ABIDE_fs-6.0.0/0051026/scripts/recon-all.log

Sat Oct  7 17:21:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051026 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051026
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Actual FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux tars-609 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    10485760 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked 64 kbytes
maxproc      1024 

             total       used       free     shared    buffers     cached
Mem:      65993848   57862780    8131068    1750584          0   53103008
-/+ buffers/cache:    4759772   61234076
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:21:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: ntraut  Machine: tars-609  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051026/session_1/anat_1/mprage.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 1, 0)
k_ras = (-0, -0, 1)
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 17:21:30 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 1, 0)
k_ras = (-0, -0, 1)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 17:21:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux tars-609 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:21:37 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.30553
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30553/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30553/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.30553/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:21:40 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.30553/nu0.mnc ./tmp.mri_nu_correct.mni.30553/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30553/0/ -iterations 1000 -distance 50
[ntraut@tars-609:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/] [2017-10-07 17:21:40] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.30553/0/ ./tmp.mri_nu_correct.mni.30553/nu0.mnc ./tmp.mri_nu_correct.mni.30553/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 46 
CV of field change: 0.000992783
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.30553/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.30553/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.30553/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 17:22:49 CEST 2017
mri_nu_correct.mni done

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 17:22:49 CEST 2017
Ended   at Sat Oct  7 17:23:20 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 17:23:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5735, pval=0.2115 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach_avi.log 

TalAviQA: 0.97279
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 17:23:22 CEST 2017

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux tars-609 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:23:22 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.31388
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31388/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.31388/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.31388/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:23:24 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.31388/nu0.mnc ./tmp.mri_nu_correct.mni.31388/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31388/0/
[ntraut@tars-609:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/] [2017-10-07 17:23:24] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.31388/0/ ./tmp.mri_nu_correct.mni.31388/nu0.mnc ./tmp.mri_nu_correct.mni.31388/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 50 
CV of field change: 0.000995075
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 17:24:15 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.31388/nu1.mnc ./tmp.mri_nu_correct.mni.31388/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.31388/1/
[ntraut@tars-609:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/] [2017-10-07 17:24:15] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.31388/1/ ./tmp.mri_nu_correct.mni.31388/nu1.mnc ./tmp.mri_nu_correct.mni.31388/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 30 
CV of field change: 0.000973775
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31388/ones.mgz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31388/ones.mgz 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.31388/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.31388/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31388/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/input.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31388/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/input.mean.dat 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.31388/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.31388/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31388/ones.mgz --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/output.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31388/ones.mgz --i ./tmp.mri_nu_correct.mni.31388/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31388/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31388/output.mean.dat 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.31388/ones.mgz
Loading ./tmp.mri_nu_correct.mni.31388/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.31388/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.31388/nu2.mnc ./tmp.mri_nu_correct.mni.31388/nu2.mnc mul .86439789201991015873
Saving result to './tmp.mri_nu_correct.mni.31388/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.31388/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.31388/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.31388/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping ( 8, 173) to ( 3, 110)
 
 
Sat Oct  7 17:25:29 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 17:25:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_normalize -g 1 -mprage nu.mgz T1.mgz 

using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
 1.02441   0.03458  -0.08275   0.58626;
 0.00769   0.91669   0.39890  -7.25849;
 0.07091  -0.37779   1.05571   4.98672;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 20
Starting OpenSpline(): npoints = 20
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 37 (37)
csf peak at 31, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 60 (60), valley at 37 (37)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 50 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 17:27:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=7.0
skull bounding box = (44, 52, 23) --> (211, 208, 224)
using (100, 104, 124) as brain centroid...
mean wm in atlas = 108, using box (79,85,99) --> (120, 123,148) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 4.7
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.358
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.284202 @ (-9.091, -9.091, -9.091)
max log p =    -4.102880 @ (4.545, -4.545, -4.545)
max log p =    -4.082741 @ (2.273, -2.273, -2.273)
max log p =    -4.058860 @ (-1.136, 1.136, 1.136)
max log p =    -4.054829 @ (1.705, -0.568, 1.705)
max log p =    -4.054829 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -15.3, -13.1): log p = -4.055
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.794, old_max_log_p =-4.055 (thresh=-4.1)
 1.00000   0.00000   0.00000  -1.70455;
 0.00000   1.14215   0.47309  -80.40340;
 0.00000  -0.40708   0.98278   54.99955;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.753, old_max_log_p =-3.794 (thresh=-3.8)
 1.00000   0.00000   0.00000  -1.70455;
 0.00000   1.05649   0.43761  -71.21009;
 0.00000  -0.37655   0.90907   51.69382;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.753, old_max_log_p =-3.753 (thresh=-3.7)
 1.00000   0.00000   0.00000  -1.70455;
 0.00000   1.05649   0.43761  -71.21009;
 0.00000  -0.37655   0.90907   51.69382;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.668, old_max_log_p =-3.753 (thresh=-3.7)
 1.01812  -0.03807  -0.01095   3.08835;
 0.03070   1.03394   0.43357  -69.09100;
-0.00404  -0.37801   0.92734   53.77422;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.668 (thresh=-3.7)
 1.03563  -0.07362  -0.02459   5.97219;
 0.06411   1.04395   0.40243  -70.98071;
-0.00303  -0.34398   0.94103   45.01742;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.654 (thresh=-3.6)
 1.03563  -0.07362  -0.02459   5.97219;
 0.06411   1.04395   0.40243  -70.98071;
-0.00303  -0.34398   0.94103   45.01742;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.626, old_max_log_p =-3.654 (thresh=-3.6)
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.626, old_max_log_p =-3.626 (thresh=-3.6)
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3243 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.626 (old=-4.358)
transform before final EM align:
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 364799 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.1  tol 0.000000
final transform:
 1.03290  -0.05625  -0.01819   3.88486;
 0.04725   1.05173   0.38778  -69.08199;
-0.00198  -0.32647   0.94638   42.55876;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1384.151576
mri_em_register stimesec    1.391788
mri_em_register ru_maxrss   609824
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157571
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  148912
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    80
mri_em_register ru_nivcsw   4715
registration took 11 minutes and 59 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=127 y=124 z=118 r=70
      first estimation of the main basin volume: 1493199 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=148, y=110, z=85, Imax=255
      CSF=12, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=9594846747 voxels, voxel volume =1.000 
                     = 9594846747 mmm3 = 9594847.232 cm3
done.
PostAnalyze...Basin Prior
 134 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=127,y=134, z=109, r=10060 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=9, CSF_MAX=34 , nb = 43803
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = -1029705146
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=17 , nb = -1048463709
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 1043219685
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 1073891898
    OTHER      CSF_MIN=0, CSF_intensity=9, CSF_MAX=19 , nb = 1078015446
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    34,      35,        36,   56
  after  analyzing :    34,      35,        36,   40
   RIGHT_CER   
  before analyzing :    18,      24,        34,   56
  after  analyzing :    18,      30,        34,   36
   LEFT_CER    
  before analyzing :    17,      22,        31,   57
  after  analyzing :    17,      28,        31,   35
  RIGHT_BRAIN  
  before analyzing :    35,      35,        36,   56
  after  analyzing :    27,      35,        36,   40
  LEFT_BRAIN   
  before analyzing :    37,      36,        36,   56
  after  analyzing :    27,      36,        36,   41
     OTHER     
  before analyzing :    19,      52,        80,   88
  after  analyzing :    19,      70,        80,   74
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...64 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.011
curvature mean = 71.621, std = 8.811

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.79, sigma = 7.35
      after  rotation: sse = 4.79, sigma = 7.35
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  6.30, its var is 10.43   
      before Erosion-Dilatation  3.92% of inacurate vertices
      after  Erosion-Dilatation  4.46% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...42 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1832135 voxels, voxel volume = 1.000 mm3
           = 1832135 mmm3 = 1832.135 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    24.026347
mri_watershed stimesec    0.417936
mri_watershed ru_maxrss   831496
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   215214
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  6016
mri_watershed ru_oublock  2896
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1658
mri_watershed ru_nivcsw   89
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 17:39:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (58, 70, 38) --> (196, 208, 198)
using (104, 116, 118) as brain centroid...
mean wm in atlas = 107, using box (87,99,98) --> (120, 132,137) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 106 +- 5.0
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.075
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.088684 @ (0.000, 0.000, 0.000)
max log p =    -3.928316 @ (-4.545, -13.636, -13.636)
max log p =    -3.842317 @ (2.273, 2.273, 2.273)
max log p =    -3.830234 @ (1.136, -1.136, -1.136)
max log p =    -3.820868 @ (0.568, 1.705, 1.705)
max log p =    -3.814574 @ (0.284, -0.284, 2.557)
Found translation: (-0.3, -11.1, -8.2): log p = -3.815
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.416, old_max_log_p =-3.815 (thresh=-3.8)
 0.99144  -0.12059  -0.04995   22.20240;
 0.14032   0.98467   0.40787  -73.27188;
 0.00000  -0.35398   0.85459   61.94067;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.416, old_max_log_p =-3.416 (thresh=-3.4)
 0.99144  -0.12059  -0.04995   22.20240;
 0.14032   0.98467   0.40787  -73.27188;
 0.00000  -0.35398   0.85459   61.94067;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.181, old_max_log_p =-3.416 (thresh=-3.4)
 1.03594  -0.05803  -0.02404   5.44814;
 0.07658   1.00902   0.41795  -69.49731;
 0.00000  -0.36726   0.88664   56.55929;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.177, old_max_log_p =-3.181 (thresh=-3.2)
 1.01652  -0.05694  -0.02359   7.72231;
 0.07802   1.02794   0.42579  -73.03706;
 0.00000  -0.36726   0.88664   56.55929;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.176, old_max_log_p =-3.177 (thresh=-3.2)
 1.03558  -0.05801  -0.02403   5.49079;
 0.07655   1.00867   0.41780  -69.43092;
 0.00000  -0.36726   0.88664   56.55929;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.147, old_max_log_p =-3.176 (thresh=-3.2)
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.147, old_max_log_p =-3.147 (thresh=-3.1)
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.147 (old=-4.075)
transform before final EM align:
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 315557 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.7  tol 0.000000
final transform:
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1036.565418
mri_em_register stimesec    1.215815
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158955
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    76
mri_em_register ru_nivcsw   3129
registration took 8 minutes and 55 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 17:48:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz 

