ABIDE_fs-6.0.0/0050564/scripts/recon-all.log

Sun Oct  8 01:37:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050564 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050564/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050564
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-575 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   57180052    8813796    1752344          0   53716072
-/+ buffers/cache:    3463980   62529868
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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-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-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $  User: ntraut  Machine: tars-575  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: 2017/10/07-23:37:07-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: ntraut  Machine: tars-575  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-6.0.0/0050564

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050564/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050564/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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/Yale/0050564/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-6.0.0/0050564/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sun Oct  8 01:37:12 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/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 float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sun Oct  8 01:37:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/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-575 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
Sun Oct  8 01:37:22 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.15440
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15440/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.15440/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.15440/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:37:25 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.15440/nu0.mnc ./tmp.mri_nu_correct.mni.15440/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15440/0/ -iterations 1000 -distance 50
[ntraut@tars-575:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/] [2017-10-08 01:37:25] 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.15440/0/ ./tmp.mri_nu_correct.mni.15440/nu0.mnc ./tmp.mri_nu_correct.mni.15440/nu1.imp

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Number of iterations: 41 
CV of field change: 0.000984704
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.15440/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.15440/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.15440/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...
 
 
Sun Oct  8 01:38:32 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 Sun Oct 8 01:38:32 CEST 2017
Ended   at Sun Oct  8 01:39:06 CEST 2017
talairach_avi done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#--------------------------------------------
#@# Talairach Failure Detection Sun Oct  8 01:39:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7121, pval=0.4932 >= 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-6.0.0/0050564/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/transforms/talairach_avi.log 

TalAviQA: 0.97672
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sun Oct  8 01:39:08 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-6.0.0/0050564/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-575 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
Sun Oct  8 01:39:08 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.16330
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16330/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.16330/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.16330/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:39:11 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.16330/nu0.mnc ./tmp.mri_nu_correct.mni.16330/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16330/0/
[ntraut@tars-575:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/] [2017-10-08 01:39:11] 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.16330/0/ ./tmp.mri_nu_correct.mni.16330/nu0.mnc ./tmp.mri_nu_correct.mni.16330/nu1.imp

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Number of iterations: 37 
CV of field change: 0.00098698
 
 
--------------------------------------------------------
Iteration 2 Sun Oct  8 01:39:58 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.16330/nu1.mnc ./tmp.mri_nu_correct.mni.16330/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.16330/1/
[ntraut@tars-575:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/] [2017-10-08 01:39:58] 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.16330/1/ ./tmp.mri_nu_correct.mni.16330/nu1.mnc ./tmp.mri_nu_correct.mni.16330/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 18 
CV of field change: 0.000963613
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.16330/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16330/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-6.0.0/0050564/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.16330/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16330/ones.mgz 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.16330/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.16330/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.16330/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16330/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.16330/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16330/input.mean.dat 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.16330/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.16330/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16330/ones.mgz --i ./tmp.mri_nu_correct.mni.16330/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16330/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.16330/ones.mgz --i ./tmp.mri_nu_correct.mni.16330/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16330/output.mean.dat 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.16330/ones.mgz
Loading ./tmp.mri_nu_correct.mni.16330/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.16330/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.16330/nu2.mnc ./tmp.mri_nu_correct.mni.16330/nu2.mnc mul 1.03246045577007865552
Saving result to './tmp.mri_nu_correct.mni.16330/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.16330/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.16330/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.16330/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 ( 7, 116) to ( 3, 110)
 
 
Sun Oct  8 01:41:20 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sun Oct  8 01:41:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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
 1.10934  -0.00921   0.03287  -40.85677;
-0.01325   1.10481   0.07398   37.50012;
-0.05769   0.05691   1.22855   4.38652;
 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 = 12
Starting OpenSpline(): npoints = 12
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 57 (57), valley at 27 (27)
csf peak at 29, setting threshold to 47
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 16 (16)
csf peak at 30, setting threshold to 49
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 Sun Oct  8 01:43:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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=18.0
skull bounding box = (54, 60, 33) --> (204, 200, 222)
using (104, 107, 128) as brain centroid...
mean wm in atlas = 108, using box (86,90,105) --> (122, 124,151) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.6
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.575
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.432574 @ (-9.091, -9.091, -9.091)
max log p =    -4.328157 @ (4.545, -4.545, -4.545)
max log p =    -4.299896 @ (2.273, 2.273, 2.273)
max log p =    -4.273440 @ (1.136, -1.136, -1.136)
max log p =    -4.262202 @ (-2.841, 0.568, 0.568)
max log p =    -4.262202 @ (0.000, 0.000, 0.000)
Found translation: (-4.0, -11.9, -11.9): log p = -4.262
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.877, old_max_log_p =-4.262 (thresh=-4.3)
 1.15000   0.00000   0.00000  -23.30515;
 0.00000   1.23625   0.00000  -40.83937;
 0.00000   0.00000   1.15000  -30.36007;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.877, old_max_log_p =-3.877 (thresh=-3.9)
 1.15000   0.00000   0.00000  -23.30515;
 0.00000   1.23625   0.00000  -40.83937;
 0.00000   0.00000   1.15000  -30.36007;
 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=-3.810, old_max_log_p =-3.877 (thresh=-3.9)
 1.12763   0.00000   0.00000  -20.42257;
 0.00000   1.30666   0.00000  -53.20788;
 0.00000   0.00000   1.08612  -26.19190;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.804, old_max_log_p =-3.810 (thresh=-3.8)
 1.12642   0.04133   0.03666  -29.20053;
-0.03757   1.32978   0.03500  -54.36811;
-0.03759  -0.04353   1.10530  -17.26101;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.802, old_max_log_p =-3.804 (thresh=-3.8)
 1.12705  -0.00220   0.03550  -24.56235;
-0.00068   1.30547   0.03550  -55.52636;
-0.03759  -0.04353   1.10530  -15.38601;
 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=-3.780, old_max_log_p =-3.802 (thresh=-3.8)
 1.12848   0.01962   0.02673  -26.89489;
-0.01883   1.30128   0.01691  -49.76498;
-0.02838  -0.02216   1.10469  -20.13219;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.778, old_max_log_p =-3.780 (thresh=-3.8)
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 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
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.778 (old=-4.575)
transform before final EM align:
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 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
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.2  tol 0.000000
final transform:
 1.12848   0.01962   0.02673  -26.89489;
-0.01881   1.29975   0.01689  -49.54005;
-0.02845  -0.02221   1.10728  -20.43935;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1251.523739
mri_em_register stimesec    1.122829
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   157576
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    89
mri_em_register ru_nivcsw   2890
registration took 10 minutes and 53 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Use the information of atlas (default parms, --help for details)

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=131 y=128 z=126 r=64
      first estimation of the main basin volume: 1098569 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        15 found in the rest of the brain 
      global maximum in x=151, y=112, z=95, Imax=255
      CSF=20, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=7969510083 voxels, voxel volume =1.000 
                     = 7969510083 mmm3 = 7969509.888 cm3
done.
PostAnalyze...Basin Prior
 14 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=129,y=132, z=120, r=9160 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=23, CSF_MAX=59 , nb = 44288
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1036172467
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1033704501
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=23, CSF_MAX=51 , nb = 1108458124
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=23, CSF_MAX=63 , nb = 1069857188
    OTHER      CSF_MIN=0, CSF_intensity=17, CSF_MAX=65 , nb = 1076035724
 Problem with the least square interpolation in GM_MIN calculation.
 Problem with the least square interpolation in GM_MIN calculation.
 (2) Problem with the least square interpolation in GM_MIN calculation.
 Problem with the least square interpolation in GM_MIN calculation.
 (2) Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    59,      42,        32,   56
  after  analyzing :    37,      42,        42,   45
   RIGHT_CER   
  before analyzing :    5,      4,        0,   23
  after  analyzing :    4,      18,        25,   19
   LEFT_CER    
  before analyzing :    5,      4,        0,   23
  after  analyzing :    4,      18,        25,   19
  RIGHT_BRAIN  
  before analyzing :    51,      24,        22,   25
  after  analyzing :    23,      24,        25,   24
  LEFT_BRAIN   
  before analyzing :    63,      39,        36,   41
  after  analyzing :    34,      39,        39,   39
     OTHER     
  before analyzing :    65,      34,        20,   42
  after  analyzing :    27,      34,        34,   36
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...69 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 69.185, std = 7.189

