919.3, rms=1.275 (8.810%) rms = 1.26, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=817518.3, rms=1.259 (1.257%) 026: dt: 0.1250, sse=809938.1, rms=1.154 (8.310%) rms = 1.15, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=809446.3, rms=1.152 (0.220%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 41 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 113 points - only 0.00% unknown deleting segment 5 with 23 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown mean border=82.4, 76 (19) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))] %90 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-6.0.0/0051026/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=832280.7, rms=1.578 rms = 1.92, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=793440.0, rms=1.082 (31.397%) 029: dt: 0.2500, sse=781115.5, rms=0.865 (20.123%) rms = 0.87, time step reduction 2 of 3 to 0.125... rms = 0.86, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=779869.8, rms=0.859 (0.653%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 7714 vertices erasing segment 1 (vno[0] = 109207) erasing segment 2 (vno[0] = 110460) erasing segment 3 (vno[0] = 113599) erasing segment 4 (vno[0] = 113647) erasing segment 5 (vno[0] = 113687) erasing segment 6 (vno[0] = 114813) erasing segment 7 (vno[0] = 115908) erasing segment 8 (vno[0] = 116914) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.area vertex spacing 0.89 +- 0.26 (0.04-->6.31) (max @ vno 36261 --> 154244) face area 0.34 +- 0.16 (0.00-->4.39) 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 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.4, 115 (115) missing vertices, mean dist 1.5 [0.6 (%0.0)->3.1 (%100.0))] %11 local maxima, %34 large gradients and %50 min vals, 579 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=32446480.0, rms=32.650 001: dt: 0.0500, sse=28340256.0, rms=30.462 (6.702%) 002: dt: 0.0500, sse=25419706.0, rms=28.804 (5.441%) 003: dt: 0.0500, sse=23199350.0, rms=27.477 (4.607%) 004: dt: 0.0500, sse=21418316.0, rms=26.365 (4.050%) 005: dt: 0.0500, sse=19933022.0, rms=25.399 (3.662%) 006: dt: 0.0500, sse=18658330.0, rms=24.540 (3.381%) 007: dt: 0.0500, sse=17542114.0, rms=23.763 (3.169%) 008: dt: 0.0500, sse=16549367.0, rms=23.049 (3.003%) 009: dt: 0.0500, sse=15655907.0, rms=22.387 (2.871%) 010: dt: 0.0500, sse=14844162.0, rms=21.769 (2.764%) positioning took 1.1 minutes mean border=50.2, 101 (72) missing vertices, mean dist 1.3 [0.2 (%0.0)->2.6 (%100.0))] %12 local maxima, %34 large gradients and %49 min vals, 546 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=15607909.0, rms=22.353 011: dt: 0.0500, sse=14861106.0, rms=21.783 (2.547%) 012: dt: 0.0500, sse=14174959.0, rms=21.247 (2.464%) 013: dt: 0.0500, sse=13542039.0, rms=20.739 (2.388%) 014: dt: 0.0500, sse=12957204.0, rms=20.259 (2.316%) 015: dt: 0.0500, sse=12415446.0, rms=19.804 (2.248%) 016: dt: 0.0500, sse=11913827.0, rms=19.372 (2.178%) 017: dt: 0.0500, sse=11447261.0, rms=18.962 (2.116%) 018: dt: 0.0500, sse=11014040.0, rms=18.574 (2.051%) 019: dt: 0.0500, sse=10610629.0, rms=18.204 (1.990%) 020: dt: 0.0500, sse=10235223.0, rms=17.853 (1.928%) positioning took 1.1 minutes mean border=50.2, 116 (64) missing vertices, mean dist 1.1 [0.1 (%0.5)->2.3 (%99.5))] %13 local maxima, %34 large gradients and %49 min vals, 550 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=10335192.0, rms=17.953 021: dt: 0.0500, sse=9981051.0, rms=17.618 (1.870%) 022: dt: 0.0500, sse=9651309.0, rms=17.299 (1.808%) 023: dt: 0.0500, sse=9342591.0, rms=16.995 (1.756%) 024: dt: 0.0500, sse=9054039.0, rms=16.706 (1.700%) 025: dt: 0.0500, sse=8783382.0, rms=16.431 (1.651%) 026: dt: 0.0500, sse=8529487.0, rms=16.168 (1.601%) 027: dt: 0.0500, sse=8290122.0, rms=15.915 (1.559%) 028: dt: 0.0500, sse=8063184.5, rms=15.673 (1.526%) 029: dt: 0.0500, sse=7847435.0, rms=15.438 (1.496%) 030: dt: 0.0500, sse=7642155.5, rms=15.212 (1.468%) positioning took 1.1 minutes mean border=50.1, 135 (55) missing vertices, mean dist 1.0 [0.1 (%4.8)->2.1 (%95.2))] %13 local maxima, %34 large gradients and %48 min vals, 513 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=7712222.0, rms=15.290 031: dt: 0.5000, sse=6280224.5, rms=13.614 (10.962%) 032: dt: 0.5000, sse=5251889.5, rms=12.262 (9.928%) 033: dt: 0.5000, sse=4447532.0, rms=11.089 (9.564%) 034: dt: 0.5000, sse=3803668.5, rms=10.048 (9.391%) 035: dt: 0.5000, sse=3282773.2, rms=9.120 (9.238%) 036: dt: 0.5000, sse=2861233.2, rms=8.291 (9.088%) 037: dt: 0.5000, sse=2506599.5, rms=7.528 (9.197%) 038: dt: 0.5000, sse=2226631.2, rms=6.865 (8.817%) 039: dt: 0.5000, sse=2012917.4, rms=6.314 (8.027%) 040: dt: 0.5000, sse=1859373.9, rms=5.885 (6.794%) 041: dt: 0.5000, sse=1755381.9, rms=5.576 (5.250%) 042: dt: 0.5000, sse=1689512.6, rms=5.369 (3.711%) 043: dt: 0.5000, sse=1650396.1, rms=5.245 (2.312%) 044: dt: 0.5000, sse=1626033.6, rms=5.162 (1.571%) 045: dt: 0.5000, sse=1607965.0, rms=5.102 (1.164%) rms = 5.06, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1596598.0, rms=5.063 (0.777%) 047: dt: 0.2500, sse=1518227.2, rms=4.749 (6.195%) 048: dt: 0.2500, sse=1495523.6, rms=4.666 (1.746%) rms = 4.66, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1495134.9, rms=4.661 (0.100%) 050: dt: 0.1250, sse=1481604.4, rms=4.606 (1.186%) rms = 4.60, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1479875.8, rms=4.599 (0.147%) positioning took 3.1 minutes mean border=49.5, 3703 (21) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.6 (%50.5))] %20 local maxima, %30 large gradients and %43 min vals, 308 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=1677294.9, rms=4.511 052: dt: 0.5000, sse=1617266.9, rms=4.291 (4.893%) rms = 4.28, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1605399.6, rms=4.275 (0.363%) 054: dt: 0.2500, sse=1535103.0, rms=3.926 (8.171%) 055: dt: 0.2500, sse=1520959.6, rms=3.866 (1.520%) rms = 3.89, time step reduction 2 of 3 to 0.125... rms = 3.84, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1515180.9, rms=3.837 (0.762%) positioning took 1.0 minutes mean border=49.1, 4110 (17) missing vertices, mean dist 0.1 [0.2 (%50.6)->0.5 (%49.4))] %28 local maxima, %23 large gradients and %42 min vals, 314 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=1551520.6, rms=3.982 rms = 4.29, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1526417.2, rms=3.866 (2.917%) rms = 3.88, time step reduction 2 of 3 to 0.125... rms = 3.85, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1523831.4, rms=3.853 (0.339%) positioning took 0.6 minutes mean border=48.7, 7515 (17) missing vertices, mean dist 0.1 [0.2 (%48.8)->0.4 (%51.2))] %32 local maxima, %18 large gradients and %41 min vals, 316 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-6.0.0/0051026/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1552112.0, rms=3.981 059: dt: 0.5000, sse=1527515.9, rms=3.920 (1.535%) rms = 4.05, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1472687.6, rms=3.662 (6.580%) 061: dt: 0.2500, sse=1442396.9, rms=3.531 (3.577%) 062: dt: 0.2500, sse=1430081.0, rms=3.477 (1.538%) rms = 3.44, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1420828.9, rms=3.439 (1.078%) 064: dt: 0.1250, sse=1404028.5, rms=3.348 (2.652%) rms = 3.33, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1399164.6, rms=3.327 (0.631%) positioning took 1.5 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.area.pial vertex spacing 1.03 +- 0.46 (0.03-->7.33) (max @ vno 11185 --> 154107) face area 0.41 +- 0.33 (0.00-->7.77) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 155300 vertices processed 25000 of 155300 vertices processed 50000 of 155300 vertices processed 75000 of 155300 vertices processed 100000 of 155300 vertices processed 125000 of 155300 vertices processed 150000 of 155300 vertices processed 0 of 155300 vertices processed 25000 of 155300 vertices processed 50000 of 155300 vertices processed 75000 of 155300 vertices processed 100000 of 155300 vertices processed 125000 of 155300 vertices processed 150000 of 155300 vertices processed thickness calculation complete, 536:1288 truncations. 29393 vertices at 0 distance 102165 vertices at 1 distance 97217 vertices at 2 distance 45032 vertices at 3 distance 15665 vertices at 4 distance 5017 vertices at 5 distance 1751 vertices at 6 distance 569 vertices at 7 distance 255 vertices at 8 distance 126 vertices at 9 distance 84 vertices at 10 distance 56 vertices at 11 distance 41 vertices at 12 distance 42 vertices at 13 distance 48 vertices at 14 distance 22 vertices at 15 distance 11 vertices at 16 distance 16 vertices at 17 distance 20 vertices at 18 distance 19 vertices at 19 distance 15 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.thickness positioning took 17.7 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 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-6.0.0/0051026/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... 26893 bright wm thresholded. 2956 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig... computing class statistics... border white: 289174 voxels (1.72%) border gray 336461 voxels (2.01%) WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0] GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70) setting MAX_BORDER_WHITE to 111.4 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 41.4 (was 40) setting MAX_GRAY to 92.