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (58, 70, 38) --> (196, 208, 198)
using (104, 116, 118) as brain centroid...
mean wm in atlas = 107, using box (87,99,98) --> (120, 132,137) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 106 +- 5.0
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
using 246344 sample points...
INFO: compute sample coordinates transform
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88005;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 69, 34) --> (192, 188, 202)
Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 555 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 70, 35) --> (128, 183, 202)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 372 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 161, 68) --> (178, 199, 124)
Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 8 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (88, 161, 67) --> (130, 201, 125)
Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0
2 of 13 (15.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 143, 102) --> (148, 207, 135)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 12 (0.0%) samples deleted
using 960 total control points for intensity normalization...
bias field = 0.960 +- 0.050
6 of 958 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 69, 34) --> (192, 188, 202)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
0 of 758 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 70, 35) --> (128, 183, 202)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
1 of 559 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 161, 68) --> (178, 199, 124)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
14 of 79 (17.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (88, 161, 67) --> (130, 201, 125)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
13 of 60 (21.7%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 143, 102) --> (148, 207, 135)
Brain_Stem: limiting intensities to 88.0 --> 132.0
16 of 91 (17.6%) samples deleted
using 1547 total control points for intensity normalization...
bias field = 1.006 +- 0.063
11 of 1494 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 69, 34) --> (192, 188, 202)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 842 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 70, 35) --> (128, 183, 202)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 618 (0.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 161, 68) --> (178, 199, 124)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
30 of 67 (44.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (88, 161, 67) --> (130, 201, 125)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
55 of 79 (69.6%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 143, 102) --> (148, 207, 135)
Brain_Stem: limiting intensities to 88.0 --> 132.0
70 of 165 (42.4%) samples deleted
using 1771 total control points for intensity normalization...
bias field = 1.012 +- 0.051
7 of 1569 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 40 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 17:50:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-regularize_mean 0.500
	-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.08 (predicted orig area = 7.4)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.804, neg=0, invalid=762
0001: dt=219.132394, rms=0.742 (7.741%), neg=0, invalid=762
0002: dt=229.788396, rms=0.720 (2.873%), neg=0, invalid=762
0003: dt=205.538462, rms=0.711 (1.292%), neg=0, invalid=762
0004: dt=221.952000, rms=0.705 (0.912%), neg=0, invalid=762
0005: dt=129.472000, rms=0.701 (0.502%), neg=0, invalid=762
0006: dt=1183.744000, rms=0.691 (1.499%), neg=0, invalid=762
0007: dt=129.472000, rms=0.687 (0.582%), neg=0, invalid=762
0008: dt=221.952000, rms=0.686 (0.142%), neg=0, invalid=762
0009: dt=221.952000, rms=0.684 (0.201%), neg=0, invalid=762
0010: dt=221.952000, rms=0.682 (0.283%), neg=0, invalid=762
0011: dt=221.952000, rms=0.681 (0.248%), neg=0, invalid=762
0012: dt=221.952000, rms=0.678 (0.417%), neg=0, invalid=762
0013: dt=221.952000, rms=0.675 (0.356%), neg=0, invalid=762
0014: dt=221.952000, rms=0.673 (0.327%), neg=0, invalid=762
0015: dt=221.952000, rms=0.671 (0.282%), neg=0, invalid=762
0016: dt=221.952000, rms=0.669 (0.362%), neg=0, invalid=762
0017: dt=221.952000, rms=0.667 (0.251%), neg=0, invalid=762
0018: dt=221.952000, rms=0.666 (0.168%), neg=0, invalid=762
0019: dt=221.952000, rms=0.665 (0.220%), neg=0, invalid=762
0020: dt=221.952000, rms=0.663 (0.189%), neg=0, invalid=762
0021: dt=221.952000, rms=0.662 (0.181%), neg=0, invalid=762
0022: dt=221.952000, rms=0.661 (0.159%), neg=0, invalid=762
0023: dt=221.952000, rms=0.660 (0.209%), neg=0, invalid=762
0024: dt=221.952000, rms=0.659 (0.157%), neg=0, invalid=762
0025: dt=221.952000, rms=0.658 (0.136%), neg=0, invalid=762
0026: dt=221.952000, rms=0.657 (0.155%), neg=0, invalid=762
0027: dt=221.952000, rms=0.656 (0.140%), neg=0, invalid=762
0028: dt=221.952000, rms=0.655 (0.136%), neg=0, invalid=762
0029: dt=221.952000, rms=0.654 (0.099%), neg=0, invalid=762
0030: dt=221.952000, rms=0.653 (0.118%), neg=0, invalid=762
0031: dt=221.952000, rms=0.653 (0.113%), neg=0, invalid=762
0032: dt=110.976000, rms=0.653 (0.006%), neg=0, invalid=762
0033: dt=110.976000, rms=0.653 (0.008%), neg=0, invalid=762
0034: dt=110.976000, rms=0.653 (0.015%), neg=0, invalid=762
0035: dt=110.976000, rms=0.652 (0.020%), neg=0, invalid=762
0036: dt=110.976000, rms=0.652 (0.024%), neg=0, invalid=762
0037: dt=110.976000, rms=0.652 (0.029%), neg=0, invalid=762
0038: dt=110.976000, rms=0.652 (0.033%), neg=0, invalid=762
0039: dt=110.976000, rms=0.652 (0.029%), neg=0, invalid=762
0040: dt=110.976000, rms=0.651 (0.027%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.652, neg=0, invalid=762
0041: dt=295.936000, rms=0.651 (0.176%), neg=0, invalid=762
0042: dt=369.920000, rms=0.651 (0.074%), neg=0, invalid=762
0043: dt=369.920000, rms=0.651 (-0.174%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.658, neg=0, invalid=762
0044: dt=207.820225, rms=0.650 (1.155%), neg=0, invalid=762
0045: dt=82.944000, rms=0.645 (0.860%), neg=0, invalid=762
0046: dt=103.680000, rms=0.642 (0.500%), neg=0, invalid=762
0047: dt=88.918768, rms=0.639 (0.454%), neg=0, invalid=762
0048: dt=90.536585, rms=0.637 (0.331%), neg=0, invalid=762
0049: dt=110.545455, rms=0.634 (0.384%), neg=0, invalid=762
0050: dt=70.974359, rms=0.632 (0.268%), neg=0, invalid=762
0051: dt=145.152000, rms=0.630 (0.376%), neg=0, invalid=762
0052: dt=64.920863, rms=0.629 (0.212%), neg=0, invalid=762
0053: dt=64.920863, rms=0.628 (0.189%), neg=0, invalid=762
0054: dt=64.920863, rms=0.626 (0.267%), neg=0, invalid=762
0055: dt=64.920863, rms=0.624 (0.355%), neg=0, invalid=762
0056: dt=64.920863, rms=0.621 (0.395%), neg=0, invalid=762
0057: dt=64.920863, rms=0.618 (0.433%), neg=0, invalid=762
0058: dt=64.920863, rms=0.616 (0.418%), neg=0, invalid=762
0059: dt=64.920863, rms=0.613 (0.390%), neg=0, invalid=762
0060: dt=64.920863, rms=0.611 (0.361%), neg=0, invalid=762
0061: dt=64.920863, rms=0.609 (0.335%), neg=0, invalid=762
0062: dt=64.920863, rms=0.607 (0.320%), neg=0, invalid=762
0063: dt=64.920863, rms=0.606 (0.275%), neg=0, invalid=762
0064: dt=64.920863, rms=0.604 (0.246%), neg=0, invalid=762
0065: dt=64.920863, rms=0.603 (0.214%), neg=0, invalid=762
0066: dt=64.920863, rms=0.602 (0.189%), neg=0, invalid=762
0067: dt=64.920863, rms=0.601 (0.161%), neg=0, invalid=762
0068: dt=64.920863, rms=0.600 (0.127%), neg=0, invalid=762
0069: dt=64.920863, rms=0.599 (0.102%), neg=0, invalid=762
0070: dt=64.920863, rms=0.599 (0.104%), neg=0, invalid=762
0071: dt=64.920863, rms=0.598 (0.114%), neg=0, invalid=762
0072: dt=64.920863, rms=0.597 (0.093%), neg=0, invalid=762
0073: dt=82.944000, rms=0.597 (0.011%), neg=0, invalid=762
0074: dt=82.944000, rms=0.597 (0.028%), neg=0, invalid=762
0075: dt=82.944000, rms=0.597 (0.028%), neg=0, invalid=762
0076: dt=82.944000, rms=0.597 (0.021%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.598, neg=0, invalid=762
0077: dt=82.944000, rms=0.596 (0.223%), neg=0, invalid=762
0078: dt=103.680000, rms=0.596 (0.044%), neg=0, invalid=762
0079: dt=103.680000, rms=0.596 (0.016%), neg=0, invalid=762
0080: dt=103.680000, rms=0.596 (0.006%), neg=0, invalid=762
0081: dt=103.680000, rms=0.596 (-0.019%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.620, neg=0, invalid=762
0082: dt=0.000000, rms=0.619 (0.102%), neg=0, invalid=762
0083: dt=0.000000, rms=0.619 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.620, neg=0, invalid=762
0084: dt=0.000000, rms=0.619 (0.102%), neg=0, invalid=762
0085: dt=0.000000, rms=0.619 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.690, neg=0, invalid=762
0086: dt=5.674286, rms=0.668 (3.209%), neg=0, invalid=762
0087: dt=2.724138, rms=0.667 (0.117%), neg=0, invalid=762
0088: dt=2.724138, rms=0.667 (-0.041%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.668, neg=0, invalid=762
0089: dt=0.000000, rms=0.667 (0.093%), neg=0, invalid=762
0090: dt=0.000000, rms=0.667 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.733, neg=0, invalid=762
0091: dt=1.280000, rms=0.728 (0.660%), neg=0, invalid=762
0092: dt=2.214815, rms=0.722 (0.842%), neg=0, invalid=762
0093: dt=0.448000, rms=0.721 (0.037%), neg=0, invalid=762
0094: dt=0.448000, rms=0.721 (0.040%), neg=0, invalid=762
0095: dt=0.448000, rms=0.721 (0.051%), neg=0, invalid=762
0096: dt=0.448000, rms=0.720 (0.043%), neg=0, invalid=762
0097: dt=0.448000, rms=0.720 (0.036%), neg=0, invalid=762
0098: dt=3.072000, rms=0.718 (0.234%), neg=0, invalid=762
0099: dt=0.096000, rms=0.718 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.719, neg=0, invalid=762
0100: dt=0.448000, rms=0.718 (0.146%), neg=0, invalid=762
0101: dt=0.448000, rms=0.718 (0.011%), neg=0, invalid=762
0102: dt=0.448000, rms=0.718 (0.005%), neg=0, invalid=762
0103: dt=0.448000, rms=0.718 (0.001%), neg=0, invalid=762
0104: dt=0.448000, rms=0.718 (-0.011%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.684, neg=0, invalid=762
0105: dt=0.838641, rms=0.666 (2.673%), neg=0, invalid=762
0106: dt=0.080000, rms=0.665 (0.143%), neg=0, invalid=762
0107: dt=0.080000, rms=0.665 (-0.077%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.665, neg=0, invalid=762
0108: dt=0.028000, rms=0.664 (0.128%), neg=0, invalid=762
0109: dt=0.007000, rms=0.664 (0.001%), neg=0, invalid=762
0110: dt=0.007000, rms=0.664 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.07098 ( 9)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (744 voxels, overlap=0.278)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (744 voxels, peak = 10), gca=10.1
gca peak = 0.15565 (16)
mri peak = 0.13221 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (800 voxels, overlap=0.300)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (800 voxels, peak =  8), gca=8.2
gca peak = 0.26829 (96)
mri peak = 0.07232 (90)
Right_Pallidum (52): linear fit = 0.93 x + 0.0 (828 voxels, overlap=0.497)
Right_Pallidum (52): linear fit = 0.93 x + 0.0 (828 voxels, peak = 89), gca=88.8
gca peak = 0.20183 (93)
mri peak = 0.06522 (86)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (747 voxels, overlap=0.442)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (747 voxels, peak = 85), gca=85.1
gca peak = 0.21683 (55)
mri peak = 0.08094 (51)
Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (530 voxels, overlap=0.985)
Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (530 voxels, peak = 50), gca=50.3
gca peak = 0.30730 (58)
mri peak = 0.07838 (56)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (396 voxels, overlap=0.993)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (396 voxels, peak = 55), gca=54.8
gca peak = 0.11430 (101)
mri peak = 0.09702 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (67387 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (67387 voxels, peak = 106), gca=105.5
gca peak = 0.12076 (102)
mri peak = 0.10198 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (71559 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (71559 voxels, peak = 107), gca=106.6
gca peak = 0.14995 (59)
mri peak = 0.04064 (56)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (27293 voxels, overlap=0.988)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (27293 voxels, peak = 56), gca=55.8
gca peak = 0.15082 (58)
mri peak = 0.03966 (54)
Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (24730 voxels, overlap=0.981)
Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (24730 voxels, peak = 55), gca=54.8
gca peak = 0.14161 (67)
mri peak = 0.12764 (67)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (567 voxels, overlap=0.938)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (567 voxels, peak = 66), gca=66.0
gca peak = 0.15243 (71)
mri peak = 0.08142 (67)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (960 voxels, overlap=0.747)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (960 voxels, peak = 66), gca=66.4
gca peak = 0.13336 (57)
mri peak = 0.03619 (46)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (23404 voxels, overlap=0.450)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (23404 voxels, peak = 49), gca=48.7
gca peak = 0.13252 (56)
mri peak = 0.02993 (41)
Right_Cerebellum_Cortex (47): linear fit = 0.77 x + 0.0 (24388 voxels, overlap=0.028)
Right_Cerebellum_Cortex (47): linear fit = 0.77 x + 0.0 (24388 voxels, peak = 43), gca=43.4
gca peak = 0.18181 (84)
mri peak = 0.06782 (87)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8100 voxels, overlap=0.929)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8100 voxels, peak = 87), gca=86.9
gca peak = 0.20573 (83)
mri peak = 0.05792 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7549 voxels, overlap=0.978)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7549 voxels, peak = 85), gca=85.1
gca peak = 0.21969 (57)
mri peak = 0.05251 (61)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (469 voxels, overlap=1.006)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (469 voxels, peak = 58), gca=58.4
gca peak = 0.39313 (56)
mri peak = 0.07993 (61)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, overlap=1.003)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, peak = 59), gca=58.5
gca peak = 0.14181 (85)
mri peak = 0.05315 (91)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6055 voxels, overlap=0.911)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6055 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.06127 (87)
Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4945 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4945 voxels, peak = 88), gca=88.4
gca peak = 0.13399 (79)
mri peak = 0.04933 (76)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2433 voxels, overlap=1.000)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2433 voxels, peak = 79), gca=78.6
gca peak = 0.14159 (79)
mri peak = 0.06141 (77)
Right_Putamen (51): linear fit = 0.98 x + 0.0 (2426 voxels, overlap=0.959)
Right_Putamen (51): linear fit = 0.98 x + 0.0 (2426 voxels, peak = 77), gca=77.0
gca peak = 0.10025 (80)
mri peak = 0.08348 (85)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (12482 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (12482 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.06858 (91)
Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1202 voxels, overlap=0.724)
Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1202 voxels, peak = 90), gca=89.9
gca peak = 0.12801 (89)
mri peak = 0.07554 (88)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1287 voxels, overlap=0.850)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1287 voxels, peak = 90), gca=90.3
gca peak = 0.20494 (23)
mri peak = 0.16031 (52)
gca peak = 0.15061 (21)
mri peak = 0.17251 ( 8)
Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (403 voxels, overlap=0.110)
Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (403 voxels, peak =  8), gca=8.1
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 0.97 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.51 x + 0.0
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.690, neg=0, invalid=762
0111: dt=140.571429, rms=0.682 (1.119%), neg=0, invalid=762
0112: dt=157.333333, rms=0.678 (0.575%), neg=0, invalid=762
0113: dt=129.472000, rms=0.676 (0.214%), neg=0, invalid=762
0114: dt=295.936000, rms=0.674 (0.294%), neg=0, invalid=762
0115: dt=92.480000, rms=0.673 (0.187%), neg=0, invalid=762
0116: dt=517.888000, rms=0.671 (0.277%), neg=0, invalid=762
0117: dt=73.984000, rms=0.670 (0.121%), neg=0, invalid=762
0118: dt=1479.680000, rms=0.668 (0.353%), neg=0, invalid=762
0119: dt=110.976000, rms=0.667 (0.236%), neg=0, invalid=762
0120: dt=110.976000, rms=0.666 (0.031%), neg=0, invalid=762
0121: dt=110.976000, rms=0.666 (0.035%), neg=0, invalid=762
0122: dt=110.976000, rms=0.666 (0.058%), neg=0, invalid=762
0123: dt=110.976000, rms=0.665 (0.071%), neg=0, invalid=762
0124: dt=110.976000, rms=0.665 (0.081%), neg=0, invalid=762
0125: dt=110.976000, rms=0.664 (0.091%), neg=0, invalid=762
0126: dt=110.976000, rms=0.663 (0.098%), neg=0, invalid=762
0127: dt=110.976000, rms=0.663 (0.095%), neg=0, invalid=762
0128: dt=110.976000, rms=0.662 (0.088%), neg=0, invalid=762
0129: dt=110.976000, rms=0.662 (0.089%), neg=0, invalid=762
0130: dt=110.976000, rms=0.661 (0.092%), neg=0, invalid=762
0131: dt=110.976000, rms=0.660 (0.093%), neg=0, invalid=762
0132: dt=110.976000, rms=0.660 (0.084%), neg=0, invalid=762
0133: dt=110.976000, rms=0.659 (0.073%), neg=0, invalid=762
0134: dt=110.976000, rms=0.659 (0.067%), neg=0, invalid=762
0135: dt=110.976000, rms=0.659 (0.067%), neg=0, invalid=762
0136: dt=110.976000, rms=0.658 (0.066%), neg=0, invalid=762
0137: dt=110.976000, rms=0.658 (0.062%), neg=0, invalid=762
0138: dt=110.976000, rms=0.657 (0.061%), neg=0, invalid=762
0139: dt=110.976000, rms=0.657 (0.057%), neg=0, invalid=762
0140: dt=110.976000, rms=0.657 (0.058%), neg=0, invalid=762
0141: dt=110.976000, rms=0.656 (0.059%), neg=0, invalid=762
0142: dt=110.976000, rms=0.656 (0.056%), neg=0, invalid=762
0143: dt=110.976000, rms=0.655 (0.051%), neg=0, invalid=762
0144: dt=110.976000, rms=0.655 (0.052%), neg=0, invalid=762
0145: dt=110.976000, rms=0.655 (0.051%), neg=0, invalid=762
0146: dt=110.976000, rms=0.654 (0.051%), neg=0, invalid=762
0147: dt=110.976000, rms=0.654 (0.049%), neg=0, invalid=762
0148: dt=110.976000, rms=0.654 (0.046%), neg=0, invalid=762
0149: dt=110.976000, rms=0.654 (0.044%), neg=0, invalid=762
0150: dt=110.976000, rms=0.653 (0.044%), neg=0, invalid=762
0151: dt=110.976000, rms=0.653 (0.042%), neg=0, invalid=762
0152: dt=110.976000, rms=0.653 (0.042%), neg=0, invalid=762
0153: dt=110.976000, rms=0.652 (0.041%), neg=0, invalid=762
0154: dt=110.976000, rms=0.652 (0.040%), neg=0, invalid=762
0155: dt=110.976000, rms=0.652 (0.040%), neg=0, invalid=762
0156: dt=110.976000, rms=0.652 (0.039%), neg=0, invalid=762
0157: dt=110.976000, rms=0.651 (0.037%), neg=0, invalid=762
0158: dt=110.976000, rms=0.651 (0.036%), neg=0, invalid=762
0159: dt=110.976000, rms=0.651 (0.035%), neg=0, invalid=762
0160: dt=110.976000, rms=0.651 (0.033%), neg=0, invalid=762
0161: dt=110.976000, rms=0.650 (0.032%), neg=0, invalid=762
0162: dt=110.976000, rms=0.650 (0.028%), neg=0, invalid=762
0163: dt=110.976000, rms=0.650 (0.027%), neg=0, invalid=762
0164: dt=110.976000, rms=0.650 (0.029%), neg=0, invalid=762
0165: dt=110.976000, rms=0.650 (0.028%), neg=0, invalid=762
0166: dt=110.976000, rms=0.650 (0.027%), neg=0, invalid=762
0167: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762
0168: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762
0169: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762
0170: dt=110.976000, rms=0.649 (0.027%), neg=0, invalid=762
0171: dt=110.976000, rms=0.649 (0.025%), neg=0, invalid=762
0172: dt=110.976000, rms=0.649 (0.025%), neg=0, invalid=762
0173: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762
0174: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762
0175: dt=110.976000, rms=0.648 (0.025%), neg=0, invalid=762
0176: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762
0177: dt=5918.720000, rms=0.648 (0.061%), neg=0, invalid=762
0178: dt=129.472000, rms=0.647 (0.066%), neg=0, invalid=762
0179: dt=23.120000, rms=0.647 (0.005%), neg=0, invalid=762
0180: dt=23.120000, rms=0.647 (0.000%), neg=0, invalid=762
0181: dt=23.120000, rms=0.647 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.648, neg=0, invalid=762
0182: dt=129.472000, rms=0.647 (0.146%), neg=0, invalid=762
0183: dt=517.888000, rms=0.646 (0.073%), neg=0, invalid=762
0184: dt=517.888000, rms=0.646 (0.081%), neg=0, invalid=762
0185: dt=110.976000, rms=0.646 (0.032%), neg=0, invalid=762
0186: dt=110.976000, rms=0.646 (0.004%), neg=0, invalid=762
0187: dt=110.976000, rms=0.646 (0.009%), neg=0, invalid=762
0188: dt=110.976000, rms=0.645 (0.020%), neg=0, invalid=762
0189: dt=110.976000, rms=0.645 (0.030%), neg=0, invalid=762
0190: dt=110.976000, rms=0.645 (0.037%), neg=0, invalid=762
0191: dt=110.976000, rms=0.645 (0.036%), neg=0, invalid=762
0192: dt=110.976000, rms=0.645 (0.033%), neg=0, invalid=762
0193: dt=110.976000, rms=0.644 (0.032%), neg=0, invalid=762
0194: dt=110.976000, rms=0.644 (0.028%), neg=0, invalid=762
0195: dt=110.976000, rms=0.644 (0.022%), neg=0, invalid=762
0196: dt=110.976000, rms=0.644 (0.024%), neg=0, invalid=762
0197: dt=110.976000, rms=0.644 (0.024%), neg=0, invalid=762
0198: dt=110.976000, rms=0.644 (0.027%), neg=0, invalid=762
0199: dt=110.976000, rms=0.643 (0.026%), neg=0, invalid=762
0200: dt=110.976000, rms=0.643 (0.022%), neg=0, invalid=762
0201: dt=110.976000, rms=0.643 (0.018%), neg=0, invalid=762
0202: dt=443.904000, rms=0.643 (0.004%), neg=0, invalid=762
0203: dt=443.904000, rms=0.643 (-0.010%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.645, neg=0, invalid=762
0204: dt=134.935961, rms=0.640 (0.672%), neg=0, invalid=762
0205: dt=96.502618, rms=0.637 (0.557%), neg=0, invalid=762
0206: dt=62.352475, rms=0.634 (0.417%), neg=0, invalid=762
0207: dt=103.680000, rms=0.632 (0.346%), neg=0, invalid=762
0208: dt=62.208000, rms=0.630 (0.351%), neg=0, invalid=762
0209: dt=88.553459, rms=0.628 (0.264%), neg=0, invalid=762
0210: dt=63.152318, rms=0.626 (0.272%), neg=0, invalid=762
0211: dt=84.087591, rms=0.625 (0.220%), neg=0, invalid=762
0212: dt=66.666667, rms=0.624 (0.229%), neg=0, invalid=762
0213: dt=82.944000, rms=0.623 (0.183%), neg=0, invalid=762
0214: dt=62.208000, rms=0.621 (0.206%), neg=0, invalid=762
0215: dt=82.944000, rms=0.620 (0.161%), neg=0, invalid=762
0216: dt=64.964824, rms=0.619 (0.182%), neg=0, invalid=762
0217: dt=82.944000, rms=0.618 (0.138%), neg=0, invalid=762
0218: dt=62.208000, rms=0.617 (0.170%), neg=0, invalid=762
0219: dt=82.944000, rms=0.616 (0.121%), neg=0, invalid=762
0220: dt=62.306878, rms=0.616 (0.157%), neg=0, invalid=762
0221: dt=82.944000, rms=0.615 (0.109%), neg=0, invalid=762
0222: dt=36.288000, rms=0.614 (0.118%), neg=0, invalid=762
0223: dt=580.608000, rms=0.609 (0.847%), neg=0, invalid=762
0224: dt=62.208000, rms=0.608 (0.104%), neg=0, invalid=762
0225: dt=62.208000, rms=0.608 (0.066%), neg=0, invalid=762
0226: dt=103.680000, rms=0.607 (0.093%), neg=0, invalid=762
0227: dt=36.288000, rms=0.607 (0.082%), neg=0, invalid=762
0228: dt=580.608000, rms=0.604 (0.484%), neg=0, invalid=762
0229: dt=36.288000, rms=0.603 (0.134%), neg=0, invalid=762
0230: dt=248.832000, rms=0.602 (0.160%), neg=0, invalid=762
0231: dt=36.288000, rms=0.602 (0.075%), neg=0, invalid=762