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.48, sigma = 6.82
      after  rotation: sse = 4.48, sigma = 6.82
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.88, its var is  6.02   
      before Erosion-Dilatation  1.73% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1448503 voxels, voxel volume = 1.000 mm3
           = 1448503 mmm3 = 1448.503 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    24.518272
mri_watershed stimesec    0.383941
mri_watershed ru_maxrss   818068
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   211268
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2328
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1439
mri_watershed ru_nivcsw   99
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct  8 01:54:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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=24.0
skull bounding box = (63, 71, 43) --> (196, 182, 208)
using (107, 108, 126) as brain centroid...
mean wm in atlas = 107, using box (91,94,106) --> (123, 121,146) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.7
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.262
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.995402 @ (-9.091, -9.091, -9.091)
max log p =    -3.865861 @ (4.545, -4.545, -4.545)
max log p =    -3.829031 @ (2.273, 2.273, 2.273)
max log p =    -3.815023 @ (-1.136, 1.136, -1.136)
max log p =    -3.809523 @ (1.705, 0.568, 0.568)
max log p =    -3.809523 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -9.7, -11.9): log p = -3.810
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.531, old_max_log_p =-3.810 (thresh=-3.8)
 1.06375   0.00000   0.00000  -9.89270;
 0.00000   1.15000   0.00000  -29.00146;
 0.00000   0.00000   1.07500  -20.73504;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.526, old_max_log_p =-3.531 (thresh=-3.5)
 1.06375   0.00000   0.00000  -9.89270;
 0.00000   1.14016  -0.14032  -11.26309;
 0.00000   0.15011   1.06580  -46.51148;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.513, old_max_log_p =-3.526 (thresh=-3.5)
 1.06375   0.00000   0.00000  -9.89270;
 0.00000   1.15000   0.00000  -29.98041;
 0.00000   0.00000   1.07500  -20.67088;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.499, old_max_log_p =-3.513 (thresh=-3.5)
 1.06375   0.00000   0.00000  -9.89270;
 0.00000   1.23625   0.00000  -41.17570;
 0.00000   0.00000   0.99438  -11.21223;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.499, old_max_log_p =-3.499 (thresh=-3.5)
 1.06375   0.00000   0.00000  -9.89270;
 0.00000   1.23625   0.00000  -41.17570;
 0.00000   0.00000   0.99438  -11.21223;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.292, old_max_log_p =-3.499 (thresh=-3.5)
 1.08311   0.04119  -0.00104  -19.48290;
-0.03415   1.21187  -0.03071  -32.01653;
 0.00000   0.04429   1.05036  -27.34835;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.288, old_max_log_p =-3.292 (thresh=-3.3)
 1.06281   0.04042  -0.00102  -16.74128;
-0.03415   1.21187  -0.03071  -30.14153;
 0.00000   0.04513   1.07006  -29.83821;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.288, old_max_log_p =-3.288 (thresh=-3.3)
 1.06281   0.04042  -0.00102  -16.74128;
-0.03415   1.21187  -0.03071  -30.14153;
 0.00000   0.04513   1.07006  -29.83821;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.252, old_max_log_p =-3.288 (thresh=-3.3)
 1.06028   0.04077   0.00773  -17.05593;
-0.03403   1.20720  -0.03935  -29.90360;
-0.00894   0.05462   1.06849  -30.67079;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 9 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.244, old_max_log_p =-3.252 (thresh=-3.2)
 1.05907   0.04028  -0.00099  -15.77296;
-0.03391   1.20296  -0.03921  -29.37950;
-0.00025   0.05489   1.06726  -31.21538;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 10 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.243, old_max_log_p =-3.244 (thresh=-3.2)
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 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
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 013: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.243 (old=-4.262)
transform before final EM align:
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 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
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.06028   0.04077   0.00775  -17.05453;
-0.03387   1.20155  -0.03916  -29.20527;
-0.00890   0.05449   1.06598  -30.35489;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 014: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 015: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 016: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 017: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 018: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 019: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 020: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 021: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 022: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
pass 2 through quasi-newton minimization...
dfp_em_step_func: 023: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 024: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 025: -log(p) = 3.8
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 026: -log(p) = 3.7
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 027: -log(p) = 3.7
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
pass 3 through quasi-newton minimization...
dfp_em_step_func: 028: -log(p) = 3.7
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.05, 1.07, -30.35)
dfp_em_step_func: 029: -log(p) = 3.7
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.06, 1.07, -30.35)
pass 4 through quasi-newton minimization...
dfp_em_step_func: 030: -log(p) = 3.7
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.06, 1.07, -30.35)
dfp_em_step_func: 031: -log(p) = 3.7
after pass:transform: ( 1.06, 0.04, 0.01, -17.05)
                      ( -0.03, 1.20, -0.04, -29.21)
                      ( -0.01, 0.06, 1.07, -30.35)
pass 5 through quasi-newton minimization...
outof QuasiNewtonEMA: 033: -log(p) =    3.7  tol 0.000000
final transform:
 1.06154   0.04178   0.00901  -17.05453;
-0.03238   1.20303  -0.03769  -29.20527;
-0.00781   0.05526   1.06661  -30.35489;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1796.855836
mri_em_register stimesec    1.615754
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   159503
mri_em_register ru_majflt   1
mri_em_register ru_nswap    0
mri_em_register ru_inblock  2888
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    318
mri_em_register ru_nivcsw   11447
registration took 15 minutes and 54 seconds.
#--------------------------------------
#@# CA Normalize Sun Oct  8 02:10:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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=24.0
skull bounding box = (63, 71, 43) --> (196, 182, 208)
using (107, 108, 126) as brain centroid...
mean wm in atlas = 107, using box (91,94,106) --> (123, 121,146) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.7
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 1.06154   0.04178   0.00901  -17.05453;
-0.03238   1.20303  -0.03769  -29.20527;
-0.00781   0.05526   1.06661  -30.35489;
 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 (128, 75, 46) --> (191, 176, 204)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
6 of 4337 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (68, 74, 47) --> (131, 174, 205)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
1 of 4468 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (129, 145, 66) --> (174, 181, 117)
Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 199 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 145, 64) --> (128, 180, 118)
Right_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0
0 of 149 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 139, 97) --> (145, 197, 128)
Brain_Stem: limiting intensities to 90.0 --> 132.0
0 of 130 (0.0%) samples deleted
using 9283 total control points for intensity normalization...
bias field = 0.958 +- 0.051
92 of 9276 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (128, 75, 46) --> (191, 176, 204)
Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
19 of 4769 (0.4%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (68, 74, 47) --> (131, 174, 205)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
1 of 5026 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (129, 145, 66) --> (174, 181, 117)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
7 of 282 (2.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 145, 64) --> (128, 180, 118)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 204 (2.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 139, 97) --> (145, 197, 128)
Brain_Stem: limiting intensities to 88.0 --> 132.0
70 of 211 (33.2%) samples deleted
using 10492 total control points for intensity normalization...
bias field = 1.011 +- 0.041
30 of 10275 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (128, 75, 46) --> (191, 176, 204)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
6 of 4632 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (68, 74, 47) --> (131, 174, 205)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 116.0
6 of 4988 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (129, 145, 66) --> (174, 181, 117)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
66 of 335 (19.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 145, 64) --> (128, 180, 118)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
46 of 256 (18.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 139, 97) --> (145, 197, 128)
Brain_Stem: limiting intensities to 88.0 --> 132.0
150 of 258 (58.1%) samples deleted
using 10469 total control points for intensity normalization...
bias field = 1.008 +- 0.037
8 of 9981 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 37 seconds.
#--------------------------------------
#@# CA Reg Sun Oct  8 02:12:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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) = 1.37 (predicted orig area = 5.9)
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=0.768, neg=0, invalid=762
0001: dt=191.083532, rms=0.712 (7.315%), neg=0, invalid=762
0002: dt=202.189055, rms=0.696 (2.235%), neg=0, invalid=762
0003: dt=131.084337, rms=0.690 (0.868%), neg=0, invalid=762
0004: dt=443.904000, rms=0.684 (0.967%), neg=0, invalid=762
0005: dt=92.689655, rms=0.680 (0.562%), neg=0, invalid=762
0006: dt=1183.744000, rms=0.672 (1.094%), neg=0, invalid=762
0007: dt=129.472000, rms=0.669 (0.421%), neg=0, invalid=762
0008: dt=129.472000, rms=0.669 (0.092%), neg=0, invalid=762
0009: dt=129.472000, rms=0.668 (0.104%), neg=0, invalid=762
0010: dt=129.472000, rms=0.667 (0.144%), neg=0, invalid=762
0011: dt=129.472000, rms=0.666 (0.174%), neg=0, invalid=762
0012: dt=129.472000, rms=0.665 (0.201%), neg=0, invalid=762
0013: dt=129.472000, rms=0.663 (0.240%), neg=0, invalid=762
0014: dt=129.472000, rms=0.661 (0.256%), neg=0, invalid=762
0015: dt=129.472000, rms=0.660 (0.251%), neg=0, invalid=762
0016: dt=129.472000, rms=0.658 (0.239%), neg=0, invalid=762
0017: dt=129.472000, rms=0.657 (0.229%), neg=0, invalid=762
0018: dt=129.472000, rms=0.655 (0.225%), neg=0, invalid=762
0019: dt=129.472000, rms=0.654 (0.197%), neg=0, invalid=762
0020: dt=129.472000, rms=0.653 (0.165%), neg=0, invalid=762
0021: dt=129.472000, rms=0.652 (0.154%), neg=0, invalid=762
0022: dt=129.472000, rms=0.651 (0.159%), neg=0, invalid=762
0023: dt=129.472000, rms=0.650 (0.161%), neg=0, invalid=762
0024: dt=129.472000, rms=0.649 (0.145%), neg=0, invalid=762
0025: dt=129.472000, rms=0.648 (0.128%), neg=0, invalid=762
0026: dt=129.472000, rms=0.647 (0.112%), neg=0, invalid=762
0027: dt=129.472000, rms=0.646 (0.113%), neg=0, invalid=762
0028: dt=129.472000, rms=0.646 (0.106%), neg=0, invalid=762
0029: dt=1775.616000, rms=0.645 (0.129%), neg=0, invalid=762
0030: dt=129.472000, rms=0.645 (0.047%), neg=0, invalid=762
0031: dt=129.472000, rms=0.645 (-0.008%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.645, neg=0, invalid=762
0032: dt=129.472000, rms=0.644 (0.146%), neg=0, invalid=762
0033: dt=369.920000, rms=0.644 (0.082%), neg=0, invalid=762
0034: dt=369.920000, rms=0.643 (0.097%), neg=0, invalid=762
0035: dt=369.920000, rms=0.643 (0.066%), neg=0, invalid=762
0036: dt=369.920000, rms=0.642 (0.034%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.647, neg=0, invalid=762
0037: dt=100.792271, rms=0.642 (0.801%), neg=0, invalid=762
0038: dt=103.680000, rms=0.636 (0.867%), neg=0, invalid=762
0039: dt=74.926829, rms=0.633 (0.447%), neg=0, invalid=762
0040: dt=118.996942, rms=0.629 (0.711%), neg=0, invalid=762
0041: dt=59.130435, rms=0.626 (0.363%), neg=0, invalid=762
0042: dt=145.152000, rms=0.622 (0.714%), neg=0, invalid=762
0043: dt=36.288000, rms=0.621 (0.167%), neg=0, invalid=762
0044: dt=36.288000, rms=0.620 (0.119%), neg=0, invalid=762
0045: dt=36.288000, rms=0.619 (0.222%), neg=0, invalid=762
0046: dt=36.288000, rms=0.617 (0.329%), neg=0, invalid=762
0047: dt=36.288000, rms=0.614 (0.408%), neg=0, invalid=762
0048: dt=36.288000, rms=0.611 (0.440%), neg=0, invalid=762
0049: dt=36.288000, rms=0.609 (0.430%), neg=0, invalid=762
0050: dt=36.288000, rms=0.606 (0.406%), neg=0, invalid=762
0051: dt=36.288000, rms=0.604 (0.382%), neg=0, invalid=762
0052: dt=36.288000, rms=0.602 (0.363%), neg=0, invalid=762
0053: dt=36.288000, rms=0.600 (0.356%), neg=0, invalid=762
0054: dt=36.288000, rms=0.598 (0.324%), neg=0, invalid=762
0055: dt=36.288000, rms=0.596 (0.286%), neg=0, invalid=762
0056: dt=36.288000, rms=0.595 (0.241%), neg=0, invalid=762
0057: dt=36.288000, rms=0.593 (0.203%), neg=0, invalid=762
0058: dt=36.288000, rms=0.592 (0.190%), neg=0, invalid=762
0059: dt=36.288000, rms=0.591 (0.183%), neg=0, invalid=762
0060: dt=36.288000, rms=0.590 (0.183%), neg=0, invalid=762
0061: dt=36.288000, rms=0.589 (0.152%), neg=0, invalid=762
0062: dt=36.288000, rms=0.588 (0.134%), neg=0, invalid=762
0063: dt=36.288000, rms=0.588 (0.115%), neg=0, invalid=762
0064: dt=36.288000, rms=0.587 (0.106%), neg=0, invalid=762
0065: dt=497.664000, rms=0.586 (0.133%), neg=0, invalid=762
0066: dt=20.736000, rms=0.586 (0.018%), neg=0, invalid=762
0067: dt=20.736000, rms=0.586 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.587, neg=0, invalid=762
0068: dt=85.333333, rms=0.585 (0.295%), neg=0, invalid=762
0069: dt=124.416000, rms=0.584 (0.133%), neg=0, invalid=762
0070: dt=124.416000, rms=0.584 (-0.232%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.606, neg=0, invalid=762
0071: dt=2.800000, rms=0.605 (0.122%), neg=0, invalid=762
0072: dt=2.800000, rms=0.605 (0.011%), neg=0, invalid=762
0073: dt=2.800000, rms=0.605 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.605, neg=0, invalid=762
0074: dt=2.800000, rms=0.605 (0.101%), neg=0, invalid=762
0075: dt=0.175000, rms=0.605 (0.000%), neg=0, invalid=762
0076: dt=0.175000, rms=0.605 (0.000%), neg=0, invalid=762
0077: dt=0.175000, rms=0.605 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.661, neg=0, invalid=762
0078: dt=5.676471, rms=0.644 (2.601%), neg=0, invalid=762
0079: dt=2.880000, rms=0.643 (0.111%), neg=0, invalid=762
0080: dt=2.880000, rms=0.643 (-0.045%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.644, neg=0, invalid=762
0081: dt=0.015750, rms=0.643 (0.075%), neg=0, invalid=762
0082: dt=0.000000, rms=0.643 (0.000%), neg=0, invalid=762
0083: dt=0.150000, rms=0.643 (-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=0.694, neg=0, invalid=762
0084: dt=1.024000, rms=0.692 (0.355%), neg=0, invalid=762
0085: dt=1.880342, rms=0.688 (0.582%), neg=0, invalid=762
0086: dt=1.024000, rms=0.687 (0.059%), neg=0, invalid=762
0087: dt=1.024000, rms=0.686 (0.153%), neg=0, invalid=762
0088: dt=1.024000, rms=0.686 (0.047%), neg=0, invalid=762
0089: dt=1.024000, rms=0.686 (-0.226%), neg=0, invalid=762
0090: dt=0.000000, rms=0.686 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.686, neg=0, invalid=762
0091: dt=1.024000, rms=0.685 (0.164%), neg=0, invalid=762
0092: dt=0.448000, rms=0.685 (0.005%), neg=0, invalid=762
0093: dt=0.448000, rms=0.685 (-0.001%), 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=0.655, neg=0, invalid=762
0094: dt=0.815841, rms=0.639 (2.472%), neg=0, invalid=762
0095: dt=0.080000, rms=0.638 (0.145%), neg=0, invalid=762
0096: dt=0.080000, rms=0.638 (-0.082%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.638, neg=0, invalid=762
0097: dt=0.028000, rms=0.638 (0.093%), neg=0, invalid=762
0098: dt=0.001750, rms=0.638 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.04921 (28)
Left_Lateral_Ventricle (4): linear fit = 1.77 x + 0.0 (753 voxels, overlap=0.147)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (753 voxels, peak = 36), gca=30.0
gca peak = 0.15565 (16)
mri peak = 0.10039 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (835 voxels, overlap=0.508)
Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (835 voxels, peak =  9), gca=8.9
gca peak = 0.26829 (96)
mri peak = 0.07751 (96)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (827 voxels, overlap=0.984)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (827 voxels, peak = 95), gca=94.6
gca peak = 0.20183 (93)
mri peak = 0.08523 (98)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (731 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (731 voxels, peak = 95), gca=95.3
gca peak = 0.21683 (55)
mri peak = 0.10379 (59)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (935 voxels, overlap=0.931)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (935 voxels, peak = 57), gca=57.5
gca peak = 0.30730 (58)
mri peak = 0.08730 (59)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (908 voxels, overlap=0.998)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (908 voxels, peak = 58), gca=58.0
gca peak = 0.11430 (101)
mri peak = 0.09301 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (54831 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (54831 voxels, peak = 107), gca=106.6
gca peak = 0.12076 (102)
mri peak = 0.08917 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (55178 voxels, overlap=0.437)
Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (55178 voxels, peak = 109), gca=108.6
gca peak = 0.14995 (59)
mri peak = 0.03657 (50)
Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (33172 voxels, overlap=0.886)
Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (33172 voxels, peak = 54), gca=54.0
gca peak = 0.15082 (58)
mri peak = 0.04214 (54)
Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (31990 voxels, overlap=0.950)
Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (31990 voxels, peak = 55), gca=54.8
gca peak = 0.14161 (67)
mri peak = 0.10911 (72)
Right_Caudate (50): linear fit = 1.03 x + 0.0 (926 voxels, overlap=0.963)
Right_Caudate (50): linear fit = 1.03 x + 0.0 (926 voxels, peak = 69), gca=69.3
gca peak = 0.15243 (71)
mri peak = 0.09726 (74)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (964 voxels, overlap=0.984)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (964 voxels, peak = 70), gca=69.9
gca peak = 0.13336 (57)
mri peak = 0.04206 (54)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (31480 voxels, overlap=0.984)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (31480 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.05209 (57)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (32272 voxels, overlap=0.923)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (32272 voxels, peak = 59), gca=58.5
gca peak = 0.18181 (84)
mri peak = 0.06026 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8414 voxels, overlap=0.730)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8414 voxels, peak = 91), gca=91.1
gca peak = 0.20573 (83)
mri peak = 0.06813 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7400 voxels, overlap=0.680)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7400 voxels, peak = 90), gca=90.1
gca peak = 0.21969 (57)
mri peak = 0.12184 (61)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (430 voxels, overlap=0.949)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (430 voxels, peak = 60), gca=59.6
gca peak = 0.39313 (56)
mri peak = 0.12753 (58)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (497 voxels, overlap=0.984)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (497 voxels, peak = 57), gca=56.8
gca peak = 0.14181 (85)
mri peak = 0.04584 (87)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5021 voxels, overlap=0.853)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5021 voxels, peak = 86), gca=86.3
gca peak = 0.11978 (83)
mri peak = 0.06627 (84)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4272 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4272 voxels, peak = 85), gca=85.1
gca peak = 0.13399 (79)
mri peak = 0.09304 (82)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2341 voxels, overlap=0.948)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2341 voxels, peak = 81), gca=81.0
gca peak = 0.14159 (79)
mri peak = 0.08785 (79)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2193 voxels, overlap=0.998)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2193 voxels, peak = 79), gca=78.6
gca peak = 0.10025 (80)
mri peak = 0.08176 (88)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11413 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11413 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.06048 (97)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1088 voxels, overlap=0.729)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1088 voxels, peak = 96), gca=95.9
gca peak = 0.12801 (89)
mri peak = 0.05800 (99)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1262 voxels, overlap=0.856)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1262 voxels, peak = 98), gca=98.3
gca peak = 0.20494 (23)
mri peak = 0.09556 (41)
gca peak = 0.15061 (21)
mri peak = 0.05357 (52)
Fourth_Ventricle (15): linear fit = 2.38 x + 0.0 (416 voxels, overlap=0.328)
Fourth_Ventricle (15): linear fit = 2.38 x + 0.0 (416 voxels, peak = 50), gca=50.1
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 0.99 x + 0.0
estimating mean wm scale to be 1.06 x + 0.0
estimating mean csf scale to be 1.03 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=0.678, neg=0, invalid=762
0099: dt=162.285714, rms=0.671 (1.006%), neg=0, invalid=762
0100: dt=129.472000, rms=0.669 (0.323%), neg=0, invalid=762
0101: dt=369.920000, rms=0.666 (0.402%), neg=0, invalid=762
0102: dt=92.480000, rms=0.665 (0.271%), neg=0, invalid=762
0103: dt=517.888000, rms=0.663 (0.291%), neg=0, invalid=762
0104: dt=92.480000, rms=0.661 (0.215%), neg=0, invalid=762
0105: dt=369.920000, rms=0.660 (0.118%), neg=0, invalid=762
0106: dt=110.976000, rms=0.660 (0.119%), neg=0, invalid=762
0107: dt=129.472000, rms=0.659 (0.059%), neg=0, invalid=762
0108: dt=369.920000, rms=0.659 (0.112%), neg=0, invalid=762
0109: dt=92.480000, rms=0.658 (0.073%), neg=0, invalid=762
0110: dt=517.888000, rms=0.657 (0.129%), neg=0, invalid=762
0111: dt=73.984000, rms=0.657 (0.070%), neg=0, invalid=762
0112: dt=2071.552000, rms=0.654 (0.372%), neg=0, invalid=762
0113: dt=92.480000, rms=0.653 (0.131%), neg=0, invalid=762
0114: dt=129.472000, rms=0.653 (0.015%), neg=0, invalid=762
0115: dt=129.472000, rms=0.653 (0.031%), neg=0, invalid=762
0116: dt=129.472000, rms=0.653 (0.042%), neg=0, invalid=762
0117: dt=129.472000, rms=0.653 (0.053%), neg=0, invalid=762
0118: dt=129.472000, rms=0.652 (0.064%), neg=0, invalid=762
0119: dt=129.472000, rms=0.652 (0.084%), neg=0, invalid=762
0120: dt=129.472000, rms=0.651 (0.085%), neg=0, invalid=762
0121: dt=129.472000, rms=0.651 (0.083%), neg=0, invalid=762
0122: dt=129.472000, rms=0.650 (0.083%), neg=0, invalid=762
0123: dt=129.472000, rms=0.649 (0.088%), neg=0, invalid=762
0124: dt=129.472000, rms=0.649 (0.085%), neg=0, invalid=762
0125: dt=129.472000, rms=0.648 (0.079%), neg=0, invalid=762
0126: dt=129.472000, rms=0.648 (0.074%), neg=0, invalid=762
0127: dt=129.472000, rms=0.647 (0.076%), neg=0, invalid=762
0128: dt=129.472000, rms=0.647 (0.076%), neg=0, invalid=762
0129: dt=129.472000, rms=0.646 (0.074%), neg=0, invalid=762
0130: dt=129.472000, rms=0.646 (0.070%), neg=0, invalid=762
0131: dt=129.472000, rms=0.646 (0.067%), neg=0, invalid=762
0132: dt=129.472000, rms=0.645 (0.065%), neg=0, invalid=762
0133: dt=129.472000, rms=0.645 (0.058%), neg=0, invalid=762
0134: dt=129.472000, rms=0.644 (0.058%), neg=0, invalid=762
0135: dt=129.472000, rms=0.644 (0.060%), neg=0, invalid=762
0136: dt=129.472000, rms=0.644 (0.060%), neg=0, invalid=762
0137: dt=129.472000, rms=0.643 (0.057%), neg=0, invalid=762
0138: dt=129.472000, rms=0.643 (0.054%), neg=0, invalid=762
0139: dt=129.472000, rms=0.643 (0.053%), neg=0, invalid=762
0140: dt=129.472000, rms=0.642 (0.051%), neg=0, invalid=762
0141: dt=129.472000, rms=0.642 (0.050%), neg=0, invalid=762
0142: dt=129.472000, rms=0.642 (0.048%), neg=0, invalid=762
0143: dt=129.472000, rms=0.641 (0.046%), neg=0, invalid=762
0144: dt=129.472000, rms=0.641 (0.045%), neg=0, invalid=762
0145: dt=129.472000, rms=0.641 (0.043%), neg=0, invalid=762
0146: dt=129.472000, rms=0.640 (0.039%), neg=0, invalid=762
0147: dt=129.472000, rms=0.640 (0.037%), neg=0, invalid=762
0148: dt=129.472000, rms=0.640 (0.036%), neg=0, invalid=762
0149: dt=129.472000, rms=0.640 (0.035%), neg=0, invalid=762
0150: dt=129.472000, rms=0.640 (0.033%), neg=0, invalid=762
0151: dt=129.472000, rms=0.639 (0.032%), neg=0, invalid=762
0152: dt=129.472000, rms=0.639 (0.031%), neg=0, invalid=762
0153: dt=129.472000, rms=0.639 (0.031%), neg=0, invalid=762
0154: dt=129.472000, rms=0.639 (0.030%), neg=0, invalid=762
0155: dt=129.472000, rms=0.639 (0.029%), neg=0, invalid=762
0156: dt=129.472000, rms=0.638 (0.029%), neg=0, invalid=762
0157: dt=129.472000, rms=0.638 (0.026%), neg=0, invalid=762
0158: dt=129.472000, rms=0.638 (0.024%), neg=0, invalid=762
0159: dt=129.472000, rms=0.638 (0.024%), neg=0, invalid=762
0160: dt=129.472000, rms=0.638 (0.025%), neg=0, invalid=762
0161: dt=129.472000, rms=0.638 (0.024%), neg=0, invalid=762
0162: dt=1479.680000, rms=0.638 (0.010%), neg=0, invalid=762
0163: dt=1479.680000, rms=0.638 (-0.880%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.638, neg=0, invalid=762
0164: dt=129.472000, rms=0.637 (0.215%), neg=0, invalid=762
0165: dt=517.888000, rms=0.636 (0.113%), neg=0, invalid=762
0166: dt=129.472000, rms=0.636 (0.036%), neg=0, invalid=762
0167: dt=129.472000, rms=0.636 (0.017%), neg=0, invalid=762
0168: dt=129.472000, rms=0.636 (0.022%), neg=0, invalid=762
0169: dt=129.472000, rms=0.635 (0.029%), neg=0, invalid=762
0170: dt=129.472000, rms=0.635 (0.030%), neg=0, invalid=762
0171: dt=129.472000, rms=0.635 (0.031%), neg=0, invalid=762
0172: dt=129.472000, rms=0.635 (0.025%), neg=0, invalid=762
0173: dt=129.472000, rms=0.635 (0.021%), neg=0, invalid=762
0174: dt=443.904000, rms=0.635 (0.015%), neg=0, invalid=762
0175: dt=443.904000, rms=0.635 (-0.117%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.636, neg=0, invalid=762
0176: dt=96.680851, rms=0.633 (0.536%), neg=0, invalid=762
0177: dt=111.319149, rms=0.628 (0.704%), neg=0, invalid=762
0178: dt=52.610169, rms=0.626 (0.378%), neg=0, invalid=762
0179: dt=145.152000, rms=0.622 (0.616%), neg=0, invalid=762
0180: dt=36.288000, rms=0.620 (0.283%), neg=0, invalid=762
0181: dt=580.608000, rms=0.612 (1.439%), neg=0, invalid=762
0182: dt=81.454545, rms=0.608 (0.537%), neg=0, invalid=762
0183: dt=36.288000, rms=0.607 (0.186%), neg=0, invalid=762
0184: dt=331.776000, rms=0.605 (0.290%), neg=0, invalid=762
0185: dt=68.319018, rms=0.603 (0.465%), neg=0, invalid=762
0186: dt=31.104000, rms=0.602 (0.038%), neg=0, invalid=762
0187: dt=31.104000, rms=0.602 (0.034%), neg=0, invalid=762
0188: dt=31.104000, rms=0.602 (0.065%), neg=0, invalid=762
0189: dt=31.104000, rms=0.601 (0.109%), neg=0, invalid=762
0190: dt=31.104000, rms=0.600 (0.164%), neg=0, invalid=762
0191: dt=31.104000, rms=0.599 (0.190%), neg=0, invalid=762
0192: dt=31.104000, rms=0.598 (0.200%), neg=0, invalid=762
0193: dt=31.104000, rms=0.597 (0.200%), neg=0, invalid=762
0194: dt=31.104000, rms=0.595 (0.196%), neg=0, invalid=762
0195: dt=31.104000, rms=0.594 (0.193%), neg=0, invalid=762
0196: dt=31.104000, rms=0.593 (0.198%), neg=0, invalid=762
0197: dt=31.104000, rms=0.592 (0.209%), neg=0, invalid=762
0198: dt=31.104000, rms=0.591 (0.206%), neg=0, invalid=762
0199: dt=31.104000, rms=0.589 (0.196%), neg=0, invalid=762
0200: dt=31.104000, rms=0.588 (0.186%), neg=0, invalid=762
0201: dt=31.104000, rms=0.588 (0.014%), neg=0, invalid=762
0202: dt=31.104000, rms=0.588 (0.019%), neg=0, invalid=762
0203: dt=3.888000, rms=0.588 (0.003%), neg=0, invalid=762
0204: dt=2.268000, rms=0.588 (0.002%), neg=0, invalid=762
0205: dt=0.567000, rms=0.588 (0.000%), neg=0, invalid=762
0206: dt=0.283500, rms=0.588 (0.000%), neg=0, invalid=762
0207: dt=0.070875, rms=0.588 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.589, neg=0, invalid=762
0208: dt=103.646018, rms=0.586 (0.514%), neg=0, invalid=762
0209: dt=36.288000, rms=0.585 (0.151%), neg=0, invalid=762
0210: dt=497.664000, rms=0.582 (0.498%), neg=0, invalid=762
0211: dt=36.288000, rms=0.581 (0.169%), neg=0, invalid=762
0212: dt=145.152000, rms=0.580 (0.122%), neg=0, invalid=762
0213: dt=82.944000, rms=0.580 (0.077%), neg=0, invalid=762
0214: dt=82.944000, rms=0.580 (0.059%), neg=0, invalid=762
0215: dt=82.944000, rms=0.579 (0.058%), neg=0, invalid=762
0216: dt=36.288000, rms=0.579 (0.038%), neg=0, invalid=762
0217: dt=36.288000, rms=0.579 (0.024%), neg=0, invalid=762
0218: dt=36.288000, rms=0.579 (0.045%), neg=0, invalid=762
0219: dt=36.288000, rms=0.578 (0.061%), neg=0, invalid=762
0220: dt=36.288000, rms=0.578 (0.078%), neg=0, invalid=762
0221: dt=36.288000, rms=0.577 (0.089%), neg=0, invalid=762
0222: dt=36.288000, rms=0.577 (0.098%), neg=0, invalid=762
0223: dt=36.288000, rms=0.576 (0.105%), neg=0, invalid=762
0224: dt=36.288000, rms=0.575 (0.108%), neg=0, invalid=762
0225: dt=36.288000, rms=0.575 (0.112%), neg=0, invalid=762
0226: dt=36.288000, rms=0.575 (0.015%), neg=0, invalid=762
0227: dt=36.288000, rms=0.575 (0.029%), neg=0, invalid=762
0228: dt=36.288000, rms=0.574 (0.041%), neg=0, invalid=762
0229: dt=9.072000, rms=0.574 (0.004%), neg=0, invalid=762
0230: dt=4.536000, rms=0.574 (0.001%), neg=0, invalid=762
0231: dt=2.268000, rms=0.574 (0.001%), neg=0, invalid=762
0232: dt=0.567000, rms=0.574 (0.000%), neg=0, invalid=762
0233: dt=0.567000, rms=0.574 (0.000%), neg=0, invalid=762
0234: dt=0.070875, rms=0.574 (0.000%), neg=0, invalid=762
0235: dt=0.017719, rms=0.574 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.581, neg=0, invalid=762
0236: dt=0.000000, rms=0.580 (0.130%), neg=0, invalid=762
0237: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0238: dt=0.000015, rms=0.580 (0.000%), neg=0, invalid=762
0239: dt=0.000008, rms=0.580 (0.000%), neg=0, invalid=762
0240: dt=0.000008, rms=0.580 (0.000%), neg=0, invalid=762
0241: dt=0.000004, rms=0.580 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.581, neg=0, invalid=762
0242: dt=0.000000, rms=0.580 (0.130%), neg=0, invalid=762
0243: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0244: dt=0.000122, rms=0.580 (0.000%), neg=0, invalid=762
0245: dt=0.000031, rms=0.580 (0.000%), neg=0, invalid=762
0246: dt=0.000015, rms=0.580 (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=0.599, neg=0, invalid=762
0247: dt=11.520000, rms=0.572 (4.534%), neg=0, invalid=762
0248: dt=4.032000, rms=0.567 (0.738%), neg=0, invalid=762
0249: dt=4.032000, rms=0.564 (0.575%), neg=0, invalid=762
0250: dt=3.456000, rms=0.562 (0.396%), neg=0, invalid=762
0251: dt=0.252000, rms=0.562 (0.026%), neg=0, invalid=762
0252: dt=0.031500, rms=0.562 (0.003%), neg=0, invalid=762
0253: dt=0.003938, rms=0.562 (0.000%), neg=0, invalid=762
0254: dt=0.001969, rms=0.562 (0.000%), neg=0, invalid=762
0255: dt=0.000984, rms=0.562 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.562, neg=0, invalid=762
0256: dt=21.205479, rms=0.554 (1.446%), neg=0, invalid=762
0257: dt=10.118919, rms=0.551 (0.516%), neg=0, invalid=762
0258: dt=16.128000, rms=0.549 (0.364%), neg=0, invalid=762
0259: dt=10.361905, rms=0.549 (0.128%), neg=0, invalid=762
0260: dt=16.827586, rms=0.548 (0.179%), neg=0, invalid=762
0261: dt=8.064000, rms=0.547 (0.093%), neg=0, invalid=762
0262: dt=33.652582, rms=0.546 (0.183%), neg=0, invalid=762
0263: dt=7.000000, rms=0.546 (0.106%), neg=0, invalid=762
0264: dt=28.307692, rms=0.545 (0.111%), neg=0, invalid=762
0265: dt=8.521739, rms=0.545 (0.066%), neg=0, invalid=762
0266: dt=16.128000, rms=0.544 (0.078%), neg=0, invalid=762
0267: dt=7.593220, rms=0.544 (0.037%), neg=0, invalid=762
0268: dt=7.593220, rms=0.544 (0.032%), neg=0, invalid=762
0269: dt=7.593220, rms=0.544 (0.052%), neg=0, invalid=762
0270: dt=7.593220, rms=0.543 (0.075%), neg=0, invalid=762
0271: dt=7.593220, rms=0.543 (0.088%), neg=0, invalid=762
0272: dt=7.593220, rms=0.542 (0.100%), neg=0, invalid=762
0273: dt=7.593220, rms=0.542 (0.102%), neg=0, invalid=762
0274: dt=7.593220, rms=0.541 (0.101%), neg=0, invalid=762
0275: dt=7.593220, rms=0.541 (0.095%), neg=0, invalid=762
0276: dt=7.593220, rms=0.540 (0.090%), neg=0, invalid=762
0277: dt=7.593220, rms=0.540 (0.088%), neg=0, invalid=762
0278: dt=7.593220, rms=0.539 (0.077%), neg=0, invalid=762
0279: dt=7.593220, rms=0.539 (0.077%), neg=0, invalid=762
0280: dt=7.593220, rms=0.538 (0.073%), neg=0, invalid=762
0281: dt=7.593220, rms=0.538 (0.061%), neg=0, invalid=762
0282: dt=7.593220, rms=0.538 (0.059%), neg=0, invalid=762
0283: dt=7.593220, rms=0.537 (0.061%), neg=0, invalid=762
0284: dt=7.593220, rms=0.537 (0.055%), neg=0, invalid=762
0285: dt=7.593220, rms=0.537 (0.041%), neg=0, invalid=762
0286: dt=7.593220, rms=0.537 (0.046%), neg=0, invalid=762
0287: dt=7.593220, rms=0.536 (0.043%), neg=0, invalid=762
0288: dt=7.593220, rms=0.536 (0.035%), neg=0, invalid=762
0289: dt=7.593220, rms=0.536 (0.030%), neg=0, invalid=762
0290: dt=7.593220, rms=0.536 (0.021%), neg=0, invalid=762
0291: dt=7.593220, rms=0.536 (0.028%), neg=0, invalid=762
0292: dt=7.593220, rms=0.536 (0.029%), neg=0, invalid=762
0293: dt=7.593220, rms=0.536 (0.023%), neg=0, invalid=762
0294: dt=7.593220, rms=0.535 (0.025%), neg=0, invalid=762
0295: dt=7.593220, rms=0.535 (0.023%), neg=0, invalid=762
0296: dt=7.593220, rms=0.535 (0.016%), neg=0, invalid=762
0297: dt=4.032000, rms=0.535 (0.000%), neg=0, invalid=762
0298: dt=4.032000, rms=0.535 (0.003%), neg=0, invalid=762
0299: dt=4.032000, rms=0.535 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.553, neg=0, invalid=762
0300: dt=0.000000, rms=0.552 (0.134%), neg=0, invalid=762
0301: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=762
0302: dt=0.100000, rms=0.552 (-0.140%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.553, neg=0, invalid=762
0303: dt=0.000000, rms=0.552 (0.134%), neg=0, invalid=762
0304: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=762
0305: dt=0.100000, rms=0.552 (-0.131%), 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=0.524, neg=0, invalid=762
0306: dt=0.448000, rms=0.511 (2.561%), neg=0, invalid=762
0307: dt=0.448000, rms=0.508 (0.645%), neg=0, invalid=762
0308: dt=0.448000, rms=0.506 (0.373%), neg=0, invalid=762
0309: dt=0.384000, rms=0.505 (0.210%), neg=0, invalid=762
0310: dt=0.384000, rms=0.504 (0.170%), neg=0, invalid=762
0311: dt=0.384000, rms=0.503 (0.123%), neg=0, invalid=762
0312: dt=0.448000, rms=0.502 (0.126%), neg=0, invalid=762
0313: dt=0.448000, rms=0.502 (0.089%), neg=0, invalid=762
0314: dt=0.448000, rms=0.502 (0.088%), neg=0, invalid=762
0315: dt=0.448000, rms=0.501 (0.054%), neg=0, invalid=762
0316: dt=0.448000, rms=0.501 (0.065%), neg=0, invalid=762
0317: dt=0.448000, rms=0.501 (0.039%), neg=0, invalid=762
0318: dt=0.448000, rms=0.501 (0.051%), neg=0, invalid=762
0319: dt=0.448000, rms=0.500 (0.069%), neg=0, invalid=762
0320: dt=0.448000, rms=0.500 (0.025%), neg=0, invalid=762
0321: dt=0.448000, rms=0.500 (0.057%), neg=0, invalid=762
0322: dt=0.448000, rms=0.500 (0.022%), neg=0, invalid=762
0323: dt=0.448000, rms=0.500 (0.026%), neg=0, invalid=762
0324: dt=0.448000, rms=0.499 (0.019%), neg=0, invalid=762
0325: dt=0.448000, rms=0.499 (0.031%), neg=0, invalid=762
0326: dt=0.224000, rms=0.499 (0.010%), neg=0, invalid=762
0327: dt=0.224000, rms=0.499 (0.012%), neg=0, invalid=762
0328: dt=0.224000, rms=0.499 (0.003%), neg=0, invalid=762
0329: dt=0.112000, rms=0.499 (0.004%), neg=0, invalid=762
0330: dt=0.320000, rms=0.499 (0.010%), neg=0, invalid=762
0331: dt=0.256000, rms=0.499 (0.003%), neg=0, invalid=762
0332: dt=0.256000, rms=0.499 (0.006%), neg=0, invalid=762
0333: dt=0.256000, rms=0.499 (0.008%), neg=0, invalid=762
0334: dt=0.256000, rms=0.499 (0.003%), neg=0, invalid=762
0335: dt=0.256000, rms=0.499 (0.009%), neg=0, invalid=762
0336: dt=0.256000, rms=0.499 (0.012%), neg=0, invalid=762
0337: dt=0.256000, rms=0.499 (0.012%), neg=0, invalid=762
0338: dt=0.256000, rms=0.499 (0.012%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.500, neg=0, invalid=762
0339: dt=0.320000, rms=0.496 (0.717%), neg=0, invalid=762
0340: dt=0.320000, rms=0.495 (0.198%), neg=0, invalid=762
0341: dt=0.320000, rms=0.495 (0.082%), neg=0, invalid=762
0342: dt=0.320000, rms=0.495 (0.025%), neg=0, invalid=762
0343: dt=0.320000, rms=0.494 (0.019%), neg=0, invalid=762
0344: dt=0.320000, rms=0.494 (0.008%), neg=0, invalid=762
0345: dt=0.160000, rms=0.494 (-0.001%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.493, neg=0, invalid=762
0346: dt=0.000000, rms=0.492 (0.175%), neg=0, invalid=762
0347: 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
0348: dt=32.368000, rms=0.492 (0.182%), neg=0, invalid=762
0349: dt=55.488000, rms=0.492 (0.005%), neg=0, invalid=762
0350: dt=55.488000, rms=0.492 (0.007%), neg=0, invalid=762
0351: dt=55.488000, rms=0.492 (0.011%), neg=0, invalid=762
0352: dt=55.488000, rms=0.492 (0.012%), neg=0, invalid=762
0353: dt=55.488000, rms=0.492 (0.017%), neg=0, invalid=762
0354: dt=55.488000, rms=0.491 (0.024%), neg=0, invalid=762
0355: dt=55.488000, rms=0.491 (0.023%), neg=0, invalid=762
0356: dt=55.488000, rms=0.491 (0.021%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0357: dt=31.104000, rms=0.491 (0.239%), neg=0, invalid=762
0358: dt=36.288000, rms=0.491 (0.036%), neg=0, invalid=762
0359: dt=36.288000, rms=0.491 (0.032%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0360: dt=36.288000, rms=0.491 (0.001%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0361: dt=36.288000, rms=0.491 (-0.075%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.491, neg=0, invalid=762
0362: dt=36.288000, rms=0.489 (0.469%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0363: dt=124.416000, rms=0.488 (0.235%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0364: dt=124.416000, rms=0.488 (-0.358%), 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 = 24
after 11 iterations, nbhd size=1, neg = 0
0365: dt=38.400000, rms=0.484 (1.040%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 9 iterations, nbhd size=1, neg = 0
0366: dt=37.857143, rms=0.482 (0.446%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0367: dt=25.600000, rms=0.480 (0.373%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 9 iterations, nbhd size=1, neg = 0
0368: dt=19.200000, rms=0.479 (0.177%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0369: dt=19.200000, rms=0.478 (0.150%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 4 iterations, nbhd size=0, neg = 0
0370: dt=19.200000, rms=0.477 (0.205%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 4 iterations, nbhd size=0, neg = 0
0371: dt=19.200000, rms=0.476 (0.223%), neg=0, invalid=762
iter 0, gcam->neg = 30
after 11 iterations, nbhd size=1, neg = 0
0372: dt=19.200000, rms=0.475 (0.188%), neg=0, invalid=762
iter 0, gcam->neg = 38
after 13 iterations, nbhd size=1, neg = 0
0373: dt=19.200000, rms=0.475 (0.140%), neg=0, invalid=762
iter 0, gcam->neg = 46
after 13 iterations, nbhd size=1, neg = 0
0374: dt=19.200000, rms=0.474 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 52
after 17 iterations, nbhd size=1, neg = 0
0375: dt=19.200000, rms=0.474 (0.093%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 12 iterations, nbhd size=1, neg = 0
0376: dt=38.400000, rms=0.473 (0.089%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 4 iterations, nbhd size=0, neg = 0
0377: dt=38.400000, rms=0.473 (-0.024%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.474, neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0378: dt=35.476543, rms=0.470 (0.960%), neg=0, invalid=762
0379: dt=20.895277, rms=0.468 (0.361%), neg=0, invalid=762
0380: dt=32.000000, rms=0.467 (0.249%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0381: dt=32.000000, rms=0.467 (0.013%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0382: dt=32.000000, rms=0.465 (0.420%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0383: dt=32.000000, rms=0.465 (-0.091%), neg=0, invalid=762
0384: dt=11.200000, rms=0.465 (0.051%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0385: dt=102.400000, rms=0.464 (0.124%), neg=0, invalid=762
0386: dt=11.200000, rms=0.464 (0.064%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.471, neg=0, invalid=762
0387: dt=4.173913, rms=0.470 (0.277%), neg=0, invalid=762
0388: dt=2.880000, rms=0.469 (0.018%), neg=0, invalid=762
0389: dt=2.880000, rms=0.469 (0.008%), neg=0, invalid=762
0390: dt=2.880000, rms=0.469 (-0.035%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.470, neg=0, invalid=762
0391: dt=9.575758, rms=0.468 (0.466%), neg=0, invalid=762
0392: dt=12.160000, rms=0.467 (0.138%), neg=0, invalid=762
0393: dt=12.160000, rms=0.467 (0.183%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 3 iterations, nbhd size=0, neg = 0
0394: dt=12.160000, rms=0.466 (0.214%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 12 iterations, nbhd size=1, neg = 0
0395: dt=12.160000, rms=0.465 (0.193%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 10 iterations, nbhd size=1, neg = 0
0396: dt=12.160000, rms=0.463 (0.336%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 3 iterations, nbhd size=0, neg = 0
0397: dt=12.160000, rms=0.461 (0.417%), neg=0, invalid=762
iter 0, gcam->neg = 23
after 13 iterations, nbhd size=1, neg = 0
0398: dt=12.160000, rms=0.460 (0.348%), neg=0, invalid=762
iter 0, gcam->neg = 25
after 11 iterations, nbhd size=1, neg = 0
0399: dt=12.160000, rms=0.459 (0.135%), neg=0, invalid=762
iter 0, gcam->neg = 28
after 11 iterations, nbhd size=1, neg = 0
0400: dt=12.160000, rms=0.459 (0.085%), neg=0, invalid=762
iter 0, gcam->neg = 61
after 16 iterations, nbhd size=1, neg = 0
0401: dt=12.160000, rms=0.459 (-0.044%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0402: dt=5.000000, rms=0.459 (0.012%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0403: dt=3.456000, rms=0.459 (-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=0.466, neg=0, invalid=762
0404: dt=0.000040, rms=0.466 (0.187%), neg=0, invalid=762
0405: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
0406: dt=0.000000, rms=0.466 (0.187%), neg=0, invalid=762
0407: dt=0.000000, rms=0.466 (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=0.455, neg=0, invalid=762
iter 0, gcam->neg = 931
after 15 iterations, nbhd size=1, neg = 0
0408: dt=1.572498, rms=0.437 (3.916%), neg=0, invalid=762
0409: dt=0.000013, rms=0.437 (0.017%), neg=0, invalid=762
0410: dt=0.000013, rms=0.437 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.438, neg=0, invalid=762
0411: dt=0.048000, rms=0.437 (0.252%), neg=0, invalid=762
0412: dt=0.007000, rms=0.437 (0.000%), neg=0, invalid=762
0413: dt=0.007000, rms=0.437 (-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=0.428, neg=0, invalid=762
0414: dt=5.780000, rms=0.428 (0.000%), neg=0, invalid=762
0415: dt=0.014450, rms=0.428 (0.000%), neg=0, invalid=762
0416: dt=0.014450, rms=0.428 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
0417: dt=32.368000, rms=0.428 (0.008%), neg=0, invalid=762
0418: dt=27.744000, rms=0.428 (0.001%), neg=0, invalid=762
0419: dt=27.744000, rms=0.428 (-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=0.428, neg=0, invalid=762
0420: dt=6.480000, rms=0.428 (0.005%), neg=0, invalid=762
0421: dt=1.944000, rms=0.428 (0.000%), neg=0, invalid=762
0422: dt=1.944000, rms=0.428 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
0423: dt=62.208000, rms=0.428 (0.076%), neg=0, invalid=762
0424: dt=82.944000, rms=0.428 (0.050%), neg=0, invalid=762
0425: dt=82.944000, rms=0.428 (0.020%), neg=0, invalid=762
0426: dt=82.944000, rms=0.427 (0.072%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0427: dt=82.944000, rms=0.427 (0.028%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 9 iterations, nbhd size=1, neg = 0
0428: dt=82.944000, rms=0.427 (0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
iter 0, gcam->neg = 9
after 10 iterations, nbhd size=1, neg = 0
0429: dt=9.600000, rms=0.427 (0.056%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0430: dt=4.800000, rms=0.427 (0.009%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0431: dt=4.800000, rms=0.427 (0.001%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 10 iterations, nbhd size=1, neg = 0
0432: dt=4.800000, rms=0.427 (-0.053%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.427, neg=0, invalid=762
iter 0, gcam->neg = 13
after 10 iterations, nbhd size=1, neg = 0
0433: dt=44.800000, rms=0.426 (0.414%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0434: dt=22.656934, rms=0.424 (0.264%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 9 iterations, nbhd size=1, neg = 0
0435: dt=32.000000, rms=0.424 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 9 iterations, nbhd size=1, neg = 0
0436: dt=32.000000, rms=0.423 (0.095%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 2 iterations, nbhd size=0, neg = 0
0437: dt=32.000000, rms=0.422 (0.290%), neg=0, invalid=762
iter 0, gcam->neg = 35
after 10 iterations, nbhd size=1, neg = 0
0438: dt=32.000000, rms=0.422 (0.108%), neg=0, invalid=762
iter 0, gcam->neg = 33
after 13 iterations, nbhd size=1, neg = 0
0439: dt=32.000000, rms=0.421 (0.258%), neg=0, invalid=762
iter 0, gcam->neg = 38
after 16 iterations, nbhd size=1, neg = 0
0440: dt=32.000000, rms=0.420 (0.113%), neg=0, invalid=762
iter 0, gcam->neg = 39
after 15 iterations, nbhd size=1, neg = 0
0441: dt=32.000000, rms=0.420 (0.113%), neg=0, invalid=762
iter 0, gcam->neg = 40
after 12 iterations, nbhd size=1, neg = 0
0442: dt=32.000000, rms=0.419 (0.088%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0443: dt=11.200000, rms=0.419 (0.035%), neg=0, invalid=762
0444: dt=11.200000, rms=0.419 (0.011%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0445: dt=11.200000, rms=0.419 (0.016%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 9 iterations, nbhd size=1, neg = 0
0446: dt=11.200000, rms=0.419 (-0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=0, neg = 0
0447: dt=3.700000, rms=0.423 (0.059%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0448: dt=1.008000, rms=0.423 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
iter 0, gcam->neg = 16
after 4 iterations, nbhd size=0, neg = 0
0449: dt=11.520000, rms=0.422 (0.231%), neg=0, invalid=762
iter 0, gcam->neg = 41
after 13 iterations, nbhd size=1, neg = 0
0450: dt=23.741935, rms=0.421 (0.200%), neg=0, invalid=762
iter 0, gcam->neg = 36
after 12 iterations, nbhd size=1, neg = 0
0451: dt=23.741935, rms=0.421 (0.031%), neg=0, invalid=762
iter 0, gcam->neg = 100
after 16 iterations, nbhd size=1, neg = 0
0452: dt=23.741935, rms=0.420 (0.202%), neg=0, invalid=762
iter 0, gcam->neg = 239
after 17 iterations, nbhd size=1, neg = 0
0453: dt=23.741935, rms=0.420 (0.133%), neg=0, invalid=762
iter 0, gcam->neg = 347
after 18 iterations, nbhd size=1, neg = 0
0454: dt=23.741935, rms=0.420 (-0.068%), neg=0, invalid=762
iter 0, gcam->neg = 25
after 14 iterations, nbhd size=1, neg = 0
0455: dt=11.520000, rms=0.419 (0.174%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 4 iterations, nbhd size=0, neg = 0
0456: dt=7.219512, rms=0.419 (0.033%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.424, neg=0, invalid=762
0457: dt=0.000060, rms=0.424 (0.000%), neg=0, invalid=762
0458: dt=0.000000, rms=0.424 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.424, neg=0, invalid=762
0459: dt=0.000000, rms=0.424 (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=0.415, neg=0, invalid=762
iter 0, gcam->neg = 623
after 13 iterations, nbhd size=1, neg = 0
0460: dt=1.024000, rms=0.409 (1.569%), neg=0, invalid=762
0461: dt=0.000027, rms=0.409 (0.000%), neg=0, invalid=762
0462: dt=0.000027, rms=0.409 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0463: dt=0.112000, rms=0.408 (0.097%), neg=0, invalid=762
0464: dt=0.112000, rms=0.408 (0.059%), neg=0, invalid=762
0465: dt=0.112000, rms=0.408 (0.051%), neg=0, invalid=762
0466: dt=0.112000, rms=0.408 (0.046%), neg=0, invalid=762
0467: dt=0.112000, rms=0.408 (-0.010%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 23 minutes and 10 seconds.
mri_ca_register utimesec    9437.213325
mri_ca_register stimesec    9.311584
mri_ca_register ru_maxrss   1334752
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4627682
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  62752
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3536
mri_ca_register ru_nivcsw   22807
FSRUNTIME@ mri_ca_register  2.3862 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 04:35:11 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-575
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-6.0.0/0050564/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 5.86
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 = 0.09689 (27)
Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (292 voxels, overlap=0.219)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (292 voxels, peak = 31), gca=30.0
gca peak = 0.17677 (13)
mri peak = 0.12735 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.62 x + 0.0 (316 voxels, overlap=0.510)
Right_Lateral_Ventricle (43): linear fit = 0.62 x + 0.0 (316 voxels, peak =  8), gca=8.1
gca peak = 0.28129 (95)
mri peak = 0.11880 (94)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (766 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (766 voxels, peak = 94), gca=93.6
gca peak = 0.16930 (96)
mri peak = 0.10989 (96)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (819 voxels, overlap=1.011)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (819 voxels, peak = 98), gca=98.4
gca peak = 0.24553 (55)
mri peak = 0.11542 (61)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (954 voxels, overlap=1.006)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (954 voxels, peak = 57), gca=57.5
gca peak = 0.30264 (59)
mri peak = 0.09198 (59)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (857 voxels, overlap=1.010)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (857 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.09916 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (28300 voxels, overlap=0.597)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (28300 voxels, peak = 107), gca=106.6
gca peak = 0.07714 (104)
mri peak = 0.10315 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (29258 voxels, overlap=0.465)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (29258 voxels, peak = 110), gca=109.7
gca peak = 0.09712 (58)
mri peak = 0.04022 (55)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (39053 voxels, overlap=0.881)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (39053 voxels, peak = 55), gca=54.8
gca peak = 0.11620 (58)
mri peak = 0.04523 (55)
Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (39604 voxels, overlap=0.967)
Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (39604 voxels, peak = 55), gca=54.8
gca peak = 0.30970 (66)
mri peak = 0.13349 (72)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (982 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (982 voxels, peak = 70), gca=70.3
gca peak = 0.15280 (69)
mri peak = 0.12129 (71)
Left_Caudate (11): linear fit = 0.96 x + 0.0 (754 voxels, overlap=0.803)
Left_Caudate (11): linear fit = 0.96 x + 0.0 (754 voxels, peak = 67), gca=66.6
gca peak = 0.13902 (56)
mri peak = 0.04936 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (32456 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (32456 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.05871 (57)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (34730 voxels, overlap=0.971)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (34730 voxels, peak = 59), gca=58.6
gca peak = 0.16765 (84)
mri peak = 0.07940 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6025 voxels, overlap=0.637)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6025 voxels, peak = 92), gca=92.0
gca peak = 0.18739 (84)
mri peak = 0.08729 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (5909 voxels, overlap=0.557)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (5909 voxels, peak = 91), gca=91.1
gca peak = 0.29869 (57)
mri peak = 0.11192 (61)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (481 voxels, overlap=1.009)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (481 voxels, peak = 60), gca=59.6
gca peak = 0.33601 (57)
mri peak = 0.09863 (63)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (546 voxels, overlap=1.021)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (546 voxels, peak = 60), gca=59.6
gca peak = 0.11131 (90)
mri peak = 0.07188 (84)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3846 voxels, overlap=0.995)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3846 voxels, peak = 88), gca=87.8
gca peak = 0.11793 (83)
mri peak = 0.08288 (84)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4085 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4085 voxels, peak = 83), gca=83.0
gca peak = 0.08324 (81)
mri peak = 0.09372 (82)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2131 voxels, overlap=0.876)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2131 voxels, peak = 83), gca=83.0
gca peak = 0.10360 (77)
mri peak = 0.10460 (79)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2390 voxels, overlap=0.950)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2390 voxels, peak = 76), gca=75.8
gca peak = 0.08424 (78)
mri peak = 0.07778 (88)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11266 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11266 voxels, peak = 85), gca=85.4
gca peak = 0.12631 (89)
mri peak = 0.06683 (99)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1424 voxels, overlap=0.796)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1424 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.05414 (95)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1455 voxels, overlap=0.869)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1455 voxels, peak = 96), gca=96.1
gca peak = 0.14975 (24)
mri peak = 0.05601 (30)
gca peak = 0.19357 (14)
mri peak = 0.07855 (11)
Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (229 voxels, overlap=0.588)
Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (229 voxels, peak = 10), gca=10.3
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.95 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.12354 (31)
mri peak = 0.09689 (27)
Left_Lateral_Ventricle (4): linear fit = 0.92 x + 0.0 (292 voxels, overlap=0.793)
Left_Lateral_Ventricle (4): linear fit = 0.92 x + 0.0 (292 voxels, peak = 28), gca=28.4
gca peak = 0.27420 ( 8)
mri peak = 0.12735 ( 9)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (316 voxels, overlap=0.906)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (316 voxels, peak =  8), gca=8.4
gca peak = 0.24586 (93)
mri peak = 0.11880 (94)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (766 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (766 voxels, peak = 93), gca=92.5
gca peak = 0.18354 (99)
mri peak = 0.10989 (96)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (819 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (819 voxels, peak = 99), gca=99.5
gca peak = 0.29355 (58)
mri peak = 0.11542 (61)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (954 voxels, overlap=1.003)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (954 voxels, peak = 58), gca=58.0
gca peak = 0.31504 (59)
mri peak = 0.09198 (59)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (857 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (857 voxels, peak = 56), gca=55.8
gca peak = 0.07494 (106)
mri peak = 0.09916 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28300 voxels, overlap=0.745)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28300 voxels, peak = 105), gca=105.5
gca peak = 0.07562 (110)
mri peak = 0.10315 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29258 voxels, overlap=0.714)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29258 voxels, peak = 110), gca=110.0
gca peak = 0.10312 (55)
mri peak = 0.04022 (55)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (39053 voxels, overlap=0.996)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (39053 voxels, peak = 56), gca=56.4
gca peak = 0.12327 (55)
mri peak = 0.04523 (55)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (39604 voxels, overlap=0.989)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (39604 voxels, peak = 54), gca=54.2
gca peak = 0.26187 (71)
mri peak = 0.13349 (72)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (982 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (982 voxels, peak = 71), gca=71.0
gca peak = 0.13032 (67)
mri peak = 0.12129 (71)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (754 voxels, overlap=0.992)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (754 voxels, peak = 66), gca=66.0
gca peak = 0.13307 (57)
mri peak = 0.04936 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (32456 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (32456 voxels, peak = 58), gca=58.4
gca peak = 0.13829 (58)
mri peak = 0.05871 (57)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (34730 voxels, overlap=0.994)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (34730 voxels, peak = 57), gca=57.1
gca peak = 0.15182 (92)
mri peak = 0.07940 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6025 voxels, overlap=0.977)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6025 voxels, peak = 92), gca=91.5
gca peak = 0.15112 (91)
mri peak = 0.08729 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, overlap=0.956)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, peak = 91), gca=90.5
gca peak = 0.26844 (61)
mri peak = 0.11192 (61)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (481 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (481 voxels, peak = 60), gca=60.1
gca peak = 0.30201 (60)
mri peak = 0.09863 (63)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (546 voxels, overlap=1.014)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (546 voxels, peak = 62), gca=61.5
gca peak = 0.11015 (86)
mri peak = 0.07188 (84)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3846 voxels, overlap=0.990)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3846 voxels, peak = 86), gca=85.6
gca peak = 0.12266 (83)
mri peak = 0.08288 (84)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4085 voxels, overlap=0.976)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4085 voxels, peak = 83), gca=83.0
gca peak = 0.09216 (77)
mri peak = 0.09372 (82)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2131 voxels, overlap=0.939)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2131 voxels, peak = 77), gca=77.0
gca peak = 0.09204 (76)
mri peak = 0.10460 (79)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2390 voxels, overlap=0.938)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2390 voxels, peak = 77), gca=77.1
gca peak = 0.08005 (86)
mri peak = 0.07778 (88)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11266 voxels, overlap=0.808)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11266 voxels, peak = 87), gca=87.3
gca peak = 0.11475 (96)
mri peak = 0.06683 (99)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1424 voxels, overlap=0.901)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1424 voxels, peak = 96), gca=95.5
gca peak = 0.15150 (94)
mri peak = 0.05414 (95)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1455 voxels, overlap=0.967)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1455 voxels, peak = 94), gca=94.0
gca peak = 0.17139 (24)
mri peak = 0.05601 (30)
gca peak = 0.22767 (12)
mri peak = 0.07855 (11)
Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (229 voxels, overlap=0.823)
Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (229 voxels, peak = 13), gca=12.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16503 (28)
gca peak Left_Thalamus = 1.00000 (95)
gca peak Third_Ventricle = 0.17139 (24)
gca peak CSF = 0.20324 (34)
gca peak Left_Accumbens_area = 0.81130 (60)
gca peak Left_undetermined = 0.95280 (34)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12475 (35)
gca peak Right_Inf_Lat_Vent = 0.24299 (24)
gca peak Right_Accumbens_area = 0.29950 (69)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.54107 (31)
gca peak WM_hypointensities = 0.06874 (81)
gca peak non_WM_hypointensities = 0.08561 (45)
gca peak Optic_Chiasm = 0.68769 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.00 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
50924 voxels changed in iteration 0 of unlikely voxel relabeling
228 voxels changed in iteration 1 of unlikely voxel relabeling
5 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
26496 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels)
418 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 61227 changed. image ll: -2.100, PF=0.500
pass 2: 17923 changed. image ll: -2.100, PF=0.500
pass 3: 6293 changed.
pass 4: 2555 changed.
31156 voxels changed in iteration 0 of unlikely voxel relabeling
210 voxels changed in iteration 1 of unlikely voxel relabeling
8 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5917 voxels changed in iteration 0 of unlikely voxel relabeling
78 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
5091 voxels changed in iteration 0 of unlikely voxel relabeling
41 voxels changed in iteration 1 of unlikely voxel relabeling
6 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
4625 voxels changed in iteration 0 of unlikely voxel relabeling
20 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    2976.393519
mri_ca_label stimesec    1.376790
mri_ca_label ru_maxrss   2104236
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   704100
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  62744
mri_ca_label ru_oublock  416
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    268
mri_ca_label ru_nivcsw   5139
auto-labeling took 48 minutes and 53 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/transforms/cc_up.lta 0050564 