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.0, GM=62+-7.0 mean inside = 91.6, mean outside = 70.7 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 (0.03-->3.78) (max @ vno 153384 --> 153404) face area 0.33 +- 0.15 (0.00-->3.64) mean absolute distance = 0.51 +- 0.74 3427 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 22 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 178 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown mean border=75.8, 97 (97) missing vertices, mean dist 0.3 [0.5 (%16.3)->0.5 (%83.7))] %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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.09-->3.84) (max @ vno 90569 --> 91721) face area 0.33 +- 0.16 (0.00-->3.65) mean absolute distance = 0.31 +- 0.52 3973 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2717593.0, rms=8.181 001: dt: 0.5000, sse=1461957.8, rms=4.948 (39.517%) 002: dt: 0.5000, sse=1194039.1, rms=3.948 (20.201%) 003: dt: 0.5000, sse=1158211.2, rms=3.803 (3.676%) 004: dt: 0.5000, sse=1116598.8, rms=3.617 (4.892%) rms = 3.72, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=918173.1, rms=2.463 (31.909%) 006: dt: 0.2500, sse=850478.4, rms=1.919 (22.094%) 007: dt: 0.2500, sse=832364.1, rms=1.735 (9.578%) rms = 1.69, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=829141.9, rms=1.689 (2.673%) 009: dt: 0.1250, sse=819302.7, rms=1.595 (5.549%) rms = 1.58, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=818189.0, rms=1.583 (0.732%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 44 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 5 with 44 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 12 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 7 points - only 0.00% unknown mean border=79.4, 76 (24) missing vertices, mean dist -0.2 [0.3 (%75.4)->0.2 (%24.6))] %84 local maxima, %12 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 (0.11-->4.05) (max @ vno 90569 --> 91721) face area 0.36 +- 0.17 (0.00-->4.24) mean absolute distance = 0.23 +- 0.38 3499 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1478565.1, rms=4.816 011: dt: 0.5000, sse=1114181.1, rms=3.229 (32.962%) rms = 3.56, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=952384.8, rms=2.308 (28.505%) 013: dt: 0.2500, sse=898221.5, rms=1.761 (23.694%) 014: dt: 0.2500, sse=863294.2, rms=1.515 (14.013%) 015: dt: 0.2500, sse=858010.1, rms=1.433 (5.376%) 016: dt: 0.2500, sse=852204.7, rms=1.383 (3.494%) rms = 1.36, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=852572.5, rms=1.364 (1.386%) 018: dt: 0.1250, sse=844609.9, rms=1.287 (5.641%) rms = 1.29, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=844554.6, rms=1.286 (0.097%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 37 points - only 0.00% unknown deleting segment 4 with 85 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown mean border=81.3, 59 (17) missing vertices, mean dist -0.1 [0.3 (%65.7)->0.2 (%34.3))] %88 local maxima, % 7 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 (0.06-->4.16) (max @ vno 90569 --> 91721) face area 0.34 +- 0.16 (0.00-->4.20) mean absolute distance = 0.22 +- 0.32 3048 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1016447.4, rms=2.918 rms = 2.89, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=1033967.8, rms=2.891 (0.937%) 021: dt: 0.2500, sse=855048.0, rms=1.666 (42.360%) 022: dt: 0.2500, sse=821322.5, rms=1.363 (18.195%) rms = 1.34, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=820083.2, rms=1.341 (1.645%) 024: dt: 0.1250, sse=807183.8, rms=1.177 (12.213%) rms = 1.17, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=806095.6, rms=1.165 (0.997%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 133 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown mean border=82.1, 71 (12) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))] %90 local maxima, % 6 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-6.0.0/0051026/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=827677.5, rms=1.587 rms = 1.96, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=789056.9, rms=1.099 (30.748%) 027: dt: 0.2500, sse=777278.4, rms=0.884 (19.581%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=776287.9, rms=0.879 (0.610%) positioning took 0.5 minutes generating cortex label... 8 non-cortical segments detected only using segment with 7533 vertices erasing segment 1 (vno[0] = 108009) erasing segment 2 (vno[0] = 108012) erasing segment 3 (vno[0] = 110042) erasing segment 4 (vno[0] = 110085) erasing segment 5 (vno[0] = 111126) erasing segment 6 (vno[0] = 112181) erasing segment 7 (vno[0] = 113450) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.area vertex spacing 0.90 +- 0.26 (0.03-->4.26) (max @ vno 113447 --> 114521) face area 0.34 +- 0.16 (0.00-->4.18) 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 1 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.2, 117 (117) missing vertices, mean dist 1.5 [0.0 (%0.0)->3.1 (%100.0))] %12 local maxima, %35 large gradients and %49 min vals, 711 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=31763528.0, rms=32.441 001: dt: 0.0500, sse=27735550.0, rms=30.262 (6.718%) 002: dt: 0.0500, sse=24869992.0, rms=28.610 (5.458%) 003: dt: 0.0500, sse=22688598.0, rms=27.286 (4.629%) 004: dt: 0.0500, sse=20937348.0, rms=26.174 (4.075%) 005: dt: 0.0500, sse=19476524.0, rms=25.209 (3.687%) 006: dt: 0.0500, sse=18223022.0, rms=24.350 (3.406%) 007: dt: 0.0500, sse=17124914.0, rms=23.572 (3.194%) 008: dt: 0.0500, sse=16147654.0, rms=22.858 (3.031%) 009: dt: 0.0500, sse=15267504.0, rms=22.195 (2.902%) 010: dt: 0.0500, sse=14469053.0, rms=21.575 (2.791%) positioning took 1.0 minutes mean border=50.0, 109 (63) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.6 (%100.0))] %13 local maxima, %35 large gradients and %48 min vals, 673 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=15220140.0, rms=22.160 011: dt: 0.0500, sse=14485679.0, rms=21.590 (2.572%) 012: dt: 0.0500, sse=13811562.0, rms=21.054 (2.486%) 013: dt: 0.0500, sse=13189933.0, rms=20.546 (2.410%) 014: dt: 0.0500, sse=12615611.0, rms=20.066 (2.337%) 015: dt: 0.0500, sse=12084454.0, rms=19.611 (2.266%) 016: dt: 0.0500, sse=11592709.0, rms=19.181 (2.196%) 017: dt: 0.0500, sse=11136938.0, rms=18.773 (2.128%) 018: dt: 0.0500, sse=10714167.0, rms=18.386 (2.060%) 019: dt: 0.0500, sse=10321429.0, rms=18.019 (1.995%) 020: dt: 0.0500, sse=9956381.0, rms=17.671 (1.930%) positioning took 1.0 minutes mean border=49.9, 122 (56) missing vertices, mean dist 1.1 [0.1 (%0.5)->2.3 (%99.5))] %13 local maxima, %36 large gradients and %47 min vals, 650 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=10045566.0, rms=17.764 021: dt: 0.0500, sse=9701816.0, rms=17.432 (1.870%) 022: dt: 0.0500, sse=9381526.0, rms=17.116 (1.810%) 023: dt: 0.0500, sse=9081780.0, rms=16.816 (1.757%) 024: dt: 0.0500, sse=8801807.0, rms=16.530 (1.700%) 025: dt: 0.0500, sse=8539536.0, rms=16.257 (1.648%) 026: dt: 0.0500, sse=8293519.0, rms=15.998 (1.598%) 027: dt: 0.0500, sse=8061346.5, rms=15.748 (1.558%) 028: dt: 0.0500, sse=7841141.0, rms=15.508 (1.525%) 029: dt: 0.0500, sse=7632145.5, rms=15.276 (1.493%) 030: dt: 0.0500, sse=7433009.0, rms=15.052 (1.467%) positioning took 1.1 minutes mean border=49.9, 146 (51) missing vertices, mean dist 1.0 [0.1 (%4.6)->2.0 (%95.4))] %14 local maxima, %36 large gradients and %47 min vals, 638 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=7501263.0, rms=15.131 031: dt: 0.5000, sse=6091755.5, rms=13.448 (11.123%) 032: dt: 0.5000, sse=5066842.0, rms=12.071 (10.241%) 033: dt: 0.5000, sse=4263149.0, rms=10.868 (9.965%) 034: dt: 0.5000, sse=3621523.8, rms=9.798 (9.847%) 035: dt: 0.5000, sse=3115775.5, rms=8.863 (9.534%) 036: dt: 0.5000, sse=2709225.0, rms=8.032 (9.379%) 037: dt: 0.5000, sse=2380262.5, rms=7.293 (9.205%) 038: dt: 0.5000, sse=2126635.8, rms=6.666 (8.599%) 039: dt: 0.5000, sse=1938475.8, rms=6.162 (7.556%) 040: dt: 0.5000, sse=1810340.8, rms=5.792 (6.012%) 041: dt: 0.5000, sse=1722856.1, rms=5.525 (4.598%) 042: dt: 0.5000, sse=1669737.0, rms=5.355 (3.082%) 043: dt: 0.5000, sse=1628962.1, rms=5.223 (2.468%) 044: dt: 0.5000, sse=1602386.1, rms=5.132 (1.734%) 045: dt: 0.5000, sse=1580629.1, rms=5.059 (1.422%) rms = 5.01, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1567357.0, rms=5.012 (0.942%) 047: dt: 0.2500, sse=1480014.8, rms=4.660 (7.017%) 048: dt: 0.2500, sse=1453969.6, rms=4.562 (2.095%) rms = 4.56, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1452807.1, rms=4.555 (0.159%) 050: dt: 0.1250, sse=1436481.2, rms=4.487 (1.491%) rms = 4.48, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1434122.2, rms=4.478 (0.206%) positioning took 3.1 minutes mean border=49.2, 3403 (22) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.6 (%52.2))] %22 local maxima, %30 large gradients and %42 min vals, 319 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=1651825.0, rms=4.466 052: dt: 0.5000, sse=1598728.1, rms=4.264 (4.527%) rms = 4.25, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1588748.8, rms=4.254 (0.227%) 054: dt: 0.2500, sse=1505262.2, rms=3.843 (9.669%) 055: dt: 0.2500, sse=1488773.5, rms=3.770 (1.903%) rms = 3.79, time step reduction 2 of 3 to 0.125... rms = 3.73, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1481424.2, rms=3.732 (0.997%) positioning took 1.0 minutes mean border=48.7, 3758 (15) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))] %31 local maxima, %22 large gradients and %41 min vals, 328 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=1529620.0, rms=3.931 rms = 4.29, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1499080.8, rms=3.787 (3.665%) rms = 3.79, time step reduction 2 of 3 to 0.125... rms = 3.77, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1495744.2, rms=3.770 (0.445%) positioning took 0.6 minutes mean border=48.3, 7191 (14) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.4 (%51.7))] %34 local maxima, %18 large gradients and %40 min vals, 355 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-6.0.0/0051026/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1526884.8, rms=3.915 rms = 3.89, time step reduction 1 of 3 to 0.250... 