0232: dt=82.944000, rms=0.601 (0.045%), neg=0, invalid=762
0233: dt=82.944000, rms=0.601 (0.083%), neg=0, invalid=762
0234: dt=82.944000, rms=0.600 (0.123%), neg=0, invalid=762
0235: dt=82.944000, rms=0.599 (0.134%), neg=0, invalid=762
0236: dt=82.944000, rms=0.598 (0.202%), neg=0, invalid=762
0237: dt=82.944000, rms=0.597 (0.205%), neg=0, invalid=762
0238: dt=82.944000, rms=0.596 (0.216%), neg=0, invalid=762
0239: dt=82.944000, rms=0.594 (0.261%), neg=0, invalid=762
0240: dt=82.944000, rms=0.593 (0.248%), neg=0, invalid=762
0241: dt=82.944000, rms=0.591 (0.226%), neg=0, invalid=762
0242: dt=82.944000, rms=0.590 (0.220%), neg=0, invalid=762
0243: dt=82.944000, rms=0.589 (0.232%), neg=0, invalid=762
0244: dt=82.944000, rms=0.588 (0.016%), neg=0, invalid=762
0245: dt=82.944000, rms=0.588 (0.046%), neg=0, invalid=762
0246: dt=82.944000, rms=0.588 (0.061%), neg=0, invalid=762
0247: dt=82.944000, rms=0.587 (0.078%), neg=0, invalid=762
0248: dt=82.944000, rms=0.587 (0.081%), neg=0, invalid=762
0249: dt=82.944000, rms=0.586 (0.100%), neg=0, invalid=762
0250: dt=82.944000, rms=0.586 (0.099%), neg=0, invalid=762
0251: dt=82.944000, rms=0.585 (0.107%), neg=0, invalid=762
0252: dt=82.944000, rms=0.584 (0.127%), neg=0, invalid=762
0253: dt=82.944000, rms=0.584 (0.107%), neg=0, invalid=762
0254: dt=82.944000, rms=0.583 (0.120%), neg=0, invalid=762
0255: dt=82.944000, rms=0.582 (0.125%), neg=0, invalid=762
0256: dt=82.944000, rms=0.582 (0.112%), neg=0, invalid=762
0257: dt=82.944000, rms=0.582 (0.008%), neg=0, invalid=762
0258: dt=82.944000, rms=0.581 (0.025%), neg=0, invalid=762
0259: dt=82.944000, rms=0.581 (0.013%), neg=0, invalid=762
0260: dt=36.288000, rms=0.581 (0.010%), neg=0, invalid=762
0261: dt=18.144000, rms=0.581 (0.002%), neg=0, invalid=762
0262: dt=0.567000, rms=0.581 (0.001%), neg=0, invalid=762
0263: dt=0.283500, rms=0.581 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.582, neg=0, invalid=762
0264: dt=110.412214, rms=0.580 (0.409%), neg=0, invalid=762
0265: dt=103.680000, rms=0.579 (0.201%), neg=0, invalid=762
0266: dt=36.288000, rms=0.578 (0.063%), neg=0, invalid=762
0267: dt=145.152000, rms=0.578 (0.087%), neg=0, invalid=762
0268: dt=124.416000, rms=0.577 (0.105%), neg=0, invalid=762
0269: dt=36.288000, rms=0.577 (0.026%), neg=0, invalid=762
0270: dt=36.288000, rms=0.577 (0.015%), neg=0, invalid=762
0271: dt=36.288000, rms=0.577 (0.031%), neg=0, invalid=762
0272: dt=36.288000, rms=0.576 (0.046%), neg=0, invalid=762
0273: dt=36.288000, rms=0.576 (0.058%), neg=0, invalid=762
0274: dt=36.288000, rms=0.576 (0.065%), neg=0, invalid=762
0275: dt=36.288000, rms=0.575 (0.065%), neg=0, invalid=762
0276: dt=36.288000, rms=0.575 (0.067%), neg=0, invalid=762
0277: dt=36.288000, rms=0.575 (0.065%), neg=0, invalid=762
0278: dt=36.288000, rms=0.574 (0.063%), neg=0, invalid=762
0279: dt=36.288000, rms=0.574 (0.067%), neg=0, invalid=762
0280: dt=36.288000, rms=0.573 (0.068%), neg=0, invalid=762
0281: dt=36.288000, rms=0.573 (0.062%), neg=0, invalid=762
0282: dt=36.288000, rms=0.573 (0.056%), neg=0, invalid=762
0283: dt=36.288000, rms=0.572 (0.057%), neg=0, invalid=762
0284: dt=36.288000, rms=0.572 (0.054%), neg=0, invalid=762
0285: dt=36.288000, rms=0.572 (0.056%), neg=0, invalid=762
0286: dt=36.288000, rms=0.572 (0.058%), neg=0, invalid=762
0287: dt=36.288000, rms=0.571 (0.056%), neg=0, invalid=762
0288: dt=36.288000, rms=0.571 (0.053%), neg=0, invalid=762
0289: dt=36.288000, rms=0.571 (0.052%), neg=0, invalid=762
0290: dt=36.288000, rms=0.570 (0.055%), neg=0, invalid=762
0291: dt=36.288000, rms=0.570 (0.054%), neg=0, invalid=762
0292: dt=36.288000, rms=0.570 (0.053%), neg=0, invalid=762
0293: dt=36.288000, rms=0.569 (0.051%), neg=0, invalid=762
0294: dt=36.288000, rms=0.569 (0.049%), neg=0, invalid=762
0295: dt=36.288000, rms=0.569 (0.047%), neg=0, invalid=762
0296: dt=36.288000, rms=0.569 (0.047%), neg=0, invalid=762
0297: dt=36.288000, rms=0.568 (0.047%), neg=0, invalid=762
0298: dt=36.288000, rms=0.568 (0.045%), neg=0, invalid=762
0299: dt=36.288000, rms=0.568 (0.044%), neg=0, invalid=762
0300: dt=36.288000, rms=0.568 (0.042%), neg=0, invalid=762
0301: dt=36.288000, rms=0.567 (0.038%), neg=0, invalid=762
0302: dt=36.288000, rms=0.567 (0.042%), neg=0, invalid=762
0303: dt=36.288000, rms=0.567 (0.040%), neg=0, invalid=762
0304: dt=36.288000, rms=0.567 (0.038%), neg=0, invalid=762
0305: dt=36.288000, rms=0.566 (0.036%), neg=0, invalid=762
0306: dt=36.288000, rms=0.566 (0.036%), neg=0, invalid=762
0307: dt=36.288000, rms=0.566 (0.034%), neg=0, invalid=762
0308: dt=36.288000, rms=0.566 (0.037%), neg=0, invalid=762
0309: dt=36.288000, rms=0.566 (0.034%), neg=0, invalid=762
0310: dt=36.288000, rms=0.565 (0.033%), neg=0, invalid=762
0311: dt=36.288000, rms=0.565 (0.032%), neg=0, invalid=762
0312: dt=36.288000, rms=0.565 (0.031%), neg=0, invalid=762
0313: dt=36.288000, rms=0.565 (0.031%), neg=0, invalid=762
0314: dt=36.288000, rms=0.565 (0.033%), neg=0, invalid=762
0315: dt=36.288000, rms=0.565 (0.029%), neg=0, invalid=762
0316: dt=36.288000, rms=0.564 (0.029%), neg=0, invalid=762
0317: dt=36.288000, rms=0.564 (0.032%), neg=0, invalid=762
0318: dt=36.288000, rms=0.564 (0.027%), neg=0, invalid=762
0319: dt=36.288000, rms=0.564 (0.027%), neg=0, invalid=762
0320: dt=36.288000, rms=0.564 (0.028%), neg=0, invalid=762
0321: dt=36.288000, rms=0.564 (0.026%), neg=0, invalid=762
0322: dt=36.288000, rms=0.563 (0.027%), neg=0, invalid=762
0323: dt=36.288000, rms=0.563 (0.026%), neg=0, invalid=762
0324: dt=36.288000, rms=0.563 (0.025%), neg=0, invalid=762
0325: dt=36.288000, rms=0.563 (0.025%), neg=0, invalid=762
0326: dt=36.288000, rms=0.563 (0.025%), neg=0, invalid=762
0327: dt=36.288000, rms=0.563 (0.027%), neg=0, invalid=762
0328: dt=36.288000, rms=0.563 (0.026%), neg=0, invalid=762
0329: dt=36.288000, rms=0.562 (0.024%), neg=0, invalid=762
0330: dt=36.288000, rms=0.562 (0.022%), neg=0, invalid=762
0331: dt=145.152000, rms=0.562 (0.005%), neg=0, invalid=762
0332: dt=145.152000, rms=0.562 (-0.016%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.571, neg=0, invalid=762
0333: dt=32.000000, rms=0.569 (0.442%), neg=0, invalid=762
0334: dt=70.736842, rms=0.566 (0.516%), neg=0, invalid=762
0335: dt=25.600000, rms=0.563 (0.436%), neg=0, invalid=762
0336: dt=72.000000, rms=0.560 (0.645%), neg=0, invalid=762
0337: dt=23.201401, rms=0.557 (0.427%), neg=0, invalid=762
0338: dt=76.800000, rms=0.554 (0.493%), neg=0, invalid=762
0339: dt=25.600000, rms=0.553 (0.354%), neg=0, invalid=762
0340: dt=44.800000, rms=0.551 (0.322%), neg=0, invalid=762
0341: dt=25.600000, rms=0.550 (0.184%), neg=0, invalid=762
0342: dt=44.800000, rms=0.548 (0.275%), neg=0, invalid=762
0343: dt=25.043478, rms=0.548 (0.120%), neg=0, invalid=762
0344: dt=44.800000, rms=0.546 (0.223%), neg=0, invalid=762
0345: dt=22.237288, rms=0.546 (0.111%), neg=0, invalid=762
0346: dt=76.800000, rms=0.544 (0.267%), neg=0, invalid=762
0347: dt=23.004016, rms=0.543 (0.152%), neg=0, invalid=762
0348: dt=128.000000, rms=0.541 (0.361%), neg=0, invalid=762
0349: dt=11.200000, rms=0.541 (0.136%), neg=0, invalid=762
0350: dt=11.200000, rms=0.540 (0.083%), neg=0, invalid=762
0351: dt=2.000000, rms=0.540 (0.019%), neg=0, invalid=762
0352: dt=0.250000, rms=0.540 (0.002%), neg=0, invalid=762
0353: dt=0.031250, rms=0.540 (0.000%), neg=0, invalid=762
0354: dt=0.007812, rms=0.540 (0.000%), neg=0, invalid=762
0355: dt=0.002734, rms=0.540 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.541, neg=0, invalid=762
0356: dt=32.000000, rms=0.538 (0.495%), neg=0, invalid=762
0357: dt=44.800000, rms=0.536 (0.329%), neg=0, invalid=762
0358: dt=11.200000, rms=0.536 (0.072%), neg=0, invalid=762
0359: dt=44.800000, rms=0.536 (0.104%), neg=0, invalid=762
0360: dt=32.000000, rms=0.535 (0.164%), neg=0, invalid=762
0361: dt=11.200000, rms=0.534 (0.047%), neg=0, invalid=762
0362: dt=11.200000, rms=0.534 (0.031%), neg=0, invalid=762
0363: dt=11.200000, rms=0.534 (0.043%), neg=0, invalid=762
0364: dt=11.200000, rms=0.534 (0.070%), neg=0, invalid=762
0365: dt=11.200000, rms=0.533 (0.104%), neg=0, invalid=762
0366: dt=11.200000, rms=0.533 (0.107%), neg=0, invalid=762
0367: dt=11.200000, rms=0.532 (0.105%), neg=0, invalid=762
0368: dt=11.200000, rms=0.531 (0.096%), neg=0, invalid=762
0369: dt=11.200000, rms=0.531 (0.107%), neg=0, invalid=762
0370: dt=11.200000, rms=0.530 (0.114%), neg=0, invalid=762
0371: dt=11.200000, rms=0.530 (0.129%), neg=0, invalid=762
0372: dt=11.200000, rms=0.529 (0.140%), neg=0, invalid=762
0373: dt=11.200000, rms=0.528 (0.136%), neg=0, invalid=762
0374: dt=11.200000, rms=0.527 (0.134%), neg=0, invalid=762
0375: dt=11.200000, rms=0.527 (0.025%), neg=0, invalid=762
0376: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=762
0377: dt=11.200000, rms=0.527 (0.052%), neg=0, invalid=762
0378: dt=11.200000, rms=0.526 (0.057%), neg=0, invalid=762
0379: dt=11.200000, rms=0.526 (0.070%), neg=0, invalid=762
0380: dt=11.200000, rms=0.526 (0.072%), neg=0, invalid=762
0381: dt=11.200000, rms=0.525 (0.079%), neg=0, invalid=762
0382: dt=11.200000, rms=0.525 (0.075%), neg=0, invalid=762
0383: dt=11.200000, rms=0.525 (0.074%), neg=0, invalid=762
0384: dt=11.200000, rms=0.524 (0.084%), neg=0, invalid=762
0385: dt=11.200000, rms=0.524 (0.085%), neg=0, invalid=762
0386: dt=11.200000, rms=0.523 (0.079%), neg=0, invalid=762
0387: dt=11.200000, rms=0.523 (0.082%), neg=0, invalid=762
0388: dt=11.200000, rms=0.522 (0.078%), neg=0, invalid=762
0389: dt=11.200000, rms=0.522 (0.078%), neg=0, invalid=762
0390: dt=11.200000, rms=0.522 (0.081%), neg=0, invalid=762
0391: dt=11.200000, rms=0.521 (0.078%), neg=0, invalid=762
0392: dt=11.200000, rms=0.521 (0.076%), neg=0, invalid=762
0393: dt=11.200000, rms=0.520 (0.073%), neg=0, invalid=762
0394: dt=11.200000, rms=0.520 (0.075%), neg=0, invalid=762
0395: dt=11.200000, rms=0.520 (0.070%), neg=0, invalid=762
0396: dt=11.200000, rms=0.519 (0.067%), neg=0, invalid=762
0397: dt=11.200000, rms=0.519 (0.067%), neg=0, invalid=762
0398: dt=11.200000, rms=0.519 (0.001%), neg=0, invalid=762
0399: dt=11.200000, rms=0.519 (0.011%), neg=0, invalid=762
0400: dt=11.200000, rms=0.519 (0.012%), neg=0, invalid=762
0401: dt=11.200000, rms=0.519 (0.018%), neg=0, invalid=762
0402: dt=11.200000, rms=0.519 (0.026%), neg=0, invalid=762
0403: dt=11.200000, rms=0.518 (0.020%), neg=0, invalid=762
0404: dt=11.200000, rms=0.518 (0.001%), neg=0, invalid=762
0405: dt=44.800000, rms=0.518 (0.020%), neg=0, invalid=762
0406: dt=11.200000, rms=0.518 (0.004%), neg=0, invalid=762
0407: dt=2.800000, rms=0.518 (0.004%), neg=0, invalid=762
0408: dt=1.400000, rms=0.518 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.539, neg=0, invalid=762
0409: dt=0.000000, rms=0.538 (0.148%), neg=0, invalid=762
0410: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762
0411: dt=0.150000, rms=0.538 (-0.020%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.539, neg=0, invalid=762
0412: dt=0.000000, rms=0.538 (0.148%), neg=0, invalid=762
0413: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762
0414: dt=0.150000, rms=0.538 (-0.021%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.579, neg=0, invalid=762
0415: dt=1.024000, rms=0.577 (0.432%), neg=0, invalid=762
0416: dt=0.112000, rms=0.577 (0.005%), neg=0, invalid=762
0417: dt=0.112000, rms=0.577 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.577, neg=0, invalid=762
0418: dt=0.448000, rms=0.576 (0.192%), neg=0, invalid=762
0419: dt=0.256000, rms=0.576 (0.010%), neg=0, invalid=762
0420: dt=0.256000, rms=0.576 (-0.005%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.526, neg=0, invalid=762
0421: dt=0.448000, rms=0.511 (2.844%), neg=0, invalid=762
0422: dt=0.448000, rms=0.508 (0.643%), neg=0, invalid=762
0423: dt=0.448000, rms=0.506 (0.343%), neg=0, invalid=762
0424: dt=0.448000, rms=0.505 (0.208%), neg=0, invalid=762
0425: dt=0.461538, rms=0.504 (0.150%), neg=0, invalid=762
0426: dt=0.448000, rms=0.504 (0.109%), neg=0, invalid=762
0427: dt=0.448000, rms=0.503 (0.086%), neg=0, invalid=762
0428: dt=0.448000, rms=0.503 (0.065%), neg=0, invalid=762
0429: dt=0.448000, rms=0.503 (0.058%), neg=0, invalid=762
0430: dt=0.448000, rms=0.503 (0.039%), neg=0, invalid=762
0431: dt=0.448000, rms=0.502 (0.042%), neg=0, invalid=762
0432: dt=0.448000, rms=0.502 (0.062%), neg=0, invalid=762
0433: dt=0.448000, rms=0.502 (0.076%), neg=0, invalid=762
0434: dt=0.448000, rms=0.501 (0.081%), neg=0, invalid=762
0435: dt=0.448000, rms=0.501 (0.065%), neg=0, invalid=762
0436: dt=0.448000, rms=0.501 (0.047%), neg=0, invalid=762
0437: dt=0.448000, rms=0.501 (-0.007%), neg=0, invalid=762
0438: dt=0.000000, rms=0.501 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.502, neg=0, invalid=762
0439: dt=0.448000, rms=0.496 (1.181%), neg=0, invalid=762
0440: dt=0.448000, rms=0.495 (0.118%), neg=0, invalid=762
0441: dt=0.448000, rms=0.495 (0.041%), neg=0, invalid=762
0442: dt=0.448000, rms=0.495 (0.007%), neg=0, invalid=762
0443: dt=0.448000, rms=0.495 (0.006%), neg=0, invalid=762
0444: dt=0.448000, rms=0.495 (-0.012%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.493, neg=0, invalid=762
0445: dt=0.000000, rms=0.492 (0.178%), neg=0, invalid=762
0446: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.493, neg=0, invalid=762
0447: dt=129.472000, rms=0.492 (0.205%), neg=0, invalid=762
0448: dt=129.472000, rms=0.492 (0.024%), neg=0, invalid=762
0449: dt=129.472000, rms=0.492 (-0.025%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.493, neg=0, invalid=762
0450: dt=9.072000, rms=0.492 (0.200%), neg=0, invalid=762
0451: dt=9.072000, rms=0.492 (0.005%), neg=0, invalid=762
0452: dt=9.072000, rms=0.492 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.493, neg=0, invalid=762
0453: dt=124.416000, rms=0.491 (0.448%), neg=0, invalid=762
0454: dt=36.288000, rms=0.490 (0.129%), neg=0, invalid=762
0455: dt=36.288000, rms=0.490 (0.046%), neg=0, invalid=762
0456: dt=36.288000, rms=0.490 (0.071%), neg=0, invalid=762
0457: dt=36.288000, rms=0.489 (0.097%), neg=0, invalid=762
0458: dt=36.288000, rms=0.489 (0.101%), neg=0, invalid=762
0459: dt=36.288000, rms=0.488 (0.097%), neg=0, invalid=762
0460: dt=36.288000, rms=0.488 (0.091%), neg=0, invalid=762
0461: dt=62.208000, rms=0.488 (0.015%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0462: dt=23.866221, rms=0.486 (0.469%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0463: dt=32.000000, rms=0.485 (0.209%), neg=0, invalid=762
0464: dt=32.000000, rms=0.485 (0.195%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 3 iterations, nbhd size=0, neg = 0
0465: dt=32.000000, rms=0.483 (0.356%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 5 iterations, nbhd size=0, neg = 0
0466: dt=32.000000, rms=0.483 (-0.016%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0467: dt=19.200000, rms=0.482 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0468: dt=32.000000, rms=0.481 (0.177%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0469: dt=11.200000, rms=0.481 (0.055%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0470: dt=38.400000, rms=0.477 (1.069%), neg=0, invalid=762
0471: dt=25.600000, rms=0.475 (0.423%), neg=0, invalid=762
0472: dt=11.200000, rms=0.474 (0.110%), neg=0, invalid=762
0473: dt=11.200000, rms=0.474 (0.089%), neg=0, invalid=762
0474: dt=11.200000, rms=0.473 (0.134%), neg=0, invalid=762
0475: dt=11.200000, rms=0.472 (0.163%), neg=0, invalid=762
0476: dt=11.200000, rms=0.471 (0.178%), neg=0, invalid=762
0477: dt=11.200000, rms=0.471 (0.177%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0478: dt=11.200000, rms=0.470 (0.169%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0479: dt=11.200000, rms=0.469 (0.156%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 4 iterations, nbhd size=0, neg = 0
0480: dt=11.200000, rms=0.468 (0.151%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 12 iterations, nbhd size=1, neg = 0
0481: dt=11.200000, rms=0.468 (0.142%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0482: dt=11.200000, rms=0.467 (0.144%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0483: dt=11.200000, rms=0.466 (0.142%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0484: dt=11.200000, rms=0.466 (0.129%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0485: dt=11.200000, rms=0.465 (0.116%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0486: dt=11.200000, rms=0.465 (0.109%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0487: dt=44.800000, rms=0.464 (0.050%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0488: dt=44.800000, rms=0.464 (-0.101%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0489: dt=2.880000, rms=0.468 (0.209%), neg=0, invalid=762
0490: dt=0.864000, rms=0.468 (0.005%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0491: dt=0.864000, rms=0.468 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0492: dt=8.000000, rms=0.468 (0.249%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0493: dt=12.081633, rms=0.467 (0.089%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0494: dt=12.081633, rms=0.467 (0.190%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0495: dt=12.081633, rms=0.465 (0.333%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0496: dt=12.081633, rms=0.463 (0.387%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 6 iterations, nbhd size=0, neg = 0
0497: dt=12.081633, rms=0.461 (0.544%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 7 iterations, nbhd size=0, neg = 0
0498: dt=12.081633, rms=0.458 (0.566%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 4 iterations, nbhd size=0, neg = 0
0499: dt=12.081633, rms=0.456 (0.477%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 9 iterations, nbhd size=0, neg = 0
0500: dt=12.081633, rms=0.455 (0.206%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 2 iterations, nbhd size=0, neg = 0
0501: dt=12.081633, rms=0.455 (0.049%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 10 iterations, nbhd size=0, neg = 0
0502: dt=12.081633, rms=0.455 (-0.088%), neg=0, invalid=762
0503: dt=0.000984, rms=0.455 (0.000%), neg=0, invalid=762
0504: dt=0.000211, rms=0.455 (0.000%), neg=0, invalid=762
0505: dt=0.000006, rms=0.455 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.462, neg=0, invalid=762
0506: dt=0.000000, rms=0.461 (0.204%), neg=0, invalid=762
0507: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.462, neg=0, invalid=762
0508: dt=0.000000, rms=0.461 (0.204%), neg=0, invalid=762
0509: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.451, neg=0, invalid=762
iter 0, gcam->neg = 794
after 17 iterations, nbhd size=1, neg = 0
0510: dt=1.921735, rms=0.424 (5.995%), neg=0, invalid=762
0511: dt=0.000013, rms=0.424 (0.001%), neg=0, invalid=762
0512: dt=0.000013, rms=0.424 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.426, neg=0, invalid=762
0513: dt=0.080000, rms=0.424 (0.315%), neg=0, invalid=762
0514: dt=0.007000, rms=0.424 (0.003%), neg=0, invalid=762
0515: dt=0.007000, rms=0.424 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0516: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0517: dt=27.744000, rms=0.413 (0.005%), neg=0, invalid=762
0518: dt=8.092000, rms=0.413 (0.000%), neg=0, invalid=762
0519: dt=8.092000, rms=0.413 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0520: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0521: dt=36.288000, rms=0.413 (0.034%), neg=0, invalid=762
0522: dt=103.680000, rms=0.412 (0.037%), neg=0, invalid=762
0523: dt=145.152000, rms=0.412 (0.037%), neg=0, invalid=762
0524: dt=145.152000, rms=0.412 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0525: dt=2.800000, rms=0.413 (0.013%), neg=0, invalid=762
0526: dt=2.800000, rms=0.413 (0.004%), neg=0, invalid=762
0527: dt=2.800000, rms=0.413 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
iter 0, gcam->neg = 5
after 11 iterations, nbhd size=1, neg = 0
0528: dt=88.510638, rms=0.411 (0.446%), neg=0, invalid=762
0529: dt=24.329588, rms=0.410 (0.300%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 4 iterations, nbhd size=0, neg = 0
0530: dt=44.800000, rms=0.409 (0.097%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0531: dt=44.800000, rms=0.409 (0.047%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 10 iterations, nbhd size=1, neg = 0
0532: dt=44.800000, rms=0.408 (0.246%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 8 iterations, nbhd size=1, neg = 0
0533: dt=44.800000, rms=0.408 (0.099%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 1 iterations, nbhd size=0, neg = 0
0534: dt=44.800000, rms=0.407 (0.182%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 7 iterations, nbhd size=1, neg = 0
0535: dt=44.800000, rms=0.406 (0.192%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 2 iterations, nbhd size=0, neg = 0
0536: dt=44.800000, rms=0.406 (0.082%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 2 iterations, nbhd size=0, neg = 0
0537: dt=44.800000, rms=0.405 (0.154%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 2 iterations, nbhd size=0, neg = 0
0538: dt=44.800000, rms=0.405 (0.144%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 4 iterations, nbhd size=0, neg = 0
0539: dt=44.800000, rms=0.404 (0.066%), neg=0, invalid=762
iter 0, gcam->neg = 22
after 7 iterations, nbhd size=0, neg = 0
0540: dt=44.800000, rms=0.404 (0.074%), neg=0, invalid=762
iter 0, gcam->neg = 23
after 19 iterations, nbhd size=1, neg = 0
0541: dt=44.800000, rms=0.404 (0.008%), neg=0, invalid=762
0542: dt=19.200000, rms=0.404 (0.028%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0543: dt=44.800000, rms=0.404 (0.023%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0544: dt=44.800000, rms=0.404 (0.008%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0545: dt=44.800000, rms=0.404 (0.014%), neg=0, invalid=762
0546: dt=44.800000, rms=0.404 (0.006%), neg=0, invalid=762
0547: dt=44.800000, rms=0.404 (0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0548: dt=0.000158, rms=0.408 (0.000%), neg=0, invalid=762
0549: dt=0.000113, rms=0.408 (0.000%), neg=0, invalid=762
0550: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0551: dt=4.032000, rms=0.407 (0.041%), neg=0, invalid=762
0552: dt=4.032000, rms=0.407 (0.017%), neg=0, invalid=762
0553: dt=4.032000, rms=0.407 (0.008%), neg=0, invalid=762
0554: dt=4.032000, rms=0.407 (-0.021%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.414, neg=0, invalid=762
0555: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.414, neg=0, invalid=762
0556: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.403, neg=0, invalid=762
iter 0, gcam->neg = 546
after 16 iterations, nbhd size=1, neg = 0
0557: dt=1.144243, rms=0.394 (2.104%), neg=0, invalid=762
0558: dt=0.000023, rms=0.394 (0.000%), neg=0, invalid=762
0559: dt=0.000023, rms=0.394 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.394, neg=0, invalid=762
0560: dt=0.112000, rms=0.394 (0.080%), neg=0, invalid=762
0561: dt=0.112000, rms=0.394 (0.034%), neg=0, invalid=762
0562: dt=0.112000, rms=0.394 (0.028%), neg=0, invalid=762
0563: dt=0.112000, rms=0.394 (-0.001%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 18 minutes and 55 seconds.
mri_ca_register utimesec    9206.880341
mri_ca_register stimesec    8.049776
mri_ca_register ru_maxrss   1346376
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4284527
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63224
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    4254
mri_ca_register ru_nivcsw   14049
FSRUNTIME@ mri_ca_register  2.3154 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 20:09:13 CEST 2017