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-6.0.0/0050564/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/norm.mgz
20201 voxels in left wm, 37111 in right wm, xrange [126, 133]
searching rotation angles z=[-9  5], y=[-6  8]

searching scale 1 Z rot -9.3  
searching scale 1 Z rot -9.0  
searching scale 1 Z rot -8.8  
searching scale 1 Z rot -8.5  
searching scale 1 Z rot -8.3  
searching scale 1 Z rot -8.0  
searching scale 1 Z rot -7.8  
searching scale 1 Z rot -7.5  
searching scale 1 Z rot -7.3  
searching scale 1 Z rot -7.0  
searching scale 1 Z rot -6.8  
searching scale 1 Z rot -6.5  
searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.0  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.5  global minimum found at slice 130.0, rotations (0.63, -2.54)
final transformation (x=130.0, yr=0.629, zr=-2.544):
 0.99895   0.04439   0.01097  -8.36197;
-0.04439   0.99901  -0.00049   18.94590;
-0.01098   0.00000   0.99994   2.43481;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 115 127
eigenvectors:
 0.00096  -0.01221   0.99993;
 0.19994  -0.97973  -0.01216;
 0.97981   0.19993   0.00150;
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.6 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 05:24:38 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 05:24:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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...
1537 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 58 (58), valley at  0 (-1)
csf peak at 29, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at  0 (-1)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 52 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 05:27:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1429462 voxels in mask (pct=  8.52)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 05:27:33 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 (103.0): 104.2 +- 5.6 [79.0 --> 125.0]
GM (71.0) : 69.8 +- 9.6 [30.0 --> 95.0]
setting bottom of white matter range to 79.3
setting top of gray matter range to 88.9
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...
3968 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4695 filled
2413 bright non-wm voxels segmented.
1968 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 0.49 minutes
reading wm segmentation from wm.seg.mgz...
321 voxels added to wm to prevent paths from MTL structures to cortex
3066 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 35108 voxels turned on, 41019 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 92   new 92
115,126,128 old 92   new 92
writing edited volume to wm.asegedit.mgz....

 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  17 found -  17 modified     |    TOTAL:  17
pass   2 (xy+):   0 found -  17 modified     |    TOTAL:  17
pass   1 (xy-):  19 found -  19 modified     |    TOTAL:  36
pass   2 (xy-):   0 found -  19 modified     |    TOTAL:  36
pass   1 (yz+):  24 found -  24 modified     |    TOTAL:  60
pass   2 (yz+):   0 found -  24 modified     |    TOTAL:  60
pass   1 (yz-):  26 found -  26 modified     |    TOTAL:  86
pass   2 (yz-):   0 found -  26 modified     |    TOTAL:  86
pass   1 (xz+):  17 found -  17 modified     |    TOTAL: 103
pass   2 (xz+):   0 found -  17 modified     |    TOTAL: 103
pass   1 (xz-):  19 found -  19 modified     |    TOTAL: 122
pass   2 (xz-):   0 found -  19 modified     |    TOTAL: 122
Iteration Number : 1
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  12
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  12
pass   1 (+++):  24 found -  24 modified     |    TOTAL:  36
pass   2 (+++):   0 found -  24 modified     |    TOTAL:  36
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  52
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  52
pass   1 (+++):  29 found -  29 modified     |    TOTAL:  81
pass   2 (+++):   0 found -  29 modified     |    TOTAL:  81
Iteration Number : 1
pass   1 (++):  61 found -  61 modified     |    TOTAL:  61
pass   2 (++):   0 found -  61 modified     |    TOTAL:  61
pass   1 (+-):  61 found -  61 modified     |    TOTAL: 122
pass   2 (+-):   0 found -  61 modified     |    TOTAL: 122
pass   1 (--):  96 found -  96 modified     |    TOTAL: 218
pass   2 (--):   0 found -  96 modified     |    TOTAL: 218
pass   1 (-+):  73 found -  73 modified     |    TOTAL: 291
pass   2 (-+):   0 found -  73 modified     |    TOTAL: 291
Iteration Number : 2
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   9 found -   9 modified     |    TOTAL:  12
pass   2 (xy-):   0 found -   9 modified     |    TOTAL:  12
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:  12
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  15
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  15
pass   1 (xz+):   6 found -   6 modified     |    TOTAL:  21
pass   2 (xz+):   0 found -   6 modified     |    TOTAL:  21
pass   1 (xz-):   4 found -   4 modified     |    TOTAL:  25
pass   2 (xz-):   0 found -   4 modified     |    TOTAL:  25
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (+++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   7
Iteration Number : 2
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   5 found -   5 modified     |    TOTAL:   8
pass   2 (+-):   0 found -   5 modified     |    TOTAL:   8
pass   1 (--):   2 found -   2 modified     |    TOTAL:  10
pass   2 (--):   0 found -   2 modified     |    TOTAL:  10
pass   1 (-+):   1 found -   1 modified     |    TOTAL:  11
pass   2 (-+):   0 found -   1 modified     |    TOTAL:  11
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 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 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 539 (out of 445882: 0.120884)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 05:29:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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
 1.06154   0.04178   0.00901  -17.05453;
-0.03238   1.20303  -0.03769  -29.20528;
-0.00781   0.05526   1.06661  -30.35489;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.06154   0.04178   0.00901  -17.05453;
-0.03238   1.20303  -0.03769  -29.20528;
-0.00781   0.05526   1.06661  -30.35489;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1243 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75)
no need to search
using seed (126, 125, 151), TAL = (2.0, 23.0, 3.0)
talairach voxel to voxel transform
 0.94097  -0.03226  -0.00909   14.82987;
 0.02550   0.82902   0.02907   25.52910;
 0.00557  -0.04319   0.93597   27.24508;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  125,  151) --> (2.0, 23.0, 3.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (2.00, 23.00, 3.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 23.00, 3.00) SRC: (111.05, 136.30, 163.78)
search lh wm seed point around talairach space (-16.00, 23.00, 3.00), SRC: (144.93, 137.22, 163.98)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 05:30:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
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 = 12 (out of 209135: 0.005738)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 1627 vertices, 1732 faces
slice 60: 5503 vertices, 5656 faces
slice 70: 11601 vertices, 11867 faces
slice 80: 19284 vertices, 19563 faces
slice 90: 27921 vertices, 28272 faces
slice 100: 37410 vertices, 37696 faces
slice 110: 47191 vertices, 47572 faces
slice 120: 58309 vertices, 58721 faces
slice 130: 69454 vertices, 69864 faces
slice 140: 79080 vertices, 79448 faces
slice 150: 87745 vertices, 88107 faces
slice 160: 95708 vertices, 96046 faces
slice 170: 102455 vertices, 102784 faces
slice 180: 108508 vertices, 108765 faces
slice 190: 113802 vertices, 114047 faces
slice 200: 116813 vertices, 116982 faces
slice 210: 117518 vertices, 117604 faces
slice 220: 117518 vertices, 117604 faces
slice 230: 117518 vertices, 117604 faces
slice 240: 117518 vertices, 117604 faces
slice 250: 117518 vertices, 117604 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...
   117518 voxel in cpt #1: X=-86 [v=117518,e=352812,f=235208] located at (-27.958448, -7.646633, 3.063301)
For the whole surface: X=-86 [v=117518,e=352812,f=235208]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 05:30:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   6
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   3 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 9 (out of 215699: 0.004172)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 933 vertices, 1023 faces
slice 60: 4258 vertices, 4434 faces
slice 70: 10836 vertices, 11088 faces
slice 80: 18693 vertices, 18966 faces
slice 90: 27630 vertices, 27924 faces
slice 100: 36481 vertices, 36799 faces
slice 110: 47423 vertices, 47812 faces
slice 120: 59158 vertices, 59574 faces
slice 130: 70663 vertices, 71097 faces
slice 140: 81910 vertices, 82348 faces
slice 150: 91535 vertices, 91896 faces
slice 160: 99113 vertices, 99448 faces
slice 170: 106257 vertices, 106590 faces
slice 180: 112791 vertices, 113102 faces
slice 190: 118364 vertices, 118649 faces
slice 200: 121793 vertices, 121966 faces
slice 210: 122494 vertices, 122592 faces
slice 220: 122494 vertices, 122592 faces
slice 230: 122494 vertices, 122592 faces
slice 240: 122494 vertices, 122592 faces
slice 250: 122494 vertices, 122592 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...
   122494 voxel in cpt #1: X=-98 [v=122494,e=367776,f=245184] located at (24.671511, -6.302701, 6.675413)
For the whole surface: X=-98 [v=122494,e=367776,f=245184]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 05:30:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 05:30:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

Waiting for PID 2485 of (2485 2488) to complete...
Waiting for PID 2488 of (2485 2488) 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 (2485 2488) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 05:30:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 05:30:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Waiting for PID 2538 of (2538 2541) to complete...
Waiting for PID 2541 of (2538 2541) to complete...

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 44.4 mm, total surface area = 62105 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.6 minutes

step 000: RMS=0.164 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.102 (target=0.015)   
step 015: RMS=0.090 (target=0.015)   
step 020: RMS=0.081 (target=0.015)   
step 025: RMS=0.073 (target=0.015)   
step 030: RMS=0.067 (target=0.015)   
step 035: RMS=0.064 (target=0.015)   
step 040: RMS=0.061 (target=0.015)   
step 045: RMS=0.060 (target=0.015)   
step 050: RMS=0.058 (target=0.015)   
step 055: RMS=0.057 (target=0.015)   
step 060: RMS=0.056 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    37.380317
mris_inflate stimesec    0.114982
mris_inflate ru_maxrss   172748
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   25754
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  8272
mris_inflate ru_oublock  8288
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    6383
mris_inflate ru_nivcsw   3442

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 44.5 mm, total surface area = 64841 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.6 minutes

step 000: RMS=0.163 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.099 (target=0.015)   
step 015: RMS=0.088 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.071 (target=0.015)   
step 030: RMS=0.067 (target=0.015)   
step 035: RMS=0.065 (target=0.015)   
step 040: RMS=0.062 (target=0.015)   
step 045: RMS=0.060 (target=0.015)   
step 050: RMS=0.058 (target=0.015)   
step 055: RMS=0.058 (target=0.015)   
step 060: RMS=0.058 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    38.907085
mris_inflate stimesec    0.081987
mris_inflate ru_maxrss   179616
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   25932
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  8624
mris_inflate ru_oublock  8640
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    3254
mris_inflate ru_nivcsw   4974
PIDs (2538 2541) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 05:31:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

#--------------------------------------------
#@# QSphere rh Sun Oct  8 05:31:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