059: dt: 0.5000, sse=1511662.8, rms=3.889 (0.670%) 060: dt: 0.2500, sse=1442113.8, rms=3.570 (8.208%) 061: dt: 0.2500, sse=1412040.2, rms=3.433 (3.826%) rms = 3.41, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1405689.6, rms=3.407 (0.757%) 063: dt: 0.1250, sse=1376256.1, rms=3.250 (4.625%) rms = 3.22, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1369910.2, rms=3.220 (0.912%) positioning took 1.2 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.area.pial vertex spacing 1.03 +- 0.46 (0.06-->7.88) (max @ vno 69901 --> 69884) face area 0.41 +- 0.33 (0.00-->7.75) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 153799 vertices processed 25000 of 153799 vertices processed 50000 of 153799 vertices processed 75000 of 153799 vertices processed 100000 of 153799 vertices processed 125000 of 153799 vertices processed 150000 of 153799 vertices processed 0 of 153799 vertices processed 25000 of 153799 vertices processed 50000 of 153799 vertices processed 75000 of 153799 vertices processed 100000 of 153799 vertices processed 125000 of 153799 vertices processed 150000 of 153799 vertices processed thickness calculation complete, 392:1318 truncations. 28689 vertices at 0 distance 99785 vertices at 1 distance 97782 vertices at 2 distance 45158 vertices at 3 distance 15448 vertices at 4 distance 4987 vertices at 5 distance 1722 vertices at 6 distance 641 vertices at 7 distance 234 vertices at 8 distance 129 vertices at 9 distance 79 vertices at 10 distance 87 vertices at 11 distance 55 vertices at 12 distance 34 vertices at 13 distance 37 vertices at 14 distance 18 vertices at 15 distance 21 vertices at 16 distance 17 vertices at 17 distance 20 vertices at 18 distance 14 vertices at 19 distance 13 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.thickness positioning took 16.8 minutes PIDs (19040 19043) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 00:38:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label Total face volume 307875 Total vertex volume 304615 (mask=0) #@# 0051026 lh 304615 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 00:38:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label Total face volume 306008 Total vertex volume 302421 (mask=0) #@# 0051026 rh 302421 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 00:38:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 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 = 261 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz mris_volmask took 13.01 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 00:51:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 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 0051026 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 00:51:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 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 0051026 rh pial Waiting for PID 20180 of (20180 20183 20186 20189) to complete... Waiting for PID 20183 of (20180 20183 20186 20189) to complete... Waiting for PID 20186 of (20180 20183 20186 20189) to complete... Waiting for PID 20189 of (20180 20183 20186 20189) 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 0051026 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 307875 Total vertex volume 304615 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1654 1135 3040 2.799 0.525 0.106 0.023 13 1.5 bankssts 743 497 1259 2.609 0.492 0.131 0.018 10 0.5 caudalanteriorcingulate 3714 2485 7194 2.714 0.516 0.109 0.023 33 3.2 caudalmiddlefrontal 2403 1649 3062 1.801 0.410 0.149 0.045 36 4.1 cuneus 695 501 2252 3.503 0.970 0.148 0.035 22 1.2 entorhinal 4906 3375 10733 2.781 0.626 0.134 0.030 67 6.0 fusiform 7404 4933 14612 2.672 0.551 0.128 0.028 93 8.4 inferiorparietal 5854 4031 13796 2.766 0.646 0.119 0.028 84 6.5 inferiortemporal 1747 1137 3261 2.349 0.896 0.127 0.032 25 2.0 isthmuscingulate 9175 6017 16600 2.308 0.615 0.146 0.045 135 17.0 lateraloccipital 4870 3270 11272 3.228 0.639 0.126 0.030 61 5.7 lateralorbitofrontal 3672 2627 6564 2.247 0.639 0.138 0.037 49 5.4 lingual 3130 2194 6482 2.715 0.585 0.115 0.029 46 3.4 medialorbitofrontal 5746 3871 14916 3.049 0.676 0.124 0.028 84 6.5 middletemporal 944 678 2289 2.892 0.659 0.116 0.023 8 0.9 parahippocampal 2339 1481 4354 2.665 0.574 0.100 0.026 16 2.1 paracentral 2384 1672 5592 3.017 0.478 0.111 0.022 23 1.9 parsopercularis 1339 868 3394 3.072 0.558 0.132 0.027 20 1.5 parsorbitalis 2328 1632 5517 2.997 0.633 0.121 0.025 28 2.2 parstriangularis 1880 1372 2235 1.784 0.411 0.131 0.036 21 2.8 pericalcarine 7341 4639 12390 2.314 0.712 0.113 0.029 84 9.0 postcentral 1787 1192 3483 2.662 0.752 0.122 0.019 24 1.3 posteriorcingulate 9624 6143 18603 2.749 0.607 0.109 0.028 95 11.1 precentral 7182 4867 13465 2.541 0.556 0.130 0.029 90 8.2 precuneus 1554 1018 3338 2.875 0.654 0.119 0.026 19 1.8 rostralanteriorcingulate 9010 6214 18914 2.631 0.566 0.138 0.035 132 12.4 rostralmiddlefrontal 13084 8991 33058 3.187 0.600 0.126 0.032 142 16.3 superiorfrontal 11067 7183 18829 2.361 0.563 0.121 0.027 121 11.6 superiorparietal 6725 4484 16554 3.131 0.688 0.111 0.024 73 6.5 superiortemporal 6986 4697 14861 2.795 0.581 0.128 0.029 90 8.0 supramarginal 496 321 1346 3.118 0.610 0.171 0.055 12 1.2 frontalpole 701 514 2361 3.492 0.915 0.140 0.040 13 1.2 temporalpole 700 430 1293 2.671 0.538 0.134 0.041 9 1.1 transversetemporal 3812 2551 7693 3.144 0.701 0.122 0.035 42 5.2 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 0051026 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 307875 Total vertex volume 304615 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1654 1029 3040 2.799 0.525 0.135 0.041 32 2.9 bankssts 743 532 1259 2.609 0.492 0.136 0.029 24 1.0 caudalanteriorcingulate 3714 2783 7194 2.714 0.516 0.127 0.029 47 4.7 caudalmiddlefrontal 2403 1818 3062 1.801 0.410 0.152 0.042 37 4.4 cuneus 695 770 2252 3.503 0.970 0.196 0.048 13 1.6 entorhinal 4906 4362 10733 2.781 0.626 0.167 0.043 92 10.5 fusiform 7404 5943 14612 2.672 0.551 0.150 0.039 110 12.9 inferiorparietal 5854 5696 13796 2.766 0.646 0.169 0.041 82 11.6 inferiortemporal 1747 1530 3261 2.349 0.896 0.165 0.047 25 3.7 isthmuscingulate 9175 7923 16600 2.308 0.615 0.160 0.045 159 18.7 lateraloccipital 4870 3764 11272 3.228 0.639 0.146 0.042 99 9.0 lateralorbitofrontal 3672 3323 6564 2.247 0.639 0.175 0.075 246 16.3 lingual 3130 2767 6482 2.715 0.585 0.168 0.044 65 6.2 medialorbitofrontal 5746 5665 14916 3.049 0.676 0.162 0.035 83 9.6 middletemporal 944 939 2289 2.892 0.659 0.187 0.050 13 2.3 parahippocampal 2339 1806 4354 2.665 0.574 0.134 0.031 31 3.3 paracentral 2384 2055 5592 3.017 0.478 0.159 0.037 38 4.0 parsopercularis 1339 1344 3394 3.072 0.558 0.163 0.034 18 2.2 parsorbitalis 2328 1986 5517 2.997 0.633 0.164 0.037 37 4.1 parstriangularis 1880 1249 2235 1.784 0.411 0.127 0.038 33 2.8 pericalcarine 7341 5986 12390 2.314 0.712 0.136 0.034 96 11.7 postcentral 1787 1425 3483 2.662 0.752 0.160 0.043 49 3.5 posteriorcingulate 9624 7253 18603 2.749 0.607 0.125 0.029 152 12.8 precentral 7182 5646 13465 2.541 0.556 0.150 0.041 117 13.7 precuneus 1554 1377 3338 2.875 0.654 0.170 0.047 30 3.3 rostralanteriorcingulate 9010 7926 18914 2.631 0.566 0.164 0.037 139 16.1 rostralmiddlefrontal 13084 11434 33058 3.187 0.600 0.151 0.038 178 22.1 superiorfrontal 11067 8548 18829 2.361 0.563 0.136 0.031 138 14.8 superiorparietal 6725 6000 16554 3.131 0.688 0.163 0.043 110 13.8 superiortemporal 6986 5898 14861 2.795 0.581 0.163 0.040 113 12.9 supramarginal 496 528 1346 3.118 0.610 0.205 0.042 9 1.0 frontalpole 701 871 2361 3.492 0.915 0.210 0.053 14 1.7 temporalpole 700 608 1293 2.671 0.538 0.176 0.055 9 1.9 transversetemporal 3812 2406 7693 3.144 0.701 0.164 0.052 94 9.4 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 0051026 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 306008 Total vertex volume 302421 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1578 1083 3223 2.747 0.430 0.128 0.035 20 2.5 bankssts 1368 971 2856 2.479 0.831 0.132 0.023 20 1.2 caudalanteriorcingulate 3337 2299 6792 2.661 0.528 0.121 0.025 36 3.5 caudalmiddlefrontal 2622 1690 4290 2.142 0.579 0.137 0.040 37 4.0 cuneus 554 415 1872 3.543 0.734 0.143 0.027 6 0.6 entorhinal 5350 3662 12204 2.888 0.595 0.128 0.029 77 6.3 fusiform 7979 5325 15855 2.647 0.523 0.122 0.028 102 9.0 inferiorparietal 5185 3558 12840 2.945 0.692 0.127 0.032 75 6.7 inferiortemporal 1650 1084 3375 2.594 0.922 0.131 0.033 24 1.7 isthmuscingulate 8874 6119 16211 2.312 0.583 0.142 0.039 124 14.1 lateraloccipital 4438 2991 10075 3.115 0.667 0.130 0.033 67 5.6 lateralorbitofrontal 4507 3196 8575 2.359 0.666 0.151 0.051 71 9.4 lingual 3625 2398 6931 2.618 0.693 0.114 0.028 53 4.0 medialorbitofrontal 5521 3821 14437 3.018 0.665 0.125 0.027 78 5.8 middletemporal 874 624 2023 2.698 0.791 0.103 0.017 6 0.5 parahippocampal 2473 1546 4267 2.597 0.502 0.105 0.026 19 2.4 paracentral 2134 1462 4728 2.916 0.488 0.119 0.026 25 2.2 parsopercularis 1764 1190 4602 3.111 0.690 0.126 0.028 24 1.9 parsorbitalis 3064 2149 7146 2.949 0.536 0.145 0.037 46 4.6 parstriangularis 2092 1414 2676 2.061 0.453 0.126 0.033 18 2.9 pericalcarine 6922 4372 11711 2.367 0.712 0.112 0.025 65 6.8 postcentral 2408 1564 4948 2.771 0.732 0.139 0.032 40 3.0 posteriorcingulate 8858 5548 16837 2.784 0.596 0.107 0.024 94 8.9 precentral 6608 4480 12389 2.584 0.567 0.136 0.034 88 8.8 precuneus 1170 792 2642 2.846 0.743 0.122 0.029 15 1.3 rostralanteriorcingulate 9372 6417 19257 2.600 0.589 0.135 0.032 126 12.5 rostralmiddlefrontal 12498 8513 30062 3.054 0.625 0.124 0.030 