 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 

sysname  Linux
hostname tars-609
machine  x86_64

setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.38
Atlas used for the 3D morph was /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16259 (20)
mri peak = 0.12777 ( 9)
Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (236 voxels, overlap=0.274)
Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (236 voxels, peak =  9), gca=8.9
gca peak = 0.17677 (13)
mri peak = 0.11596 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (809 voxels, overlap=0.650)
Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (809 voxels, peak =  8), gca=7.6
gca peak = 0.28129 (95)
mri peak = 0.08869 (90)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (653 voxels, overlap=0.480)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (653 voxels, peak = 89), gca=88.8
gca peak = 0.16930 (96)
mri peak = 0.09128 (92)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (728 voxels, overlap=0.839)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (728 voxels, peak = 91), gca=90.7
gca peak = 0.24553 (55)
mri peak = 0.08646 (55)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, overlap=1.008)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, peak = 54), gca=54.2
gca peak = 0.30264 (59)
mri peak = 0.09387 (56)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (683 voxels, overlap=1.010)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (683 voxels, peak = 58), gca=58.1
gca peak = 0.07580 (103)
mri peak = 0.10501 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (50629 voxels, overlap=0.643)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (50629 voxels, peak = 106), gca=105.6
gca peak = 0.07714 (104)
mri peak = 0.10932 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (54747 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (54747 voxels, peak = 106), gca=105.6
gca peak = 0.09712 (58)
mri peak = 0.04631 (56)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (37176 voxels, overlap=0.948)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (37176 voxels, peak = 55), gca=54.8
gca peak = 0.11620 (58)
mri peak = 0.04428 (52)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (34228 voxels, overlap=0.967)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (34228 voxels, peak = 53), gca=53.1
gca peak = 0.30970 (66)
mri peak = 0.12527 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, peak = 66), gca=66.0
gca peak = 0.15280 (69)
mri peak = 0.11513 (69)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (735 voxels, overlap=0.590)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (735 voxels, peak = 64), gca=63.8
gca peak = 0.13902 (56)
mri peak = 0.04322 (51)
Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (21214 voxels, overlap=0.782)
Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (21214 voxels, peak = 50), gca=50.1
gca peak = 0.14777 (55)
mri peak = 0.03979 (45)
Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (21478 voxels, overlap=0.680)
Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (21478 voxels, peak = 46), gca=45.9
gca peak = 0.16765 (84)
mri peak = 0.07523 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6641 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6641 voxels, peak = 86), gca=86.1
gca peak = 0.18739 (84)
mri peak = 0.06973 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6517 voxels, overlap=0.968)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6517 voxels, peak = 85), gca=85.3
gca peak = 0.29869 (57)
mri peak = 0.07809 (56)
Left_Amygdala (18): linear fit = 0.96 x + 0.0 (474 voxels, overlap=1.036)
Left_Amygdala (18): linear fit = 0.96 x + 0.0 (474 voxels, peak = 55), gca=55.0
gca peak = 0.33601 (57)
mri peak = 0.08585 (56)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (548 voxels, overlap=1.028)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (548 voxels, peak = 60), gca=59.6
gca peak = 0.11131 (90)
mri peak = 0.06187 (91)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4898 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4898 voxels, peak = 90), gca=89.6
gca peak = 0.11793 (83)
mri peak = 0.07494 (87)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4844 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4844 voxels, peak = 87), gca=86.7
gca peak = 0.08324 (81)
mri peak = 0.07322 (75)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (1901 voxels, overlap=0.847)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (1901 voxels, peak = 78), gca=78.2
gca peak = 0.10360 (77)
mri peak = 0.06990 (79)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (1949 voxels, overlap=0.771)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (1949 voxels, peak = 74), gca=74.3
gca peak = 0.08424 (78)
mri peak = 0.08412 (85)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (14342 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (14342 voxels, peak = 82), gca=82.3
gca peak = 0.12631 (89)
mri peak = 0.07196 (91)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1692 voxels, overlap=0.824)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1692 voxels, peak = 91), gca=91.2
gca peak = 0.14500 (87)
mri peak = 0.07553 (92)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1771 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1771 voxels, peak = 88), gca=88.3
gca peak = 0.14975 (24)
mri peak = 0.03440 (20)
gca peak = 0.19357 (14)
mri peak = 0.12752 ( 8)
Fourth_Ventricle (15): linear fit = 0.50 x + 0.0 (293 voxels, overlap=0.230)
Fourth_Ventricle (15): linear fit = 0.50 x + 0.0 (293 voxels, peak =  7), gca=6.9
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.97 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.51 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.29483 ( 9)
mri peak = 0.12777 ( 9)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (236 voxels, overlap=0.999)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (236 voxels, peak =  9), gca=9.5
gca peak = 0.23941 ( 8)
mri peak = 0.11596 ( 9)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (809 voxels, overlap=0.968)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (809 voxels, peak =  8), gca=8.4
gca peak = 0.27103 (88)
mri peak = 0.08869 (90)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (653 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (653 voxels, peak = 88), gca=87.6
gca peak = 0.17605 (89)
mri peak = 0.09128 (92)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (728 voxels, overlap=1.004)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (728 voxels, peak = 89), gca=88.6
gca peak = 0.28560 (55)
mri peak = 0.08646 (55)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, overlap=1.008)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (774 voxels, peak = 54), gca=54.2
gca peak = 0.30921 (58)
mri peak = 0.09387 (56)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (683 voxels, overlap=1.012)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (683 voxels, peak = 57), gca=56.6
gca peak = 0.07610 (105)
mri peak = 0.10501 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50629 voxels, overlap=0.749)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50629 voxels, peak = 105), gca=105.0
gca peak = 0.07820 (106)
mri peak = 0.10932 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54747 voxels, overlap=0.679)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (54747 voxels, peak = 106), gca=106.0
gca peak = 0.10325 (55)
mri peak = 0.04631 (56)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37176 voxels, overlap=0.996)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37176 voxels, peak = 54), gca=54.2
gca peak = 0.12642 (53)
mri peak = 0.04428 (52)
Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (34228 voxels, overlap=0.977)
Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (34228 voxels, peak = 55), gca=55.4
gca peak = 0.30221 (66)
mri peak = 0.12527 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (943 voxels, peak = 66), gca=66.0
gca peak = 0.13199 (64)
mri peak = 0.11513 (69)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (735 voxels, overlap=0.999)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (735 voxels, peak = 64), gca=64.0
gca peak = 0.15841 (49)
mri peak = 0.04322 (51)
Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (21214 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (21214 voxels, peak = 48), gca=47.8
gca peak = 0.17082 (46)
mri peak = 0.03979 (45)
Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (21478 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (21478 voxels, peak = 49), gca=48.5
gca peak = 0.15784 (86)
mri peak = 0.07523 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6641 voxels, overlap=0.985)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6641 voxels, peak = 86), gca=85.6
gca peak = 0.15488 (85)
mri peak = 0.06973 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6517 voxels, overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6517 voxels, peak = 85), gca=84.6
gca peak = 0.31099 (56)
mri peak = 0.07809 (56)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (474 voxels, overlap=1.036)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (474 voxels, peak = 59), gca=58.5
gca peak = 0.28860 (60)
mri peak = 0.08585 (56)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (548 voxels, overlap=1.021)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (548 voxels, peak = 62), gca=61.5
gca peak = 0.10627 (89)
mri peak = 0.06187 (91)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4898 voxels, overlap=1.001)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4898 voxels, peak = 90), gca=90.3
gca peak = 0.09747 (90)
mri peak = 0.07494 (87)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4844 voxels, overlap=0.983)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4844 voxels, peak = 89), gca=88.7
gca peak = 0.08891 (78)
mri peak = 0.07322 (75)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1901 voxels, overlap=0.966)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1901 voxels, peak = 78), gca=78.0
gca peak = 0.09182 (72)
mri peak = 0.06990 (79)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1949 voxels, overlap=0.942)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1949 voxels, peak = 72), gca=72.0
gca peak = 0.07773 (85)
mri peak = 0.08412 (85)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (14342 voxels, overlap=0.714)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (14342 voxels, peak = 87), gca=87.1
gca peak = 0.11601 (91)
mri peak = 0.07196 (91)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1692 voxels, overlap=0.861)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1692 voxels, peak = 91), gca=90.5
gca peak = 0.16257 (87)
mri peak = 0.07553 (92)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1771 voxels, overlap=0.932)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1771 voxels, peak = 87), gca=86.6
gca peak = 0.26228 (13)
mri peak = 0.03440 (20)
gca peak = 0.31432 ( 8)
mri peak = 0.12752 ( 8)
Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (293 voxels, overlap=0.845)
Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (293 voxels, peak =  9), gca=8.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18140 (33)
gca peak Left_Thalamus = 0.72551 (92)
gca peak Third_Ventricle = 0.26228 (13)
gca peak CSF = 0.26789 (19)
gca peak Left_Accumbens_area = 0.54630 (57)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.26998 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82280 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.51764 (17)
gca peak WM_hypointensities = 0.07134 (78)
gca peak non_WM_hypointensities = 0.08683 (44)
gca peak Optic_Chiasm = 0.70942 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.06 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
65881 voxels changed in iteration 0 of unlikely voxel relabeling
174 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
33092 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels)
374 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 73377 changed. image ll: -2.137, PF=0.500
pass 2: 20498 changed. image ll: -2.137, PF=0.500
pass 3: 6951 changed.
pass 4: 2666 changed.
35503 voxels changed in iteration 0 of unlikely voxel relabeling
245 voxels changed in iteration 1 of unlikely voxel relabeling
5 voxels changed in iteration 2 of unlikely voxel relabeling
1 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
6082 voxels changed in iteration 0 of unlikely voxel relabeling
70 voxels changed in iteration 1 of unlikely voxel relabeling
80 voxels changed in iteration 2 of unlikely voxel relabeling
10 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
5706 voxels changed in iteration 0 of unlikely voxel relabeling
50 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
5068 voxels changed in iteration 0 of unlikely voxel relabeling
12 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3357.288614
mri_ca_label stimesec    1.563762
mri_ca_label ru_maxrss   2119452
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   660702
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63216
mri_ca_label ru_oublock  496
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    291
mri_ca_label ru_nivcsw   9996
auto-labeling took 55 minutes and 11 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/cc_up.lta 0051026 