Waiting for PID 2672 of (2672 2675) to complete...
Waiting for PID 2675 of (2672 2675) 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 1.04 +- 0.65 (0.00-->8.46) (max @ vno 43768 --> 44837)
face area 0.03 +- 0.04 (-0.41-->0.88)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.319...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.597, avgs=0
005/300: dt: 0.9000, rms radial error=177.337, avgs=0
010/300: dt: 0.9000, rms radial error=176.778, avgs=0
015/300: dt: 0.9000, rms radial error=176.044, avgs=0
020/300: dt: 0.9000, rms radial error=175.207, avgs=0
025/300: dt: 0.9000, rms radial error=174.311, avgs=0
030/300: dt: 0.9000, rms radial error=173.383, avgs=0
035/300: dt: 0.9000, rms radial error=172.437, avgs=0
040/300: dt: 0.9000, rms radial error=171.483, avgs=0
045/300: dt: 0.9000, rms radial error=170.527, avgs=0
050/300: dt: 0.9000, rms radial error=169.572, avgs=0
055/300: dt: 0.9000, rms radial error=168.620, avgs=0
060/300: dt: 0.9000, rms radial error=167.671, avgs=0
065/300: dt: 0.9000, rms radial error=166.727, avgs=0
070/300: dt: 0.9000, rms radial error=165.787, avgs=0
075/300: dt: 0.9000, rms radial error=164.852, avgs=0
080/300: dt: 0.9000, rms radial error=163.922, avgs=0
085/300: dt: 0.9000, rms radial error=162.997, avgs=0
090/300: dt: 0.9000, rms radial error=162.078, avgs=0
095/300: dt: 0.9000, rms radial error=161.163, avgs=0
100/300: dt: 0.9000, rms radial error=160.253, avgs=0
105/300: dt: 0.9000, rms radial error=159.348, avgs=0
110/300: dt: 0.9000, rms radial error=158.448, avgs=0
115/300: dt: 0.9000, rms radial error=157.553, avgs=0
120/300: dt: 0.9000, rms radial error=156.662, avgs=0
125/300: dt: 0.9000, rms radial error=155.776, avgs=0
130/300: dt: 0.9000, rms radial error=154.896, avgs=0
135/300: dt: 0.9000, rms radial error=154.023, avgs=0
140/300: dt: 0.9000, rms radial error=153.155, avgs=0
145/300: dt: 0.9000, rms radial error=152.293, avgs=0
150/300: dt: 0.9000, rms radial error=151.435, avgs=0
155/300: dt: 0.9000, rms radial error=150.583, avgs=0
160/300: dt: 0.9000, rms radial error=149.734, avgs=0
165/300: dt: 0.9000, rms radial error=148.891, avgs=0
170/300: dt: 0.9000, rms radial error=148.052, avgs=0
175/300: dt: 0.9000, rms radial error=147.218, avgs=0
180/300: dt: 0.9000, rms radial error=146.389, avgs=0
185/300: dt: 0.9000, rms radial error=145.565, avgs=0
190/300: dt: 0.9000, rms radial error=144.745, avgs=0
195/300: dt: 0.9000, rms radial error=143.930, avgs=0
200/300: dt: 0.9000, rms radial error=143.120, avgs=0
205/300: dt: 0.9000, rms radial error=142.313, avgs=0
210/300: dt: 0.9000, rms radial error=141.512, avgs=0
215/300: dt: 0.9000, rms radial error=140.714, avgs=0
220/300: dt: 0.9000, rms radial error=139.922, avgs=0
225/300: dt: 0.9000, rms radial error=139.133, avgs=0
230/300: dt: 0.9000, rms radial error=138.349, avgs=0
235/300: dt: 0.9000, rms radial error=137.570, avgs=0
240/300: dt: 0.9000, rms radial error=136.794, avgs=0
245/300: dt: 0.9000, rms radial error=136.023, avgs=0
250/300: dt: 0.9000, rms radial error=135.257, avgs=0
255/300: dt: 0.9000, rms radial error=134.495, avgs=0
260/300: dt: 0.9000, rms radial error=133.737, avgs=0
265/300: dt: 0.9000, rms radial error=132.983, avgs=0
270/300: dt: 0.9000, rms radial error=132.233, avgs=0
275/300: dt: 0.9000, rms radial error=131.488, avgs=0
280/300: dt: 0.9000, rms radial error=130.747, avgs=0
285/300: dt: 0.9000, rms radial error=130.010, avgs=0
290/300: dt: 0.9000, rms radial error=129.277, avgs=0
295/300: dt: 0.9000, rms radial error=128.548, avgs=0
300/300: dt: 0.9000, rms radial error=127.824, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 13675.50
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 2 (K=40.0), pass 1, starting sse = 2319.94
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
epoch 3 (K=160.0), pass 1, starting sse = 271.14
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/10 = 0.00552
epoch 4 (K=640.0), pass 1, starting sse = 25.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/10 = 0.00673
final distance error %28.05
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.06 hours
mris_sphere utimesec    208.772261
mris_sphere stimesec    0.135979
mris_sphere ru_maxrss   172944
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   25294
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  8272
mris_sphere ru_oublock  8312
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8269
mris_sphere ru_nivcsw   15261
FSRUNTIME@ mris_sphere  0.0580 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 1.02 +- 0.63 (0.00-->7.21) (max @ vno 87431 --> 87453)
face area 0.03 +- 0.03 (-0.08-->0.61)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.319...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.241, avgs=0
005/300: dt: 0.9000, rms radial error=176.982, avgs=0
010/300: dt: 0.9000, rms radial error=176.424, avgs=0
015/300: dt: 0.9000, rms radial error=175.692, avgs=0
020/300: dt: 0.9000, rms radial error=174.860, avgs=0
025/300: dt: 0.9000, rms radial error=173.969, avgs=0
030/300: dt: 0.9000, rms radial error=173.047, avgs=0
035/300: dt: 0.9000, rms radial error=172.107, avgs=0
040/300: dt: 0.9000, rms radial error=171.160, avgs=0
045/300: dt: 0.9000, rms radial error=170.210, avgs=0
050/300: dt: 0.9000, rms radial error=169.260, avgs=0
055/300: dt: 0.9000, rms radial error=168.314, avgs=0
060/300: dt: 0.9000, rms radial error=167.370, avgs=0
065/300: dt: 0.9000, rms radial error=166.431, avgs=0
070/300: dt: 0.9000, rms radial error=165.497, avgs=0
075/300: dt: 0.9000, rms radial error=164.567, avgs=0
080/300: dt: 0.9000, rms radial error=163.642, avgs=0
085/300: dt: 0.9000, rms radial error=162.722, avgs=0
090/300: dt: 0.9000, rms radial error=161.807, avgs=0
095/300: dt: 0.9000, rms radial error=160.897, avgs=0
100/300: dt: 0.9000, rms radial error=159.991, avgs=0
105/300: dt: 0.9000, rms radial error=159.091, avgs=0
110/300: dt: 0.9000, rms radial error=158.195, avgs=0
115/300: dt: 0.9000, rms radial error=157.304, avgs=0
120/300: dt: 0.9000, rms radial error=156.418, avgs=0
125/300: dt: 0.9000, rms radial error=155.537, avgs=0
130/300: dt: 0.9000, rms radial error=154.662, avgs=0
135/300: dt: 0.9000, rms radial error=153.791, avgs=0
140/300: dt: 0.9000, rms radial error=152.925, avgs=0
145/300: dt: 0.9000, rms radial error=152.064, avgs=0
150/300: dt: 0.9000, rms radial error=151.207, avgs=0
155/300: dt: 0.9000, rms radial error=150.355, avgs=0
160/300: dt: 0.9000, rms radial error=149.509, avgs=0
165/300: dt: 0.9000, rms radial error=148.667, avgs=0
170/300: dt: 0.9000, rms radial error=147.829, avgs=0
175/300: dt: 0.9000, rms radial error=146.996, avgs=0
180/300: dt: 0.9000, rms radial error=146.168, avgs=0
185/300: dt: 0.9000, rms radial error=145.345, avgs=0
190/300: dt: 0.9000, rms radial error=144.526, avgs=0
195/300: dt: 0.9000, rms radial error=143.711, avgs=0
200/300: dt: 0.9000, rms radial error=142.901, avgs=0
205/300: dt: 0.9000, rms radial error=142.096, avgs=0
210/300: dt: 0.9000, rms radial error=141.294, avgs=0
215/300: dt: 0.9000, rms radial error=140.497, avgs=0
220/300: dt: 0.9000, rms radial error=139.705, avgs=0
225/300: dt: 0.9000, rms radial error=138.917, avgs=0
230/300: dt: 0.9000, rms radial error=138.134, avgs=0
235/300: dt: 0.9000, rms radial error=137.355, avgs=0
240/300: dt: 0.9000, rms radial error=136.580, avgs=0
245/300: dt: 0.9000, rms radial error=135.810, avgs=0
250/300: dt: 0.9000, rms radial error=135.044, avgs=0
255/300: dt: 0.9000, rms radial error=134.282, avgs=0
260/300: dt: 0.9000, rms radial error=133.525, avgs=0
265/300: dt: 0.9000, rms radial error=132.771, avgs=0
270/300: dt: 0.9000, rms radial error=132.022, avgs=0
275/300: dt: 0.9000, rms radial error=131.277, avgs=0
280/300: dt: 0.9000, rms radial error=130.536, avgs=0
285/300: dt: 0.9000, rms radial error=129.799, avgs=0
290/300: dt: 0.9000, rms radial error=129.067, avgs=0
295/300: dt: 0.9000, rms radial error=128.338, avgs=0
300/300: dt: 0.9000, rms radial error=127.614, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 14225.15
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 2385.09
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00021
epoch 3 (K=160.0), pass 1, starting sse = 275.27
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/11 = 0.00870
epoch 4 (K=640.0), pass 1, starting sse = 26.36
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00726
final distance error %26.81
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.06 hours
mris_sphere utimesec    224.755831
mris_sphere stimesec    0.117982
mris_sphere ru_maxrss   179820
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   26493
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  8664
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8360
mris_sphere ru_nivcsw   14668
FSRUNTIME@ mris_sphere  0.0607 hours 1 threads
PIDs (2672 2675) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 05:34:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 cp ../surf/lh.orig.nofix ../surf/lh.orig 


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated 

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 05:34:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology lh Sun Oct  8 05:34:43 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050564 lh 

#@# Fix Topology rh Sun Oct  8 05:34:43 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050564 rh 

Waiting for PID 3275 of (3275 3278) to complete...
Waiting for PID 3278 of (3275 3278) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050564 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=-86 (nv=117518, nf=235208, ne=352812, g=44)
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...
8330 ambiguous faces found in tessellation
segmenting defects...
63 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 22 into 18
      -merging segment 26 into 21
61 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2673  (-4.6336)
      -vertex     loglikelihood: -6.3181  (-3.1591)
      -normal dot loglikelihood: -3.5978  (-3.5978)
      -quad curv  loglikelihood: -6.0726  (-3.0363)
      Total Loglikelihood : -25.2558

CORRECTING DEFECT 0 (vertices=76, convex hull=105, v0=46)
After retessellation of defect 0 (v0=46), euler #=-57 (112475,335479,222947) : difference with theory (-58) = -1 

CORRECTING DEFECT 1 (vertices=78, convex hull=100, v0=2115)
After retessellation of defect 1 (v0=2115), euler #=-56 (112505,335616,223055) : difference with theory (-57) = -1 

CORRECTING DEFECT 2 (vertices=128, convex hull=140, v0=3501)
After retessellation of defect 2 (v0=3501), euler #=-55 (112566,335866,223245) : difference with theory (-56) = -1 

CORRECTING DEFECT 3 (vertices=15, convex hull=30, v0=7013)
After retessellation of defect 3 (v0=7013), euler #=-54 (112566,335877,223257) : difference with theory (-55) = -1 

CORRECTING DEFECT 4 (vertices=19, convex hull=25, v0=7794)
After retessellation of defect 4 (v0=7794), euler #=-53 (112567,335887,223267) : difference with theory (-54) = -1 

CORRECTING DEFECT 5 (vertices=206, convex hull=166, v0=8740)
After retessellation of defect 5 (v0=8740), euler #=-53 (112601,336074,223420) : difference with theory (-53) = 0 

CORRECTING DEFECT 6 (vertices=54, convex hull=106, v0=8970)
After retessellation of defect 6 (v0=8970), euler #=-52 (112637,336222,223533) : difference with theory (-52) = 0 

CORRECTING DEFECT 7 (vertices=30, convex hull=23, v0=9712)
After retessellation of defect 7 (v0=9712), euler #=-51 (112639,336235,223545) : difference with theory (-51) = 0 

CORRECTING DEFECT 8 (vertices=90, convex hull=117, v0=10443)
After retessellation of defect 8 (v0=10443), euler #=-50 (112672,336387,223665) : difference with theory (-50) = 0 

CORRECTING DEFECT 9 (vertices=78, convex hull=79, v0=13052)
After retessellation of defect 9 (v0=13052), euler #=-49 (112698,336500,223753) : difference with theory (-49) = 0 

CORRECTING DEFECT 10 (vertices=32, convex hull=35, v0=13671)
After retessellation of defect 10 (v0=13671), euler #=-48 (112706,336539,223785) : difference with theory (-48) = 0 

CORRECTING DEFECT 11 (vertices=109, convex hull=109, v0=14949)
After retessellation of defect 11 (v0=14949), euler #=-47 (112744,336699,223908) : difference with theory (-47) = 0 

CORRECTING DEFECT 12 (vertices=105, convex hull=102, v0=16848)
After retessellation of defect 12 (v0=16848), euler #=-46 (112767,336811,223998) : difference with theory (-46) = 0 

CORRECTING DEFECT 13 (vertices=46, convex hull=85, v0=17150)
After retessellation of defect 13 (v0=17150), euler #=-45 (112785,336900,224070) : difference with theory (-45) = 0 

CORRECTING DEFECT 14 (vertices=180, convex hull=144, v0=21767)
After retessellation of defect 14 (v0=21767), euler #=-44 (112832,337110,224234) : difference with theory (-44) = 0 

CORRECTING DEFECT 15 (vertices=9, convex hull=23, v0=27649)
After retessellation of defect 15 (v0=27649), euler #=-43 (112834,337124,224247) : difference with theory (-43) = 0 

CORRECTING DEFECT 16 (vertices=41, convex hull=64, v0=32838)
After retessellation of defect 16 (v0=32838), euler #=-42 (112850,337201,224309) : difference with theory (-42) = 0 

CORRECTING DEFECT 17 (vertices=128, convex hull=171, v0=38277)
After retessellation of defect 17 (v0=38277), euler #=-41 (112937,337542,224564) : difference with theory (-41) = 0 

CORRECTING DEFECT 18 (vertices=226, convex hull=167, v0=38900)
After retessellation of defect 18 (v0=38900), euler #=-39 (113025,337882,224818) : difference with theory (-40) = -1 

CORRECTING DEFECT 19 (vertices=40, convex hull=52, v0=39972)
After retessellation of defect 19 (v0=39972), euler #=-38 (113046,337964,224880) : difference with theory (-39) = -1 

CORRECTING DEFECT 20 (vertices=7, convex hull=18, v0=41981)
After retessellation of defect 20 (v0=41981), euler #=-37 (113047,337972,224888) : difference with theory (-38) = -1 

CORRECTING DEFECT 21 (vertices=155, convex hull=220, v0=42390)
After retessellation of defect 21 (v0=42390), euler #=-35 (113139,338359,225185) : difference with theory (-37) = -2 

CORRECTING DEFECT 22 (vertices=39, convex hull=67, v0=43830)
After retessellation of defect 22 (v0=43830), euler #=-34 (113148,338412,225230) : difference with theory (-36) = -2 

CORRECTING DEFECT 23 (vertices=30, convex hull=58, v0=44265)
After retessellation of defect 23 (v0=44265), euler #=-33 (113159,338465,225273) : difference with theory (-35) = -2 

CORRECTING DEFECT 24 (vertices=28, convex hull=30, v0=45727)
After retessellation of defect 24 (v0=45727), euler #=-33 (113163,338492,225296) : difference with theory (-34) = -1 

CORRECTING DEFECT 25 (vertices=12, convex hull=33, v0=47182)
After retessellation of defect 25 (v0=47182), euler #=-32 (113164,338506,225310) : difference with theory (-33) = -1 

CORRECTING DEFECT 26 (vertices=85, convex hull=47, v0=47204)
After retessellation of defect 26 (v0=47204), euler #=-31 (113172,338548,225345) : difference with theory (-32) = -1 

CORRECTING DEFECT 27 (vertices=49, convex hull=51, v0=49048)
After retessellation of defect 27 (v0=49048), euler #=-30 (113201,338655,225424) : difference with theory (-31) = -1 

CORRECTING DEFECT 28 (vertices=24, convex hull=30, v0=49647)
After retessellation of defect 28 (v0=49647), euler #=-29 (113202,338667,225436) : difference with theory (-30) = -1 

CORRECTING DEFECT 29 (vertices=45, convex hull=43, v0=54215)
After retessellation of defect 29 (v0=54215), euler #=-28 (113215,338721,225478) : difference with theory (-29) = -1 

CORRECTING DEFECT 30 (vertices=35, convex hull=37, v0=56682)
After retessellation of defect 30 (v0=56682), euler #=-27 (113222,338758,225509) : difference with theory (-28) = -1 

CORRECTING DEFECT 31 (vertices=116, convex hull=136, v0=59607)
After retessellation of defect 31 (v0=59607), euler #=-26 (113272,338966,225668) : difference with theory (-27) = -1 

CORRECTING DEFECT 32 (vertices=69, convex hull=81, v0=63231)
After retessellation of defect 32 (v0=63231), euler #=-25 (113303,339091,225763) : difference with theory (-26) = -1 

CORRECTING DEFECT 33 (vertices=33, convex hull=64, v0=64559)
After retessellation of defect 33 (v0=64559), euler #=-24 (113324,339182,225834) : difference with theory (-25) = -1 

CORRECTING DEFECT 34 (vertices=62, convex hull=36, v0=64640)
After retessellation of defect 34 (v0=64640), euler #=-23 (113335,339230,225872) : difference with theory (-24) = -1 

CORRECTING DEFECT 35 (vertices=26, convex hull=23, v0=65520)
After retessellation of defect 35 (v0=65520), euler #=-22 (113337,339243,225884) : difference with theory (-23) = -1 

CORRECTING DEFECT 36 (vertices=85, convex hull=122, v0=69450)
After retessellation of defect 36 (v0=69450), euler #=-21 (113354,339348,225973) : difference with theory (-22) = -1 

CORRECTING DEFECT 37 (vertices=159, convex hull=74, v0=70539)
After retessellation of defect 37 (v0=70539), euler #=-20 (113405,339535,226110) : difference with theory (-21) = -1 

CORRECTING DEFECT 38 (vertices=91, convex hull=139, v0=71285)
After retessellation of defect 38 (v0=71285), euler #=-19 (113427,339659,226213) : difference with theory (-20) = -1 

CORRECTING DEFECT 39 (vertices=29, convex hull=72, v0=72889)
After retessellation of defect 39 (v0=72889), euler #=-18 (113445,339741,226278) : difference with theory (-19) = -1 

CORRECTING DEFECT 40 (vertices=328, convex hull=162, v0=73501)
After retessellation of defect 40 (v0=73501), euler #=-17 (113473,339903,226413) : difference with theory (-18) = -1 

CORRECTING DEFECT 41 (vertices=74, convex hull=41, v0=74584)
After retessellation of defect 41 (v0=74584), euler #=-16 (113483,339948,226449) : difference with theory (-17) = -1 

CORRECTING DEFECT 42 (vertices=7, convex hull=24, v0=77267)
After retessellation of defect 42 (v0=77267), euler #=-15 (113487,339965,226463) : difference with theory (-16) = -1 

CORRECTING DEFECT 43 (vertices=74, convex hull=89, v0=78041)
After retessellation of defect 43 (v0=78041), euler #=-14 (113507,340063,226542) : difference with theory (-15) = -1 

CORRECTING DEFECT 44 (vertices=31, convex hull=32, v0=78220)
After retessellation of defect 44 (v0=78220), euler #=-13 (113513,340091,226565) : difference with theory (-14) = -1 

CORRECTING DEFECT 45 (vertices=579, convex hull=127, v0=79711)
After retessellation of defect 45 (v0=79711), euler #=-13 (113544,340254,226697) : difference with theory (-13) = 0 

CORRECTING DEFECT 46 (vertices=16, convex hull=41, v0=80448)
After retessellation of defect 46 (v0=80448), euler #=-12 (113553,340298,226733) : difference with theory (-12) = 0 

CORRECTING DEFECT 47 (vertices=31, convex hull=35, v0=82996)
After retessellation of defect 47 (v0=82996), euler #=-11 (113559,340328,226758) : difference with theory (-11) = 0 

CORRECTING DEFECT 48 (vertices=358, convex hull=130, v0=85904)
After retessellation of defect 48 (v0=85904), euler #=-10 (113595,340493,226888) : difference with theory (-10) = 0 

CORRECTING DEFECT 49 (vertices=12, convex hull=42, v0=85920)
After retessellation of defect 49 (v0=85920), euler #=-9 (113598,340516,226909) : difference with theory (-9) = 0 

CORRECTING DEFECT 50 (vertices=39, convex hull=46, v0=89325)
After retessellation of defect 50 (v0=89325), euler #=-8 (113606,340557,226943) : difference with theory (-8) = 0 

CORRECTING DEFECT 51 (vertices=12, convex hull=27, v0=90208)
After retessellation of defect 51 (v0=90208), euler #=-7 (113607,340567,226953) : difference with theory (-7) = 0 

CORRECTING DEFECT 52 (vertices=24, convex hull=31, v0=91672)
After retessellation of defect 52 (v0=91672), euler #=-6 (113613,340595,226976) : difference with theory (-6) = 0 

CORRECTING DEFECT 53 (vertices=51, convex hull=71, v0=96176)
After retessellation of defect 53 (v0=96176), euler #=-5 (113630,340677,227042) : difference with theory (-5) = 0 

CORRECTING DEFECT 54 (vertices=99, convex hull=46, v0=101707)
After retessellation of defect 54 (v0=101707), euler #=-4 (113639,340725,227082) : difference with theory (-4) = 0 

CORRECTING DEFECT 55 (vertices=16, convex hull=28, v0=104232)
After retessellation of defect 55 (v0=104232), euler #=-3 (113640,340740,227097) : difference with theory (-3) = 0 

CORRECTING DEFECT 56 (vertices=130, convex hull=88, v0=104545)
After retessellation of defect 56 (v0=104545), euler #=-2 (113668,340863,227193) : difference with theory (-2) = 0 

CORRECTING DEFECT 57 (vertices=164, convex hull=82, v0=105223)
After retessellation of defect 57 (v0=105223), euler #=-1 (113698,340992,227293) : difference with theory (-1) = 0 

CORRECTING DEFECT 58 (vertices=66, convex hull=102, v0=110999)
After retessellation of defect 58 (v0=110999), euler #=0 (113723,341109,227386) : difference with theory (0) = 0 

CORRECTING DEFECT 59 (vertices=33, convex hull=41, v0=112260)
After retessellation of defect 59 (v0=112260), euler #=1 (113727,341136,227410) : difference with theory (1) = 0 

CORRECTING DEFECT 60 (vertices=59, convex hull=87, v0=115416)
After retessellation of defect 60 (v0=115416), euler #=2 (113752,341250,227500) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.25 (0.04-->8.64) (max @ vno 16007 --> 21338)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.25 (0.04-->8.64) (max @ vno 16007 --> 21338)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
207 mutations (33.9%), 404 crossovers (66.1%), 296 vertices were eliminated
building final representation...
3766 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=113752, nf=227500, ne=341250, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 30.7 minutes
0 defective edges
removing intersecting faces
000: 464 intersecting
001: 3 intersecting
mris_fix_topology utimesec    1841.147103
mris_fix_topology stimesec    0.154976
mris_fix_topology ru_maxrss   374276
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   52951
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23632
mris_fix_topology ru_oublock  11040
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    547
mris_fix_topology ru_nivcsw   3909
FSRUNTIME@ mris_fix_topology lh  0.5113 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050564 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=-98 (nv=122494, nf=245184, ne=367776, g=50)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
12656 ambiguous faces found in tessellation
segmenting defects...
58 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 39 into 37
      -merging segment 40 into 38
56 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2370  (-4.6185)
      -vertex     loglikelihood: -6.2909  (-3.1454)
      -normal dot loglikelihood: -3.6262  (-3.6262)
      -quad curv  loglikelihood: -6.1061  (-3.0531)
      Total Loglikelihood : -25.2602

CORRECTING DEFECT 0 (vertices=200, convex hull=162, v0=46)
After retessellation of defect 0 (v0=46), euler #=-54 (115149,343252,228049) : difference with theory (-53) = 1 

CORRECTING DEFECT 1 (vertices=23, convex hull=32, v0=394)
After retessellation of defect 1 (v0=394), euler #=-53 (115151,343268,228064) : difference with theory (-52) = 1 

CORRECTING DEFECT 2 (vertices=5, convex hull=17, v0=1870)
After retessellation of defect 2 (v0=1870), euler #=-52 (115152,343275,228071) : difference with theory (-51) = 1 

CORRECTING DEFECT 3 (vertices=37, convex hull=64, v0=2110)
After retessellation of defect 3 (v0=2110), euler #=-51 (115166,343345,228128) : difference with theory (-50) = 1 

CORRECTING DEFECT 4 (vertices=42, convex hull=31, v0=2635)
After retessellation of defect 4 (v0=2635), euler #=-50 (115170,343368,228148) : difference with theory (-49) = 1 

CORRECTING DEFECT 5 (vertices=398, convex hull=205, v0=3172)
After retessellation of defect 5 (v0=3172), euler #=-49 (115251,343710,228410) : difference with theory (-48) = 1 

CORRECTING DEFECT 6 (vertices=118, convex hull=111, v0=3821)
After retessellation of defect 6 (v0=3821), euler #=-48 (115303,343918,228567) : difference with theory (-47) = 1 

CORRECTING DEFECT 7 (vertices=157, convex hull=63, v0=4717)
After retessellation of defect 7 (v0=4717), euler #=-47 (115327,344016,228642) : difference with theory (-46) = 1 

CORRECTING DEFECT 8 (vertices=68, convex hull=111, v0=7373)
After retessellation of defect 8 (v0=7373), euler #=-46 (115353,344140,228741) : difference with theory (-45) = 1 

CORRECTING DEFECT 9 (vertices=100, convex hull=112, v0=10890)
After retessellation of defect 9 (v0=10890), euler #=-45 (115395,344318,228878) : difference with theory (-44) = 1 

CORRECTING DEFECT 10 (vertices=64, convex hull=123, v0=14026)
After retessellation of defect 10 (v0=14026), euler #=-44 (115435,344487,229008) : difference with theory (-43) = 1 

CORRECTING DEFECT 11 (vertices=50, convex hull=49, v0=16901)
After retessellation of defect 11 (v0=16901), euler #=-43 (115448,344546,229055) : difference with theory (-42) = 1 

CORRECTING DEFECT 12 (vertices=44, convex hull=47, v0=17885)
After retessellation of defect 12 (v0=17885), euler #=-42 (115459,344598,229097) : difference with theory (-41) = 1 

CORRECTING DEFECT 13 (vertices=33, convex hull=51, v0=20867)
After retessellation of defect 13 (v0=20867), euler #=-41 (115467,344641,229133) : difference with theory (-40) = 1 

CORRECTING DEFECT 14 (vertices=66, convex hull=76, v0=21041)
After retessellation of defect 14 (v0=21041), euler #=-41 (115502,344786,229243) : difference with theory (-39) = 2 

CORRECTING DEFECT 15 (vertices=156, convex hull=186, v0=21270)
After retessellation of defect 15 (v0=21270), euler #=-40 (115580,345108,229488) : difference with theory (-38) = 2 

CORRECTING DEFECT 16 (vertices=797, convex hull=340, v0=27630)
After retessellation of defect 16 (v0=27630), euler #=-39 (115748,345794,230007) : difference with theory (-37) = 2 

CORRECTING DEFECT 17 (vertices=78, convex hull=83, v0=29393)
After retessellation of defect 17 (v0=29393), euler #=-38 (115770,345895,230087) : difference with theory (-36) = 2 

CORRECTING DEFECT 18 (vertices=121, convex hull=142, v0=34002)
After retessellation of defect 18 (v0=34002), euler #=-37 (115829,346137,230271) : difference with theory (-35) = 2 

CORRECTING DEFECT 19 (vertices=24, convex hull=32, v0=35652)
After retessellation of defect 19 (v0=35652), euler #=-36 (115829,346150,230285) : difference with theory (-34) = 2 

CORRECTING DEFECT 20 (vertices=82, convex hull=101, v0=39315)
After retessellation of defect 20 (v0=39315), euler #=-35 (115876,346337,230426) : difference with theory (-33) = 2 

CORRECTING DEFECT 21 (vertices=17, convex hull=27, v0=41817)
After retessellation of defect 21 (v0=41817), euler #=-34 (115877,346351,230440) : difference with theory (-32) = 2 

CORRECTING DEFECT 22 (vertices=32, convex hull=64, v0=44213)
After retessellation of defect 22 (v0=44213), euler #=-33 (115890,346416,230493) : difference with theory (-31) = 2 

CORRECTING DEFECT 23 (vertices=93, convex hull=109, v0=47360)
After retessellation of defect 23 (v0=47360), euler #=-32 (115936,346602,230634) : difference with theory (-30) = 2 

CORRECTING DEFECT 24 (vertices=240, convex hull=222, v0=47414)
After retessellation of defect 24 (v0=47414), euler #=-31 (116055,347067,230981) : difference with theory (-29) = 2 

CORRECTING DEFECT 25 (vertices=22, convex hull=34, v0=49576)
After retessellation of defect 25 (v0=49576), euler #=-30 (116059,347090,231001) : difference with theory (-28) = 2 

CORRECTING DEFECT 26 (vertices=32, convex hull=69, v0=52006)
After retessellation of defect 26 (v0=52006), euler #=-29 (116073,347162,231060) : difference with theory (-27) = 2 

CORRECTING DEFECT 27 (vertices=39, convex hull=59, v0=59181)
After retessellation of defect 27 (v0=59181), euler #=-28 (116094,347248,231126) : difference with theory (-26) = 2 

CORRECTING DEFECT 28 (vertices=12, convex hull=29, v0=63295)
After retessellation of defect 28 (v0=63295), euler #=-27 (116098,347271,231146) : difference with theory (-25) = 2 

CORRECTING DEFECT 29 (vertices=75, convex hull=103, v0=63906)
After retessellation of defect 29 (v0=63906), euler #=-26 (116116,347367,231225) : difference with theory (-24) = 2 

CORRECTING DEFECT 30 (vertices=59, convex hull=24, v0=64728)
After retessellation of defect 30 (v0=64728), euler #=-25 (116122,347391,231244) : difference with theory (-23) = 2 

CORRECTING DEFECT 31 (vertices=78, convex hull=96, v0=69108)
After retessellation of defect 31 (v0=69108), euler #=-24 (116161,347550,231365) : difference with theory (-22) = 2 

CORRECTING DEFECT 32 (vertices=377, convex hull=77, v0=69591)
After retessellation of defect 32 (v0=69591), euler #=-23 (116172,347615,231420) : difference with theory (-21) = 2 

CORRECTING DEFECT 33 (vertices=118, convex hull=37, v0=73708)
After retessellation of defect 33 (v0=73708), euler #=-22 (116184,347664,231458) : difference with theory (-20) = 2 

CORRECTING DEFECT 34 (vertices=10, convex hull=21, v0=74023)
After retessellation of defect 34 (v0=74023), euler #=-21 (116184,347672,231467) : difference with theory (-19) = 2 

CORRECTING DEFECT 35 (vertices=62, convex hull=37, v0=74041)
After retessellation of defect 35 (v0=74041), euler #=-20 (116189,347698,231489) : difference with theory (-18) = 2 

CORRECTING DEFECT 36 (vertices=11, convex hull=27, v0=74841)
After retessellation of defect 36 (v0=74841), euler #=-19 (116190,347713,231504) : difference with theory (-17) = 2 

CORRECTING DEFECT 37 (vertices=1275, convex hull=551, v0=77213)
L defect detected...
After retessellation of defect 37 (v0=77213), euler #=-17 (116334,348420,232069) : difference with theory (-16) = 1 

CORRECTING DEFECT 38 (vertices=251, convex hull=104, v0=82794)
After retessellation of defect 38 (v0=82794), euler #=-15 (116354,348532,232163) : difference with theory (-15) = 0 

CORRECTING DEFECT 39 (vertices=27, convex hull=43, v0=85840)
After retessellation of defect 39 (v0=85840), euler #=-14 (116359,348562,232189) : difference with theory (-14) = 0 

CORRECTING DEFECT 40 (vertices=58, convex hull=41, v0=86522)
After retessellation of defect 40 (v0=86522), euler #=-13 (116370,348612,232229) : difference with theory (-13) = 0 

CORRECTING DEFECT 41 (vertices=59, convex hull=72, v0=87477)
After retessellation of defect 41 (v0=87477), euler #=-12 (116382,348669,232275) : difference with theory (-12) = 0 

CORRECTING DEFECT 42 (vertices=52, convex hull=34, v0=90528)
After retessellation of defect 42 (v0=90528), euler #=-11 (116394,348720,232315) : difference with theory (-11) = 0 

CORRECTING DEFECT 43 (vertices=63, convex hull=112, v0=90846)
After retessellation of defect 43 (v0=90846), euler #=-10 (116420,348846,232416) : difference with theory (-10) = 0 