131 14.2 superiorfrontal 10676 6898 17908 2.352 0.475 0.124 0.028 124 11.4 superiorparietal 6345 4276 15346 3.133 0.684 0.110 0.026 78 7.3 superiortemporal 6190 4156 13382 2.801 0.563 0.118 0.025 68 6.2 supramarginal 492 342 1556 3.221 0.568 0.161 0.037 9 0.8 frontalpole 720 515 2813 3.702 0.631 0.126 0.029 10 0.9 temporalpole 542 338 1140 2.887 0.545 0.111 0.038 5 0.7 transversetemporal 3926 2629 7420 2.925 0.675 0.120 0.036 55 5.0 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 0051026 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 306008 Total vertex volume 302421 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1578 1222 3223 2.747 0.430 0.149 0.038 23 2.5 bankssts 1368 1234 2856 2.479 0.831 0.171 0.044 31 2.7 caudalanteriorcingulate 3337 2758 6792 2.661 0.528 0.139 0.028 48 4.3 caudalmiddlefrontal 2622 2261 4290 2.142 0.579 0.159 0.039 38 4.9 cuneus 554 621 1872 3.543 0.734 0.198 0.046 11 1.1 entorhinal 5350 4699 12204 2.888 0.595 0.163 0.046 120 10.8 fusiform 7979 6462 15855 2.647 0.523 0.143 0.034 107 12.5 inferiorparietal 5185 5060 12840 2.945 0.692 0.174 0.044 82 10.6 inferiortemporal 1650 1423 3375 2.594 0.922 0.161 0.045 27 3.1 isthmuscingulate 8874 7884 16211 2.312 0.583 0.159 0.040 143 16.8 lateraloccipital 4438 3573 10075 3.115 0.667 0.161 0.044 102 9.3 lateralorbitofrontal 4507 4027 8575 2.359 0.666 0.175 0.049 89 10.9 lingual 3625 3029 6931 2.618 0.693 0.164 0.044 64 7.5 medialorbitofrontal 5521 5498 14437 3.018 0.665 0.162 0.037 76 9.6 middletemporal 874 860 2023 2.698 0.791 0.202 0.055 17 2.4 parahippocampal 2473 1724 4267 2.597 0.502 0.119 0.028 33 3.1 paracentral 2134 1828 4728 2.916 0.488 0.154 0.037 27 3.7 parsopercularis 1764 1707 4602 3.111 0.690 0.158 0.033 26 2.7 parsorbitalis 3064 2696 7146 2.949 0.536 0.164 0.043 45 5.9 parstriangularis 2092 1256 2676 2.061 0.453 0.116 0.030 29 2.7 pericalcarine 6922 5470 11711 2.367 0.712 0.129 0.029 65 8.9 postcentral 2408 2042 4948 2.771 0.732 0.175 0.049 110 4.9 posteriorcingulate 8858 6350 16837 2.784 0.596 0.113 0.029 180 11.9 precentral 6608 5011 12389 2.584 0.567 0.145 0.038 91 11.6 precuneus 1170 1044 2642 2.846 0.743 0.178 0.050 30 2.4 rostralanteriorcingulate 9372 8055 19257 2.600 0.589 0.161 0.039 147 16.9 rostralmiddlefrontal 12498 10832 30062 3.054 0.625 0.155 0.039 185 22.1 superiorfrontal 10676 8193 17908 2.352 0.475 0.131 0.030 133 13.3 superiorparietal 6345 5681 15346 3.133 0.684 0.169 0.044 105 13.6 superiortemporal 6190 5147 13382 2.801 0.563 0.155 0.038 97 11.3 supramarginal 492 615 1556 3.221 0.568 0.216 0.044 7 1.1 frontalpole 720 997 2813 3.702 0.631 0.230 0.054 11 1.8 temporalpole 542 447 1140 2.887 0.545 0.155 0.044 7 1.1 transversetemporal 3926 2576 7420 2.925 0.675 0.167 0.056 101 9.7 insula PIDs (20180 20183 20186 20189) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 00:53:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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 00:53:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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 20292 of (20292 20295) to complete... Waiting for PID 20295 of (20292 20295) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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... 133 labels changed using aseg relabeling using gibbs priors... 000: 10185 changed, 155300 examined... 001: 2465 changed, 39863 examined... 002: 717 changed, 12853 examined... 003: 303 changed, 4019 examined... 004: 142 changed, 1713 examined... 005: 81 changed, 796 examined... 006: 30 changed, 432 examined... 007: 22 changed, 184 examined... 008: 8 changed, 120 examined... 009: 1 changed, 47 examined... 010: 0 changed, 6 examined... 22 labels changed using aseg 000: 302 total segments, 217 labels (2779 vertices) changed 001: 96 total segments, 12 labels (35 vertices) changed 002: 85 total segments, 1 labels (2 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1170 vertices marked for relabeling... 1170 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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... 16 labels changed using aseg relabeling using gibbs priors... 000: 9951 changed, 153799 examined... 001: 2349 changed, 38804 examined... 002: 672 changed, 12208 examined... 003: 285 changed, 3781 examined... 004: 119 changed, 1559 examined... 005: 72 changed, 671 examined... 006: 48 changed, 412 examined... 007: 21 changed, 254 examined... 008: 7 changed, 141 examined... 009: 1 changed, 35 examined... 010: 1 changed, 7 examined... 011: 0 changed, 7 examined... 1 labels changed using aseg 000: 290 total segments, 206 labels (3279 vertices) changed 001: 96 total segments, 13 labels (92 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1284 vertices marked for relabeling... 1284 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. PIDs (20292 20295) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 00:53:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 00:53:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 rh white Waiting for PID 20339 of (20339 20342) to complete... Waiting for PID 20342 of (20339 20342) 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 0051026 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 307875 Total vertex volume 304615 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1450 976 2923 2.719 0.565 0.137 0.033 20 2.0 G&S_frontomargin 1856 1243 4146 2.493 0.793 0.141 0.048 26 3.5 G&S_occipital_inf 2028 1152 3539 2.598 0.620 0.109 0.034 19 2.4 G&S_paracentral 1851 1236 4261 2.909 0.529 0.122 0.025 20 1.9 G&S_subcentral 999 661 2530 2.931 0.626 0.147 0.040 20 1.4 G&S_transv_frontopol 2692 1802 5907 3.018 0.518 0.114 0.023 27 2.6 G&S_cingul-Ant 1367 953 2556 2.775 0.484 0.110 0.019 9 1.0 G&S_cingul-Mid-Ant 1181 849 2344 2.733 0.427 0.097 0.016 8 0.7 G&S_cingul-Mid-Post 725 477 2201 3.341 0.661 0.145 0.029 13 0.8 G_cingul-Post-dorsal 330 212 804 2.772 0.957 0.155 0.049 8 0.5 G_cingul-Post-ventral 2223 1559 3239 1.820 0.510 0.153 0.048 37 4.0 G_cuneus 1323 892 3642 3.026 0.506 0.117 0.027 18 1.3 G_front_inf-Opercular 548 346 1693 3.232 0.596 0.153 0.033 11 0.7 G_front_inf-Orbital 1368 946 3949 3.239 0.645 0.142 0.035 25 1.7 G_front_inf-Triangul 5074 3474 12578 2.788 0.577 0.140 0.037 83 7.3 G_front_middle 9066 6092 25282 3.301 0.619 0.138 0.039 135 14.6 G_front_sup 900 587 1831 3.140 0.693 0.137 0.048 14 1.6 G_Ins_lg&S_cent_ins 783 506 2360 3.576 0.742 0.133 0.040 12 1.1 G_insular_short 2864 1834 5969 2.549 0.618 0.141 0.040 44 4.4 G_occipital_middle 2313 1431 3836 2.213 0.588 0.132 0.042 29 3.4 G_occipital_sup 1959 1297 4956 2.852 0.612 0.144 0.036 33 2.8 G_oc-temp_lat-fusifor 2465 1733 4721 2.245 0.675 0.152 0.044 40 4.4 G_oc-temp_med-Lingual 1388 983 4275 3.278 0.885 0.139 0.032 30 2.0 G_oc-temp_med-Parahip 3155 2020 8523 3.134 0.650 0.133 0.036 53 4.5 G_orbital 3056 1995 7144 2.722 0.551 0.146 0.037 57 4.3 G_pariet_inf-Angular 3736 2455 9130 2.949 0.622 0.135 0.032 58 4.7 G_pariet_inf-Supramar 4464 2796 8998 2.509 0.629 0.124 0.029 58 5.0 G_parietal_sup 2754 1593 5172 2.447 0.704 0.119 0.041 46 4.7 G_postcentral 3740 2297 8584 2.936 0.663 0.116 0.033 39 4.7 G_precentral 3270 2215 7686 2.685 0.535 0.140 0.032 54 4.1 G_precuneus 1195 898 3244 2.655 0.608 0.149 0.038 27 2.0 G_rectus 713 457 1289 2.663 0.913 0.110 0.056 15 1.4 G_subcallosal 566 347 1131 2.647 0.548 0.127 0.040 7 1.0 G_temp_sup-G_T_transv 2516 1645 8023 3.310 0.757 0.139 0.035 49 3.3 G_temp_sup-Lateral 920 625 2683 3.681 0.795 0.085 0.026 6 1.0 G_temp_sup-Plan_polar 1060 709 2323 2.809 0.501 0.100 0.018 9 0.9 G_temp_sup-Plan_tempo 3317 2268 8962 2.801 0.718 0.136 0.037 68 5.0 G_temporal_inf 3141 2098 10268 3.286 0.659 0.134 0.034 60 4.2 G_temporal_middle 411 286 667 2.834 0.424 0.089 0.013 2 0.2 Lat_Fis-ant-Horizont 390 302 687 2.918 0.534 0.101 0.010 2 0.2 Lat_Fis-ant-Vertical 1137 770 1713 2.781 0.408 0.112 0.026 8 1.2 Lat_Fis-post 2526 1723 4972 2.247 0.654 0.169 0.058 51 6.3 Pole_occipital 1700 1180 5321 3.091 0.735 0.153 0.045 38 3.1 Pole_temporal 2241 1665 3045 2.031 0.557 0.139 0.036 27 3.3 S_calcarine 3643 2459 4340 1.974 0.523 0.108 0.021 23 3.2 S_central 1438 1007 2210 2.370 0.464 0.104 0.018 9 1.1 S_cingul-Marginalis 678 455 1242 3.436 0.362 0.102 0.018 3 0.5 S_circular_insula_ant 1649 1108 3024 3.287 0.626 0.090 0.017 7 1.1 S_circular_insula_inf 1820 1278 2902 2.877 0.433 0.106 0.019 9 1.5 S_circular_insula_sup 1080 764 1882 2.725 0.601 0.108 0.016 8 0.8 S_collat_transv_ant 724 459 867 2.251 0.373 0.127 0.033 6 1.0 S_collat_transv_post 2081 1463 3663 2.466 0.478 0.117 0.026 18 2.1 S_front_inf 1503 1071 2644 2.408 0.492 0.125 0.029 17 1.7 S_front_middle 3482 2439 6230 2.739 0.428 0.100 0.019 20 2.7 S_front_sup 397 292 648 2.425 0.425 0.123 0.019 3 0.4 S_interm_prim-Jensen 3386 2350 4599 2.216 0.419 0.108 0.018 24 2.6 S_intrapariet&P_trans 1105 746 1376 2.135 0.402 0.114 0.024 7 1.1 S_oc_middle&Lunatus 1715 1128 2410 2.188 0.452 0.121 0.026 17 1.8 S_oc_sup&transversal 546 365 730 2.581 0.384 0.151 0.037 6 0.9 S_occipital_ant 1055 753 1876 2.670 0.418 0.101 0.017 6 0.6 S_oc-temp_lat 2091 1497 3517 2.507 0.678 0.115 0.022 17 1.9 S_oc-temp_med&Lingual 442 293 618 2.533 0.494 0.121 0.020 3 0.4 S_orbital_lateral 745 546 1216 2.721 0.593 0.113 0.016 5 0.4 S_orbital_med-olfact 1810 1235 3855 3.373 0.571 0.121 0.028 18 2.0 S_orbital-H_Shaped 2955 1931 4209 2.354 0.568 0.121 0.027 28 3.2 S_parieto_occipital 1363 805 1237 1.920 0.751 0.117 0.018 21 0.8 S_pericallosal 3353 2262 4924 2.390 0.461 0.111 0.022 25 2.7 S_postcentral 1837 1257 3188 2.784 0.374 0.094 0.015 11 1.1 S_precentral-inf-part 2055 1405 3245 2.655 0.398 0.105 0.021 14 1.6 S_precentral-sup-part 727 496 1174 2.867 0.405 0.095 0.013 3 0.4 