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/norm.mgz
41778 voxels in left wm, 46425 in right wm, xrange [122, 131]
searching rotation angles z=[-3 11], y=[-8  6]

searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.7  
searching scale 1 Z rot 6.9  
searching scale 1 Z rot 7.2  
searching scale 1 Z rot 7.4  
searching scale 1 Z rot 7.7  
searching scale 1 Z rot 7.9  
searching scale 1 Z rot 8.2  
searching scale 1 Z rot 8.4  
searching scale 1 Z rot 8.7  
searching scale 1 Z rot 8.9  
searching scale 1 Z rot 9.2  
searching scale 1 Z rot 9.4  
searching scale 1 Z rot 9.7  
searching scale 1 Z rot 9.9  
searching scale 1 Z rot 10.2  
searching scale 1 Z rot 10.4  global minimum found at slice 126.2, rotations (-1.18, 3.68)
final transformation (x=126.2, yr=-1.185, zr=3.681):
 0.99772  -0.06420  -0.02064   11.75817;
 0.06418   0.99794  -0.00133   5.28474;
 0.02068   0.00000   0.99979   14.41391;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 115 111
eigenvectors:
-0.00045  -0.00520   0.99999;
-0.27178  -0.96234  -0.00512;
 0.96236  -0.27178  -0.00098;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.8 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 21:05:14 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 21:05:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 

assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.presurf.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
1819 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 56 (56), valley at 22 (22)
csf peak at 11, setting threshold to 41
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 59 (59), valley at 22 (22)
csf peak at 11, setting threshold to 43
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 50 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 21:08:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1794232 voxels in mask (pct= 10.69)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 21:08:07 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (106.0): 106.5 +- 5.1 [79.0 --> 125.0]
GM (68.0) : 66.8 +- 9.6 [30.0 --> 95.0]
setting bottom of white matter range to 76.4
setting top of gray matter range to 85.9
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
6652 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5139 filled
2669 bright non-wm voxels segmented.
2973 diagonally connected voxels added...
white matter segmentation took 1.4 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 

preserving editing changes in input volume...
auto filling took 0.44 minutes
reading wm segmentation from wm.seg.mgz...
37 voxels added to wm to prevent paths from MTL structures to cortex
2550 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 39715 voxels turned on, 38126 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  24 found -  24 modified     |    TOTAL:  24
pass   2 (xy+):   0 found -  24 modified     |    TOTAL:  24
pass   1 (xy-):  19 found -  19 modified     |    TOTAL:  43
pass   2 (xy-):   0 found -  19 modified     |    TOTAL:  43
pass   1 (yz+):  30 found -  30 modified     |    TOTAL:  73
pass   2 (yz+):   0 found -  30 modified     |    TOTAL:  73
pass   1 (yz-):  17 found -  17 modified     |    TOTAL:  90
pass   2 (yz-):   0 found -  17 modified     |    TOTAL:  90
pass   1 (xz+):  18 found -  18 modified     |    TOTAL: 108
pass   2 (xz+):   0 found -  18 modified     |    TOTAL: 108
pass   1 (xz-):  20 found -  20 modified     |    TOTAL: 128
pass   2 (xz-):   0 found -  20 modified     |    TOTAL: 128
Iteration Number : 1
pass   1 (+++):  44 found -  44 modified     |    TOTAL:  44
pass   2 (+++):   0 found -  44 modified     |    TOTAL:  44
pass   1 (+++):  24 found -  24 modified     |    TOTAL:  68
pass   2 (+++):   0 found -  24 modified     |    TOTAL:  68
pass   1 (+++):  32 found -  32 modified     |    TOTAL: 100
pass   2 (+++):   0 found -  32 modified     |    TOTAL: 100
pass   1 (+++):  18 found -  18 modified     |    TOTAL: 118
pass   2 (+++):   0 found -  18 modified     |    TOTAL: 118
Iteration Number : 1
pass   1 (++): 115 found - 115 modified     |    TOTAL: 115
pass   2 (++):   0 found - 115 modified     |    TOTAL: 115
pass   1 (+-): 102 found - 102 modified     |    TOTAL: 217
pass   2 (+-):   0 found - 102 modified     |    TOTAL: 217
pass   1 (--): 110 found - 110 modified     |    TOTAL: 327
pass   2 (--):   0 found - 110 modified     |    TOTAL: 327
pass   1 (-+):  93 found -  93 modified     |    TOTAL: 420
pass   2 (-+):   0 found -  93 modified     |    TOTAL: 420
Iteration Number : 2
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (yz+):   8 found -   8 modified     |    TOTAL:  13
pass   2 (yz+):   0 found -   8 modified     |    TOTAL:  13
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  17
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  17
pass   1 (xz+):   7 found -   7 modified     |    TOTAL:  24
pass   2 (xz+):   0 found -   7 modified     |    TOTAL:  24
pass   1 (xz-):   5 found -   5 modified     |    TOTAL:  29
pass   2 (xz-):   0 found -   5 modified     |    TOTAL:  29
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   3
pass   1 (--):   3 found -   3 modified     |    TOTAL:   6
pass   2 (--):   0 found -   3 modified     |    TOTAL:   6
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  10
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  10
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 711 (out of 625633: 0.113645)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 21:10:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88007;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.03415  -0.07150  -0.03810   8.52905;
 0.09327   1.00522   0.41638  -71.88007;
 0.00846  -0.36699   0.88428   55.23253;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2872 (min = 350, max = 1400), aspect = 1.25 (min = 0.10, max = 0.75)
need search nearby
using seed (124, 121, 145), TAL = (4.0, 17.0, 7.0)
talairach voxel to voxel transform
 0.96049   0.07119   0.00786  -3.50887;
-0.07280   0.84348  -0.40030   83.36012;
-0.03940   0.34938   0.96466  -27.83098;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (124,  121,  145) --> (4.0, 17.0, 7.0)
done.
writing output to filled.mgz...
filling took 0.6 minutes
talairach cc position changed to (4.00, 17.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(22.00, 17.00, 7.00) SRC: (108.06, 119.66, 150.14)
search lh wm seed point around talairach space (-14.00, 17.00, 7.00), SRC: (142.63, 117.04, 148.72)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 21:10:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   7
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   8
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  12
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  12
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:  12
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (--):   1 found -   1 modified     |    TOTAL:   3
pass   2 (--):   0 found -   1 modified     |    TOTAL:   3
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 16 (out of 301317: 0.005310)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 455 vertices, 512 faces
slice 50: 6527 vertices, 6789 faces
slice 60: 17670 vertices, 18173 faces
slice 70: 31184 vertices, 31623 faces
slice 80: 43810 vertices, 44301 faces
slice 90: 56963 vertices, 57396 faces
slice 100: 69489 vertices, 69975 faces
slice 110: 82002 vertices, 82475 faces
slice 120: 93775 vertices, 94260 faces
slice 130: 105416 vertices, 105880 faces
slice 140: 117248 vertices, 117737 faces
slice 150: 127597 vertices, 127998 faces
slice 160: 137191 vertices, 137568 faces
slice 170: 144700 vertices, 145018 faces
slice 180: 151345 vertices, 151621 faces
slice 190: 156060 vertices, 156303 faces
slice 200: 158460 vertices, 158552 faces
slice 210: 158460 vertices, 158552 faces
slice 220: 158460 vertices, 158552 faces
slice 230: 158460 vertices, 158552 faces
slice 240: 158460 vertices, 158552 faces
slice 250: 158460 vertices, 158552 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   158460 voxel in cpt #1: X=-92 [v=158460,e=475656,f=317104] located at (-27.342358, -18.675875, 3.579446)
For the whole surface: X=-92 [v=158460,e=475656,f=317104]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 21:10:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   7
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   7
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   9
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 15 (out of 299486: 0.005009)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 464 vertices, 547 faces
slice 50: 6638 vertices, 6919 faces
slice 60: 17456 vertices, 17904 faces
slice 70: 30814 vertices, 31277 faces
slice 80: 43547 vertices, 44011 faces
slice 90: 56485 vertices, 56910 faces
slice 100: 68926 vertices, 69418 faces
slice 110: 81186 vertices, 81660 faces
slice 120: 92576 vertices, 93033 faces
slice 130: 103729 vertices, 104187 faces
slice 140: 114844 vertices, 115291 faces
slice 150: 125370 vertices, 125773 faces
slice 160: 134664 vertices, 135052 faces
slice 170: 142422 vertices, 142750 faces
slice 180: 149147 vertices, 149443 faces
slice 190: 154020 vertices, 154249 faces
slice 200: 156741 vertices, 156836 faces
slice 210: 156808 vertices, 156880 faces
slice 220: 156808 vertices, 156880 faces
slice 230: 156808 vertices, 156880 faces
slice 240: 156808 vertices, 156880 faces
slice 250: 156808 vertices, 156880 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   156808 voxel in cpt #1: X=-72 [v=156808,e=470640,f=313760] located at (29.297466, -18.371065, -0.228923)
For the whole surface: X=-72 [v=156808,e=470640,f=313760]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 21:10:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 21:10:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

Waiting for PID 10884 of (10884 10887) to complete...
Waiting for PID 10887 of (10884 10887) to complete...

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

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...

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

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
PIDs (10884 10887) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 21:10:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 21:10:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

Waiting for PID 10929 of (10929 10932) to complete...
Waiting for PID 10932 of (10929 10932) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 49.1 mm, total surface area = 83230 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.120 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.059 (target=0.015)   
step 030: RMS=0.055 (target=0.015)   
step 035: RMS=0.050 (target=0.015)   
step 040: RMS=0.047 (target=0.015)   
step 045: RMS=0.044 (target=0.015)   
step 050: RMS=0.044 (target=0.015)   
step 055: RMS=0.043 (target=0.015)   
step 060: RMS=0.043 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.681447
mris_inflate stimesec    0.101984
mris_inflate ru_maxrss   231260
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33224
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11152
mris_inflate ru_oublock  11168
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2369
mris_inflate ru_nivcsw   3501

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 49.6 mm, total surface area = 82072 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.158 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.066 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.052 (target=0.015)   
step 035: RMS=0.049 (target=0.015)   
step 040: RMS=0.047 (target=0.015)   
step 045: RMS=0.045 (target=0.015)   
step 050: RMS=0.044 (target=0.015)   
step 055: RMS=0.043 (target=0.015)   
step 060: RMS=0.043 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.010549
mris_inflate stimesec    0.111982
mris_inflate ru_maxrss   228780
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33114
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11048
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2057
mris_inflate ru_nivcsw   3632
PIDs (10929 10932) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 21:11:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 21:11:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

Waiting for PID 11004 of (11004 11008) to complete...
Waiting for PID 11008 of (11004 11008) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.56 (0.00-->7.92) (max @ vno 111050 --> 111068)
face area 0.02 +- 0.03 (-0.21-->0.69)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.305...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.795, avgs=0
005/300: dt: 0.9000, rms radial error=175.539, avgs=0
010/300: dt: 0.9000, rms radial error=174.988, avgs=0
015/300: dt: 0.9000, rms radial error=174.265, avgs=0
020/300: dt: 0.9000, rms radial error=173.443, avgs=0
025/300: dt: 0.9000, rms radial error=172.563, avgs=0
030/300: dt: 0.9000, rms radial error=171.651, avgs=0
035/300: dt: 0.9000, rms radial error=170.723, avgs=0
040/300: dt: 0.9000, rms radial error=169.786, avgs=0
045/300: dt: 0.9000, rms radial error=168.847, avgs=0
050/300: dt: 0.9000, rms radial error=167.907, avgs=0
055/300: dt: 0.9000, rms radial error=166.970, avgs=0
060/300: dt: 0.9000, rms radial error=166.036, avgs=0
065/300: dt: 0.9000, rms radial error=165.105, avgs=0
070/300: dt: 0.9000, rms radial error=164.178, avgs=0
075/300: dt: 0.9000, rms radial error=163.257, avgs=0
080/300: dt: 0.9000, rms radial error=162.339, avgs=0
085/300: dt: 0.9000, rms radial error=161.425, avgs=0
090/300: dt: 0.9000, rms radial error=160.516, avgs=0
095/300: dt: 0.9000, rms radial error=159.611, avgs=0
100/300: dt: 0.9000, rms radial error=158.710, avgs=0
105/300: dt: 0.9000, rms radial error=157.813, avgs=0
110/300: dt: 0.9000, rms radial error=156.921, avgs=0
115/300: dt: 0.9000, rms radial error=156.033, avgs=0
120/300: dt: 0.9000, rms radial error=155.150, avgs=0
125/300: dt: 0.9000, rms radial error=154.271, avgs=0
130/300: dt: 0.9000, rms radial error=153.398, avgs=0
135/300: dt: 0.9000, rms radial error=152.531, avgs=0
140/300: dt: 0.9000, rms radial error=151.669, avgs=0
145/300: dt: 0.9000, rms radial error=150.813, avgs=0
150/300: dt: 0.9000, rms radial error=149.960, avgs=0
155/300: dt: 0.9000, rms radial error=149.113, avgs=0
160/300: dt: 0.9000, rms radial error=148.271, avgs=0
165/300: dt: 0.9000, rms radial error=147.433, avgs=0
170/300: dt: 0.9000, rms radial error=146.599, avgs=0
175/300: dt: 0.9000, rms radial error=145.771, avgs=0
180/300: dt: 0.9000, rms radial error=144.948, avgs=0
185/300: dt: 0.9000, rms radial error=144.130, avgs=0
190/300: dt: 0.9000, rms radial error=143.316, avgs=0
195/300: dt: 0.9000, rms radial error=142.507, avgs=0
200/300: dt: 0.9000, rms radial error=141.702, avgs=0
205/300: dt: 0.9000, rms radial error=140.902, avgs=0
210/300: dt: 0.9000, rms radial error=140.106, avgs=0
215/300: dt: 0.9000, rms radial error=139.314, avgs=0
220/300: dt: 0.9000, rms radial error=138.527, avgs=0
225/300: dt: 0.9000, rms radial error=137.744, avgs=0
230/300: dt: 0.9000, rms radial error=136.966, avgs=0
235/300: dt: 0.9000, rms radial error=136.192, avgs=0
240/300: dt: 0.9000, rms radial error=135.422, avgs=0
245/300: dt: 0.9000, rms radial error=134.657, avgs=0
250/300: dt: 0.9000, rms radial error=133.896, avgs=0
255/300: dt: 0.9000, rms radial error=133.139, avgs=0
260/300: dt: 0.9000, rms radial error=132.387, avgs=0
265/300: dt: 0.9000, rms radial error=131.639, avgs=0
270/300: dt: 0.9000, rms radial error=130.895, avgs=0
275/300: dt: 0.9000, rms radial error=130.155, avgs=0
280/300: dt: 0.9000, rms radial error=129.419, avgs=0
285/300: dt: 0.9000, rms radial error=128.689, avgs=0
290/300: dt: 0.9000, rms radial error=127.963, avgs=0
295/300: dt: 0.9000, rms radial error=127.241, avgs=0
300/300: dt: 0.9000, rms radial error=126.523, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18704.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 3214.10
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 345.02
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00355
epoch 4 (K=640.0), pass 1, starting sse = 26.90
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00762
final distance error %29.41
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    283.492902
mris_sphere stimesec    0.132979
mris_sphere ru_maxrss   231456
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33781
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11192
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8381
mris_sphere ru_nivcsw   19937
FSRUNTIME@ mris_sphere  0.0787 hours 1 threads