CORRECTING DEFECT 44 (vertices=45, convex hull=111, v0=92369)
After retessellation of defect 44 (v0=92369), euler #=-9 (116451,348985,232525) : difference with theory (-9) = 0 

CORRECTING DEFECT 45 (vertices=162, convex hull=77, v0=93115)
After retessellation of defect 45 (v0=93115), euler #=-8 (116478,349101,232615) : difference with theory (-8) = 0 

CORRECTING DEFECT 46 (vertices=777, convex hull=203, v0=96128)
After retessellation of defect 46 (v0=96128), euler #=-7 (116565,349464,232892) : difference with theory (-7) = 0 

CORRECTING DEFECT 47 (vertices=61, convex hull=77, v0=98271)
After retessellation of defect 47 (v0=98271), euler #=-6 (116589,349568,232973) : difference with theory (-6) = 0 

CORRECTING DEFECT 48 (vertices=156, convex hull=93, v0=102789)
After retessellation of defect 48 (v0=102789), euler #=-5 (116637,349752,233110) : difference with theory (-5) = 0 

CORRECTING DEFECT 49 (vertices=36, convex hull=69, v0=110751)
After retessellation of defect 49 (v0=110751), euler #=-4 (116657,349839,233178) : difference with theory (-4) = 0 

CORRECTING DEFECT 50 (vertices=47, convex hull=62, v0=111578)
After retessellation of defect 50 (v0=111578), euler #=-3 (116673,349911,233235) : difference with theory (-3) = 0 

CORRECTING DEFECT 51 (vertices=9, convex hull=17, v0=113946)
After retessellation of defect 51 (v0=113946), euler #=-2 (116674,349920,233244) : difference with theory (-2) = 0 

CORRECTING DEFECT 52 (vertices=186, convex hull=44, v0=116182)
After retessellation of defect 52 (v0=116182), euler #=-1 (116699,350010,233310) : difference with theory (-1) = 0 

CORRECTING DEFECT 53 (vertices=9, convex hull=18, v0=120049)
After retessellation of defect 53 (v0=120049), euler #=0 (116700,350020,233320) : difference with theory (0) = 0 

CORRECTING DEFECT 54 (vertices=152, convex hull=130, v0=120580)
After retessellation of defect 54 (v0=120580), euler #=1 (116745,350214,233470) : difference with theory (1) = 0 

CORRECTING DEFECT 55 (vertices=38, convex hull=41, v0=121529)
After retessellation of defect 55 (v0=121529), euler #=2 (116748,350238,233492) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.25 (0.04-->11.11) (max @ vno 50515 --> 59567)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.25 (0.04-->11.11) (max @ vno 50515 --> 59567)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
165 mutations (34.8%), 309 crossovers (65.2%), 432 vertices were eliminated
building final representation...
5746 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=116748, nf=233492, ne=350238, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 41.3 minutes
0 defective edges
removing intersecting faces
000: 520 intersecting
001: 11 intersecting
mris_fix_topology utimesec    2478.729175
mris_fix_topology stimesec    0.180972
mris_fix_topology ru_maxrss   412604
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   58560
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23984
mris_fix_topology ru_oublock  11392
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    538
mris_fix_topology ru_nivcsw   5424
FSRUNTIME@ mris_fix_topology rh  0.6882 hours 1 threads
PIDs (3275 3278) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 113752 - 341250 + 227500 = 2 --> 0 holes
      F =2V-4:          227500 = 227504-4 (0)
      2E=3F:            682500 = 682500 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 116748 - 350238 + 233492 = 2 --> 0 holes
      F =2V-4:          233492 = 233496-4 (0)
      2E=3F:            700476 = 700476 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 75 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 64 intersecting
001: 3 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 06:16:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050564 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 06:16:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050564 rh 

Waiting for PID 5652 of (5652 5655) to complete...
Waiting for PID 5655 of (5652 5655) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050564 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-6.0.0/0050564/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
9576 bright wm thresholded.
2610 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.orig...
computing class statistics...
border white:    218071 voxels (1.30%)
border gray      265543 voxels (1.58%)
WM (95.0): 95.7 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.7 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 55.5 (was 70)
setting MAX_BORDER_WHITE to 108.5 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 45.0 (was 40)
setting MAX_GRAY to 91.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 34.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.02-->4.25) (max @ vno 21554 --> 27646)
face area 0.28 +- 0.13 (0.00-->3.16)
mean absolute distance = 0.64 +- 0.76
3070 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=100+-7.8,    GM=66+-7.8
mean inside = 91.3, mean outside = 73.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=78.2, 110 (110) missing vertices, mean dist 0.3 [0.5 (%35.8)->0.7 (%64.2))]
%68 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.26 (0.06-->4.34) (max @ vno 39230 --> 112992)
face area 0.28 +- 0.13 (0.00-->4.08)
mean absolute distance = 0.28 +- 0.52
2181 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2496323.0, rms=9.661
001: dt: 0.5000, sse=1477343.9, rms=6.861 (28.981%)
002: dt: 0.5000, sse=1046750.4, rms=5.246 (23.543%)
003: dt: 0.5000, sse=844824.8, rms=4.264 (18.707%)
004: dt: 0.5000, sse=751310.6, rms=3.733 (12.469%)
005: dt: 0.5000, sse=713710.9, rms=3.486 (6.595%)
006: dt: 0.5000, sse=695317.7, rms=3.362 (3.571%)
007: dt: 0.5000, sse=687619.8, rms=3.306 (1.674%)
rms = 3.26, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=683669.6, rms=3.260 (1.372%)
009: dt: 0.2500, sse=546434.0, rms=1.978 (39.329%)
010: dt: 0.2500, sse=525311.8, rms=1.697 (14.224%)
011: dt: 0.2500, sse=521031.2, rms=1.625 (4.198%)
rms = 1.59, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=519704.6, rms=1.586 (2.406%)
rms = 1.54, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=515212.2, rms=1.537 (3.097%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=80.0, 79 (22) missing vertices, mean dist -0.1 [0.3 (%66.3)->0.3 (%33.7))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.25 (0.07-->4.70) (max @ vno 39230 --> 112992)
face area 0.36 +- 0.17 (0.00-->5.58)
mean absolute distance = 0.25 +- 0.41
2410 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=820436.4, rms=3.311
014: dt: 0.5000, sse=700459.3, rms=2.345 (29.172%)
rms = 2.58, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=647359.3, rms=1.741 (25.784%)
016: dt: 0.2500, sse=627995.6, rms=1.429 (17.896%)
017: dt: 0.2500, sse=621183.9, rms=1.336 (6.484%)
rms = 1.32, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=619704.9, rms=1.319 (1.310%)
rms = 1.28, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=617268.8, rms=1.278 (3.082%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=81.3, 56 (8) missing vertices, mean dist -0.1 [0.3 (%60.9)->0.2 (%39.1))]
%78 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.25 (0.05-->4.80) (max @ vno 39230 --> 112992)
face area 0.35 +- 0.17 (0.00-->5.69)
mean absolute distance = 0.24 +- 0.37
2399 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=679783.0, rms=2.196
020: dt: 0.5000, sse=667159.3, rms=2.051 (6.598%)
rms = 2.38, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=620846.3, rms=1.449 (29.347%)
022: dt: 0.2500, sse=608866.1, rms=1.247 (13.934%)
023: dt: 0.2500, sse=605434.6, rms=1.188 (4.765%)
rms = 1.20, time step reduction 2 of 3 to 0.125...
rms = 1.17, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=604127.8, rms=1.168 (1.699%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=81.9, 60 (2) missing vertices, mean dist -0.0 [0.3 (%53.4)->0.2 (%46.6))]
%81 local maxima, %14 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-6.0.0/0050564/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=614201.4, rms=1.428
rms = 1.48, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=596093.2, rms=1.079 (24.464%)
026: dt: 0.2500, sse=587956.2, rms=0.898 (16.738%)
rms = 0.91, time step reduction 2 of 3 to 0.125...
rms = 0.89, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=586902.4, rms=0.889 (1.026%)
positioning took 0.4 minutes
generating cortex label...
5 non-cortical segments detected
only using segment with 6885 vertices
erasing segment 0 (vno[0] = 26436)
erasing segment 1 (vno[0] = 28317)
erasing segment 3 (vno[0] = 81505)
erasing segment 4 (vno[0] = 113491)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.area
vertex spacing 0.91 +- 0.26 (0.02-->4.85) (max @ vno 39230 --> 112992)
face area 0.35 +- 0.17 (0.00-->5.76)
refinement took 3.9 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050564 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-6.0.0/0050564/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
9576 bright wm thresholded.
2610 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.orig...
computing class statistics...
border white:    218071 voxels (1.30%)
border gray      265543 voxels (1.58%)
WM (95.0): 95.7 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.7 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 55.5 (was 70)
setting MAX_BORDER_WHITE to 107.5 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 45.0 (was 40)
setting MAX_GRAY to 90.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 34.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.03-->5.98) (max @ vno 98503 --> 116501)
face area 0.28 +- 0.13 (0.00-->4.77)
mean absolute distance = 0.65 +- 0.77
3684 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=99+-6.1,    GM=66+-7.8
mean inside = 91.4, mean outside = 74.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=78.3, 119 (119) missing vertices, mean dist 0.3 [0.5 (%35.2)->0.7 (%64.8))]
%72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.26 (0.09-->5.76) (max @ vno 98503 --> 116501)
face area 0.28 +- 0.14 (0.00-->4.19)
mean absolute distance = 0.29 +- 0.53
2242 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2553202.2, rms=9.646
001: dt: 0.5000, sse=1533318.0, rms=6.924 (28.222%)
002: dt: 0.5000, sse=1098697.2, rms=5.343 (22.835%)
003: dt: 0.5000, sse=891424.1, rms=4.368 (18.238%)
004: dt: 0.5000, sse=792194.2, rms=3.785 (13.343%)
005: dt: 0.5000, sse=738590.9, rms=3.501 (7.522%)
006: dt: 0.5000, sse=715034.4, rms=3.348 (4.364%)
007: dt: 0.5000, sse=706308.1, rms=3.289 (1.772%)
008: dt: 0.5000, sse=699711.3, rms=3.237 (1.561%)
rms = 3.23, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=699608.9, rms=3.231 (0.204%)
010: dt: 0.2500, sse=574422.8, rms=1.985 (38.543%)
011: dt: 0.2500, sse=548242.6, rms=1.721 (13.307%)
012: dt: 0.2500, sse=552170.6, rms=1.662 (3.455%)
rms = 1.62, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=537456.4, rms=1.617 (2.708%)
014: dt: 0.1250, sse=533039.4, rms=1.558 (3.627%)
rms = 1.55, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=535089.0, rms=1.546 (0.775%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=80.2, 96 (31) missing vertices, mean dist -0.1 [0.3 (%67.9)->0.3 (%32.1))]
%77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.26 (0.04-->5.75) (max @ vno 98503 --> 116501)
face area 0.36 +- 0.17 (0.00-->5.26)
mean absolute distance = 0.26 +- 0.42
2447 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=860345.5, rms=3.379
016: dt: 0.5000, sse=725671.1, rms=2.324 (31.200%)
rms = 2.54, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=672077.1, rms=1.750 (24.728%)
018: dt: 0.2500, sse=654172.2, rms=1.470 (15.984%)
019: dt: 0.2500, sse=651363.4, rms=1.389 (5.539%)
rms = 1.38, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=646254.5, rms=1.378 (0.772%)
rms = 1.33, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=643589.0, rms=1.333 (3.257%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
mean border=81.6, 105 (16) missing vertices, mean dist -0.1 [0.3 (%61.7)->0.2 (%38.3))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.26 (0.08-->5.66) (max @ vno 98503 --> 116501)
face area 0.35 +- 0.17 (0.00-->5.32)
mean absolute distance = 0.25 +- 0.37
2510 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=717737.2, rms=2.329
022: dt: 0.5000, sse=695186.1, rms=2.081 (10.678%)
rms = 2.38, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=647300.0, rms=1.500 (27.918%)
024: dt: 0.2500, sse=634722.4, rms=1.290 (14.000%)
rms = 1.24, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=630697.8, rms=1.244 (3.520%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=628812.4, rms=1.198 (3.720%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=82.2, 140 (11) missing vertices, mean dist -0.0 [0.3 (%53.3)->0.2 (%46.7))]
%83 local maxima, %11 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-6.0.0/0050564/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=640999.8, rms=1.501
rms = 1.48, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=641551.8, rms=1.478 (1.574%)
028: dt: 0.2500, sse=622590.7, rms=1.152 (22.021%)
029: dt: 0.2500, sse=612991.9, rms=1.061 (7.958%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
rms = 1.01, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=610312.6, rms=1.014 (4.374%)
positioning took 0.4 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 6745 vertices
erasing segment 0 (vno[0] = 26674)
erasing segment 1 (vno[0] = 29221)
erasing segment 3 (vno[0] = 77545)
erasing segment 4 (vno[0] = 79529)
erasing segment 5 (vno[0] = 83692)
erasing segment 6 (vno[0] = 85204)
erasing segment 7 (vno[0] = 87459)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.area
vertex spacing 0.91 +- 0.26 (0.03-->5.62) (max @ vno 98503 --> 116501)
face area 0.35 +- 0.17 (0.00-->5.48)
refinement took 4.2 minutes
PIDs (5652 5655) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 06:20:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm 

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 06:20:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm 

Waiting for PID 6105 of (6105 6108) to complete...
Waiting for PID 6108 of (6105 6108) 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 (6105 6108) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 06:20:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 06:20:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 6176 of (6176 6179) to complete...
Waiting for PID 6179 of (6176 6179) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 44.5 mm, total surface area = 71681 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.183 (target=0.015)   
step 005: RMS=0.131 (target=0.015)   
step 010: RMS=0.101 (target=0.015)   
step 015: RMS=0.083 (target=0.015)   
step 020: RMS=0.071 (target=0.015)   
step 025: RMS=0.059 (target=0.015)   
step 030: RMS=0.050 (target=0.015)   
step 035: RMS=0.044 (target=0.015)   
step 040: RMS=0.039 (target=0.015)   
step 045: RMS=0.035 (target=0.015)   
step 050: RMS=0.032 (target=0.015)   
step 055: RMS=0.030 (target=0.015)   
step 060: RMS=0.028 (target=0.015)   
inflation complete.
inflation took 0.6 minutes
mris_inflate utimesec    36.184499
mris_inflate stimesec    0.100984
mris_inflate ru_maxrss   167460
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   25063
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  8920
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5523
mris_inflate ru_nivcsw   3118

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 44.4 mm, total surface area = 73650 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.181 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.097 (target=0.015)   
step 015: RMS=0.081 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.050 (target=0.015)   
step 035: RMS=0.043 (target=0.015)   
step 040: RMS=0.038 (target=0.015)   
step 045: RMS=0.035 (target=0.015)   
step 050: RMS=0.031 (target=0.015)   
step 055: RMS=0.029 (target=0.015)   
step 060: RMS=0.028 (target=0.015)   
inflation complete.
inflation took 0.6 minutes
mris_inflate utimesec    37.467304
mris_inflate stimesec    0.074988
mris_inflate ru_maxrss   171652
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   25602
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  8216
mris_inflate ru_oublock  9152
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2743
mris_inflate ru_nivcsw   4622
PIDs (6176 6179) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 06:21:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf

 mris_curvature -w lh.white.preaparc 

rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K

 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated 

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 06:21:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 6265 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6268 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6271 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6274 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6277 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6280 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6283 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6286 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6290 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6293 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6296 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...
Waiting for PID 6300 of (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 12.222*4pi (153.591) --> -11 handles
ICI = 154.1, FI = 1459.5, variation=23356.861
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
122 vertices thresholded to be in k1 ~ [-0.31 0.95], k2 ~ [-0.14 0.09]
total integrated curvature = 0.257*4pi (3.228) --> 1 handles
ICI = 1.2, FI = 7.6, variation=134.693
92 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
97 vertices thresholded to be in [-0.17 0.28]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 27.724*4pi (348.385) --> -27 handles
ICI = 171.0, FI = 1619.0, variation=25644.405
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
145 vertices thresholded to be in k1 ~ [-0.42 1.32], k2 ~ [-0.21 0.17]
total integrated curvature = 0.148*4pi (1.862) --> 1 handles
ICI = 1.2, FI = 8.3, variation=146.316
111 vertices thresholded to be in [-0.07 0.04]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
94 vertices thresholded to be in [-0.22 0.29]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.024
done.
PIDs (6265 6268 6271 6274 6277 6280 6283 6286 6290 6293 6296 6300) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 06:22:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050564 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      [ 0050564/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                      [ 245 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.474360
WARN:    S explicit min:                          0.000000	vertex = 16

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 06:22:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050564 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      [ 0050564/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                      [ 222 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.161728
WARN:    S explicit min:                          0.000000	vertex = 361
#--------------------------------------------
#@# Sphere lh Sun Oct  8 06:22:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 06:22:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 6498 of (6498 6505) to complete...
Waiting for PID 6505 of (6498 6505) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0.295...
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 %22.14
pass 1: epoch 2 of 3 starting distance error %22.12
unfolding complete - removing small folds...
starting distance error %21.92
removing remaining folds...
final distance error %21.96
MRISunfold() return, current seed 1234
-01: dt=0.0000, 86 negative triangles
240: dt=0.9900, 86 negative triangles
241: dt=0.9900, 39 negative triangles
242: dt=0.9900, 23 negative triangles
243: dt=0.9900, 23 negative triangles
244: dt=0.9900, 18 negative triangles
245: dt=0.9900, 18 negative triangles
246: dt=0.9900, 17 negative triangles
247: dt=0.9900, 11 negative triangles
248: dt=0.9900, 8 negative triangles
249: dt=0.9900, 11 negative triangles
250: dt=0.9900, 9 negative triangles
251: dt=0.9900, 10 negative triangles
252: dt=0.9900, 6 negative triangles
253: dt=0.9900, 8 negative triangles
254: dt=0.9900, 5 negative triangles
255: dt=0.9900, 4 negative triangles
256: dt=0.9900, 6 negative triangles
257: dt=0.9900, 4 negative triangles
258: dt=0.9900, 4 negative triangles
259: dt=0.9900, 4 negative triangles
260: dt=0.9900, 6 negative triangles
261: dt=0.9900, 5 negative triangles
262: dt=0.9900, 4 negative triangles
263: dt=0.9900, 5 negative triangles
264: dt=0.9900, 3 negative triangles
265: dt=0.9900, 3 negative triangles
266: dt=0.9900, 1 negative triangles
267: dt=0.9900, 2 negative triangles
268: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.79 hours
mris_sphere utimesec    2835.660914
mris_sphere stimesec    0.804877
mris_sphere ru_maxrss   234132
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   41870
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  8048
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    117450
mris_sphere ru_nivcsw   244777
FSRUNTIME@ mris_sphere  0.7880 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0.299...
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 %21.46
pass 1: epoch 2 of 3 starting distance error %21.41
unfolding complete - removing small folds...
starting distance error %21.30
removing remaining folds...
final distance error %21.33
MRISunfold() return, current seed 1234
-01: dt=0.0000, 61 negative triangles
281: dt=0.9900, 61 negative triangles
282: dt=0.9900, 15 negative triangles
283: dt=0.9900, 8 negative triangles
284: dt=0.9900, 5 negative triangles
285: dt=0.9900, 6 negative triangles
286: dt=0.9900, 4 negative triangles
287: dt=0.9900, 5 negative triangles
288: dt=0.9900, 6 negative triangles
289: dt=0.9900, 5 negative triangles
290: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.87 hours
mris_sphere utimesec    3364.288550
mris_sphere stimesec    0.809876
mris_sphere ru_maxrss   240844
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   43047
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  8240
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    123494
mris_sphere ru_nivcsw   246172
FSRUNTIME@ mris_sphere  0.8733 hours 1 threads
PIDs (6498 6505) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 07:14:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 07:14:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 9536 of (9536 9539) to complete...
Waiting for PID 9539 of (9536 9539) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 5.604
curvature mean = 0.045, std = 0.812
curvature mean = 0.009, std = 0.875
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 248121.1, tmin=0.8686
  d=32.00 min @ (0.00, 8.00, 0.00) sse = 206984.6, tmin=1.7624
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 200494.7, tmin=2.6578
  d=8.00 min @ (-2.00, -2.00, 0.00) sse = 197603.2, tmin=3.5625
  d=4.00 min @ (1.00, 1.00, 0.00) sse = 196701.6, tmin=4.4748
  d=2.00 min @ (0.00, -0.50, 0.00) sse = 196432.4, tmin=5.3940
  d=1.00 min @ (-0.25, 0.00, 0.00) sse = 196408.9, tmin=6.3076
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 196406.6, tmin=7.2215
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   7.22 min
curvature mean = 0.012, std = 0.852
curvature mean = 0.003, std = 0.953
curvature mean = 0.009, std = 0.864
curvature mean = 0.001, std = 0.981
curvature mean = 0.007, std = 0.867
curvature mean = 0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.039, std = 0.363
curvature mean = 0.042, std = 0.249
curvature mean = 0.052, std = 0.308
curvature mean = 0.033, std = 0.311
curvature mean = 0.041, std = 0.448
curvature mean = 0.032, std = 0.337
curvature mean = 0.024, std = 0.559
curvature mean = 0.031, std = 0.348
curvature mean = 0.008, std = 0.654
MRISregister() return, current seed 0
-01: dt=0.0000, 65 negative triangles
114: dt=0.9900, 65 negative triangles
expanding nbhd size to 1
115: dt=0.9900, 91 negative triangles
116: dt=0.9900, 63 negative triangles
117: dt=0.9900, 55 negative triangles
118: dt=0.9900, 50 negative triangles
119: dt=0.9900, 42 negative triangles
120: dt=0.9900, 40 negative triangles
121: dt=0.9900, 40 negative triangles
122: dt=0.9900, 34 negative triangles
123: dt=0.9900, 32 negative triangles
124: dt=0.9900, 24 negative triangles
125: dt=0.9900, 19 negative triangles
126: dt=0.9900, 22 negative triangles
127: dt=0.9900, 16 negative triangles
128: dt=0.9900, 16 negative triangles
129: dt=0.9900, 15 negative triangles
130: dt=0.9900, 16 negative triangles
131: dt=0.9900, 13 negative triangles
132: dt=0.9900, 15 negative triangles
133: dt=0.9900, 16 negative triangles
134: dt=0.9900, 14 negative triangles
135: dt=0.9900, 12 negative triangles
136: dt=0.9900, 13 negative triangles
137: dt=0.9900, 13 negative triangles
138: dt=0.9900, 8 negative triangles
139: dt=0.9900, 7 negative triangles
140: dt=0.9900, 5 negative triangles
141: dt=0.9900, 6 negative triangles
142: dt=0.9900, 9 negative triangles
143: dt=0.9900, 7 negative triangles
144: dt=0.9900, 5 negative triangles
145: dt=0.9900, 3 negative triangles
146: dt=0.9900, 2 negative triangles
147: dt=0.9900, 4 negative triangles
148: dt=0.9900, 4 negative triangles
149: dt=0.9900, 2 negative triangles
150: dt=0.9900, 2 negative triangles
151: dt=0.9900, 1 negative triangles
152: dt=0.9900, 2 negative triangles
153: dt=0.9900, 2 negative triangles
154: dt=0.9900, 3 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 0.99 hours
mris_register utimesec    3555.633461
mris_register stimesec    0.871867
mris_register ru_maxrss   221424
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   30869
mris_register ru_majflt   1
mris_register ru_nswap    0
mris_register ru_inblock  1672
mris_register ru_oublock  8104
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    234477
mris_register ru_nivcsw   190410
FSRUNTIME@ mris_register  0.9873 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 5.694
curvature mean = 0.046, std = 0.810
curvature mean = 0.009, std = 0.877
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 276932.6, tmin=0.8923
  d=32.00 min @ (8.00, 8.00, 8.00) sse = 204551.2, tmin=1.8104
  d=16.00 min @ (-4.00, -4.00, -4.00) sse = 187874.0, tmin=2.7379
  d=8.00 min @ (0.00, 2.00, 2.00) sse = 177095.0, tmin=3.6900
  d=4.00 min @ (0.00, 0.00, -1.00) sse = 176488.0, tmin=4.6500
  d=2.00 min @ (0.50, 0.00, 0.50) sse = 176173.3, tmin=5.6117
  d=1.00 min @ (0.00, 0.00, -0.25) sse = 176095.9, tmin=6.5637
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   7.52 min
curvature mean = 0.017, std = 0.833
curvature mean = 0.003, std = 0.953
curvature mean = 0.015, std = 0.844
curvature mean = 0.001, std = 0.981
curvature mean = 0.014, std = 0.847
curvature mean = -0.000, std = 0.993
2 Reading smoothwm
curvature mean = -0.034, std = 0.288
curvature mean = 0.041, std = 0.239
curvature mean = 0.055, std = 0.382
curvature mean = 0.033, std = 0.300
curvature mean = 0.042, std = 0.558
curvature mean = 0.032, std = 0.326
curvature mean = 0.024, std = 0.690
curvature mean = 0.032, std = 0.337
curvature mean = 0.009, std = 0.791
MRISregister() return, current seed 0
-01: dt=0.0000, 50 negative triangles
112: dt=0.9900, 50 negative triangles
expanding nbhd size to 1
113: dt=0.9900, 65 negative triangles
114: dt=0.9900, 52 negative triangles
115: dt=0.9900, 47 negative triangles
116: dt=0.9900, 52 negative triangles
117: dt=0.9900, 45 negative triangles
118: dt=0.9900, 53 negative triangles
119: dt=0.9900, 49 negative triangles
120: dt=0.9900, 34 negative triangles
121: dt=0.9900, 28 negative triangles
122: dt=0.9900, 24 negative triangles
123: dt=0.9900, 27 negative triangles
124: dt=0.9900, 21 negative triangles
125: dt=0.9900, 25 negative triangles
126: dt=0.9900, 19 negative triangles
127: dt=0.9900, 17 negative triangles
128: dt=0.9900, 16 negative triangles
129: dt=0.9900, 19 negative triangles
130: dt=0.9900, 16 negative triangles
131: dt=0.9900, 11 negative triangles
132: dt=0.9900, 12 negative triangles
133: dt=0.9900, 9 negative triangles
134: dt=0.9900, 13 negative triangles
135: dt=0.9900, 12 negative triangles
136: dt=0.9900, 8 negative triangles
137: dt=0.9900, 9 negative triangles
138: dt=0.9900, 7 negative triangles
139: dt=0.9900, 9 negative triangles
140: dt=0.9900, 9 negative triangles
141: dt=0.9900, 10 negative triangles
142: dt=0.9900, 5 negative triangles
143: dt=0.9900, 4 negative triangles
144: dt=0.9900, 5 negative triangles
145: dt=0.9900, 4 negative triangles
146: dt=0.9900, 3 negative triangles
147: dt=0.9900, 2 negative triangles
148: dt=0.9900, 3 negative triangles
149: dt=0.9900, 5 negative triangles
150: dt=0.9900, 2 negative triangles
151: dt=0.9900, 1 negative triangles
152: dt=0.9900, 1 negative triangles
153: dt=0.9900, 2 negative triangles
154: dt=0.9900, 2 negative triangles
155: dt=0.9900, 1 negative triangles
156: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.01 hours
mris_register utimesec    3670.077063
mris_register stimesec    1.402786
mris_register ru_maxrss   225156
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   33178
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  8304
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    281705
mris_register ru_nivcsw   188447
FSRUNTIME@ mris_register  1.0072 hours 1 threads
PIDs (9536 9539) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 08:15:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white 

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 08:15:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white 

Waiting for PID 11989 of (11989 11992) to complete...
Waiting for PID 11992 of (11989 11992) 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 (11989 11992) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 08:15:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 08:15:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 12037 of (12037 12040) to complete...
Waiting for PID 12040 of (12037 12040) 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 (12037 12040) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 08:15:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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 08:15:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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 12083 of (12083 12086) to complete...
Waiting for PID 12086 of (12083 12086) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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...
1057 labels changed using aseg
relabeling using gibbs priors...
000:   2683 changed, 113752 examined...
001:    631 changed, 11356 examined...
002:    148 changed, 3616 examined...
003:     39 changed, 892 examined...
004:     16 changed, 241 examined...
005:      6 changed, 95 examined...
006:      2 changed, 41 examined...
007:      0 changed, 14 examined...
209 labels changed using aseg
000: 101 total segments, 51 labels (244 vertices) changed
001: 51 total segments, 3 labels (3 vertices) changed
002: 48 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1043 vertices marked for relabeling...
1043 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 12 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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...
1023 labels changed using aseg
relabeling using gibbs priors...
000:   2499 changed, 116748 examined...
001:    537 changed, 10775 examined...
002:    146 changed, 3004 examined...
003:     43 changed, 861 examined...
004:     15 changed, 253 examined...
005:      7 changed, 86 examined...
006:      2 changed, 42 examined...
007:      0 changed, 16 examined...
176 labels changed using aseg
000: 90 total segments, 52 labels (259 vertices) changed
001: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1164 vertices marked for relabeling...
1164 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 12 seconds.
PIDs (12083 12086) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 08:15:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050564 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 08:15:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050564 rh 