S_suborbital 1351 940 2126 2.430 0.492 0.111 0.020 8 1.2 S_subparietal 2078 1397 3168 2.638 0.416 0.104 0.018 14 1.4 S_temporal_inf 6751 4626 11820 2.770 0.501 0.109 0.020 50 5.7 S_temporal_sup 374 258 569 2.425 0.408 0.133 0.026 4 0.4 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 0051026 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 306008 Total vertex volume 302421 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1060 748 2247 2.638 0.613 0.144 0.039 20 1.6 G&S_frontomargin 1514 1125 3172 2.344 0.696 0.157 0.045 27 2.7 G&S_occipital_inf 1669 943 2701 2.468 0.556 0.108 0.032 17 2.2 G&S_paracentral 1503 1012 3420 2.997 0.546 0.136 0.031 19 1.8 G&S_subcentral 1179 821 3044 2.751 0.618 0.170 0.048 25 2.6 G&S_transv_frontopol 3582 2438 7435 2.888 0.609 0.111 0.023 33 3.3 G&S_cingul-Ant 1794 1249 3759 2.863 0.558 0.121 0.023 21 1.6 G&S_cingul-Mid-Ant 2000 1347 4031 2.910 0.551 0.123 0.029 21 2.3 G&S_cingul-Mid-Post 682 454 2022 3.318 0.546 0.153 0.040 13 1.0 G_cingul-Post-dorsal 317 208 914 3.183 0.594 0.148 0.049 8 0.4 G_cingul-Post-ventral 2453 1569 4222 2.146 0.582 0.143 0.041 38 4.0 G_cuneus 1516 1027 4137 3.002 0.539 0.135 0.034 26 1.9 G_front_inf-Opercular 542 357 1760 3.188 0.527 0.154 0.040 11 0.9 G_front_inf-Orbital 1277 922 3718 3.088 0.558 0.173 0.053 29 2.5 G_front_inf-Triangul 4221 2889 11375 2.837 0.611 0.146 0.037 70 6.5 G_front_middle 8158 5430 22509 3.212 0.602 0.134 0.035 108 10.8 G_front_sup 742 500 1534 2.852 0.696 0.126 0.038 12 1.1 G_Ins_lg&S_cent_ins 1170 752 2456 2.909 0.823 0.145 0.056 30 2.1 G_insular_short 2230 1426 5378 2.794 0.535 0.139 0.037 41 3.0 G_occipital_middle 2395 1443 3983 2.346 0.462 0.130 0.038 30 3.3 G_occipital_sup 2482 1646 6003 2.944 0.564 0.134 0.036 46 3.5 G_oc-temp_lat-fusifor 2770 1928 5731 2.307 0.718 0.163 0.061 53 6.9 G_oc-temp_med-Lingual 1275 898 4237 3.333 0.781 0.145 0.032 19 1.7 G_oc-temp_med-Parahip 3518 2361 10028 3.154 0.680 0.142 0.043 78 5.9 G_orbital 3342 2173 8620 2.839 0.603 0.141 0.038 64 5.1 G_pariet_inf-Angular 2985 2001 7342 2.892 0.554 0.126 0.027 39 3.4 G_pariet_inf-Supramar 3921 2493 7494 2.444 0.520 0.124 0.026 50 3.8 G_parietal_sup 2755 1626 5314 2.511 0.691 0.110 0.026 28 2.9 G_postcentral 3308 1966 7900 3.008 0.549 0.110 0.029 56 3.7 G_precentral 2974 1943 6962 2.749 0.530 0.150 0.041 55 4.8 G_precuneus 868 595 2297 2.651 0.696 0.135 0.039 18 1.3 G_rectus 484 310 853 2.491 0.965 0.122 0.056 13 0.9 G_subcallosal 405 247 987 2.908 0.621 0.101 0.039 4 0.6 G_temp_sup-G_T_transv 2434 1609 7226 3.257 0.654 0.145 0.040 44 4.3 G_temp_sup-Lateral 804 571 2489 3.765 0.623 0.101 0.018 6 0.7 G_temp_sup-Plan_polar 871 572 1927 2.809 0.616 0.099 0.051 23 2.5 G_temp_sup-Plan_tempo 2797 1910 8161 3.094 0.670 0.142 0.040 55 4.1 G_temporal_inf 3229 2222 10217 3.146 0.701 0.135 0.035 57 4.4 G_temporal_middle 582 388 936 2.872 0.423 0.102 0.015 3 0.4 Lat_Fis-ant-Horizont 328 226 564 2.837 0.423 0.105 0.016 2 0.3 Lat_Fis-ant-Vertical 1380 961 2223 2.825 0.438 0.091 0.016 5 0.8 Lat_Fis-post 3975 2835 7176 2.090 0.546 0.163 0.052 67 8.6 Pole_occipital 1835 1285 6218 3.254 0.851 0.144 0.030 33 2.4 Pole_temporal 2359 1656 3531 2.484 0.622 0.131 0.034 23 3.4 S_calcarine 3648 2371 4208 2.070 0.587 0.104 0.022 22 3.5 S_central 1280 894 2058 2.453 0.444 0.093 0.017 8 0.8 S_cingul-Marginalis 841 566 1342 2.970 0.869 0.097 0.017 3 0.6 S_circular_insula_ant 1436 957 2366 2.971 0.691 0.088 0.016 6 1.0 S_circular_insula_inf 1491 1024 2621 3.092 0.428 0.108 0.019 7 1.2 S_circular_insula_sup 1292 904 2538 3.020 0.598 0.090 0.012 5 0.7 S_collat_transv_ant 365 250 394 1.962 0.363 0.131 0.022 3 0.4 S_collat_transv_post 2332 1630 3684 2.407 0.400 0.106 0.019 16 2.0 S_front_inf 2486 1677 4265 2.466 0.557 0.126 0.027 25 2.6 S_front_middle 2979 2064 5016 2.574 0.498 0.104 0.020 18 2.3 S_front_sup 601 413 885 2.390 0.388 0.100 0.013 3 0.4 S_interm_prim-Jensen 4041 2735 5659 2.265 0.393 0.110 0.021 30 3.2 S_intrapariet&P_trans 913 632 1301 2.300 0.479 0.094 0.015 5 0.6 S_oc_middle&Lunatus 1606 1072 2315 2.381 0.400 0.121 0.027 15 1.9 S_oc_sup&transversal 835 574 1215 2.466 0.343 0.117 0.024 7 0.8 S_occipital_ant 1129 795 1945 2.691 0.464 0.113 0.026 8 1.2 S_oc-temp_lat 2247 1608 3784 2.447 0.508 0.099 0.017 14 1.6 S_oc-temp_med&Lingual 704 486 1037 2.536 0.420 0.130 0.026 6 0.9 S_orbital_lateral 764 533 1250 2.837 0.832 0.105 0.014 5 0.4 S_orbital_med-olfact 1655 1133 3185 3.042 0.588 0.119 0.021 14 1.3 S_orbital-H_Shaped 2698 1832 3798 2.271 0.562 0.132 0.035 29 3.5 S_parieto_occipital 1829 1135 1707 1.868 0.677 0.119 0.020 26 1.1 S_pericallosal 2680 1776 3866 2.402 0.436 0.111 0.020 22 2.1 S_postcentral 1901 1274 2976 2.752 0.444 0.104 0.018 12 1.5 S_precentral-inf-part 1862 1250 2948 2.578 0.570 0.103 0.018 11 1.4 S_precentral-sup-part 569 389 807 2.500 0.454 0.113 0.015 4 0.3 S_suborbital 1601 1110 2724 2.597 0.461 0.118 0.024 12 1.7 S_subparietal 1459 1004 2258 2.578 0.522 0.114 0.019 12 1.3 S_temporal_inf 6496 4470 11427 2.765 0.482 0.105 0.019 45 5.0 S_temporal_sup 305 213 586 3.037 0.459 0.116 0.020 2 0.2 S_temporal_transverse PIDs (20339 20342) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 00:54:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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 00:54:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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 20412 of (20412 20415) to complete... Waiting for PID 20415 of (20412 20415) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 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... 1479 labels changed using aseg relabeling using gibbs priors... 000: 2147 changed, 155300 examined... 001: 472 changed, 9831 examined... 002: 132 changed, 2765 examined... 003: 55 changed, 802 examined... 004: 25 changed, 336 examined... 005: 21 changed, 134 examined... 006: 13 changed, 117 examined... 007: 7 changed, 61 examined... 008: 7 changed, 44 examined... 009: 8 changed, 37 examined... 010: 5 changed, 45 examined... 011: 2 changed, 27 examined... 012: 2 changed, 14 examined... 013: 1 changed, 11 examined... 014: 0 changed, 7 examined... 248 labels changed using aseg 000: 78 total segments, 45 labels (349 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 871 vertices marked for relabeling... 871 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 0051026 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... 1237 labels changed using aseg relabeling using gibbs priors... 000: 2183 changed, 153799 examined... 001: 507 changed, 10042 examined... 002: 125 changed, 2811 examined... 003: 48 changed, 803 examined... 004: 18 changed, 287 examined... 005: 8 changed, 115 examined... 006: 4 changed, 45 examined... 007: 2 changed, 22 examined... 008: 1 changed, 15 examined... 009: 1 changed, 7 examined... 010: 0 changed, 8 examined... 111 labels changed using aseg 000: 59 total segments, 26 labels (292 vertices) changed 001: 35 total segments, 2 labels (4 vertices) changed 002: 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... 1072 vertices marked for relabeling... 1072 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. PIDs (20412 20415) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 00:54:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 00:54:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 rh white Waiting for PID 20464 of (20464 20467) to complete... Waiting for PID 20467 of (20464 20467) 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 0051026 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 307875 Total vertex volume 304615 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1656 1124 3500 2.871 0.624 0.122 0.022 20 1.3 caudalanteriorcingulate 3982 2674 7755 2.713 0.506 0.111 0.023 36 3.5 caudalmiddlefrontal 3505 2364 4916 1.935 0.526 0.138 0.041 46 5.4 cuneus 613 447 2126 3.663 0.924 0.145 0.035 20 1.0 entorhinal 4672 3200 9880 2.760 0.625 0.131 0.028 57 5.5 fusiform 7252 4853 14346 2.662 0.554 0.130 0.029 93 8.5 inferiorparietal 5940 4093 14290 2.758 0.657 0.125 0.032 96 7.7 inferiortemporal 1710 1119 3218 2.373 0.884 0.128 0.032 25 2.0 isthmuscingulate 9164 6001 16666 2.306 0.622 0.146 0.045 135 16.6 lateraloccipital 5329 3538 12487 3.188 0.665 0.127 0.034 71 6.7 lateralorbitofrontal 3842 2726 6859 2.257 0.632 0.139 0.038 54 5.9 lingual 2595 1839 5728 2.731 0.608 0.119 0.032 43 3.5 medialorbitofrontal 7459 5049 17983 2.977 0.647 0.121 0.027 99 8.0 middletemporal 969 691 2342 2.881 0.680 0.116 0.022 8 0.9 parahippocampal 2840 1806 5254 2.657 0.582 0.105 0.033 34 3.8 paracentral 2153 1513 4918 3.004 0.470 0.110 0.021 20 1.6 parsopercularis 1312 877 3290 3.199 0.543 0.124 0.023 15 1.2 parsorbitalis 2734 1927 6447 2.950 0.653 0.126 0.028 36 2.8 parstriangularis 1819 1327 2151 1.795 0.409 0.131 0.035 20 2.7 pericalcarine 8287 5277 13881 2.330 0.696 0.114 0.029 91 10.1 postcentral 1981 1318 3753 2.635 0.751 0.121 0.019 26 1.5 posteriorcingulate 9369 6006 18283 2.763 0.603 0.108 0.026 80 9.5 precentral 7097 4812 13442 2.548 0.551 0.133 0.029 92 8.2 precuneus 2218 1464 4676 2.893 0.658 0.124 0.030 28 2.9 rostralanteriorcingulate 6726 4600 14260 2.631 0.552 0.138 0.034 101 9.3 rostralmiddlefrontal 13777 9450 34038 3.120 0.620 0.129 0.033 159 17.5 superiorfrontal 8878 5780 15109 2.363 0.556 0.118 0.026 93 8.7 superiorparietal 8625 5814 21241 3.141 0.718 0.113 0.026 96 9.2 superiortemporal 6613 4431 13953 2.802 0.583 0.128 0.029 84 7.4 supramarginal 682 417 1254 2.673 0.535 0.136 0.041 9 1.1 transversetemporal 3196 2135 6570 3.162 0.675 0.116 0.029 31 3.7 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 0051026 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 306008 Total vertex volume 302421 