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.56 (0.00-->6.92) (max @ vno 66136 --> 67326)
face area 0.02 +- 0.03 (-0.32-->0.76)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.304...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.704, avgs=0
005/300: dt: 0.9000, rms radial error=175.448, avgs=0
010/300: dt: 0.9000, rms radial error=174.898, avgs=0
015/300: dt: 0.9000, rms radial error=174.175, avgs=0
020/300: dt: 0.9000, rms radial error=173.351, avgs=0
025/300: dt: 0.9000, rms radial error=172.469, avgs=0
030/300: dt: 0.9000, rms radial error=171.555, avgs=0
035/300: dt: 0.9000, rms radial error=170.623, avgs=0
040/300: dt: 0.9000, rms radial error=169.684, avgs=0
045/300: dt: 0.9000, rms radial error=168.743, avgs=0
050/300: dt: 0.9000, rms radial error=167.802, avgs=0
055/300: dt: 0.9000, rms radial error=166.863, avgs=0
060/300: dt: 0.9000, rms radial error=165.927, avgs=0
065/300: dt: 0.9000, rms radial error=164.995, avgs=0
070/300: dt: 0.9000, rms radial error=164.067, avgs=0
075/300: dt: 0.9000, rms radial error=163.143, avgs=0
080/300: dt: 0.9000, rms radial error=162.223, avgs=0
085/300: dt: 0.9000, rms radial error=161.307, avgs=0
090/300: dt: 0.9000, rms radial error=160.396, avgs=0
095/300: dt: 0.9000, rms radial error=159.489, avgs=0
100/300: dt: 0.9000, rms radial error=158.587, avgs=0
105/300: dt: 0.9000, rms radial error=157.689, avgs=0
110/300: dt: 0.9000, rms radial error=156.796, avgs=0
115/300: dt: 0.9000, rms radial error=155.907, avgs=0
120/300: dt: 0.9000, rms radial error=155.023, avgs=0
125/300: dt: 0.9000, rms radial error=154.148, avgs=0
130/300: dt: 0.9000, rms radial error=153.278, avgs=0
135/300: dt: 0.9000, rms radial error=152.413, avgs=0
140/300: dt: 0.9000, rms radial error=151.552, avgs=0
145/300: dt: 0.9000, rms radial error=150.697, avgs=0
150/300: dt: 0.9000, rms radial error=149.845, avgs=0
155/300: dt: 0.9000, rms radial error=148.999, avgs=0
160/300: dt: 0.9000, rms radial error=148.157, avgs=0
165/300: dt: 0.9000, rms radial error=147.321, avgs=0
170/300: dt: 0.9000, rms radial error=146.490, avgs=0
175/300: dt: 0.9000, rms radial error=145.663, avgs=0
180/300: dt: 0.9000, rms radial error=144.841, avgs=0
185/300: dt: 0.9000, rms radial error=144.023, avgs=0
190/300: dt: 0.9000, rms radial error=143.210, avgs=0
195/300: dt: 0.9000, rms radial error=142.402, avgs=0
200/300: dt: 0.9000, rms radial error=141.599, avgs=0
205/300: dt: 0.9000, rms radial error=140.800, avgs=0
210/300: dt: 0.9000, rms radial error=140.006, avgs=0
215/300: dt: 0.9000, rms radial error=139.216, avgs=0
220/300: dt: 0.9000, rms radial error=138.432, avgs=0
225/300: dt: 0.9000, rms radial error=137.651, avgs=0
230/300: dt: 0.9000, rms radial error=136.875, avgs=0
235/300: dt: 0.9000, rms radial error=136.103, avgs=0
240/300: dt: 0.9000, rms radial error=135.336, avgs=0
245/300: dt: 0.9000, rms radial error=134.573, avgs=0
250/300: dt: 0.9000, rms radial error=133.814, avgs=0
255/300: dt: 0.9000, rms radial error=133.059, avgs=0
260/300: dt: 0.9000, rms radial error=132.308, avgs=0
265/300: dt: 0.9000, rms radial error=131.562, avgs=0
270/300: dt: 0.9000, rms radial error=130.820, avgs=0
275/300: dt: 0.9000, rms radial error=130.082, avgs=0
280/300: dt: 0.9000, rms radial error=129.348, avgs=0
285/300: dt: 0.9000, rms radial error=128.618, avgs=0
290/300: dt: 0.9000, rms radial error=127.892, avgs=0
295/300: dt: 0.9000, rms radial error=127.171, avgs=0
300/300: dt: 0.9000, rms radial error=126.453, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18527.60
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
epoch 2 (K=40.0), pass 1, starting sse = 3164.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 3 (K=160.0), pass 1, starting sse = 343.26
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00598
epoch 4 (K=640.0), pass 1, starting sse = 25.61
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/12 = 0.00869
final distance error %28.86
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    289.765948
mris_sphere stimesec    0.161975
mris_sphere ru_maxrss   228976
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33168
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11032
mris_sphere ru_oublock  11080
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8945
mris_sphere ru_nivcsw   20444
FSRUNTIME@ mris_sphere  0.0799 hours 1 threads
PIDs (11004 11008) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 21:16:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 21:16:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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


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

#@# Fix Topology lh Sat Oct  7 21:16:36 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 lh 

#@# Fix Topology rh Sat Oct  7 21:16:36 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 rh 

Waiting for PID 11230 of (11230 11233) to complete...
Waiting for PID 11233 of (11230 11233) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 lh

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-92 (nv=158460, nf=317104, ne=475656, g=47)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
7112 ambiguous faces found in tessellation
segmenting defects...
49 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 4 into 3
      -merging segment 32 into 22
      -merging segment 35 into 27
      -merging segment 36 into 27
      -merging segment 44 into 41
      -merging segment 45 into 41
43 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5149  (-4.7575)
      -vertex     loglikelihood: -6.4071  (-3.2036)
      -normal dot loglikelihood: -3.6311  (-3.6311)
      -quad curv  loglikelihood: -6.4013  (-3.2007)
      Total Loglikelihood : -25.9545

CORRECTING DEFECT 0 (vertices=59, convex hull=70, v0=5710)
After retessellation of defect 0 (v0=5710), euler #=-42 (154062,460300,306196) : difference with theory (-40) = 2 

CORRECTING DEFECT 1 (vertices=31, convex hull=23, v0=6517)
After retessellation of defect 1 (v0=6517), euler #=-41 (154066,460319,306212) : difference with theory (-39) = 2 

CORRECTING DEFECT 2 (vertices=100, convex hull=123, v0=8169)
After retessellation of defect 2 (v0=8169), euler #=-40 (154097,460470,306333) : difference with theory (-38) = 2 

CORRECTING DEFECT 3 (vertices=133, convex hull=176, v0=9232)
After retessellation of defect 3 (v0=9232), euler #=-38 (154136,460683,306509) : difference with theory (-37) = 1 

CORRECTING DEFECT 4 (vertices=13, convex hull=21, v0=12496)
After retessellation of defect 4 (v0=12496), euler #=-37 (154137,460693,306519) : difference with theory (-36) = 1 

CORRECTING DEFECT 5 (vertices=25, convex hull=40, v0=17354)
After retessellation of defect 5 (v0=17354), euler #=-36 (154144,460729,306549) : difference with theory (-35) = 1 

CORRECTING DEFECT 6 (vertices=76, convex hull=67, v0=21337)
After retessellation of defect 6 (v0=21337), euler #=-35 (154155,460789,306599) : difference with theory (-34) = 1 

CORRECTING DEFECT 7 (vertices=88, convex hull=112, v0=25494)
After retessellation of defect 7 (v0=25494), euler #=-34 (154197,460967,306736) : difference with theory (-33) = 1 

CORRECTING DEFECT 8 (vertices=311, convex hull=198, v0=26629)
After retessellation of defect 8 (v0=26629), euler #=-33 (154267,461271,306971) : difference with theory (-32) = 1 

CORRECTING DEFECT 9 (vertices=14, convex hull=23, v0=34933)
After retessellation of defect 9 (v0=34933), euler #=-32 (154268,461280,306980) : difference with theory (-31) = 1 

CORRECTING DEFECT 10 (vertices=16, convex hull=34, v0=39537)
After retessellation of defect 10 (v0=39537), euler #=-31 (154270,461301,307000) : difference with theory (-30) = 1 

CORRECTING DEFECT 11 (vertices=29, convex hull=41, v0=43397)
After retessellation of defect 11 (v0=43397), euler #=-30 (154278,461340,307032) : difference with theory (-29) = 1 

CORRECTING DEFECT 12 (vertices=1007, convex hull=647, v0=43420)
XL defect detected...
After retessellation of defect 12 (v0=43420), euler #=-32 (154615,462733,308086) : difference with theory (-28) = 4 

CORRECTING DEFECT 13 (vertices=40, convex hull=78, v0=55303)
After retessellation of defect 13 (v0=55303), euler #=-31 (154634,462819,308154) : difference with theory (-27) = 4 

CORRECTING DEFECT 14 (vertices=31, convex hull=54, v0=58170)
After retessellation of defect 14 (v0=58170), euler #=-30 (154643,462868,308195) : difference with theory (-26) = 4 

CORRECTING DEFECT 15 (vertices=25, convex hull=48, v0=60856)
After retessellation of defect 15 (v0=60856), euler #=-29 (154655,462919,308235) : difference with theory (-25) = 4 

CORRECTING DEFECT 16 (vertices=55, convex hull=102, v0=61919)
After retessellation of defect 16 (v0=61919), euler #=-28 (154689,463064,308347) : difference with theory (-24) = 4 

CORRECTING DEFECT 17 (vertices=13, convex hull=37, v0=65754)
After retessellation of defect 17 (v0=65754), euler #=-27 (154690,463078,308361) : difference with theory (-23) = 4 

CORRECTING DEFECT 18 (vertices=9, convex hull=26, v0=66640)
After retessellation of defect 18 (v0=66640), euler #=-26 (154695,463101,308380) : difference with theory (-22) = 4 

CORRECTING DEFECT 19 (vertices=44, convex hull=77, v0=67758)
After retessellation of defect 19 (v0=67758), euler #=-25 (154713,463191,308453) : difference with theory (-21) = 4 

CORRECTING DEFECT 20 (vertices=38, convex hull=73, v0=68151)
After retessellation of defect 20 (v0=68151), euler #=-24 (154737,463294,308533) : difference with theory (-20) = 4 

CORRECTING DEFECT 21 (vertices=603, convex hull=466, v0=88744)
L defect detected...
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
normal vector of length zero at vertex 156729 with 3 faces
After retessellation of defect 21 (v0=88744), euler #=-22 (154865,463904,309017) : difference with theory (-19) = 3 

CORRECTING DEFECT 22 (vertices=36, convex hull=91, v0=90235)
After retessellation of defect 22 (v0=90235), euler #=-21 (154889,464015,309105) : difference with theory (-18) = 3 

CORRECTING DEFECT 23 (vertices=45, convex hull=64, v0=98098)
After retessellation of defect 23 (v0=98098), euler #=-20 (154910,464104,309174) : difference with theory (-17) = 3 

CORRECTING DEFECT 24 (vertices=47, convex hull=41, v0=102803)
After retessellation of defect 24 (v0=102803), euler #=-19 (154930,464179,309230) : difference with theory (-16) = 3 

CORRECTING DEFECT 25 (vertices=7, convex hull=12, v0=105270)
After retessellation of defect 25 (v0=105270), euler #=-18 (154930,464180,309232) : difference with theory (-15) = 3 

CORRECTING DEFECT 26 (vertices=361, convex hull=257, v0=106117)
After retessellation of defect 26 (v0=106117), euler #=-16 (154975,464465,309474) : difference with theory (-14) = 2 

CORRECTING DEFECT 27 (vertices=16, convex hull=36, v0=107444)
After retessellation of defect 27 (v0=107444), euler #=-15 (154979,464488,309494) : difference with theory (-13) = 2 

CORRECTING DEFECT 28 (vertices=38, convex hull=75, v0=107713)
After retessellation of defect 28 (v0=107713), euler #=-14 (155000,464582,309568) : difference with theory (-12) = 2 

CORRECTING DEFECT 29 (vertices=22, convex hull=26, v0=109915)
After retessellation of defect 29 (v0=109915), euler #=-13 (155004,464601,309584) : difference with theory (-11) = 2 

CORRECTING DEFECT 30 (vertices=10, convex hull=14, v0=110941)
After retessellation of defect 30 (v0=110941), euler #=-12 (155006,464609,309591) : difference with theory (-10) = 2 

CORRECTING DEFECT 31 (vertices=26, convex hull=70, v0=112326)
After retessellation of defect 31 (v0=112326), euler #=-11 (155019,464674,309644) : difference with theory (-9) = 2 

CORRECTING DEFECT 32 (vertices=34, convex hull=60, v0=113650)
After retessellation of defect 32 (v0=113650), euler #=-10 (155035,464746,309701) : difference with theory (-8) = 2 

CORRECTING DEFECT 33 (vertices=68, convex hull=45, v0=117904)
After retessellation of defect 33 (v0=117904), euler #=-9 (155044,464787,309734) : difference with theory (-7) = 2 

CORRECTING DEFECT 34 (vertices=11, convex hull=24, v0=120616)
After retessellation of defect 34 (v0=120616), euler #=-8 (155045,464799,309746) : difference with theory (-6) = 2 

CORRECTING DEFECT 35 (vertices=23, convex hull=42, v0=121483)
After retessellation of defect 35 (v0=121483), euler #=-7 (155051,464833,309775) : difference with theory (-5) = 2 

CORRECTING DEFECT 36 (vertices=48, convex hull=31, v0=123033)
After retessellation of defect 36 (v0=123033), euler #=-6 (155059,464867,309802) : difference with theory (-4) = 2 

CORRECTING DEFECT 37 (vertices=421, convex hull=340, v0=130071)
After retessellation of defect 37 (v0=130071), euler #=-3 (155191,465431,310237) : difference with theory (-3) = 0 

CORRECTING DEFECT 38 (vertices=180, convex hull=102, v0=132119)
After retessellation of defect 38 (v0=132119), euler #=-2 (155241,465626,310383) : difference with theory (-2) = 0 

CORRECTING DEFECT 39 (vertices=89, convex hull=39, v0=134913)
After retessellation of defect 39 (v0=134913), euler #=-1 (155250,465665,310414) : difference with theory (-1) = 0 

CORRECTING DEFECT 40 (vertices=42, convex hull=72, v0=148285)
After retessellation of defect 40 (v0=148285), euler #=0 (155272,465760,310488) : difference with theory (0) = 0 

CORRECTING DEFECT 41 (vertices=32, convex hull=48, v0=148798)
After retessellation of defect 41 (v0=148798), euler #=1 (155282,465808,310527) : difference with theory (1) = 0 

CORRECTING DEFECT 42 (vertices=96, convex hull=75, v0=151826)
After retessellation of defect 42 (v0=151826), euler #=2 (155300,465894,310596) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.24 (0.02-->12.52) (max @ vno 128501 --> 157949)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.24 (0.02-->12.52) (max @ vno 128501 --> 157949)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
127 mutations (33.0%), 258 crossovers (67.0%), 339 vertices were eliminated
building final representation...
3160 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=155300, nf=310596, ne=465894, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 34.2 minutes
0 defective edges
removing intersecting faces
000: 430 intersecting
001: 15 intersecting
mris_fix_topology utimesec    2054.864613
mris_fix_topology stimesec    0.252961
mris_fix_topology ru_maxrss   500724
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   55723
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22304
mris_fix_topology ru_oublock  14896
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    650
mris_fix_topology ru_nivcsw   7078
FSRUNTIME@ mris_fix_topology lh  0.5705 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051026 rh

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-72 (nv=156808, nf=313760, ne=470640, g=37)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
6584 ambiguous faces found in tessellation
segmenting defects...
59 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 24 into 20
      -merging segment 33 into 29
57 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5286  (-4.7643)
      -vertex     loglikelihood: -6.4769  (-3.2384)
      -normal dot loglikelihood: -3.5897  (-3.5897)
      -quad curv  loglikelihood: -6.5179  (-3.2590)
      Total Loglikelihood : -26.1131

CORRECTING DEFECT 0 (vertices=33, convex hull=41, v0=1205)
After retessellation of defect 0 (v0=1205), euler #=-56 (152809,456929,304064) : difference with theory (-54) = 2 

CORRECTING DEFECT 1 (vertices=8, convex hull=32, v0=1674)
After retessellation of defect 1 (v0=1674), euler #=-55 (152810,456942,304077) : difference with theory (-53) = 2 

CORRECTING DEFECT 2 (vertices=189, convex hull=92, v0=2699)
After retessellation of defect 2 (v0=2699), euler #=-54 (152855,457119,304210) : difference with theory (-52) = 2 

CORRECTING DEFECT 3 (vertices=178, convex hull=91, v0=3356)
After retessellation of defect 3 (v0=3356), euler #=-53 (152871,457212,304288) : difference with theory (-51) = 2 

CORRECTING DEFECT 4 (vertices=65, convex hull=46, v0=3973)
After retessellation of defect 4 (v0=3973), euler #=-52 (152878,457251,304321) : difference with theory (-50) = 2 

CORRECTING DEFECT 5 (vertices=18, convex hull=23, v0=4949)
After retessellation of defect 5 (v0=4949), euler #=-51 (152879,457261,304331) : difference with theory (-49) = 2 