Waiting for PID 12131 of (12131 12134) to complete...
Waiting for PID 12134 of (12131 12134) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050564 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-6.0.0/0050564/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
9576 bright wm thresholded.
2610 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.orig...
computing class statistics...
border white:    218071 voxels (1.30%)
border gray      265543 voxels (1.58%)
WM (95.0): 95.7 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.7 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 55.5 (was 70)
setting MAX_BORDER_WHITE to 108.5 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 45.0 (was 40)
setting MAX_GRAY to 91.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 34.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-7.8,    GM=66+-7.8
mean inside = 91.3, mean outside = 73.6
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.91 +- 0.26 (0.02-->4.85) (max @ vno 39230 --> 112992)
face area 0.35 +- 0.16 (0.00-->5.73)
mean absolute distance = 0.44 +- 0.74
2347 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 140 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 51 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 19 points - only 0.00% unknown
deleting segment 7 with 114 points - only 0.00% unknown
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=77.8, 120 (113) missing vertices, mean dist 0.2 [0.5 (%20.2)->0.4 (%79.8))]
%65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.26 (0.11-->4.64) (max @ vno 39230 --> 112992)
face area 0.35 +- 0.17 (0.00-->5.30)
mean absolute distance = 0.29 +- 0.55
1974 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1271536.6, rms=5.695
001: dt: 0.5000, sse=845377.4, rms=3.565 (37.396%)
002: dt: 0.5000, sse=759939.1, rms=2.993 (16.043%)
rms = 3.04, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=678658.5, rms=2.257 (24.585%)
004: dt: 0.2500, sse=645938.4, rms=1.873 (17.037%)
005: dt: 0.2500, sse=637257.1, rms=1.735 (7.382%)
006: dt: 0.2500, sse=632249.2, rms=1.676 (3.381%)
rms = 1.64, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=629407.1, rms=1.637 (2.327%)
rms = 1.59, time step reduction 3 of 3 to 0.062...
008: dt: 0.1250, sse=626666.2, rms=1.594 (2.604%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 149 points - only 0.00% unknown
deleting segment 1 with 19 points - only 0.00% unknown
deleting segment 2 with 50 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 79 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
mean border=79.9, 49 (15) missing vertices, mean dist -0.1 [0.3 (%67.4)->0.2 (%32.6))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.26 (0.10-->4.89) (max @ vno 39230 --> 112992)
face area 0.36 +- 0.18 (0.00-->5.93)
mean absolute distance = 0.25 +- 0.44
2359 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=832512.8, rms=3.291
009: dt: 0.5000, sse=707720.6, rms=2.245 (31.795%)
rms = 2.45, time step reduction 1 of 3 to 0.250...
010: dt: 0.2500, sse=659721.1, rms=1.693 (24.587%)
011: dt: 0.2500, sse=639917.0, rms=1.397 (17.475%)
012: dt: 0.2500, sse=635018.4, rms=1.314 (5.931%)
rms = 1.30, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=633881.0, rms=1.301 (0.988%)
rms = 1.27, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=632998.2, rms=1.266 (2.665%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 152 points - only 0.00% unknown
deleting segment 1 with 15 points - only 0.00% unknown
deleting segment 2 with 50 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 13 points - only 0.00% unknown
deleting segment 5 with 78 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
mean border=81.2, 61 (9) missing vertices, mean dist -0.1 [0.3 (%61.2)->0.2 (%38.8))]
%78 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.26 (0.08-->4.95) (max @ vno 39230 --> 112992)
face area 0.36 +- 0.17 (0.00-->5.91)
mean absolute distance = 0.25 +- 0.38
2474 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=690749.6, rms=2.199
015: dt: 0.5000, sse=677067.1, rms=2.039 (7.299%)
rms = 2.37, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=630631.5, rms=1.439 (29.428%)
017: dt: 0.2500, sse=617856.6, rms=1.235 (14.153%)
018: dt: 0.2500, sse=616501.9, rms=1.181 (4.384%)
rms = 1.19, time step reduction 2 of 3 to 0.125...
rms = 1.16, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=614269.0, rms=1.161 (1.736%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 146 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 2 with 51 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 13 points - only 0.00% unknown
deleting segment 5 with 82 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
mean border=81.8, 64 (5) missing vertices, mean dist -0.0 [0.3 (%53.4)->0.2 (%46.6))]
%81 local maxima, %14 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-6.0.0/0050564/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=623195.0, rms=1.420
rms = 1.49, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=603865.1, rms=1.066 (24.955%)
021: dt: 0.2500, sse=596598.2, rms=0.897 (15.854%)
rms = 0.92, time step reduction 2 of 3 to 0.125...
rms = 0.89, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=595592.2, rms=0.885 (1.281%)
positioning took 0.4 minutes
generating cortex label...
4 non-cortical segments detected
only using segment with 6885 vertices
erasing segment 0 (vno[0] = 26436)
erasing segment 2 (vno[0] = 66636)
erasing segment 3 (vno[0] = 81505)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.area
vertex spacing 0.91 +- 0.26 (0.02-->4.97) (max @ vno 39230 --> 112992)
face area 0.35 +- 0.17 (0.00-->5.92)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 62 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=53.8, 125 (125) missing vertices, mean dist 1.6 [4.1 (%0.0)->2.6 (%100.0))]
%11 local maxima, %48 large gradients and %37 min vals, 965 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=18322378.0, rms=28.640
001: dt: 0.0500, sse=16170235.0, rms=26.848 (6.258%)
002: dt: 0.0500, sse=14616992.0, rms=25.476 (5.110%)
003: dt: 0.0500, sse=13417986.0, rms=24.364 (4.365%)
004: dt: 0.0500, sse=12442086.0, rms=23.420 (3.875%)
005: dt: 0.0500, sse=11615810.0, rms=22.589 (3.545%)
006: dt: 0.0500, sse=10897652.0, rms=21.842 (3.309%)
007: dt: 0.0500, sse=10259800.0, rms=21.156 (3.141%)
008: dt: 0.0500, sse=9685052.0, rms=20.518 (3.015%)
009: dt: 0.0500, sse=9162008.0, rms=19.920 (2.916%)
010: dt: 0.0500, sse=8682350.0, rms=19.355 (2.837%)
positioning took 0.8 minutes
mean border=53.6, 117 (77) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.2 (%100.0))]
%11 local maxima, %48 large gradients and %36 min vals, 977 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=9295489.0, rms=20.071
011: dt: 0.0500, sse=8849688.0, rms=19.551 (2.593%)
012: dt: 0.0500, sse=8437053.0, rms=19.057 (2.529%)
013: dt: 0.0500, sse=8053771.0, rms=18.585 (2.472%)
014: dt: 0.0500, sse=7697728.5, rms=18.137 (2.414%)
015: dt: 0.0500, sse=7367083.0, rms=17.710 (2.354%)
016: dt: 0.0500, sse=7060354.0, rms=17.304 (2.291%)
017: dt: 0.0500, sse=6775639.5, rms=16.919 (2.227%)
018: dt: 0.0500, sse=6511853.0, rms=16.553 (2.158%)
019: dt: 0.0500, sse=6266769.0, rms=16.207 (2.095%)
020: dt: 0.0500, sse=6039048.5, rms=15.877 (2.031%)
positioning took 0.8 minutes
mean border=53.4, 137 (58) missing vertices, mean dist 1.2 [0.1 (%1.4)->1.9 (%98.6))]
%12 local maxima, %47 large gradients and %36 min vals, 954 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=6162845.0, rms=16.060
021: dt: 0.0500, sse=5942492.0, rms=15.739 (2.001%)
022: dt: 0.0500, sse=5738772.0, rms=15.436 (1.926%)
023: dt: 0.0500, sse=5548318.0, rms=15.147 (1.873%)
024: dt: 0.0500, sse=5371637.0, rms=14.873 (1.804%)
025: dt: 0.0500, sse=5207630.5, rms=14.615 (1.737%)
026: dt: 0.0500, sse=5054940.0, rms=14.370 (1.675%)
027: dt: 0.0500, sse=4912425.0, rms=14.138 (1.618%)
028: dt: 0.0500, sse=4778205.0, rms=13.915 (1.575%)
029: dt: 0.0500, sse=4651294.0, rms=13.701 (1.538%)
030: dt: 0.0500, sse=4531141.0, rms=13.495 (1.502%)
positioning took 0.8 minutes
mean border=53.4, 159 (46) missing vertices, mean dist 1.0 [0.1 (%16.6)->2.0 (%83.4))]
%12 local maxima, %48 large gradients and %35 min vals, 901 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=4586913.0, rms=13.587
031: dt: 0.5000, sse=3730450.8, rms=12.031 (11.452%)
032: dt: 0.5000, sse=3200432.0, rms=10.948 (9.000%)
033: dt: 0.5000, sse=2833726.2, rms=10.130 (7.467%)
034: dt: 0.5000, sse=2591796.0, rms=9.545 (5.783%)
035: dt: 0.5000, sse=2404606.8, rms=9.065 (5.024%)
036: dt: 0.5000, sse=2240034.0, rms=8.621 (4.901%)
037: dt: 0.5000, sse=2065677.2, rms=8.128 (5.716%)
038: dt: 0.5000, sse=1901186.2, rms=7.635 (6.063%)
039: dt: 0.5000, sse=1750445.0, rms=7.156 (6.275%)
040: dt: 0.5000, sse=1631836.2, rms=6.755 (5.608%)
041: dt: 0.5000, sse=1532417.6, rms=6.401 (5.243%)
042: dt: 0.5000, sse=1469118.5, rms=6.162 (3.720%)
043: dt: 0.5000, sse=1416658.2, rms=5.960 (3.287%)
044: dt: 0.5000, sse=1385983.4, rms=5.836 (2.078%)
045: dt: 0.5000, sse=1356664.5, rms=5.717 (2.043%)
046: dt: 0.5000, sse=1342486.5, rms=5.656 (1.071%)
047: dt: 0.5000, sse=1325192.6, rms=5.584 (1.274%)
rms = 5.56, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1318820.2, rms=5.556 (0.501%)
049: dt: 0.2500, sse=1275838.4, rms=5.344 (3.817%)
050: dt: 0.2500, sse=1264649.6, rms=5.293 (0.944%)
rms = 5.29, time step reduction 2 of 3 to 0.125...
051: dt: 0.2500, sse=1263921.2, rms=5.288 (0.096%)
052: dt: 0.1250, sse=1252016.5, rms=5.232 (1.067%)
rms = 5.21, time step reduction 3 of 3 to 0.062...
053: dt: 0.1250, sse=1248121.1, rms=5.214 (0.331%)
positioning took 2.3 minutes
mean border=52.8, 2012 (19) missing vertices, mean dist 0.2 [0.2 (%53.5)->1.0 (%46.5))]
%20 local maxima, %42 large gradients and %32 min vals, 473 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=1430827.5, rms=5.105
054: dt: 0.5000, sse=1370666.0, rms=4.833 (5.319%)
055: dt: 0.5000, sse=1313483.1, rms=4.571 (5.421%)
rms = 4.59, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1273775.5, rms=4.338 (5.098%)
057: dt: 0.2500, sse=1262125.9, rms=4.265 (1.682%)
rms = 4.26, time step reduction 2 of 3 to 0.125...
058: dt: 0.2500, sse=1260073.2, rms=4.256 (0.214%)
059: dt: 0.1250, sse=1241383.0, rms=4.147 (2.565%)
rms = 4.11, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1234561.9, rms=4.109 (0.903%)
positioning took 0.9 minutes
mean border=52.1, 2470 (14) missing vertices, mean dist 0.2 [0.2 (%52.0)->0.8 (%48.0))]
%30 local maxima, %33 large gradients and %31 min vals, 507 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=1302730.9, rms=4.373
rms = 4.40, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1279730.0, rms=4.247 (2.885%)
062: dt: 0.2500, sse=1261971.6, rms=4.153 (2.211%)
rms = 4.13, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1256942.0, rms=4.132 (0.510%)
064: dt: 0.1250, sse=1237970.6, rms=4.020 (2.714%)
rms = 3.97, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1229433.0, rms=3.974 (1.148%)
positioning took 0.7 minutes
mean border=51.5, 4636 (12) missing vertices, mean dist 0.1 [0.2 (%49.0)->0.6 (%51.0))]
%36 local maxima, %25 large gradients and %30 min vals, 602 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-6.0.0/0050564/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1259061.9, rms=4.077
rms = 4.11, time step reduction 1 of 3 to 0.250...
066: dt: 0.2500, sse=1239953.4, rms=3.966 (2.729%)
067: dt: 0.2500, sse=1218975.6, rms=3.855 (2.794%)
rms = 3.82, time step reduction 2 of 3 to 0.125...
068: dt: 0.2500, sse=1212243.0, rms=3.824 (0.807%)
069: dt: 0.1250, sse=1190830.2, rms=3.689 (3.522%)
070: dt: 0.1250, sse=1181655.0, rms=3.636 (1.430%)
rms = 3.61, time step reduction 3 of 3 to 0.062...
071: dt: 0.1250, sse=1176789.9, rms=3.610 (0.733%)
positioning took 0.8 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.area.pial
vertex spacing 1.09 +- 0.50 (0.06-->7.16) (max @ vno 44144 --> 43136)
face area 0.47 +- 0.40 (0.00-->6.96)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 113752 vertices processed
25000 of 113752 vertices processed
50000 of 113752 vertices processed
75000 of 113752 vertices processed
100000 of 113752 vertices processed
0 of 113752 vertices processed
25000 of 113752 vertices processed
50000 of 113752 vertices processed
75000 of 113752 vertices processed
100000 of 113752 vertices processed
thickness calculation complete, 622:2858 truncations.
24887 vertices at 0 distance
73686 vertices at 1 distance
68651 vertices at 2 distance
32006 vertices at 3 distance
11006 vertices at 4 distance
3680 vertices at 5 distance
1322 vertices at 6 distance
559 vertices at 7 distance
286 vertices at 8 distance
151 vertices at 9 distance
91 vertices at 10 distance
68 vertices at 11 distance
58 vertices at 12 distance
53 vertices at 13 distance
42 vertices at 14 distance
34 vertices at 15 distance
18 vertices at 16 distance
20 vertices at 17 distance
14 vertices at 18 distance
15 vertices at 19 distance
17 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.thickness
positioning took 12.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050564 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-6.0.0/0050564/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
9576 bright wm thresholded.
2610 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.orig...
computing class statistics...
border white:    218071 voxels (1.30%)
border gray      265543 voxels (1.58%)
WM (95.0): 95.7 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.7 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 55.5 (was 70)
setting MAX_BORDER_WHITE to 107.5 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 45.0 (was 40)
setting MAX_GRAY to 90.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 34.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=99+-6.1,    GM=66+-7.8
mean inside = 91.4, mean outside = 74.0
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 0.91 +- 0.26 (0.03-->5.62) (max @ vno 98503 --> 116501)
face area 0.35 +- 0.17 (0.00-->5.44)
mean absolute distance = 0.46 +- 0.73
2663 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 32 points - only 0.00% unknown
deleting segment 1 with 31 points - only 0.00% unknown
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 4 with 25 points - only 0.00% unknown
deleting segment 7 with 213 points - only 0.00% unknown
deleting segment 8 with 14 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 154 points - only 0.00% unknown
deleting segment 11 with 11 points - only 0.00% unknown
mean border=77.8, 189 (186) missing vertices, mean dist 0.3 [0.5 (%19.5)->0.4 (%80.5))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.94 +- 0.27 (0.07-->5.58) (max @ vno 56157 --> 115599)
face area 0.35 +- 0.17 (0.00-->4.95)
mean absolute distance = 0.30 +- 0.56
2257 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1397699.0, rms=6.039
001: dt: 0.5000, sse=904046.8, rms=3.781 (37.394%)
002: dt: 0.5000, sse=794227.0, rms=3.062 (19.005%)
rms = 3.02, time step reduction 1 of 3 to 0.250...
003: dt: 0.5000, sse=787578.8, rms=3.024 (1.263%)
004: dt: 0.2500, sse=667908.9, rms=1.898 (37.239%)
005: dt: 0.2500, sse=654599.4, rms=1.723 (9.198%)
006: dt: 0.2500, sse=650850.6, rms=1.660 (3.641%)
rms = 1.63, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=649499.5, rms=1.633 (1.655%)
008: dt: 0.1250, sse=644865.2, rms=1.573 (3.682%)
rms = 1.56, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=644276.1, rms=1.560 (0.803%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 11 points - only 0.00% unknown
deleting segment 1 with 30 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 23 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 132 points - only 0.00% unknown
deleting segment 7 with 8 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 147 points - only 0.00% unknown
deleting segment 10 with 22 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
mean border=80.1, 103 (47) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.2 (%30.5))]
%77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.93 +- 0.26 (0.07-->5.49) (max @ vno 98503 --> 116501)
face area 0.37 +- 0.18 (0.00-->5.29)
mean absolute distance = 0.26 +- 0.44
2585 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=877375.3, rms=3.400
010: dt: 0.5000, sse=741485.7, rms=2.272 (33.160%)
rms = 2.46, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=685212.6, rms=1.714 (24.561%)
012: dt: 0.2500, sse=666190.2, rms=1.433 (16.379%)
013: dt: 0.2500, sse=660931.6, rms=1.358 (5.296%)
rms = 1.35, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=660259.8, rms=1.348 (0.700%)
rms = 1.31, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=657808.4, rms=1.313 (2.633%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 11 points - only 0.00% unknown
deleting segment 1 with 32 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 11 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 25 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 134 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
deleting segment 10 with 149 points - only 0.00% unknown
deleting segment 11 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 11 points - only 0.00% unknown
mean border=81.5, 106 (29) missing vertices, mean dist -0.1 [0.3 (%62.0)->0.2 (%38.0))]
%82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.26 (0.07-->5.44) (max @ vno 56157 --> 115599)
face area 0.36 +- 0.18 (0.00-->5.45)
mean absolute distance = 0.25 +- 0.38
2635 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=728340.5, rms=2.349
016: dt: 0.5000, sse=706133.3, rms=2.091 (10.968%)
rms = 2.36, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=657262.0, rms=1.510 (27.805%)
018: dt: 0.2500, sse=643843.4, rms=1.299 (13.930%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=640876.1, rms=1.256 (3.352%)
020: dt: 0.1250, sse=637304.9, rms=1.204 (4.138%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=637080.2, rms=1.201 (0.260%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 11 points - only 0.00% unknown
deleting segment 1 with 32 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 23 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 113 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 149 points - only 0.00% unknown
deleting segment 12 with 14 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
deleting segment 15 with 11 points - only 0.00% unknown
mean border=82.1, 131 (22) missing vertices, mean dist -0.0 [0.3 (%53.5)->0.2 (%46.5))]
%84 local maxima, %11 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-6.0.0/0050564/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=647949.7, rms=1.505
rms = 1.49, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=647236.8, rms=1.491 (0.889%)
023: dt: 0.2500, sse=626866.5, rms=1.151 (22.852%)
024: dt: 0.2500, sse=619610.8, rms=1.040 (9.615%)
rms = 1.10, time step reduction 2 of 3 to 0.125...
rms = 1.00, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=617207.4, rms=1.000 (3.861%)
positioning took 0.4 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 6727 vertices
erasing segment 0 (vno[0] = 27489)
erasing segment 1 (vno[0] = 28332)
erasing segment 3 (vno[0] = 67028)
erasing segment 4 (vno[0] = 79529)
erasing segment 5 (vno[0] = 83692)
erasing segment 6 (vno[0] = 85204)
erasing segment 7 (vno[0] = 87459)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.area
vertex spacing 0.91 +- 0.26 (0.03-->5.63) (max @ vno 85925 --> 85939)
face area 0.35 +- 0.17 (0.00-->5.65)
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
deleting segment 0 with 2 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=54.1, 195 (195) missing vertices, mean dist 1.5 [3.3 (%0.1)->2.7 (%99.9))]
%10 local maxima, %44 large gradients and %41 min vals, 1002 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=18901504.0, rms=28.688
001: dt: 0.0500, sse=16748722.0, rms=26.949 (6.062%)
002: dt: 0.0500, sse=15188492.0, rms=25.615 (4.951%)
003: dt: 0.0500, sse=13981902.0, rms=24.533 (4.223%)
004: dt: 0.0500, sse=12997257.0, rms=23.614 (3.748%)
005: dt: 0.0500, sse=12162042.0, rms=22.805 (3.426%)
006: dt: 0.0500, sse=11433710.0, rms=22.075 (3.200%)
007: dt: 0.0500, sse=10785801.0, rms=21.405 (3.036%)
008: dt: 0.0500, sse=10200614.0, rms=20.781 (2.915%)
009: dt: 0.0500, sse=9667119.0, rms=20.195 (2.819%)
010: dt: 0.0500, sse=9176832.0, rms=19.641 (2.742%)
positioning took 0.8 minutes
mean border=53.8, 169 (128) missing vertices, mean dist 1.3 [1.7 (%0.1)->2.3 (%99.9))]
%11 local maxima, %44 large gradients and %40 min vals, 922 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=9905206.0, rms=20.456
011: dt: 0.0500, sse=9446619.0, rms=19.946 (2.496%)
012: dt: 0.0500, sse=9021082.0, rms=19.460 (2.436%)
013: dt: 0.0500, sse=8625441.0, rms=18.997 (2.379%)
014: dt: 0.0500, sse=8257533.5, rms=18.556 (2.321%)
015: dt: 0.0500, sse=7914903.5, rms=18.136 (2.266%)
016: dt: 0.0500, sse=7595731.5, rms=17.735 (2.209%)
017: dt: 0.0500, sse=7298222.0, rms=17.353 (2.154%)
018: dt: 0.0500, sse=7021516.0, rms=16.990 (2.092%)
019: dt: 0.0500, sse=6763592.5, rms=16.644 (2.035%)
020: dt: 0.0500, sse=6523423.5, rms=16.316 (1.974%)
positioning took 0.8 minutes
mean border=53.7, 182 (102) missing vertices, mean dist 1.1 [0.2 (%1.4)->2.0 (%98.6))]
%11 local maxima, %44 large gradients and %40 min vals, 937 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=6638495.0, rms=16.478
021: dt: 0.0500, sse=6406852.5, rms=16.158 (1.943%)
022: dt: 0.0500, sse=6192102.5, rms=15.855 (1.873%)
023: dt: 0.0500, sse=5991184.0, rms=15.566 (1.820%)
024: dt: 0.0500, sse=5804862.5, rms=15.294 (1.751%)
025: dt: 0.0500, sse=5631630.0, rms=15.036 (1.687%)
026: dt: 0.0500, sse=5469939.5, rms=14.791 (1.629%)
027: dt: 0.0500, sse=5318790.0, rms=14.558 (1.575%)
028: dt: 0.0500, sse=5176056.0, rms=14.334 (1.535%)
029: dt: 0.0500, sse=5040600.5, rms=14.119 (1.503%)
030: dt: 0.0500, sse=4912072.0, rms=13.911 (1.471%)
positioning took 0.8 minutes
mean border=53.6, 206 (89) missing vertices, mean dist 1.0 [0.1 (%14.6)->2.0 (%85.4))]
%12 local maxima, %44 large gradients and %40 min vals, 953 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=5007355.0, rms=14.062
031: dt: 0.5000, sse=4086982.8, rms=12.494 (11.150%)
032: dt: 0.5000, sse=3498716.0, rms=11.370 (8.998%)
033: dt: 0.5000, sse=3088046.8, rms=10.513 (7.534%)
034: dt: 0.5000, sse=2807380.8, rms=9.877 (6.053%)
035: dt: 0.5000, sse=2607293.8, rms=9.396 (4.869%)
036: dt: 0.5000, sse=2435509.8, rms=8.960 (4.635%)
037: dt: 0.5000, sse=2270432.5, rms=8.526 (4.851%)
038: dt: 0.5000, sse=2098036.5, rms=8.047 (5.617%)
039: dt: 0.5000, sse=1938893.6, rms=7.582 (5.772%)
040: dt: 0.5000, sse=1800293.2, rms=7.152 (5.681%)
041: dt: 0.5000, sse=1690600.1, rms=6.794 (5.006%)
042: dt: 0.5000, sse=1607229.1, rms=6.507 (4.218%)
043: dt: 0.5000, sse=1548006.6, rms=6.297 (3.232%)
044: dt: 0.5000, sse=1501984.0, rms=6.127 (2.688%)
045: dt: 0.5000, sse=1470539.5, rms=6.009 (1.931%)
046: dt: 0.5000, sse=1446361.8, rms=5.916 (1.551%)
047: dt: 0.5000, sse=1431622.8, rms=5.859 (0.960%)
048: dt: 0.5000, sse=1418118.6, rms=5.804 (0.935%)
rms = 5.77, time step reduction 1 of 3 to 0.250...
049: dt: 0.5000, sse=1408409.0, rms=5.768 (0.632%)
050: dt: 0.2500, sse=1367472.9, rms=5.577 (3.306%)
051: dt: 0.2500, sse=1349424.0, rms=5.503 (1.332%)
rms = 5.50, time step reduction 2 of 3 to 0.125...
rms = 5.48, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1343547.9, rms=5.477 (0.468%)
positioning took 2.4 minutes
mean border=53.0, 2247 (32) missing vertices, mean dist 0.2 [0.2 (%53.4)->1.0 (%46.6))]
%20 local maxima, %38 large gradients and %36 min vals, 400 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=1518848.9, rms=5.280
053: dt: 0.5000, sse=1441291.6, rms=4.942 (6.395%)
054: dt: 0.5000, sse=1383795.1, rms=4.691 (5.088%)
rms = 4.69, time step reduction 1 of 3 to 0.250...
055: dt: 0.2500, sse=1339133.0, rms=4.442 (5.293%)
056: dt: 0.2500, sse=1329091.4, rms=4.380 (1.414%)
rms = 4.38, time step reduction 2 of 3 to 0.125...
rms = 4.34, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1321730.0, rms=4.338 (0.940%)
positioning took 0.8 minutes
mean border=52.4, 2780 (22) missing vertices, mean dist 0.2 [0.2 (%50.7)->0.8 (%49.3))]
%29 local maxima, %29 large gradients and %35 min vals, 498 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=1375447.0, rms=4.558
rms = 4.67, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1346990.4, rms=4.409 (3.273%)
059: dt: 0.2500, sse=1336028.9, rms=4.354 (1.260%)
rms = 4.34, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1332961.2, rms=4.343 (0.233%)
061: dt: 0.1250, sse=1309632.6, rms=4.215 (2.961%)
rms = 4.17, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1300892.8, rms=4.170 (1.055%)
positioning took 0.7 minutes
mean border=51.8, 5115 (19) missing vertices, mean dist 0.1 [0.2 (%48.2)->0.6 (%51.8))]
%35 local maxima, %23 large gradients and %34 min vals, 569 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-6.0.0/0050564/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1331239.4, rms=4.271
rms = 4.31, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1311564.2, rms=4.164 (2.504%)
064: dt: 0.2500, sse=1290251.0, rms=4.058 (2.531%)
rms = 4.02, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1281771.4, rms=4.020 (0.950%)
066: dt: 0.1250, sse=1258038.2, rms=3.881 (3.459%)
067: dt: 0.1250, sse=1247752.4, rms=3.825 (1.435%)
rms = 3.79, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1241813.4, rms=3.794 (0.801%)
positioning took 0.9 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.area.pial
vertex spacing 1.09 +- 0.51 (0.07-->7.16) (max @ vno 56157 --> 115599)
face area 0.47 +- 0.39 (0.00-->6.59)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 116748 vertices processed
25000 of 116748 vertices processed
50000 of 116748 vertices processed
75000 of 116748 vertices processed
100000 of 116748 vertices processed
0 of 116748 vertices processed
25000 of 116748 vertices processed
50000 of 116748 vertices processed
75000 of 116748 vertices processed
100000 of 116748 vertices processed
thickness calculation complete, 412:2601 truncations.
25253 vertices at 0 distance
76224 vertices at 1 distance
70891 vertices at 2 distance
32664 vertices at 3 distance
11655 vertices at 4 distance
3749 vertices at 5 distance
1268 vertices at 6 distance
524 vertices at 7 distance
198 vertices at 8 distance
105 vertices at 9 distance
57 vertices at 10 distance
80 vertices at 11 distance
63 vertices at 12 distance
43 vertices at 13 distance
35 vertices at 14 distance
28 vertices at 15 distance
22 vertices at 16 distance
10 vertices at 17 distance
12 vertices at 18 distance
14 vertices at 19 distance
7 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.thickness
positioning took 13.0 minutes
PIDs (12131 12134) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 08:28:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/lh.cortex.label
Total face volume 232168
Total vertex volume 227835 (mask=0)
#@# 0050564 lh 227835
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 08:28:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/rh.cortex.label
Total face volume 244008
Total vertex volume 240206 (mask=0)
#@# 0050564 rh 240206
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 08:28:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 