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1523 1072 3126 2.461 0.848 0.132 0.023 22 1.3 caudalanteriorcingulate 3415 2360 6905 2.669 0.521 0.120 0.025 36 3.4 caudalmiddlefrontal 3164 2055 5115 2.125 0.554 0.136 0.039 44 4.8 cuneus 483 367 1679 3.516 0.663 0.140 0.025 5 0.5 entorhinal 5072 3464 11268 2.870 0.569 0.127 0.030 72 6.4 fusiform 8090 5402 16249 2.665 0.533 0.124 0.028 105 9.3 inferiorparietal 5527 3803 13835 2.965 0.705 0.128 0.031 79 6.8 inferiortemporal 1635 1078 3319 2.592 0.893 0.130 0.032 23 1.7 isthmuscingulate 8873 6113 16157 2.305 0.570 0.142 0.039 124 13.9 lateraloccipital 5112 3485 12038 3.134 0.667 0.139 0.039 100 7.5 lateralorbitofrontal 4410 3130 8358 2.340 0.653 0.152 0.051 70 9.4 lingual 2321 1563 4837 2.584 0.722 0.122 0.036 40 3.0 medialorbitofrontal 6571 4536 16443 2.968 0.645 0.123 0.027 88 6.7 middletemporal 1000 704 2328 2.754 0.829 0.108 0.020 8 0.7 parahippocampal 2611 1639 4585 2.611 0.503 0.105 0.026 20 2.5 paracentral 2573 1768 5662 2.902 0.494 0.123 0.027 31 2.8 parsopercularis 1513 1019 3863 3.059 0.674 0.117 0.027 18 1.5 parsorbitalis 2946 2049 6615 2.932 0.538 0.145 0.037 44 4.5 parstriangularis 2109 1426 2722 2.062 0.453 0.126 0.033 19 2.9 pericalcarine 7733 4906 12842 2.351 0.696 0.112 0.025 73 7.7 postcentral 2467 1611 5127 2.805 0.716 0.137 0.031 39 3.1 posteriorcingulate 8397 5253 16150 2.795 0.588 0.108 0.025 92 8.5 precentral 6814 4608 12949 2.592 0.559 0.135 0.034 91 9.0 precuneus 1696 1119 3304 2.782 0.748 0.116 0.026 20 1.8 rostralanteriorcingulate 6963 4745 14294 2.605 0.586 0.128 0.030 82 8.4 rostralmiddlefrontal 15917 10791 37083 2.967 0.649 0.126 0.029 177 18.7 superiorfrontal 8989 5790 15183 2.368 0.478 0.124 0.028 104 9.3 superiorparietal 8326 5633 20727 3.129 0.701 0.115 0.029 107 10.8 superiortemporal 5590 3767 12081 2.794 0.569 0.115 0.024 59 5.5 supramarginal 559 346 1172 2.928 0.569 0.114 0.037 5 0.8 transversetemporal 3331 2250 6406 2.911 0.653 0.117 0.031 37 3.8 insula PIDs (20464 20467) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 00:55:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts pctsurfcon --s 0051026 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 00:55:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts pctsurfcon --s 0051026 --rh-only Waiting for PID 20539 of (20539 20551) to complete... Waiting for PID 20551 of (20539 20551) to complete... pctsurfcon --s 0051026 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts/pctsurfcon.log Sun Oct 8 00:55:07 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-6.0.0/0051026/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-609 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-6.0.0/0051026/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.wm.mgh --regheader 0051026 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 75940 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.wm.mgh Dim: 155300 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.gm.mgh --projfrac 0.3 --regheader 0051026 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 91157 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.gm.mgh Dim: 155300 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.w-g.pct.mgh --annot 0051026 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/lh.w-g.pct.mgh --annot 0051026 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-609 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/lh.w-g.pct.mgh Vertex Area is 0.669866 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 0051026 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts/pctsurfcon.log Sun Oct 8 00:55:07 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-6.0.0/0051026/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-609 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-6.0.0/0051026/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.wm.mgh --regheader 0051026 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 75225 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.wm.mgh Dim: 153799 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.gm.mgh --projfrac 0.3 --regheader 0051026 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 90234 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.gm.mgh Dim: 153799 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.w-g.pct.mgh --annot 0051026 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.w-g.pct.mgh --annot 0051026 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-609 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.w-g.pct.mgh Vertex Area is 0.670808 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 (20539 20551) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 00:55:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1172 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1668 voxels changed to hypointensity... 2855 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 00:55:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 mri_aparc2aseg --s 0051026 --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 00:55:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 mri_aparc2aseg --s 0051026 --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 00:55:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 mri_aparc2aseg --s 0051026 --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 20719 of (20719 20722 20725) to complete... Waiting for PID 20722 of (20719 20722 20725) to complete... Waiting for PID 20725 of (20719 20722 20725) to complete... mri_aparc2aseg --s 0051026 --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 0051026 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/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-6.0.0/0051026/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 7.38 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 48 rescaling Left_Thalamus from 94 --> 93 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 64 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 89 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 9 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 57 rescaling Left_Amygdala from 56 --> 59 rescaling CSF from 32 --> 20 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 87 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 55 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 49 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 88 rescaling Right_Hippocampus from 53 --> 54 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 91 rescaling Fifth_Ventricle from 40 --> 18 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 601104 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 419 changed. pass 2: 70 changed. pass 3: 8 changed. pass 4: 4 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc+aseg.mgz mri_aparc2aseg --s 0051026 --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 0051026 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/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-6.0.0/0051026/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 7.38 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 48 rescaling Left_Thalamus from 94 --> 93 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 64 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 89 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 9 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 57 rescaling Left_Amygdala from 56 --> 59 rescaling CSF from 32 --> 20 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 87 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 55 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 49 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 88 rescaling Right_Hippocampus from 53 --> 54 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 91 rescaling Fifth_Ventricle from 40 --> 18 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 601124 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 419 changed. pass 2: 70 changed. pass 3: 8 changed. pass 4: 4 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0051026 --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 0051026 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/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-6.0.0/0051026/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 7.38 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 48 rescaling Left_Thalamus from 94 --> 93 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 64 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 89 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 9 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 57 rescaling Left_Amygdala from 56 --> 59 rescaling CSF from 32 --> 20 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 87 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 55 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 49 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 88 rescaling Right_Hippocampus from 53 --> 54 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 91 rescaling Fifth_Ventricle from 40 --> 18 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 601124 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 419 changed. pass 2: 70 changed. pass 3: 8 changed. pass 4: 4 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (20719 20722 20725) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 01:03:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 01:03:46 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-6.0.0/0051026/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-609 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-6.0.0/0051026/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-609 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 01:03:46 CEST 2017 Ended at Sun Oct 8 01:03:52 CEST 2017 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 01:03:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 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 0051026 $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 0051026 sysname Linux hostname tars-609 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1690943 mm^3 (det: 1.152082 ) Computing euler number orig.nofix lheno = -92, rheno = -72 orig.nofix lhholes = 47, rhholes = 37 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 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 01:05:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026 mri_aparc2aseg --s 0051026 --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 0051026 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-6.0.0/0051026/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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-6.0.0/0051026/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8304 vertices from left hemi Ripped 8083 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-6.0.0/0051026/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 = 1130085 Used brute-force search on 60 voxels Fixing Parahip LH WM Found 9 clusters 0 k 2.000000 1 k 1.000000 2 k 40.000000 3 k 1.000000 4 k 1410.000000 5 k 3.000000 6 k 23.000000 7 k 1.000000 8 k 1.000000 Fixing Parahip RH WM Found 11 clusters 0 k 3.