CORRECTING DEFECT 6 (vertices=60, convex hull=47, v0=6630)
After retessellation of defect 6 (v0=6630), euler #=-50 (152886,457304,304368) : difference with theory (-48) = 2 

CORRECTING DEFECT 7 (vertices=80, convex hull=77, v0=7155)
After retessellation of defect 7 (v0=7155), euler #=-49 (152909,457408,304450) : difference with theory (-47) = 2 

CORRECTING DEFECT 8 (vertices=18, convex hull=23, v0=8395)
After retessellation of defect 8 (v0=8395), euler #=-48 (152912,457420,304460) : difference with theory (-46) = 2 

CORRECTING DEFECT 9 (vertices=223, convex hull=129, v0=8450)
After retessellation of defect 9 (v0=8450), euler #=-47 (152969,457653,304637) : difference with theory (-45) = 2 

CORRECTING DEFECT 10 (vertices=12, convex hull=38, v0=8895)
After retessellation of defect 10 (v0=8895), euler #=-46 (152971,457673,304656) : difference with theory (-44) = 2 

CORRECTING DEFECT 11 (vertices=49, convex hull=62, v0=12465)
After retessellation of defect 11 (v0=12465), euler #=-45 (152996,457773,304732) : difference with theory (-43) = 2 

CORRECTING DEFECT 12 (vertices=33, convex hull=30, v0=13790)
After retessellation of defect 12 (v0=13790), euler #=-44 (153003,457805,304758) : difference with theory (-42) = 2 

CORRECTING DEFECT 13 (vertices=15, convex hull=31, v0=16243)
After retessellation of defect 13 (v0=16243), euler #=-43 (153006,457825,304776) : difference with theory (-41) = 2 

CORRECTING DEFECT 14 (vertices=58, convex hull=77, v0=18661)
After retessellation of defect 14 (v0=18661), euler #=-42 (153028,457924,304854) : difference with theory (-40) = 2 

CORRECTING DEFECT 15 (vertices=89, convex hull=87, v0=19916)
After retessellation of defect 15 (v0=19916), euler #=-41 (153050,458028,304937) : difference with theory (-39) = 2 

CORRECTING DEFECT 16 (vertices=37, convex hull=83, v0=19962)
After retessellation of defect 16 (v0=19962), euler #=-40 (153068,458114,305006) : difference with theory (-38) = 2 

CORRECTING DEFECT 17 (vertices=6, convex hull=29, v0=21079)
After retessellation of defect 17 (v0=21079), euler #=-39 (153070,458128,305019) : difference with theory (-37) = 2 

CORRECTING DEFECT 18 (vertices=19, convex hull=42, v0=25106)
After retessellation of defect 18 (v0=25106), euler #=-38 (153076,458159,305045) : difference with theory (-36) = 2 

CORRECTING DEFECT 19 (vertices=68, convex hull=66, v0=26338)
After retessellation of defect 19 (v0=26338), euler #=-37 (153087,458218,305094) : difference with theory (-35) = 2 

CORRECTING DEFECT 20 (vertices=37, convex hull=76, v0=26869)
After retessellation of defect 20 (v0=26869), euler #=-35 (153099,458286,305152) : difference with theory (-34) = 1 

CORRECTING DEFECT 21 (vertices=101, convex hull=112, v0=27908)
After retessellation of defect 21 (v0=27908), euler #=-34 (153120,458406,305252) : difference with theory (-33) = 1 

CORRECTING DEFECT 22 (vertices=12, convex hull=20, v0=28273)
After retessellation of defect 22 (v0=28273), euler #=-33 (153122,458419,305264) : difference with theory (-32) = 1 

CORRECTING DEFECT 23 (vertices=235, convex hull=114, v0=30506)
After retessellation of defect 23 (v0=30506), euler #=-32 (153158,458579,305389) : difference with theory (-31) = 1 

CORRECTING DEFECT 24 (vertices=146, convex hull=123, v0=37008)
After retessellation of defect 24 (v0=37008), euler #=-31 (153203,458762,305528) : difference with theory (-30) = 1 

CORRECTING DEFECT 25 (vertices=6, convex hull=19, v0=38210)
After retessellation of defect 25 (v0=38210), euler #=-30 (153203,458769,305536) : difference with theory (-29) = 1 

CORRECTING DEFECT 26 (vertices=25, convex hull=60, v0=43067)
After retessellation of defect 26 (v0=43067), euler #=-29 (153211,458816,305576) : difference with theory (-28) = 1 

CORRECTING DEFECT 27 (vertices=60, convex hull=93, v0=43109)
After retessellation of defect 27 (v0=43109), euler #=-28 (153238,458939,305673) : difference with theory (-27) = 1 

CORRECTING DEFECT 28 (vertices=233, convex hull=155, v0=45713)
After retessellation of defect 28 (v0=45713), euler #=-26 (153313,459252,305913) : difference with theory (-26) = 0 

CORRECTING DEFECT 29 (vertices=22, convex hull=44, v0=47663)
After retessellation of defect 29 (v0=47663), euler #=-25 (153322,459295,305948) : difference with theory (-25) = 0 

CORRECTING DEFECT 30 (vertices=29, convex hull=44, v0=47762)
After retessellation of defect 30 (v0=47762), euler #=-24 (153331,459338,305983) : difference with theory (-24) = 0 

CORRECTING DEFECT 31 (vertices=68, convex hull=81, v0=51368)
After retessellation of defect 31 (v0=51368), euler #=-23 (153355,459440,306062) : difference with theory (-23) = 0 

CORRECTING DEFECT 32 (vertices=167, convex hull=188, v0=61072)
After retessellation of defect 32 (v0=61072), euler #=-22 (153415,459708,306271) : difference with theory (-22) = 0 

CORRECTING DEFECT 33 (vertices=44, convex hull=48, v0=61524)
After retessellation of defect 33 (v0=61524), euler #=-21 (153428,459765,306316) : difference with theory (-21) = 0 

CORRECTING DEFECT 34 (vertices=8, convex hull=18, v0=63835)
After retessellation of defect 34 (v0=63835), euler #=-20 (153428,459770,306322) : difference with theory (-20) = 0 

CORRECTING DEFECT 35 (vertices=89, convex hull=53, v0=63854)
After retessellation of defect 35 (v0=63854), euler #=-19 (153456,459874,306399) : difference with theory (-19) = 0 

CORRECTING DEFECT 36 (vertices=36, convex hull=23, v0=68372)
After retessellation of defect 36 (v0=68372), euler #=-18 (153462,459899,306419) : difference with theory (-18) = 0 

CORRECTING DEFECT 37 (vertices=156, convex hull=89, v0=75863)
After retessellation of defect 37 (v0=75863), euler #=-17 (153508,460079,306554) : difference with theory (-17) = 0 

CORRECTING DEFECT 38 (vertices=28, convex hull=79, v0=76369)
After retessellation of defect 38 (v0=76369), euler #=-16 (153522,460149,306611) : difference with theory (-16) = 0 

CORRECTING DEFECT 39 (vertices=311, convex hull=129, v0=84492)
After retessellation of defect 39 (v0=84492), euler #=-15 (153579,460388,306794) : difference with theory (-15) = 0 

CORRECTING DEFECT 40 (vertices=18, convex hull=29, v0=92476)
After retessellation of defect 40 (v0=92476), euler #=-14 (153581,460405,306810) : difference with theory (-14) = 0 

CORRECTING DEFECT 41 (vertices=19, convex hull=28, v0=101106)
After retessellation of defect 41 (v0=101106), euler #=-13 (153587,460431,306831) : difference with theory (-13) = 0 

CORRECTING DEFECT 42 (vertices=55, convex hull=72, v0=102304)
After retessellation of defect 42 (v0=102304), euler #=-12 (153608,460527,306907) : difference with theory (-12) = 0 

CORRECTING DEFECT 43 (vertices=9, convex hull=19, v0=106950)
After retessellation of defect 43 (v0=106950), euler #=-11 (153609,460534,306914) : difference with theory (-11) = 0 

CORRECTING DEFECT 44 (vertices=318, convex hull=92, v0=109744)
After retessellation of defect 44 (v0=109744), euler #=-10 (153636,460659,307013) : difference with theory (-10) = 0 

CORRECTING DEFECT 45 (vertices=54, convex hull=34, v0=111265)
After retessellation of defect 45 (v0=111265), euler #=-9 (153647,460705,307049) : difference with theory (-9) = 0 

CORRECTING DEFECT 46 (vertices=9, convex hull=26, v0=114576)
After retessellation of defect 46 (v0=114576), euler #=-8 (153651,460724,307065) : difference with theory (-8) = 0 

CORRECTING DEFECT 47 (vertices=121, convex hull=57, v0=116644)
After retessellation of defect 47 (v0=116644), euler #=-7 (153660,460769,307102) : difference with theory (-7) = 0 

CORRECTING DEFECT 48 (vertices=22, convex hull=36, v0=116750)
After retessellation of defect 48 (v0=116750), euler #=-6 (153663,460790,307121) : difference with theory (-6) = 0 

CORRECTING DEFECT 49 (vertices=50, convex hull=83, v0=116903)
After retessellation of defect 49 (v0=116903), euler #=-5 (153698,460930,307227) : difference with theory (-5) = 0 

CORRECTING DEFECT 50 (vertices=64, convex hull=84, v0=122189)
After retessellation of defect 50 (v0=122189), euler #=-4 (153732,461068,307332) : difference with theory (-4) = 0 

CORRECTING DEFECT 51 (vertices=56, convex hull=95, v0=122482)
After retessellation of defect 51 (v0=122482), euler #=-3 (153766,461211,307442) : difference with theory (-3) = 0 

CORRECTING DEFECT 52 (vertices=25, convex hull=76, v0=122577)
After retessellation of defect 52 (v0=122577), euler #=-2 (153781,461287,307504) : difference with theory (-2) = 0 

CORRECTING DEFECT 53 (vertices=19, convex hull=22, v0=142391)
After retessellation of defect 53 (v0=142391), euler #=-1 (153781,461293,307511) : difference with theory (-1) = 0 

CORRECTING DEFECT 54 (vertices=16, convex hull=29, v0=150272)
After retessellation of defect 54 (v0=150272), euler #=0 (153783,461306,307523) : difference with theory (0) = 0 

CORRECTING DEFECT 55 (vertices=39, convex hull=34, v0=155582)
After retessellation of defect 55 (v0=155582), euler #=1 (153789,461336,307548) : difference with theory (1) = 0 

CORRECTING DEFECT 56 (vertices=37, convex hull=66, v0=156639)
After retessellation of defect 56 (v0=156639), euler #=2 (153799,461391,307594) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.03-->7.59) (max @ vno 20310 --> 25806)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.03-->7.59) (max @ vno 20310 --> 25806)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
180 mutations (34.4%), 344 crossovers (65.6%), 83 vertices were eliminated
building final representation...
3009 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=153799, nf=307594, ne=461391, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 28.1 minutes
0 defective edges
removing intersecting faces
000: 339 intersecting
001: 11 intersecting
002: 3 intersecting
mris_fix_topology utimesec    1684.829866
mris_fix_topology stimesec    0.190970
mris_fix_topology ru_maxrss   480080
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56173
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22072
mris_fix_topology ru_oublock  14800
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    738
mris_fix_topology ru_nivcsw   4475
FSRUNTIME@ mris_fix_topology rh  0.4678 hours 1 threads
PIDs (11230 11233) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 155300 - 465894 + 310596 = 2 --> 0 holes
      F =2V-4:          310596 = 310600-4 (0)
      2E=3F:            931788 = 931788 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 153799 - 461391 + 307594 = 2 --> 0 holes
      F =2V-4:          307594 = 307598-4 (0)
      2E=3F:            922782 = 922782 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 129 intersecting
001: 17 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 21 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 21:51:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 21:51:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 rh 

Waiting for PID 12593 of (12593 12596) to complete...
Waiting for PID 12596 of (12593 12596) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 lh

using white.preaparc as white matter name...
only generating white matter surface
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
26893 bright wm thresholded.
2956 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig...
computing class statistics...
border white:    289174 voxels (1.72%)
border gray      336461 voxels (2.01%)
WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0]
GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70)
setting MAX_BORDER_WHITE to 112.4 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 41.4 (was 40)
setting MAX_GRAY to 93.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->6.56) (max @ vno 36261 --> 154244)
face area 0.28 +- 0.13 (0.00-->3.54)
mean absolute distance = 0.61 +- 0.76
4682 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-7.8,    GM=62+-7.8
mean inside = 92.0, mean outside = 71.1
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=76.7, 95 (95) missing vertices, mean dist 0.3 [0.5 (%37.8)->0.7 (%62.2))]
%80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.08-->6.78) (max @ vno 36261 --> 154244)
face area 0.28 +- 0.13 (0.00-->3.18)
mean absolute distance = 0.31 +- 0.51
4227 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4237459.0, rms=10.978
001: dt: 0.5000, sse=2323469.2, rms=7.582 (30.929%)
002: dt: 0.5000, sse=1608527.0, rms=5.804 (23.458%)
003: dt: 0.5000, sse=1284634.9, rms=4.777 (17.687%)
004: dt: 0.5000, sse=1140978.5, rms=4.242 (11.204%)
005: dt: 0.5000, sse=1085455.5, rms=3.992 (5.901%)
006: dt: 0.5000, sse=1054390.9, rms=3.876 (2.888%)
rms = 3.83, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=1043708.2, rms=3.827 (1.286%)
008: dt: 0.2500, sse=793741.1, rms=2.394 (37.429%)
009: dt: 0.2500, sse=741274.1, rms=1.986 (17.073%)
010: dt: 0.2500, sse=727388.1, rms=1.856 (6.499%)
011: dt: 0.2500, sse=719200.0, rms=1.779 (4.186%)
rms = 1.74, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=715649.3, rms=1.741 (2.124%)
013: dt: 0.1250, sse=704674.8, rms=1.622 (6.850%)
rms = 1.61, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=703162.6, rms=1.608 (0.875%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=79.9, 91 (27) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.2 (%26.5))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.11-->6.65) (max @ vno 36261 --> 154244)
face area 0.35 +- 0.16 (0.00-->4.35)
mean absolute distance = 0.23 +- 0.37
3655 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1467843.6, rms=4.803
015: dt: 0.5000, sse=1102273.4, rms=3.274 (31.842%)
rms = 3.62, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=947479.0, rms=2.360 (27.927%)
017: dt: 0.2500, sse=882242.4, rms=1.835 (22.254%)
018: dt: 0.2500, sse=859392.9, rms=1.590 (13.343%)
019: dt: 0.2500, sse=849371.6, rms=1.507 (5.211%)
020: dt: 0.2500, sse=845542.6, rms=1.447 (4.006%)
rms = 1.42, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=843350.0, rms=1.419 (1.882%)
022: dt: 0.1250, sse=835869.6, rms=1.341 (5.512%)
rms = 1.33, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=835307.7, rms=1.334 (0.500%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
mean border=81.8, 86 (16) missing vertices, mean dist -0.1 [0.3 (%65.1)->0.2 (%34.9))]
%89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.24 (0.07-->6.57) (max @ vno 36261 --> 154244)
face area 0.34 +- 0.16 (0.00-->4.30)
mean absolute distance = 0.21 +- 0.32
3171 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1013774.0, rms=2.919
rms = 2.87, time step reduction 1 of 3 to 0.250...
024: dt: 0.5000, sse=1009442.2, rms=2.874 (1.563%)
025: dt: 0.2500, sse=853382.6, rms=1.682 (41.470%)
026: dt: 0.2500, sse=818416.8, rms=1.383 (17.754%)
rms = 1.36, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=817121.0, rms=1.365 (1.358%)
028: dt: 0.1250, sse=817001.8, rms=1.202 (11.905%)
rms = 1.19, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=802714.8, rms=1.190 (1.021%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=82.5, 85 (12) missing vertices, mean dist -0.0 [0.2 (%54.7)->0.2 (%45.3))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=823905.6, rms=1.575
rms = 1.93, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=785920.6, rms=1.096 (30.433%)
031: dt: 0.2500, sse=773736.1, rms=0.891 (18.653%)
rms = 0.89, time step reduction 2 of 3 to 0.125...
rms = 0.89, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=773111.1, rms=0.887 (0.540%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7713 vertices
erasing segment 1 (vno[0] = 108007)
erasing segment 2 (vno[0] = 109207)
erasing segment 3 (vno[0] = 113599)
erasing segment 4 (vno[0] = 113687)
erasing segment 5 (vno[0] = 114755)
erasing segment 6 (vno[0] = 114813)
erasing segment 7 (vno[0] = 116914)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.04-->6.58) (max @ vno 36261 --> 154244)
face area 0.33 +- 0.16 (0.00-->4.20)
refinement took 5.9 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051026 rh