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 = 153
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/ribbon.mgz
mris_volmask took 9.20 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 08:37:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 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 0050564 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 08:37:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 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 0050564 rh pial 

Waiting for PID 13490 of (13490 13493 13496 13499) to complete...
Waiting for PID 13493 of (13490 13493 13496 13499) to complete...
Waiting for PID 13496 of (13490 13493 13496 13499) to complete...
Waiting for PID 13499 of (13490 13493 13496 13499) 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 0050564 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 232168
Total vertex volume 227835 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
 1034    699   1413  1.971 0.530     0.099     0.014        8     0.6  bankssts
  676    415   1167  2.559 0.786     0.125     0.012        9     0.3  caudalanteriorcingulate
 3108   2161   6515  2.598 0.599     0.119     0.026       30     3.4  caudalmiddlefrontal
 1984   1406   2766  1.834 0.535     0.156     0.034       28     2.7  cuneus
  643    455   2515  3.840 0.801     0.115     0.037        7     1.0  entorhinal
 3297   2430   8069  2.825 0.816     0.151     0.039       54     5.7  fusiform
 5304   3703  10529  2.330 0.720     0.135     0.034       72     8.2  inferiorparietal
 3074   2184   7641  2.468 0.884     0.138     0.037       60     4.9  inferiortemporal
 1314    934   2861  2.520 1.027     0.130     0.037       18     1.8  isthmuscingulate
 6714   4706  11606  2.106 0.654     0.149     0.037       98    10.7  lateraloccipital
 3464   2416   9515  3.053 0.922     0.127     0.036       36     4.9  lateralorbitofrontal
 3311   2494   6385  2.269 0.729     0.148     0.041       45     5.4  lingual
 2064   1483   5592  2.965 0.755     0.135     0.038       26     3.1  medialorbitofrontal
 2997   2091   7266  2.497 0.913     0.130     0.035       43     4.5  middletemporal
  837    558   2032  2.953 0.891     0.109     0.025        9     0.8  parahippocampal
 1739   1243   3422  2.458 0.564     0.129     0.030       17     2.1  paracentral
 2691   1825   6110  2.562 0.787     0.120     0.025       31     2.9  parsopercularis
  838    617   2791  2.999 0.915     0.176     0.061       17     2.2  parsorbitalis
 1780   1251   4169  2.467 0.729     0.135     0.035       25     2.3  parstriangularis
 1822   1336   2074  1.662 0.443     0.149     0.036       23     2.9  pericalcarine
 5248   3672   9445  2.151 0.781     0.128     0.029       62     6.3  postcentral
 1425   1086   3706  2.693 0.967     0.152     0.032       22     2.1  posteriorcingulate
 6335   4311  10719  2.236 0.666     0.125     0.032       81     8.8  precentral
 4710   3289  10008  2.529 0.726     0.131     0.035       54     6.8  precuneus
  562    386   1625  3.364 0.879     0.145     0.039        9     1.0  rostralanteriorcingulate
 6743   4767  14978  2.529 0.747     0.129     0.032       94     8.7  rostralmiddlefrontal
 9975   6824  26091  3.057 0.723     0.120     0.027       97    10.3  superiorfrontal
 6910   4911  13817  2.376 0.715     0.128     0.028       70     8.2  superiorparietal
 4688   3271   9017  2.322 0.794     0.114     0.026       53     5.3  superiortemporal
 6284   4483  12114  2.309 0.742     0.140     0.039       94     9.9  supramarginal
  350    270   1276  2.859 0.818     0.209     0.067       10     1.1  frontalpole
  590    488   2440  3.185 1.048     0.172     0.048       12     1.6  temporalpole
  686    481   1195  2.241 0.554     0.142     0.027        9     0.7  transversetemporal
 3102   2168   6946  3.176 0.768     0.114     0.025       24     3.2  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 0050564 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 232168
Total vertex volume 227835 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
 1034    751   1413  1.971 0.530     0.110     0.023        8     1.0  bankssts
  676    529   1167  2.559 0.786     0.142     0.030       17     0.8  caudalanteriorcingulate
 3108   2801   6515  2.598 0.599     0.147     0.032       39     4.6  caudalmiddlefrontal
 1984   1683   2766  1.834 0.535     0.162     0.036       28     3.4  cuneus
  643    923   2515  3.840 0.801     0.209     0.043       13     1.4  entorhinal
 3297   3298   8069  2.825 0.816     0.185     0.044       53     7.0  fusiform
 5304   5363  10529  2.330 0.720     0.183     0.045       74    11.6  inferiorparietal
 3074   3561   7641  2.468 0.884     0.200     0.048       41     7.6  inferiortemporal
 1314   1259   2861  2.520 1.027     0.170     0.037       21     2.2  isthmuscingulate
 6714   6191  11606  2.106 0.654     0.169     0.038       95    12.3  lateraloccipital
 3464   3515   9515  3.053 0.922     0.190     0.047       74     7.9  lateralorbitofrontal
 3311   3168   6385  2.269 0.729     0.178     0.044       45     7.2  lingual
 2064   2286   5592  2.965 0.755     0.197     0.049       31     4.8  medialorbitofrontal
 2997   3372   7266  2.497 0.913     0.192     0.041       35     6.1  middletemporal
  837    842   2032  2.953 0.891     0.173     0.046        9     1.7  parahippocampal
 1739   1558   3422  2.458 0.564     0.150     0.035       22     2.9  paracentral
 2691   2749   6110  2.562 0.787     0.173     0.037       31     4.6  parsopercularis
  838   1161   2791  2.999 0.915     0.254     0.071       19     3.0  parsorbitalis
 1780   1932   4169  2.467 0.729     0.207     0.048       29     4.2  parstriangularis
 1822   1265   2074  1.662 0.443     0.148     0.042       26     3.5  pericalcarine
 5248   5076   9445  2.151 0.781     0.164     0.035       57     8.9  postcentral
 1425   1429   3706  2.693 0.967     0.185     0.042       25     2.9  posteriorcingulate
 6335   5090  10719  2.236 0.666     0.140     0.037      380     9.9  precentral
 4710   4339  10008  2.529 0.726     0.171     0.042       71    10.0  precuneus
  562    631   1625  3.364 0.879     0.232     0.067       14     1.5  rostralanteriorcingulate
 6743   6705  14978  2.529 0.747     0.177     0.039       91    12.4  rostralmiddlefrontal
 9975   9599  26091  3.057 0.723     0.159     0.037      128    17.2  superiorfrontal
 6910   6480  13817  2.376 0.715     0.163     0.036       90    12.4  superiorparietal
 4688   4453   9017  2.322 0.794     0.166     0.038       62     8.5  superiortemporal
 6284   6037  12114  2.309 0.742     0.177     0.045      121    13.4  supramarginal
  350    612   1276  2.859 0.818     0.303     0.057        6     1.1  frontalpole
  590   1062   2440  3.185 1.048     0.301     0.060        8     2.0  temporalpole
  686    652   1195  2.241 0.554     0.163     0.044        8     1.2  transversetemporal
 3102   2146   6946  3.176 0.768     0.155     0.043       59     6.3  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 0050564 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 244008
Total vertex volume 240206 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  972    669   1529  2.295 0.526     0.098     0.016        6     0.6  bankssts
  868    584   1891  2.540 0.842     0.126     0.021       10     0.9  caudalanteriorcingulate
 2221   1611   4710  2.590 0.659     0.112     0.020       18     1.8  caudalmiddlefrontal
 1955   1430   3784  2.315 0.677     0.172     0.043       34     3.7  cuneus
  521    376   1782  3.601 0.708     0.121     0.025        4     0.6  entorhinal
 3746   2648   8589  2.701 0.750     0.140     0.034       53     5.2  fusiform
 8139   5850  17968  2.521 0.709     0.139     0.034      109    12.4  inferiorparietal
 3702   2642   8963  2.629 0.779     0.140     0.045       56     7.4  inferiortemporal
 1274    887   2999  2.658 1.015     0.122     0.024       16     1.1  isthmuscingulate
 6852   4673  12359  2.291 0.720     0.146     0.039       93    11.0  lateraloccipital
 2800   2006   8294  3.137 0.974     0.140     0.039       34     4.5  lateralorbitofrontal
 3263   2427   7070  2.543 0.777     0.155     0.042       50     5.9  lingual
 2119   1546   5607  2.749 0.758     0.144     0.041       31     3.9  medialorbitofrontal
 3526   2509   8932  2.658 0.826     0.127     0.027       47     4.0  middletemporal
  769    511   1745  3.059 0.863     0.111     0.020        8     0.5  parahippocampal
 1934   1342   3574  2.450 0.698     0.115     0.026       16     2.1  paracentral
 2181   1516   5946  2.954 0.871     0.134     0.030       30     2.8  parsopercularis
  988    693   2772  2.692 0.923     0.131     0.045       14     1.6  parsorbitalis
 2104   1506   5109  2.505 0.770     0.139     0.035       33     3.2  parstriangularis
 1761   1247   2057  1.800 0.446     0.140     0.036       19     2.6  pericalcarine
 5815   3871   8576  1.877 0.670     0.127     0.035       85     9.1  postcentral
 1455   1097   3011  2.303 0.725     0.144     0.031       22     2.0  posteriorcingulate
 6312   4297  11601  2.348 0.703     0.121     0.030       73     8.0  precentral
 5145   3553  10576  2.541 0.776     0.125     0.032       56     7.4  precuneus
  617    421   1684  3.090 0.892     0.145     0.030       11     0.8  rostralanteriorcingulate
 7826   5571  16747  2.441 0.716     0.143     0.037      121    13.4  rostralmiddlefrontal
 8788   6114  22447  2.933 0.811     0.126     0.028       89     9.8  superiorfrontal
 7415   5181  14566  2.430 0.803     0.130     0.030       92     9.1  superiorparietal
 4427   3136  10502  2.616 0.768     0.120     0.029       51     5.5  superiortemporal
 4768   3453  11485  2.667 0.750     0.139     0.032       62     6.8  supramarginal
  424    302   1538  2.940 0.988     0.192     0.069       16     1.4  frontalpole
  776    556   3212  3.726 0.714     0.148     0.040       12     1.4  temporalpole
  528    378    871  2.122 0.467     0.162     0.036        7     0.8  transversetemporal
 3483   2375   7618  3.218 0.718     0.116     0.032       41     3.9  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 0050564 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 244008
Total vertex volume 240206 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  972    637   1529  2.295 0.526     0.128     0.029       13     1.3  bankssts
  868    794   1891  2.540 0.842     0.153     0.034       17     1.2  caudalanteriorcingulate
 2221   2040   4710  2.590 0.659     0.138     0.029       22     3.0  caudalmiddlefrontal
 1955   1906   3784  2.315 0.677     0.173     0.038       32     3.4  cuneus
  521    583   1782  3.601 0.708     0.172     0.043       15     1.1  entorhinal
 3746   3634   8589  2.701 0.750     0.168     0.039      152     6.8  fusiform
 8139   7998  17968  2.521 0.709     0.171     0.038      106    15.2  inferiorparietal
 3702   3946   8963  2.629 0.779     0.194     0.049       63     9.6  inferiortemporal
 1274   1174   2999  2.658 1.015     0.154     0.035       16     1.8  isthmuscingulate
 6852   6001  12359  2.291 0.720     0.157     0.038      104    11.9  lateraloccipital
 2800   3019   8294  3.137 0.974     0.197     0.051       44     6.6  lateralorbitofrontal
 3263   3120   7070  2.543 0.777     0.176     0.093       77    19.3  lingual
 2119   2401   5607  2.749 0.758     0.202     0.047       32     5.0  medialorbitofrontal
 3526   3958   8932  2.658 0.826     0.180     0.035       43     5.7  middletemporal
  769    638   1745  3.059 0.863     0.157     0.042        9     1.6  parahippocampal
 1934   1572   3574  2.450 0.698     0.137     0.031       21     2.7  paracentral
 2181   2377   5946  2.954 0.871     0.195     0.044       35     4.7  parsopercularis
  988   1282   2772  2.692 0.923     0.215     0.048       11     2.3  parsorbitalis
 2104   2378   5109  2.505 0.770     0.201     0.042       29     4.4  parstriangularis
 1761   1143   2057  1.800 0.446     0.128     0.038       39     2.7  pericalcarine
 5815   5007   8576  1.877 0.670     0.150     0.034       70     9.5  postcentral
 1455   1420   3011  2.303 0.725     0.182     0.042       22     2.9  posteriorcingulate
 6312   5250  11601  2.348 0.703     0.137     0.032       77     9.3  precentral
 5145   4605  10576  2.541 0.776     0.164     0.038       77     9.4  precuneus
  617    632   1684  3.090 0.892     0.178     0.045       12     1.3  rostralanteriorcingulate
 7826   7863  16747  2.441 0.716     0.186     0.042      115    16.7  rostralmiddlefrontal
 8788   8661  22447  2.933 0.811     0.163     0.038      106    15.5  superiorfrontal
 7415   6742  14566  2.430 0.803     0.156     0.038       90    13.2  superiorparietal
 4427   4564  10502  2.616 0.768     0.188     0.042       62     9.2  superiortemporal
 4768   4742  11485  2.667 0.750     0.178     0.042       60     9.4  supramarginal
  424    716   1538  2.940 0.988     0.290     0.056        5     1.4  frontalpole
  776   1237   3212  3.726 0.714     0.251     0.050        9     2.1  temporalpole
  528    477    871  2.122 0.467     0.170     0.048        7     1.2  transversetemporal
 3483   2419   7618  3.218 0.718     0.164     0.053       69     8.5  insula
PIDs (13490 13493 13496 13499) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 08:38:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 08:38:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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 13624 of (13624 13627) to complete...
Waiting for PID 13627 of (13624 13627) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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...
154 labels changed using aseg
relabeling using gibbs priors...
000:   7607 changed, 113752 examined...
001:   1780 changed, 29568 examined...
002:    504 changed, 9271 examined...
003:    232 changed, 2955 examined...
004:    118 changed, 1310 examined...
005:     61 changed, 695 examined...
006:     30 changed, 337 examined...
007:     13 changed, 164 examined...
008:     16 changed, 91 examined...
009:      5 changed, 63 examined...
010:      5 changed, 32 examined...
011:      2 changed, 30 examined...
012:      1 changed, 12 examined...
013:      2 changed, 6 examined...
014:      1 changed, 11 examined...
015:      0 changed, 4 examined...
76 labels changed using aseg
000: 246 total segments, 162 labels (1832 vertices) changed
001: 94 total segments, 10 labels (29 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 26 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
667 vertices marked for relabeling...
667 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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...
44 labels changed using aseg
relabeling using gibbs priors...
000:   7600 changed, 116748 examined...
001:   1684 changed, 30102 examined...
002:    479 changed, 8975 examined...
003:    205 changed, 2761 examined...
004:     91 changed, 1162 examined...
005:     59 changed, 545 examined...
006:     37 changed, 326 examined...
007:     15 changed, 193 examined...
008:      5 changed, 83 examined...
009:      9 changed, 40 examined...
010:      5 changed, 44 examined...
011:      1 changed, 26 examined...
012:      1 changed, 5 examined...
013:      0 changed, 7 examined...
42 labels changed using aseg
000: 210 total segments, 130 labels (2178 vertices) changed
001: 87 total segments, 8 labels (167 vertices) changed
002: 79 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 47 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1040 vertices marked for relabeling...
1040 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 16 seconds.
PIDs (13624 13627) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 08:39:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 08:39:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 rh white 

Waiting for PID 13673 of (13673 13676) to complete...
Waiting for PID 13676 of (13673 13676) 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 0050564 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 232168
Total vertex volume 227835 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  958    692   2520  2.474 0.945     0.139     0.047       14     1.5  G&S_frontomargin
 1748   1233   3478  2.310 0.614     0.138     0.029       24     2.0  G&S_occipital_inf
 1632   1134   3111  2.245 0.637     0.134     0.029       16     2.0  G&S_paracentral
 1351    968   3940  2.917 0.828     0.145     0.040       19     2.1  G&S_subcentral
  609    465   1890  2.751 0.699     0.174     0.050       14     1.2  G&S_transv_frontopol
 1595   1110   3953  3.056 0.815     0.120     0.026       15     1.8  G&S_cingul-Ant
 1066    725   1934  2.571 0.604     0.103     0.013        7     0.5  G&S_cingul-Mid-Ant
 1102    823   2732  2.845 0.726     0.127     0.028       11     1.3  G&S_cingul-Mid-Post
  399    330   1734  3.440 0.640     0.187     0.057        7     1.0  G_cingul-Post-dorsal
  254    178    633  2.775 0.996     0.166     0.061        6     0.5  G_cingul-Post-ventral
 1790   1342   2719  1.812 0.489     0.168     0.038       30     2.9  G_cuneus
 1379    985   3995  2.865 0.739     0.137     0.033       21     2.0  G_front_inf-Opercular
  398    296   1318  2.905 0.575     0.186     0.068       10     1.0  G_front_inf-Orbital
 1148    810   3559  2.757 0.809     0.157     0.040       25     1.8  G_front_inf-Triangul
 3998   2833  10642  2.800 0.669     0.145     0.035       67     6.0  G_front_middle
 6958   4698  20799  3.264 0.667     0.132     0.032       88     8.7  G_front_sup
  572    417   1402  3.372 0.978     0.141     0.038        6     0.9  G_Ins_lg&S_cent_ins
  701    476   2165  3.321 0.663     0.136     0.034       10     1.0  G_insular_short
 1815   1335   4507  2.498 0.650     0.171     0.058       38     4.6  G_occipital_middle
 1320    916   2546  2.173 0.659     0.152     0.040       20     2.2  G_occipital_sup
 1596   1215   4345  2.783 0.628     0.189     0.055       40     4.0  G_oc-temp_lat-fusifor
 2404   1820   5062  2.316 0.673     0.177     0.052       45     5.2  G_oc-temp_med-Lingual
 1136    769   3641  3.499 0.873     0.111     0.027       11     1.2  G_oc-temp_med-Parahip
 2089   1533   7904  3.305 0.957     0.159     0.054       35     4.5  G_orbital
 2623   1831   6192  2.398 0.816     0.158     0.048       53     5.7  G_pariet_inf-Angular
 3245   2315   7517  2.444 0.727     0.161     0.049       67     6.5  G_pariet_inf-Supramar
 2608   1916   6907  2.612 0.752     0.152     0.037       36     4.3  G_parietal_sup
 2108   1433   3853  2.065 0.644     0.135     0.034       31     3.0  G_postcentral
 2387   1560   4082  2.134 0.663     0.142     0.049       51     5.2  G_precentral
 2116   1565   6570  2.835 0.806     0.167     0.048       37     4.9  G_precuneus
  877    660   2972  2.998 0.807     0.184     0.062       18     2.3  G_rectus
  172    120    540  3.486 0.506     0.120     0.040        2     0.2  G_subcallosal
  585    402   1092  2.112 0.511     0.149     0.029        9     0.8  G_temp_sup-G_T_transv
 1629   1177   4216  2.477 0.854     0.146     0.039       30     3.0  G_temp_sup-Lateral
  631    472   1724  2.962 1.076     0.101     0.027        5     0.6  G_temp_sup-Plan_polar
  973    677   1803  2.297 0.690     0.091     0.017        7     0.7  G_temp_sup-Plan_tempo
 1539   1156   4645  2.625 0.860     0.167     0.050       45     3.5  G_temporal_inf
 1617   1133   4736  2.661 0.925     0.148     0.049       31     3.5  G_temporal_middle
  264    181    378  2.041 0.486     0.112     0.019        2     0.2  Lat_Fis-ant-Horizont
  280    197    522  2.593 0.602     0.093     0.017        1     0.1  Lat_Fis-ant-Vertical
 1119    752   1670  2.844 0.856     0.098     0.017        5     0.8  Lat_Fis-post
 2005   1387   2588  1.732 0.433     0.153     0.034       29     3.2  Pole_occipital
 1492   1130   5766  3.048 1.029     0.161     0.044       30     3.3  Pole_temporal
 2373   1736   3014  1.932 0.704     0.125     0.035       22     3.1  S_calcarine
 2252   1602   2659  1.855 0.518     0.110     0.020       16     1.7  S_central
  885    628   1462  2.495 0.572     0.115     0.017        7     0.7  S_cingul-Marginalis
  625    416   1104  3.111 0.735     0.090     0.015        3     0.4  S_circular_insula_ant
 1154    809   1936  2.833 0.769     0.099     0.016        6     0.8  S_circular_insula_inf
 1600   1089   2445  2.659 0.601     0.093     0.016        6     1.1  S_circular_insula_sup
  638    438   1435  3.273 0.944     0.096     0.016        3     0.3  S_collat_transv_ant
  395    261    433  1.806 0.373     0.106     0.018        2     0.3  S_collat_transv_post
 2147   1504   3331  2.140 0.573     0.105     0.019       15     1.8  S_front_inf
  987    687   1793  2.503 0.716     0.095     0.017        4     0.7  S_front_middle
 2829   1938   4803  2.506 0.571     0.094     0.018       13     2.0  S_front_sup
  460    323    460  1.602 0.314     0.083     0.009        2     0.2  S_interm_prim-Jensen
 2766   1911   3913  2.187 0.631     0.113     0.022       21     2.4  S_intrapariet&P_trans
  978    680   1554  2.217 0.762     0.127     0.034        9     1.3  S_oc_middle&Lunatus
  833    584   1083  2.045 0.568     0.110     0.020        5     0.7  S_oc_sup&transversal
  431    305    546  1.933 0.457     0.110     0.023        2     0.4  S_occipital_ant
  409    287    753  2.330 0.645     0.114     0.029        3     0.3  S_oc-temp_lat
 1357    966   2218  2.432 0.756     0.096     0.018        6     0.8  S_oc-temp_med&Lingual
  378    250    759  2.255 0.783     0.121     0.033        7     0.5  S_orbital_lateral
  484    342    810  2.506 0.749     0.111     0.023        3     0.4  S_orbital_med-olfact
 1136    780   2310  2.735 0.866     0.118     0.030       10     1.4  S_orbital-H_Shaped
 2231   1458   3050  2.189 0.682     0.099     0.018       14     1.5  S_parieto_occipital
 1016    661    920  1.808 0.729     0.118     0.016       18     0.5  S_pericallosal
 2713   1918   4274  2.316 0.652     0.115     0.021       20     2.1  S_postcentral
 1401    948   2072  2.163 0.589     0.117     0.023       12     1.4  S_precentral-inf-part
 1278    866   1862  2.329 0.444     0.086     0.014        5     0.7  S_precentral-sup-part
  441    312    791  2.805 0.587     0.110     0.018        2     0.4  S_suborbital
  746    488   1121  2.384 0.644     0.122     0.026        6     0.8  S_subparietal
  995    668   1176  1.988 0.813     0.106     0.018        6     0.8  S_temporal_inf
 3687   2533   5039  1.959 0.554     0.102     0.019       29     2.9  S_temporal_sup
  382    258    407  1.788 0.365     0.096     0.012        2     0.2  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050564 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 244008
Total vertex volume 240206 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  723    519   1485  2.121 0.748     0.143     0.039       19     1.3  G&S_frontomargin
 1119    749   2408  2.571 0.772     0.150     0.049       19     2.2  G&S_occipital_inf
 1265    913   2097  1.991 0.645     0.153     0.045       18     2.5  G&S_paracentral
 1199    886   2911  2.369 0.764     0.146     0.037       21     1.8  G&S_subcentral
  897    709   2959  2.813 0.944     0.189     0.059       23     2.5  G&S_transv_frontopol
 2429   1681   5705  2.825 0.746     0.125     0.027       28     2.5  G&S_cingul-Ant
  987    694   2142  2.736 0.599     0.119     0.026        7     1.1  G&S_cingul-Mid-Ant
 1084    828   2384  2.569 0.693     0.125     0.026       11     1.2  G&S_cingul-Mid-Post
  440    340   1540  3.094 0.623     0.185     0.041        8     0.8  G_cingul-Post-dorsal
  238    155    882  3.274 1.034     0.130     0.031        3     0.2  G_cingul-Post-ventral
 1743   1313   3569  2.250 0.652     0.182     0.046       34     3.5  G_cuneus
 1305    915   4485  3.245 0.928     0.149     0.036       24     2.1  G_front_inf-Opercular
  375    268   1202  2.811 0.835     0.149     0.052        7     0.7  G_front_inf-Orbital
  878    646   2804  2.810 0.692     0.169     0.048       21     1.9  G_front_inf-Triangul
 2962   2150   8264  2.633 0.778     0.162     0.047       56     6.6  G_front_middle
 5615   3862  16082  3.115 0.780     0.134     0.031       65     6.8  G_front_sup
 1051    689   2152  3.029 0.788     0.126     0.038       16     1.1  G_Ins_lg&S_cent_ins
  575    382   1859  3.518 0.615     0.140     0.057       14     1.2  G_insular_short
 2246   1586   5615  2.679 0.668     0.164     0.044       39     4.4  G_occipital_middle
 1344    967   2938  2.380 0.708     0.149     0.039       17     2.3  G_occipital_sup
 1605   1157   4213  2.788 0.725     0.164     0.045       33     3.1  G_oc-temp_lat-fusifor
 2126   1553   5222  2.646 0.824     0.167     0.048       39     4.3  G_oc-temp_med-Lingual
 1082    741   3397  3.444 0.761     0.125     0.028       11     1.0  G_oc-temp_med-Parahip
 2172   1594   8359  3.314 0.897     0.168     0.053       41     5.3  G_orbital
 2910   2134   8428  2.797 0.801     0.163     0.048       54     6.1  G_pariet_inf-Angular
 2618   1945   7995  2.882 0.814     0.169     0.042       52     5.0  G_pariet_inf-Supramar
 2722   1927   6736  2.626 0.774     0.147     0.033       38     3.5  G_parietal_sup
 2365   1472   3467  1.826 0.680     0.151     0.051       51     5.6  G_postcentral
 2203   1470   5299  2.571 0.760     0.142     0.048       43     4.5  G_precentral
 2390   1734   6104  2.547 0.817     0.163     0.053       57     6.5  G_precuneus
  691    576   2638  2.907 0.861     0.184     0.063       14     1.9  G_rectus
  100     74    226  2.365 0.895     0.190     0.114        3     0.7  G_subcallosal
  383    290    817  2.174 0.644     0.175     0.056        6     0.8  G_temp_sup-G_T_transv
 1345   1009   4713  2.988 0.767     0.160     0.043       24     2.6  G_temp_sup-Lateral
  714    535   2058  3.146 0.946     0.133     0.041       10     1.2  G_temp_sup-Plan_polar
  754    548   1614  2.505 0.586     0.080     0.010        2     0.3  G_temp_sup-Plan_tempo
 2166   1538   5977  2.648 0.857     0.167     0.062       48     6.1  G_temporal_inf
 1996   1446   5986  2.767 0.833     0.142     0.034       33     3.0  G_temporal_middle
  374    251    445  1.906 0.585     0.087     0.011        2     0.1  Lat_Fis-ant-Horizont
  217    162    358  2.190 0.516     0.104     0.012        1     0.1  Lat_Fis-ant-Vertical
 1392    956   2065  2.589 0.622     0.106     0.019        8     1.1  Lat_Fis-post
 2877   2003   4914  2.126 0.714     0.163     0.042       45     5.3  Pole_occipital
 1778   1277   6478  3.325 0.865     0.152     0.044       32     3.5  Pole_temporal
 2001   1409   2971  2.352 0.940     0.117     0.031       17     2.6  S_calcarine
 2776   1867   3014  1.812 0.554     0.102     0.020       17     2.5  S_central
 1157    801   1806  2.331 0.615     0.097     0.018        6     0.8  S_cingul-Marginalis
  509    355    904  2.975 0.474     0.104     0.023        3     0.4  S_circular_insula_ant
  952    656   1604  2.795 0.900     0.088     0.018        4     0.7  S_circular_insula_inf
 1430    964   2399  2.838 0.677     0.093     0.014        6     0.9  S_circular_insula_sup
 1025    701   1652  2.564 0.407     0.098     0.013        5     0.6  S_collat_transv_ant
  410    288    543  2.353 0.482     0.129     0.037        3     0.4  S_collat_transv_post
 2086   1447   3437  2.400 0.607     0.117     0.025       21     2.0  S_front_inf
 2356   1680   4715  2.428 0.705     0.130     0.031       26     2.9  S_front_middle
 2628   1841   5299  2.630 0.744     0.107     0.020       18     2.0  S_front_sup
  359    265    582  2.260 0.475     0.113     0.026        2     0.5  S_interm_prim-Jensen
 3127   2181   5083  2.421 0.779     0.109     0.020       21     2.3  S_intrapariet&P_trans
 1054    706   1328  2.032 0.528     0.117     0.027        8     1.1  S_oc_middle&Lunatus
 1115    777   1434  2.039 0.515     0.113     0.023        8     0.9  S_oc_sup&transversal
  530    355    830  2.520 0.664     0.105     0.022        3     0.4  S_occipital_ant
  746    514   1084  2.351 0.545     0.107     0.021        4     0.6  S_oc-temp_lat
 1422   1019   2349  2.373 0.736     0.105     0.017        9     1.0  S_oc-temp_med&Lingual
  378    270    599  2.137 0.542     0.113     0.022        2     0.4  S_orbital_lateral
  471    313   1149  3.425 0.864     0.097     0.027        4     0.5  S_orbital_med-olfact
 1000    703   1958  2.441 0.964     0.122     0.031       10     1.3  S_orbital-H_Shaped
 2130   1414   3092  2.284 0.645     0.104     0.018       12     1.5  S_parieto_occipital
 1381    868   1126  1.769 0.513     0.109     0.014       21     0.7  S_pericallosal
 1960   1304   2578  2.124 0.632     0.093     0.017       11     1.2  S_postcentral
 1718   1176   2751  2.370 0.606     0.103     0.016       12     1.2  S_precentral-inf-part
 1160    853   1796  2.362 0.559     0.119     0.018        8     0.9  S_precentral-sup-part
  283    195    293  1.975 0.354     0.122     0.014        2     0.2  S_suborbital
 1030    720   1799  2.500 0.690     0.110     0.021        6     0.9  S_subparietal
  729    513    934  2.105 0.419     0.114     0.015        5     0.5  S_temporal_inf
 5775   3970   9660  2.350 0.586     0.105     0.020       46     5.2  S_temporal_sup
  337    221    448  2.221 0.634     0.104     0.013        2     0.1  S_temporal_transverse
PIDs (13673 13676) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 08:39:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 08:39:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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 13740 of (13740 13743) to complete...
Waiting for PID 13743 of (13740 13743) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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...
1183 labels changed using aseg
relabeling using gibbs priors...
000:   1772 changed, 113752 examined...
001:    395 changed, 8230 examined...
002:    110 changed, 2186 examined...
003:     51 changed, 631 examined...
004:     32 changed, 300 examined...
005:     15 changed, 193 examined...
006:     12 changed, 93 examined...
007:      6 changed, 60 examined...
008:      2 changed, 44 examined...
009:      2 changed, 13 examined...
010:      2 changed, 12 examined...
011:      2 changed, 10 examined...
012:      0 changed, 13 examined...
208 labels changed using aseg
000: 57 total segments, 24 labels (194 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
500 vertices marked for relabeling...
500 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 13 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050564 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...
916 labels changed using aseg
relabeling using gibbs priors...
000:   1709 changed, 116748 examined...
001:    412 changed, 8165 examined...
002:    110 changed, 2350 examined...
003:     37 changed, 637 examined...
004:     21 changed, 221 examined...
005:      9 changed, 112 examined...
006:      7 changed, 55 examined...
007:      8 changed, 37 examined...
008:      6 changed, 39 examined...
009:      4 changed, 22 examined...
010:      3 changed, 16 examined...
011:      5 changed, 18 examined...
012:      4 changed, 24 examined...
013:      4 changed, 25 examined...
014:      2 changed, 22 examined...
015:      0 changed, 12 examined...
155 labels changed using aseg
000: 48 total segments, 15 labels (91 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
784 vertices marked for relabeling...
784 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 13 seconds.
PIDs (13740 13743) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 08:39:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 08:39:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 rh white 