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 2.000000 5 k 1443.000000 6 k 4.000000 7 k 5.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 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 0051026 --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 0051026 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-609 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1690943 mm^3 (det: 1.152082 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 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-6.0.0/0051026/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 01:14:25 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 22405 of (22405 22411 22417 22423 22429) to complete... Waiting for PID 22411 of (22405 22411 22417 22423 22429) to complete... Waiting for PID 22417 of (22405 22411 22417 22423 22429) to complete... Waiting for PID 22423 of (22405 22411 22417 22423 22429) to complete... Waiting for PID 22429 of (22405 22411 22417 22423 22429) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 526 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4655 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 840 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8749 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4230 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 510 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6493 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 995 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6779 mri_label2label: Done PIDs (22405 22411 22417 22423 22429) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 22505 of (22505 22511 22517 22521) to complete... Waiting for PID 22511 of (22505 22511 22517 22521) to complete... Waiting for PID 22517 of (22505 22511 22517 22521) to complete... Waiting for PID 22521 of (22505 22511 22517 22521) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 475 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4545 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 2712 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 16301 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 334 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4515 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 877 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4299 mri_label2label: Done PIDs (22505 22511 22517 22521) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 22627 of (22627 22633 22639 22645 22651) to complete... Waiting for PID 22633 of (22627 22633 22639 22645 22651) to complete... Waiting for PID 22639 of (22627 22633 22639 22645 22651) to complete... Waiting for PID 22645 of (22627 22633 22639 22645 22651) to complete... Waiting for PID 22651 of (22627 22633 22639 22645 22651) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 1351 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5992 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 3486 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11600 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 459 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2477 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1396 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 147 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1346 mri_label2label: Done PIDs (22627 22633 22639 22645 22651) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 23163 of (23163 23169 23175 23182 23188) to complete... Waiting for PID 23169 of (23163 23169 23175 23182 23188) to complete... Waiting for PID 23175 of (23163 23169 23175 23182 23188) to complete... Waiting for PID 23182 of (23163 23169 23175 23182 23188) to complete... Waiting for PID 23188 of (23163 23169 23175 23182 23188) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 171 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1185 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2312 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2186 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 405 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2724 mri_label2label: Done PIDs (23163 23169 23175 23182 23188) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 23350 of (23350 23356 23362 23367) to complete... Waiting for PID 23356 of (23350 23356 23362 23367) to complete... Waiting for PID 23362 of (23350 23356 23362 23367) to complete... Waiting for PID 23367 of (23350 23356 23362 23367) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1677 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 1275 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8310 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2020 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 346 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1497 mri_label2label: Done PIDs (23350 23356 23362 23367) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 23636 of (23636 23642 23648 23654 23659) to complete... Waiting for PID 23642 of (23636 23642 23648 23654 23659) to complete... Waiting for PID 23648 of (23636 23642 23648 23654 23659) to complete... Waiting for PID 23654 of (23636 23642 23648 23654 23659) to complete... Waiting for PID 23659 of (23636 23642 23648 23654 23659) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 850 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4255 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 1600 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4934 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 627 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 507 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 155300 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 520 mri_label2label: Done PIDs (23636 23642 23648 23654 23659) completed and logs appended. mris_label2annot --s 0051026 --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-6.0.0/0051026/label cmdline mris_label2annot --s 0051026 --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-609 machine x86_64 user ntraut subject 0051026 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-6.0.0/0051026/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 108317 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.BA_exvivo.annot mris_label2annot --s 0051026 --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-6.0.0/0051026/label cmdline mris_label2annot --s 0051026 --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-609 machine x86_64 user ntraut subject 0051026 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-6.0.0/0051026/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 127772 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 307875 Total vertex volume 304615 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1334 762 2514 2.510 0.673 0.126 0.038 17 1.8 BA1_exvivo 4498 2921 7837 2.504 0.541 0.111 0.025 41 4.1 BA2_exvivo 1091 743 1065 1.835 0.370 0.136 0.030 10 1.1 BA3a_exvivo 2675 1726 4031 2.029 0.744 0.111 0.032 38 3.9 BA3b_exvivo 2207 1213 4026 2.849 0.557 0.098 0.028 17 2.6 BA4a_exvivo 1496 1029 2188 2.272 0.485 0.113 0.024 9 1.7 BA4p_exvivo 12251 8101 28854 3.039 0.603 0.115 0.029 127 13.6 BA6_exvivo 2263 1560 5085 2.944 0.460 0.102 0.020 21 1.7 BA44_exvivo 3439 2424 8353 2.921 0.664 0.134 0.031 48 4.1 BA45_exvivo 3323 2460 5236 1.961 0.577 0.151 0.047 55 6.3 V1_exvivo 9003 6005 14076 2.093 0.579 0.147 0.045 130 15.9 V2_exvivo 2139 1415 4507 2.662 0.585 0.141 0.033 27 2.8 MT_exvivo 516 366 1884 3.602 0.880 0.125 0.025 5 0.4 perirhinal_exvivo 748 563 1761 3.011 0.744 0.150 0.030 11 0.8 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051026 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 307875 Total vertex volume 304615 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 884 463 1697 2.566 0.645 0.130 0.064 24 2.6 BA1_exvivo 1767 1127 3150 2.496 0.589 0.104 0.024 15 1.6 BA2_exvivo 931 629 860 1.794 0.322 0.139 0.032 9 1.0 BA3a_exvivo 1684 1109 1893 1.657 0.415 0.104 0.022 13 1.6 BA3b_exvivo 2157 1236 3918 2.781 0.573 0.100 0.028 15 2.5 BA4a_exvivo 1234 853 1770 2.229 0.461 0.110 0.023 8 1.3 BA4p_exvivo 6818 4416 15548 3.014 0.597 0.115 0.031 78 8.2 BA6_exvivo 1416 986 3318 3.011 0.419 0.108 0.021 15 1.1 BA44_exvivo 1366 974 3877 3.153 0.698 0.138 0.033 23 1.6 BA45_exvivo 3503 2605 5583 1.965 0.565 0.151 0.046 