Waiting for PID 13791 of (13791 13794) to complete...
Waiting for PID 13794 of (13791 13794) 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 0050564 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 232168
Total vertex volume 227835 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
 1487    939   3019  2.719 0.742     0.121     0.017       19     1.0  caudalanteriorcingulate
 3362   2335   6915  2.579 0.602     0.119     0.026       32     3.6  caudalmiddlefrontal
 2863   2016   4101  1.880 0.560     0.139     0.029       36     3.4  cuneus
  550    385   2106  3.780 0.821     0.101     0.028        4     0.5  entorhinal
 2944   2152   6645  2.686 0.743     0.148     0.038       47     4.7  fusiform
 5657   3956  11169  2.297 0.741     0.136     0.035       77     9.3  inferiorparietal
 3286   2396   9259  2.679 0.991     0.144     0.041       64     6.1  inferiortemporal
 1295    917   2839  2.542 1.006     0.130     0.038       18     1.8  isthmuscingulate
 6711   4690  11480  2.103 0.657     0.149     0.037       98    10.6  lateraloccipital
 3643   2549  10531  3.088 0.966     0.127     0.037       40     5.2  lateralorbitofrontal
 3421   2577   6529  2.254 0.721     0.152     0.041       48     5.8  lingual
 1742   1276   4914  2.912 0.782     0.147     0.043       25     3.1  medialorbitofrontal
 3870   2674   8628  2.444 0.861     0.126     0.031       51     5.0  middletemporal
  890    596   2146  2.920 0.893     0.107     0.025        8     0.8  parahippocampal
 2055   1453   4230  2.570 0.615     0.129     0.030       20     2.4  paracentral
 2425   1653   5555  2.603 0.761     0.123     0.026       29     2.7  parsopercularis
  924    671   2817  3.019 0.802     0.162     0.054       16     2.0  parsorbitalis
 2276   1597   5205  2.432 0.743     0.132     0.033       35     2.9  parstriangularis
 1750   1288   1976  1.662 0.460     0.145     0.035       21     2.7  pericalcarine
 6026   4208  10611  2.179 0.765     0.126     0.028       66     6.9  postcentral
 1552   1181   3916  2.682 0.958     0.149     0.033       24     2.3  posteriorcingulate
 6203   4228  10647  2.246 0.676     0.124     0.033       79     8.7  precentral
 4402   3111   9665  2.560 0.722     0.135     0.036       52     6.5  precuneus
  916    637   2609  3.334 0.838     0.142     0.035       13     1.3  rostralanteriorcingulate
 4609   3255  10126  2.485 0.755     0.132     0.032       65     6.3  rostralmiddlefrontal
10704   7370  27706  2.993 0.745     0.122     0.028      109    11.9  superiorfrontal
 5476   3881  11359  2.420 0.724     0.130     0.029       59     6.6  superiorparietal
 6146   4343  12563  2.369 0.882     0.119     0.028       75     7.9  superiortemporal
 5752   4117  11440  2.385 0.745     0.140     0.037       86     8.5  supramarginal
  680    472   1179  2.223 0.542     0.142     0.028        9     0.7  transversetemporal
 2678   1891   5951  3.108 0.686     0.115     0.024       22     2.8  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050564 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 244008
Total vertex volume 240206 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  949    638   1995  2.506 0.832     0.124     0.021       11     0.9  caudalanteriorcingulate
 2415   1737   5080  2.580 0.701     0.118     0.023       22     2.4  caudalmiddlefrontal
 2407   1753   4515  2.273 0.695     0.163     0.039       38     4.1  cuneus
  492    356   1681  3.533 0.706     0.127     0.030        4     0.6  entorhinal
 3296   2335   7232  2.643 0.710     0.137     0.032       46     4.2  fusiform
 7956   5732  17480  2.515 0.709     0.139     0.034      106    11.9  inferiorparietal
 4108   2921  10385  2.717 0.809     0.142     0.045       62     8.2  inferiortemporal
 1267    875   2894  2.627 1.005     0.120     0.023       16     1.1  isthmuscingulate
 6872   4647  12224  2.281 0.717     0.145     0.039       93    10.8  lateraloccipital
 3369   2399   9551  3.002 1.027     0.147     0.044       56     6.2  lateralorbitofrontal
 3202   2388   6954  2.526 0.784     0.156     0.043       50     5.9  lingual
 1528   1161   4286  2.683 0.823     0.155     0.048       26     3.5  medialorbitofrontal
 4276   3039  10295  2.635 0.788     0.126     0.026       54     4.7  middletemporal
  807    539   1871  3.074 0.888     0.110     0.019        8     0.6  parahippocampal
 1980   1375   3794  2.491 0.709     0.115     0.026       16     2.1  paracentral
 2421   1681   6276  2.899 0.851     0.137     0.031       34     3.5  parsopercularis
  877    587   2340  2.844 0.822     0.108     0.036        9     1.1  parsorbitalis
 2100   1523   5134  2.492 0.776     0.139     0.033       33     2.9  parstriangularis
 1785   1254   2077  1.801 0.440     0.142     0.038       20     2.8  pericalcarine
 6623   4456   9773  1.860 0.683     0.133     0.037      115    11.7  postcentral
 1488   1121   3084  2.322 0.728     0.145     0.032       23     2.0  posteriorcingulate
 6109   4127  11310  2.347 0.716     0.120     0.031       71     7.8  precentral
 5261   3695  11243  2.565 0.768     0.128     0.032       59     7.7  precuneus
  790    531   1917  3.023 0.820     0.139     0.028       13     0.9  rostralanteriorcingulate
 5788   4060  12229  2.446 0.721     0.141     0.036       83     9.4  rostralmiddlefrontal
11270   7934  28658  2.865 0.806     0.130     0.030      127    13.9  superiorfrontal
 6080   4235  12552  2.547 0.779     0.123     0.026       57     6.0  superiorparietal
 6019   4231  15092  2.728 0.846     0.122     0.029       71     7.9  superiortemporal
 4526   3268  10741  2.669 0.742     0.136     0.031       55     6.2  supramarginal
  537    385    910  2.127 0.479     0.161     0.044        7     0.8  transversetemporal
 2892   2004   6633  3.282 0.637     0.117     0.031       35     3.3  insula
PIDs (13791 13794) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 08:40:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 pctsurfcon --s 0050564 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 08:40:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts

 pctsurfcon --s 0050564 --rh-only 

Waiting for PID 13883 of (13883 13890) to complete...
Waiting for PID 13890 of (13883 13890) to complete...

 pctsurfcon --s 0050564 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts/pctsurfcon.log
Sun Oct  8 08:40:25 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-575 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-6.0.0/0050564/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13883/lh.wm.mgh --regheader 0050564 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 64579
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13883/lh.wm.mgh
Dim: 113752 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13883/lh.gm.mgh --projfrac 0.3 --regheader 0050564 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 77347
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13883/lh.gm.mgh
Dim: 113752 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13883/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13883/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.w-g.pct.mgh --annot 0050564 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/lh.w-g.pct.mgh --annot 0050564 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/lh.w-g.pct.mgh
Vertex Area is 0.700566 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 0050564 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/scripts/pctsurfcon.log
Sun Oct  8 08:40:25 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-575 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-6.0.0/0050564/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13890/rh.wm.mgh --regheader 0050564 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 66645
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13890/rh.wm.mgh
Dim: 116748 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13890/rh.gm.mgh --projfrac 0.3 --regheader 0050564 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 79025
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13890/rh.gm.mgh
Dim: 116748 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13890/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/tmp.pctsurfcon.13890/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.w-g.pct.mgh --annot 0050564 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.w-g.pct.mgh --annot 0050564 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.w-g.pct.mgh
Vertex Area is 0.699769 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 (13883 13890) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 08:40:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz 

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2731 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1761 voxels changed to hypointensity...
4780 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 08:40:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564

 mri_aparc2aseg --s 0050564 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 08:40:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564

 mri_aparc2aseg --s 0050564 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 08:40:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564

 mri_aparc2aseg --s 0050564 --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 14054 of (14054 14057 14060) to complete...
Waiting for PID 14057 of (14054 14057 14060) to complete...
Waiting for PID 14060 of (14054 14057 14060) to complete...

 mri_aparc2aseg --s 0050564 --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 0050564
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/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-6.0.0/0050564/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 5.86
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 110
rescaling Left_Cerebral_Cortex from 61 --> 56
rescaling Left_Lateral_Ventricle from 13 --> 28
rescaling Left_Inf_Lat_Vent from 34 --> 26
rescaling Left_Cerebellum_White_Matter from 86 --> 92
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 94
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 66
rescaling Left_Putamen from 80 --> 77
rescaling Left_Pallidum from 98 --> 99
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 56
rescaling Left_Amygdala from 56 --> 60
rescaling CSF from 32 --> 34
rescaling Left_Accumbens_area from 62 --> 59
rescaling Left_VentralDC from 87 --> 94
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 54
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 71
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 58
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 69
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 31
rescaling WM_hypointensities from 78 --> 81
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 464424
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 116 changed.
pass 2: 2 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050564 --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 0050564
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/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-6.0.0/0050564/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 5.86
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 110
rescaling Left_Cerebral_Cortex from 61 --> 56
rescaling Left_Lateral_Ventricle from 13 --> 28
rescaling Left_Inf_Lat_Vent from 34 --> 26
rescaling Left_Cerebellum_White_Matter from 86 --> 92
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 94
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 66
rescaling Left_Putamen from 80 --> 77
rescaling Left_Pallidum from 98 --> 99
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 56
rescaling Left_Amygdala from 56 --> 60
rescaling CSF from 32 --> 34
rescaling Left_Accumbens_area from 62 --> 59
rescaling Left_VentralDC from 87 --> 94
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 54
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 71
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 58
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 69
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 31
rescaling WM_hypointensities from 78 --> 81
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 464397
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 116 changed.
pass 2: 2 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050564 --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 0050564
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/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-6.0.0/0050564/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 5.86
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 110
rescaling Left_Cerebral_Cortex from 61 --> 56
rescaling Left_Lateral_Ventricle from 13 --> 28
rescaling Left_Inf_Lat_Vent from 34 --> 26
rescaling Left_Cerebellum_White_Matter from 86 --> 92
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 94
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 66
rescaling Left_Putamen from 80 --> 77
rescaling Left_Pallidum from 98 --> 99
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 56
rescaling Left_Amygdala from 56 --> 60
rescaling CSF from 32 --> 34
rescaling Left_Accumbens_area from 62 --> 59
rescaling Left_VentralDC from 87 --> 94
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 54
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 71
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 58
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 69
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 31
rescaling WM_hypointensities from 78 --> 81
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 464397
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 116 changed.
pass 2: 2 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (14054 14057 14060) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 08:47:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri

 apas2aseg --i aparc+aseg.mgz --o aseg.mgz 

Sun Oct  8 08:47:57 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-6.0.0/0050564/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-575 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-6.0.0/0050564/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-575
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 08:47:57 CEST 2017 
Ended   at Sun Oct  8 08:48:03 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 08:48:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564

 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 0050564 


$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 0050564 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1296133 mm^3    (det: 1.503013 )
Computing euler number
orig.nofix lheno =  -86, rheno = -98
orig.nofix lhholes =   44, rhholes = 50
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 08:49:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564

 mri_aparc2aseg --s 0050564 --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 0050564
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-6.0.0/0050564/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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-6.0.0/0050564/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7453 vertices from left hemi
Ripped 7274 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-6.0.0/0050564/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 = 846776
Used brute-force search on 454 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 1188.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 2.000000
     5 k 1.000000
Fixing Parahip RH WM
  Found 10 clusters
     0 k 1.000000
     1 k 1290.000000
     2 k 2.000000
     3 k 1.000000
     4 k 3.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1.000000
     9 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 0050564 --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 0050564 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-575
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1296133 mm^3    (det: 1.503013 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
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-6.0.0/0050564/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 08:57:40 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 14789 of (14789 14795 14801 14807 14813) to complete...
Waiting for PID 14795 of (14789 14795 14801 14807 14813) to complete...
Waiting for PID 14801 of (14789 14795 14801 14807 14813) to complete...
Waiting for PID 14807 of (14789 14795 14801 14807 14813) to complete...
Waiting for PID 14813 of (14789 14795 14801 14807 14813) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 206
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4335
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 350
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8259
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 48
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4125
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 188
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6171
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 401
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6185
mri_label2label: Done

PIDs (14789 14795 14801 14807 14813) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 14857 of (14857 14863 14871 14877) to complete...
Waiting for PID 14863 of (14857 14863 14871 14877) to complete...
Waiting for PID 14871 of (14857 14863 14871 14877) to complete...
Waiting for PID 14877 of (14857 14863 14871 14877) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 141
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4211
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 922
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14511
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 441
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4622
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 603
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4025
mri_label2label: Done

PIDs (14857 14863 14871 14877) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 14936 of (14936 14942 14948 14953 14958) to complete...
Waiting for PID 14942 of (14936 14942 14948 14953 14958) to complete...
Waiting for PID 14948 of (14936 14942 14948 14953 14958) to complete...
Waiting for PID 14953 of (14936 14942 14948 14953 14958) to complete...
Waiting for PID 14958 of (14936 14942 14948 14953 14958) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 904
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5545
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 1846
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 9960
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 208
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2226
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 90
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1380
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 84
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1283
mri_label2label: Done

PIDs (14936 14942 14948 14953 14958) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 15004 of (15004 15010 15016 15021 15026) to complete...
Waiting for PID 15010 of (15004 15010 15016 15021 15026) to complete...
Waiting for PID 15016 of (15004 15010 15016 15021 15026) to complete...
Waiting for PID 15021 of (15004 15010 15016 15021 15026) to complete...
Waiting for PID 15026 of (15004 15010 15016 15021 15026) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 90
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1104
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 74
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2166
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 24
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1528
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 52
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2048
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2390
mri_label2label: Done

PIDs (15004 15010 15016 15021 15026) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 15072 of (15072 15078 15084 15089) to complete...
Waiting for PID 15078 of (15072 15078 15084 15089) to complete...
Waiting for PID 15084 of (15072 15078 15084 15089) to complete...
Waiting for PID 15089 of (15072 15078 15084 15089) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 13
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1562
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 520
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7555
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 238
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2150
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 292
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1443
mri_label2label: Done

PIDs (15072 15078 15084 15089) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 15147 of (15147 15153 15159 15164 15170) to complete...
Waiting for PID 15153 of (15147 15153 15159 15164 15170) to complete...
Waiting for PID 15159 of (15147 15153 15159 15164 15170) to complete...
Waiting for PID 15164 of (15147 15153 15159 15164 15170) to complete...
Waiting for PID 15170 of (15147 15153 15159 15164 15170) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 596
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4001
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 852
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4186
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 43
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 556
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 22
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 492
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 113752
Number of reverse mapping hits = 16
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 466
mri_label2label: Done

PIDs (15147 15153 15159 15164 15170) completed and logs appended.

 mris_label2annot --s 0050564 --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-6.0.0/0050564/label
cmdline mris_label2annot --s 0050564 --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-575
machine  x86_64
user     ntraut

subject 0050564
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-6.0.0/0050564/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 77639 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050564 --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-6.0.0/0050564/label
cmdline mris_label2annot --s 0050564 --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-575
machine  x86_64
user     ntraut

subject 0050564
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-6.0.0/0050564/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 92431 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 232168
Total vertex volume 227835 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  949    663   1829  2.088 0.667     0.148     0.039       15     1.3  BA1_exvivo
 3513   2482   5874  2.263 0.614     0.121     0.026       35     3.6  BA2_exvivo
  886    568    852  1.834 0.501     0.141     0.029        9     0.9  BA3a_exvivo
 1952   1387   3753  2.097 0.853     0.133     0.030       27     2.6  BA3b_exvivo
 1387    928   2647  2.362 0.641     0.123     0.036       18     2.2  BA4a_exvivo
  971    705   1491  2.163 0.442     0.094     0.016        5     0.6  BA4p_exvivo
 8356   5685  19512  2.796 0.824     0.125     0.032       97    10.8  BA6_exvivo
 2299   1635   5363  2.484 0.760     0.141     0.032       33     3.4  BA44_exvivo
 2819   2027   7034  2.547 0.766     0.134     0.033       46     4.0  BA45_exvivo
 3100   2285   3924  1.677 0.446     0.152     0.036       43     4.8  V1_exvivo
 7169   5119  11768  2.090 0.628     0.156     0.042      103    12.1  V2_exvivo
 1530   1111   3684  2.440 0.752     0.151     0.042       27     2.5  MT_exvivo
  576    369   1628  3.446 0.917     0.098     0.033        5     0.8  perirhinal_exvivo
  606    470   2445  3.807 0.656     0.138     0.040        7     1.1  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 0050564 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 232168
Total vertex volume 227835 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  618    393   1284  2.318 0.679     0.166     0.058       15     1.4  BA1_exvivo
 1380    979   2246  2.068 0.566     0.112     0.018       11     1.0  BA2_exvivo
  762    480    688  1.865 0.481     0.142     0.029        7     0.9  BA3a_exvivo
 1094    809   1545  1.671 0.682     0.105     0.020        9     0.9  BA3b_exvivo
 1248    890   2492  2.438 0.523     0.111     0.025       10     1.2  BA4a_exvivo
  795    577   1184  2.079 0.439     0.093     0.017        4     0.5  BA4p_exvivo
 4732   3123  10247  2.660 0.899     0.127     0.038       67     7.6  BA6_exvivo
 1544   1085   3483  2.444 0.772     0.145     0.034       26     2.3  BA44_exvivo
 1275    910   3671  2.631 0.815     0.144     0.032       22     1.5  BA45_exvivo
 3250   2421   4345  1.698 0.466     0.152     0.037       43     5.2  V1_exvivo
 3614   2620   5488  1.994 0.652     0.165     0.047       58     6.7  V2_exvivo
  421    283    773  2.313 0.725     0.123     0.025        6     0.4  MT_exvivo
  284    179    888  3.414 0.896     0.056     0.010        1     0.1  perirhinal_exvivo
  304    232   1240  3.923 0.628     0.105     0.029        2     0.3  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 09:00:22 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 15351 of (15351 15357 15363 15368 15375) to complete...
Waiting for PID 15357 of (15351 15357 15363 15368 15375) to complete...
Waiting for PID 15363 of (15351 15357 15363 15368 15375) to complete...
Waiting for PID 15368 of (15351 15357 15363 15368 15375) to complete...
Waiting for PID 15375 of (15351 15357 15363 15368 15375) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 450
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4412
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 473
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7160
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 86
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4066
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 212
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4734
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 225
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 5972
mri_label2label: Done

PIDs (15351 15357 15363 15368 15375) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 15416 of (15416 15422 15428 15434) to complete...
Waiting for PID 15422 of (15416 15422 15428 15434) to complete...
Waiting for PID 15428 of (15416 15422 15428 15434) to complete...
Waiting for PID 15434 of (15416 15422 15428 15434) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 113
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4586
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 429
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 12685
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 702
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7614
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 830
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6185
mri_label2label: Done

PIDs (15416 15422 15428 15434) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 15619 of (15619 15625 15631 15636 15642) to complete...
Waiting for PID 15625 of (15619 15625 15631 15636 15642) to complete...
Waiting for PID 15631 of (15619 15625 15631 15636 15642) to complete...
Waiting for PID 15636 of (15619 15625 15631 15636 15642) to complete...
Waiting for PID 15642 of (15619 15625 15631 15636 15642) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 805
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 5532
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 1571
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 9587
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 290
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2222
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1123
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 65
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 817
mri_label2label: Done

PIDs (15619 15625 15631 15636 15642) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 15705 of (15705 15711 15717 15721 15729) to complete...
Waiting for PID 15711 of (15705 15711 15717 15721 15729) to complete...
Waiting for PID 15717 of (15705 15711 15717 15721 15729) to complete...
Waiting for PID 15721 of (15705 15711 15717 15721 15729) to complete...
Waiting for PID 15729 of (15705 15711 15717 15721 15729) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 129
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1005
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 153
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2841
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1728
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 93
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2276
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 43
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1431
mri_label2label: Done

PIDs (15705 15711 15717 15721 15729) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 15770 of (15770 15776 15782 15787) to complete...
Waiting for PID 15776 of (15770 15776 15782 15787) to complete...
Waiting for PID 15782 of (15770 15776 15782 15787) to complete...
Waiting for PID 15787 of (15770 15776 15782 15787) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 34
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1523
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 263
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7222
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 186
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1198
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 107
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1285
mri_label2label: Done

PIDs (15770 15776 15782 15787) 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 0050564 --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 0050564 --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 0050564 --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 0050564 --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 0050564 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 15830 of (15830 15836 15842 15845 15853) to complete...
Waiting for PID 15836 of (15830 15836 15842 15845 15853) to complete...
Waiting for PID 15842 of (15830 15836 15842 15845 15853) to complete...
Waiting for PID 15845 of (15830 15836 15842 15845 15853) to complete...
Waiting for PID 15853 of (15830 15836 15842 15845 15853) 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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 497
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 3729
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 703
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4140
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 51
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 319
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 64
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 758
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 0050564 --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 = 0050564
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-6.0.0/0050564/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 116748
Number of reverse mapping hits = 27
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 318
mri_label2label: Done

PIDs (15830 15836 15842 15845 15853) completed and logs appended.

 mris_label2annot --s 0050564 --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-6.0.0/0050564/label
cmdline mris_label2annot --s 0050564 --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-575
machine  x86_64
user     ntraut

subject 0050564
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-6.0.0/0050564/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 81138 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050564 --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-6.0.0/0050564/label
cmdline mris_label2annot --s 0050564 --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-575
machine  x86_64
user     ntraut

subject 0050564
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-6.0.0/0050564/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 96924 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/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 0050564 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 244008
Total vertex volume 240206 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
 1071    678   1680  1.878 0.813     0.179     0.071       30     3.6  BA1_exvivo
 2937   1949   4437  2.098 0.718     0.114     0.028       32     3.5  BA2_exvivo
  994    653    956  1.847 0.528     0.126     0.026        9     0.9  BA3a_exvivo
 1778   1221   2438  1.626 0.600     0.122     0.032       21     2.7  BA3b_exvivo
 1214    842   2309  2.381 0.598     0.113     0.029       11     1.4  BA4a_exvivo
 1111    759   1621  2.130 0.497     0.108     0.021        7     1.0  BA4p_exvivo
 6472   4456  15192  2.775 0.785     0.128     0.031       78     8.3  BA6_exvivo
 3644   2504   8580  2.719 0.863     0.126     0.029       46     4.5  BA44_exvivo
 3904   2772   9406  2.531 0.785     0.141     0.037       60     6.3  BA45_exvivo
 3101   2225   4959  2.008 0.649     0.148     0.039       40     5.1  V1_exvivo
 6634   4742  12615  2.377 0.775     0.160     0.042      105    11.9  V2_exvivo
 1809   1263   3439  2.421 0.687     0.142     0.037       22     2.9  MT_exvivo
  579    406   1908  3.443 0.735     0.116     0.025        4     0.6  perirhinal_exvivo
  362    253   1121  3.505 0.717     0.142     0.034        5     0.5  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 0050564 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050564/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 244008
Total vertex volume 240206 (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) = 1296133 mm^3    (det: 1.503013 )
lhCtxGM: 227383.268 227276.000  diff=  107.3  pctdiff= 0.047
rhCtxGM: 239444.469 239316.000  diff=  128.5  pctdiff= 0.054
lhCtxWM: 189166.878 189183.500  diff=  -16.6  pctdiff=-0.009
rhCtxWM: 192907.540 193758.500  diff= -851.0  pctdiff=-0.441
SubCortGMVol  56722.000
SupraTentVol  915699.155 (914357.000) diff=1342.155 pctdiff=0.147
SupraTentVolNotVent  907607.155 (906265.000) diff=1342.155 pctdiff=0.148
BrainSegVol  1066218.000 (1063777.000) diff=2441.000 pctdiff=0.229
BrainSegVolNotVent  1054817.000 (1054043.155) diff=773.845 pctdiff=0.073
BrainSegVolNotVent  1054817.000
CerebellumVol 148410.000
VentChorVol    8092.000
3rd4th5thCSF   3309.000
CSFVol   868.000, OptChiasmVol   142.000
MaskVol 1440310.000
  672    413    920  1.717 0.606     0.160     0.062       16     1.8  BA1_exvivo
 1757   1112   2474  1.977 0.602     0.108     0.030       21     2.4  BA2_exvivo
  903    589    768  1.794 0.493     0.126     0.024        7     0.9  BA3a_exvivo
 1400    961   1578  1.516 0.404     0.099     0.023       11     1.5  BA3b_exvivo
  743    504   1499  2.548 0.586     0.129     0.033        7     0.9  BA4a_exvivo
  918    641   1359  2.169 0.465     0.100     0.020        5     0.7  BA4p_exvivo
 4250   2908   9906  2.755 0.768     0.134     0.035       59     6.2  BA6_exvivo
 1002    688   2941  3.051 1.055     0.143     0.038       14     1.6  BA44_exvivo
  919    691   2843  2.723 0.774     0.152     0.037       16     1.4  BA45_exvivo
 2926   2103   4429  1.971 0.615     0.147     0.038       36     4.7  V1_exvivo
 3465   2555   7157  2.420 0.857     0.177     0.049       65     7.5  V2_exvivo
  250    169    669  2.689 0.457     0.158     0.047        5     0.5  MT_exvivo
  364    242   1206  3.436 0.666     0.090     0.015        2     0.2  perirhinal_exvivo
  255    189    706  3.545 0.783     0.136     0.020        3     0.2  entorhinal_exvivo

Started at Sun Oct 8 01:37:07 CEST 2017 
Ended   at Sun Oct 8 09:03:04 CEST 2017
#@#%# recon-all-run-time-hours 7.432
recon-all -s 0050564 finished without error at Sun Oct  8 09:03:04 CEST 2017