56 6.5 V1_exvivo 4521 3052 7026 1.999 0.549 0.158 0.051 76 9.4 V2_exvivo 569 389 1156 2.614 0.448 0.161 0.036 9 0.9 MT_exvivo 260 182 939 3.680 0.688 0.135 0.024 3 0.3 perirhinal_exvivo 418 298 949 3.010 0.607 0.137 0.024 6 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 01:17:46 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 23938 of (23938 23944 23950 23956 23962) to complete... Waiting for PID 23944 of (23938 23944 23950 23956 23962) to complete... Waiting for PID 23950 of (23938 23944 23950 23956 23962) to complete... Waiting for PID 23956 of (23938 23944 23950 23956 23962) to complete... Waiting for PID 23962 of (23938 23944 23950 23956 23962) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 520 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4482 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 591 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7278 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 301 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4281 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 478 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5000 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 896 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6643 mri_label2label: Done PIDs (23938 23944 23950 23956 23962) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 24008 of (24008 24014 24020 24026) to complete... Waiting for PID 24014 of (24008 24014 24020 24026) to complete... Waiting for PID 24020 of (24008 24014 24020 24026) to complete... Waiting for PID 24026 of (24008 24014 24020 24026) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 512 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4985 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 1807 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14063 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 1016 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7928 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 1811 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7166 mri_label2label: Done PIDs (24008 24014 24020 24026) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 24085 of (24085 24091 24097 24103 24109) to complete... Waiting for PID 24091 of (24085 24091 24097 24103 24109) to complete... Waiting for PID 24097 of (24085 24091 24097 24103 24109) to complete... Waiting for PID 24103 of (24085 24091 24097 24103 24109) to complete... Waiting for PID 24109 of (24085 24091 24097 24103 24109) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 1616 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6343 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 3524 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11540 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2361 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1182 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 886 mri_label2label: Done PIDs (24085 24091 24097 24103 24109) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 24158 of (24158 24164 24170 24175 24182) to complete... Waiting for PID 24164 of (24158 24164 24170 24175 24182) to complete... Waiting for PID 24170 of (24158 24164 24170 24175 24182) to complete... Waiting for PID 24175 of (24158 24164 24170 24175 24182) to complete... Waiting for PID 24182 of (24158 24164 24170 24175 24182) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 999 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2873 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1770 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 277 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2460 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1653 mri_label2label: Done PIDs (24158 24164 24170 24175 24182) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 24225 of (24225 24231 24237 24243) to complete... Waiting for PID 24231 of (24225 24231 24237 24243) to complete... Waiting for PID 24237 of (24225 24231 24237 24243) to complete... Waiting for PID 24243 of (24225 24231 24237 24243) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1671 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 1078 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8037 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1201 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 336 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1514 mri_label2label: Done PIDs (24225 24231 24237 24243) 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 0051026 --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 0051026 --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 0051026 --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 0051026 --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 0051026 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 24334 of (24334 24341 24347 24353 24358) to complete... Waiting for PID 24341 of (24334 24341 24347 24353 24358) to complete... Waiting for PID 24347 of (24334 24341 24347 24353 24358) to complete... Waiting for PID 24353 of (24334 24341 24347 24353 24358) to complete... Waiting for PID 24358 of (24334 24341 24347 24353 24358) 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 945 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4177 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 1592 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5029 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 337 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 783 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 0051026 --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 = 0051026 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-6.0.0/0051026/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 153799 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 362 mri_label2label: Done PIDs (24334 24341 24347 24353 24358) completed and logs appended. mris_label2annot --s 0051026 --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-6.0.0/0051026/label cmdline mris_label2annot --s 0051026 --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-609 machine x86_64 user ntraut subject 0051026 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-6.0.0/0051026/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 107098 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.BA_exvivo.annot mris_label2annot --s 0051026 --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-6.0.0/0051026/label cmdline mris_label2annot --s 0051026 --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-609 machine x86_64 user ntraut subject 0051026 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-6.0.0/0051026/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 127356 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/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 0051026 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 306008 Total vertex volume 302421 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 1047 598 2280 2.649 0.573 0.128 0.036 15 1.3 BA1_exvivo 3540 2289 6088 2.510 0.551 0.108 0.020 30 2.9 BA2_exvivo 1147 799 1147 1.860 0.462 0.127 0.030 9 1.4 BA3a_exvivo 2387 1473 3163 1.924 0.617 0.105 0.024 21 2.3 BA3b_exvivo 2042 1110 3646 2.791 0.441 0.100 0.030 39 2.6 BA4a_exvivo 1525 922 2306 2.620 0.484 0.098 0.025 10 1.5 BA4p_exvivo 9760 6397 22705 3.011 0.634 0.113 0.026 88 9.5 BA6_exvivo 3751 2539 7767 2.902 0.503 0.112 0.023 35 3.4 BA44_exvivo 5544 3842 12860 2.888 0.577 0.138 0.033 79 7.5 BA45_exvivo 3824 2744 6769 2.130 0.593 0.157 0.051 62 8.3 V1_exvivo 8982 6003 15315 2.238 0.576 0.145 0.044 128 15.2 V2_exvivo 2049 1377 3464 2.498 0.496 0.121 0.026 21 2.1 MT_exvivo 657 491 2283 3.559 0.746 0.140 0.024 7 0.6 perirhinal_exvivo 446 290 1532 3.379 0.752 0.148 0.040 9 0.8 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 0051026 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 306008 Total vertex volume 302421 (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) = 1690943 mm^3 (det: 1.152082 ) lhCtxGM: 302187.450 301335.000 diff= 852.5 pctdiff= 0.282 rhCtxGM: 300149.670 299367.000 diff= 782.7 pctdiff= 0.261 lhCtxWM: 267570.720 267576.500 diff= -5.8 pctdiff=-0.002 rhCtxWM: 263312.855 264187.500 diff= -874.6 pctdiff=-0.332 SubCortGMVol 63995.000 SupraTentVol 1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349 SupraTentVolNotVent 1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353 BrainSegVol 1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171 BrainSegVolNotVent 1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045 BrainSegVolNotVent 1356048.000 CerebellumVol 159428.000 VentChorVol 10963.000 3rd4th5thCSF 3112.000 CSFVol 766.000, OptChiasmVol 140.000 MaskVol 1826083.000 751 423 1637 2.655 0.565 0.122 0.032 9 0.8 BA1_exvivo 2022 1288 3801 2.612 0.540 0.103 0.020 16 1.6 BA2_exvivo 1023 702 907 1.838 0.408 0.131 0.029 8 1.2 BA3a_exvivo 1895 1214 2096 1.717 0.432 0.099 0.020 13 1.6 BA3b_exvivo 1308 641 2237 2.927 0.446 0.102 0.035 13 1.7 BA4a_exvivo 1295 800 1921 2.612 0.482 0.098 0.026 7 1.4 BA4p_exvivo 6491 4211 15174 2.991 0.649 0.113 0.026 82 6.6 BA6_exvivo 996 677 2368 3.039 0.512 0.120 0.028 12 1.1 BA44_exvivo 1385 998 3817 3.111 0.514 0.161 0.049 27 2.6 BA45_exvivo 3599 2578 6138 2.119 0.583 0.155 0.049 57 7.6 V1_exvivo 4658 3186 8133 2.182 0.563 0.155 0.048 74 8.9 V2_exvivo 313 198 735 2.834 0.446 0.122 0.026 4 0.3 MT_exvivo 381 291 1494 3.708 0.681 0.135 0.021 4 0.3 perirhinal_exvivo 326 226 917 3.346 0.665 0.154 0.041 5 0.7 entorhinal_exvivo Started at Sat Oct 7 17:21:27 CEST 2017 Ended at Sun Oct 8 01:21:01 CEST 2017 #@#%# recon-all-run-time-hours 7.993 recon-all -s 0051026 finished without error at Sun Oct 8 01:21:01 CEST 2017