using white.preaparc as white matter name...
only generating white matter surface
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
26893 bright wm thresholded.
2956 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig...
computing class statistics...
border white:    289174 voxels (1.72%)
border gray      336461 voxels (2.01%)
WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0]
GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70)
setting MAX_BORDER_WHITE to 111.4 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 41.4 (was 40)
setting MAX_GRAY to 92.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->3.78) (max @ vno 153384 --> 153404)
face area 0.28 +- 0.12 (0.00-->2.21)
mean absolute distance = 0.61 +- 0.73
4484 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-7.0,    GM=62+-7.0
mean inside = 91.6, mean outside = 70.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=76.3, 37 (37) missing vertices, mean dist 0.3 [0.5 (%38.2)->0.7 (%61.8))]
%79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.10-->3.59) (max @ vno 7675 --> 8624)
face area 0.28 +- 0.13 (0.00-->2.57)
mean absolute distance = 0.30 +- 0.51
4050 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4253042.5, rms=11.085
001: dt: 0.5000, sse=2342605.0, rms=7.674 (30.772%)
002: dt: 0.5000, sse=1607994.1, rms=5.849 (23.780%)
003: dt: 0.5000, sse=1275656.0, rms=4.791 (18.092%)
004: dt: 0.5000, sse=1131521.4, rms=4.254 (11.209%)
005: dt: 0.5000, sse=1070876.5, rms=3.997 (6.041%)
006: dt: 0.5000, sse=1048886.5, rms=3.902 (2.378%)
007: dt: 0.5000, sse=1036944.9, rms=3.845 (1.462%)
rms = 3.82, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=1032159.2, rms=3.821 (0.607%)
009: dt: 0.2500, sse=782325.4, rms=2.380 (37.723%)
010: dt: 0.2500, sse=729933.4, rms=1.959 (17.661%)
011: dt: 0.2500, sse=718221.4, rms=1.849 (5.641%)
012: dt: 0.2500, sse=710742.1, rms=1.776 (3.955%)
rms = 1.74, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=708455.8, rms=1.745 (1.742%)
014: dt: 0.1250, sse=696465.6, rms=1.624 (6.931%)
rms = 1.61, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=695435.2, rms=1.611 (0.779%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=79.5, 55 (4) missing vertices, mean dist -0.2 [0.3 (%73.4)->0.2 (%26.6))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.07-->3.53) (max @ vno 7675 --> 8624)
face area 0.35 +- 0.16 (0.00-->3.61)
mean absolute distance = 0.23 +- 0.38
3652 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1445717.5, rms=4.762
016: dt: 0.5000, sse=1086688.9, rms=3.250 (31.744%)
rms = 3.64, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=937696.7, rms=2.336 (28.130%)
018: dt: 0.2500, sse=875905.9, rms=1.838 (21.333%)
019: dt: 0.2500, sse=853190.2, rms=1.606 (12.625%)
020: dt: 0.2500, sse=845931.8, rms=1.529 (4.758%)
021: dt: 0.2500, sse=840943.7, rms=1.464 (4.291%)
rms = 1.43, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=839135.0, rms=1.434 (2.029%)
023: dt: 0.1250, sse=831255.1, rms=1.352 (5.692%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=830365.5, rms=1.343 (0.709%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=81.5, 61 (2) missing vertices, mean dist -0.1 [0.3 (%65.2)->0.2 (%34.8))]
%88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.24 (0.10-->3.54) (max @ vno 84062 --> 82939)
face area 0.34 +- 0.16 (0.00-->3.65)
mean absolute distance = 0.21 +- 0.32
3054 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1003716.2, rms=2.898
rms = 2.90, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=885804.0, rms=2.091 (27.832%)
026: dt: 0.2500, sse=818895.2, rms=1.416 (32.311%)
027: dt: 0.2500, sse=808405.7, rms=1.290 (8.842%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=806505.0, rms=1.261 (2.308%)
029: dt: 0.1250, sse=799436.8, rms=1.195 (5.250%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=799887.6, rms=1.197 (-0.214%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=82.1, 82 (2) missing vertices, mean dist -0.0 [0.2 (%54.3)->0.2 (%45.7))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=822026.9, rms=1.592
rms = 1.95, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=784586.8, rms=1.124 (29.395%)
032: dt: 0.2500, sse=775378.9, rms=0.910 (19.038%)
rms = 0.91, time step reduction 2 of 3 to 0.125...
rms = 0.90, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=772723.5, rms=0.905 (0.610%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 7531 vertices
erasing segment 1 (vno[0] = 108009)
erasing segment 2 (vno[0] = 110000)
erasing segment 3 (vno[0] = 110055)
erasing segment 4 (vno[0] = 110085)
erasing segment 5 (vno[0] = 110101)
erasing segment 6 (vno[0] = 111126)
erasing segment 7 (vno[0] = 112181)
erasing segment 8 (vno[0] = 113450)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.03-->3.78) (max @ vno 153384 --> 153404)
face area 0.34 +- 0.15 (0.00-->3.66)
refinement took 6.1 minutes
PIDs (12593 12596) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 21:57:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 21:57:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

Waiting for PID 12824 of (12824 12827) to complete...
Waiting for PID 12827 of (12824 12827) to complete...

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

smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...

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

smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
PIDs (12824 12827) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 21:57:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 21:57:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 12871 of (12871 12874) to complete...
Waiting for PID 12874 of (12871 12874) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.3 mm, total surface area = 94212 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.044 (target=0.015)   
step 035: RMS=0.038 (target=0.015)   
step 040: RMS=0.033 (target=0.015)   
step 045: RMS=0.030 (target=0.015)   
step 050: RMS=0.028 (target=0.015)   
step 055: RMS=0.026 (target=0.015)   
step 060: RMS=0.025 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    49.081538
mris_inflate stimesec    0.117982
mris_inflate ru_maxrss   226956
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32786
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10928
mris_inflate ru_oublock  12160
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2320
mris_inflate ru_nivcsw   3616

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 49.7 mm, total surface area = 93561 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.043 (target=0.015)   
step 035: RMS=0.037 (target=0.015)   
step 040: RMS=0.032 (target=0.015)   
step 045: RMS=0.029 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    48.612609
mris_inflate stimesec    0.110983
mris_inflate ru_maxrss   224584
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32192
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  12048
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2069
mris_inflate ru_nivcsw   3463
PIDs (12871 12874) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 21:58:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sat Oct  7 21:58:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf

 mris_curvature -w rh.white.preaparc 

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

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

cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd
Waiting for PID 12982 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 12985 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 12988 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 12991 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 12994 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 12997 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 13000 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 13003 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 13006 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 13009 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 13013 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...
Waiting for PID 13019 of (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = -4.936*4pi (-62.025) --> 6 handles
ICI = 186.7, FI = 1914.6, variation=30438.390
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.

 rm -f lh.white.H


 ln -s lh.white.preaparc.H lh.white.H


 rm -f lh.white.K


 ln -s lh.white.preaparc.K lh.white.K


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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
201 vertices thresholded to be in k1 ~ [-0.57 0.65], k2 ~ [-0.15 0.21]
total integrated curvature = 0.363*4pi (4.556) --> 1 handles
ICI = 1.6, FI = 9.8, variation=170.629
173 vertices thresholded to be in [-0.06 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
118 vertices thresholded to be in [-0.20 0.25]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = -9.204*4pi (-115.662) --> 10 handles
ICI = 184.5, FI = 1900.3, variation=30243.861
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.

 rm -f rh.white.H


 ln -s rh.white.preaparc.H rh.white.H


 rm -f rh.white.K


 ln -s rh.white.preaparc.K rh.white.K


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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
171 vertices thresholded to be in k1 ~ [-0.24 0.43], k2 ~ [-0.13 0.06]
total integrated curvature = 0.570*4pi (7.159) --> 0 handles
ICI = 1.5, FI = 10.3, variation=172.318
137 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
150 vertices thresholded to be in [-0.13 0.18]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022
done.
PIDs (12982 12985 12988 12991 12994 12997 13000 13003 13006 13009 13013 13019) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 21:59:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051026 lh curv sulc 

             Toggling save flag on curvature files                       [ ok ]
                 Outputting results using filestem   [ ../stats/lh.curv.stats ]
             Toggling save flag on curvature files                       [ ok ]
                                   Setting surface      [ 0051026/lh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 311 ]
Gb_filter = 0

WARN:    S lookup   min:                          -1.058048
WARN:    S explicit min:                          0.000000	vertex = 26

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 21:59:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051026 rh curv sulc 

             Toggling save flag on curvature files                       [ ok ]
                 Outputting results using filestem   [ ../stats/rh.curv.stats ]
             Toggling save flag on curvature files                       [ ok ]
                                   Setting surface      [ 0051026/rh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 309 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.592156
WARN:    S explicit min:                          0.000000	vertex = 213
#--------------------------------------------
#@# Sphere lh Sat Oct  7 21:59:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 21:59:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 13181 of (13181 13185) to complete...
Waiting for PID 13185 of (13181 13185) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.285...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.46
pass 1: epoch 2 of 3 starting distance error %21.46
unfolding complete - removing small folds...
starting distance error %21.40
removing remaining folds...
final distance error %21.42
MRISunfold() return, current seed 1234
-01: dt=0.0000, 203 negative triangles
195: dt=0.9900, 203 negative triangles
196: dt=0.9900, 97 negative triangles
197: dt=0.9900, 77 negative triangles
198: dt=0.9900, 60 negative triangles
199: dt=0.9900, 55 negative triangles
200: dt=0.9900, 53 negative triangles
201: dt=0.9900, 47 negative triangles
202: dt=0.9900, 50 negative triangles
203: dt=0.9900, 50 negative triangles
204: dt=0.9900, 46 negative triangles
205: dt=0.9900, 45 negative triangles
206: dt=0.9900, 37 negative triangles
207: dt=0.9900, 44 negative triangles
208: dt=0.9900, 37 negative triangles
209: dt=0.9900, 31 negative triangles
210: dt=0.9900, 35 negative triangles
211: dt=0.9900, 33 negative triangles
212: dt=0.9900, 28 negative triangles
213: dt=0.9900, 33 negative triangles
214: dt=0.9900, 31 negative triangles
215: dt=0.9900, 25 negative triangles
216: dt=0.9900, 30 negative triangles
217: dt=0.9900, 28 negative triangles
218: dt=0.9900, 28 negative triangles
219: dt=0.9900, 32 negative triangles
220: dt=0.9900, 29 negative triangles
221: dt=0.9900, 24 negative triangles
222: dt=0.9900, 23 negative triangles
223: dt=0.9900, 20 negative triangles
224: dt=0.9900, 19 negative triangles
225: dt=0.9900, 17 negative triangles
226: dt=0.9900, 20 negative triangles
227: dt=0.9900, 18 negative triangles
228: dt=0.9900, 15 negative triangles
229: dt=0.9900, 17 negative triangles
230: dt=0.9900, 17 negative triangles
231: dt=0.9900, 16 negative triangles
232: dt=0.9900, 15 negative triangles
233: dt=0.9900, 18 negative triangles
234: dt=0.9900, 18 negative triangles
235: dt=0.9900, 16 negative triangles
236: dt=0.9900, 17 negative triangles
237: dt=0.9900, 16 negative triangles
238: dt=0.9405, 18 negative triangles
239: dt=0.9405, 17 negative triangles
240: dt=0.9405, 16 negative triangles
241: dt=0.9405, 18 negative triangles
242: dt=0.9405, 20 negative triangles
243: dt=0.9405, 16 negative triangles
244: dt=0.9405, 20 negative triangles
245: dt=0.9405, 16 negative triangles
246: dt=0.9405, 21 negative triangles
247: dt=0.9405, 16 negative triangles
248: dt=0.8935, 17 negative triangles
249: dt=0.8935, 14 negative triangles
250: dt=0.8935, 10 negative triangles
251: dt=0.8935, 15 negative triangles
252: dt=0.8935, 11 negative triangles
253: dt=0.8935, 13 negative triangles
254: dt=0.8935, 17 negative triangles
255: dt=0.8935, 14 negative triangles
256: dt=0.8935, 9 negative triangles
257: dt=0.8935, 13 negative triangles
258: dt=0.8935, 12 negative triangles
259: dt=0.8935, 13 negative triangles
260: dt=0.8935, 17 negative triangles
261: dt=0.8935, 13 negative triangles
262: dt=0.8935, 10 negative triangles
263: dt=0.8935, 12 negative triangles
264: dt=0.8935, 9 negative triangles
265: dt=0.8935, 13 negative triangles
266: dt=0.8488, 13 negative triangles
267: dt=0.8488, 17 negative triangles
268: dt=0.8488, 13 negative triangles
269: dt=0.8488, 9 negative triangles
270: dt=0.8488, 13 negative triangles
271: dt=0.8488, 9 negative triangles
272: dt=0.8488, 13 negative triangles
273: dt=0.8488, 11 negative triangles
274: dt=0.8488, 14 negative triangles
275: dt=0.8488, 17 negative triangles
276: dt=0.8064, 13 negative triangles
277: dt=0.8064, 9 negative triangles
278: dt=0.8064, 11 negative triangles
279: dt=0.8064, 11 negative triangles
280: dt=0.8064, 10 negative triangles
281: dt=0.8064, 13 negative triangles
282: dt=0.8064, 12 negative triangles
283: dt=0.8064, 9 negative triangles
284: dt=0.8064, 12 negative triangles
285: dt=0.8064, 10 negative triangles
286: dt=0.7660, 10 negative triangles
287: dt=0.7660, 9 negative triangles
288: dt=0.7660, 10 negative triangles
289: dt=0.7660, 7 negative triangles
290: dt=0.7660, 11 negative triangles
291: dt=0.7660, 8 negative triangles
292: dt=0.7660, 8 negative triangles
293: dt=0.7660, 10 negative triangles
294: dt=0.7660, 8 negative triangles
295: dt=0.7660, 6 negative triangles
296: dt=0.7660, 10 negative triangles
297: dt=0.7660, 9 negative triangles
298: dt=0.7660, 9 negative triangles
299: dt=0.7660, 12 negative triangles
300: dt=0.7660, 11 negative triangles
301: dt=0.7660, 4 negative triangles
302: dt=0.7660, 5 negative triangles
303: dt=0.7660, 5 negative triangles
304: dt=0.7660, 4 negative triangles
305: dt=0.7660, 3 negative triangles
306: dt=0.7660, 2 negative triangles
307: dt=0.7660, 3 negative triangles
308: dt=0.7660, 2 negative triangles
309: dt=0.7660, 2 negative triangles
310: dt=0.7660, 1 negative triangles
311: dt=0.7660, 1 negative triangles
312: dt=0.7660, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.11 hours
mris_sphere utimesec    3981.195766
mris_sphere stimesec    1.239811
mris_sphere ru_maxrss   319176
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55980
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11040
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    143430
mris_sphere ru_nivcsw   325635
FSRUNTIME@ mris_sphere  1.1054 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.283...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.14
pass 1: epoch 2 of 3 starting distance error %21.14
unfolding complete - removing small folds...
starting distance error %21.08
removing remaining folds...
final distance error %21.09
MRISunfold() return, current seed 1234
-01: dt=0.0000, 180 negative triangles
190: dt=0.9900, 180 negative triangles
191: dt=0.9900, 72 negative triangles
192: dt=0.9900, 62 negative triangles
193: dt=0.9900, 51 negative triangles
194: dt=0.9900, 51 negative triangles
195: dt=0.9900, 43 negative triangles
196: dt=0.9900, 38 negative triangles
197: dt=0.9900, 40 negative triangles
198: dt=0.9900, 33 negative triangles
199: dt=0.9900, 40 negative triangles
200: dt=0.9900, 43 negative triangles
201: dt=0.9900, 42 negative triangles
202: dt=0.9900, 41 negative triangles
203: dt=0.9900, 38 negative triangles
204: dt=0.9900, 37 negative triangles
205: dt=0.9900, 39 negative triangles
206: dt=0.9900, 34 negative triangles
207: dt=0.9900, 22 negative triangles
208: dt=0.9900, 26 negative triangles
209: dt=0.9900, 26 negative triangles
210: dt=0.9900, 27 negative triangles
211: dt=0.9900, 28 negative triangles
212: dt=0.9900, 26 negative triangles
213: dt=0.9900, 25 negative triangles
214: dt=0.9900, 29 negative triangles
215: dt=0.9900, 24 negative triangles
216: dt=0.9900, 18 negative triangles
217: dt=0.9900, 20 negative triangles
218: dt=0.9900, 27 negative triangles
219: dt=0.9900, 18 negative triangles
220: dt=0.9900, 15 negative triangles
221: dt=0.9900, 16 negative triangles
222: dt=0.9900, 21 negative triangles
223: dt=0.9900, 26 negative triangles
224: dt=0.9900, 18 negative triangles
225: dt=0.9900, 18 negative triangles
226: dt=0.9900, 22 negative triangles
227: dt=0.9900, 17 negative triangles
228: dt=0.9900, 16 negative triangles
229: dt=0.9900, 14 negative triangles
230: dt=0.9900, 15 negative triangles
231: dt=0.9900, 14 negative triangles
232: dt=0.9900, 12 negative triangles
233: dt=0.9900, 14 negative triangles
234: dt=0.9900, 13 negative triangles
235: dt=0.9900, 14 negative triangles
236: dt=0.9900, 16 negative triangles
237: dt=0.9900, 15 negative triangles
238: dt=0.9900, 12 negative triangles
239: dt=0.9900, 18 negative triangles
240: dt=0.9900, 15 negative triangles
241: dt=0.9900, 16 negative triangles
242: dt=0.9405, 14 negative triangles
243: dt=0.9405, 11 negative triangles
244: dt=0.9405, 14 negative triangles
245: dt=0.9405, 11 negative triangles
246: dt=0.9405, 15 negative triangles
247: dt=0.9405, 12 negative triangles
248: dt=0.9405, 15 negative triangles
249: dt=0.9405, 14 negative triangles
250: dt=0.9405, 11 negative triangles
251: dt=0.9405, 13 negative triangles
252: dt=0.9405, 11 negative triangles
253: dt=0.8935, 15 negative triangles
254: dt=0.8935, 15 negative triangles
255: dt=0.8935, 14 negative triangles
256: dt=0.8935, 14 negative triangles
257: dt=0.8935, 12 negative triangles
258: dt=0.8935, 13 negative triangles
259: dt=0.8935, 11 negative triangles
260: dt=0.8935, 14 negative triangles
261: dt=0.8935, 13 negative triangles
262: dt=0.8935, 14 negative triangles
263: dt=0.8488, 15 negative triangles
264: dt=0.8488, 11 negative triangles
265: dt=0.8488, 10 negative triangles
266: dt=0.8488, 10 negative triangles
267: dt=0.8488, 10 negative triangles
268: dt=0.8488, 10 negative triangles
269: dt=0.8488, 10 negative triangles
270: dt=0.8488, 11 negative triangles
271: dt=0.8488, 9 negative triangles
272: dt=0.8488, 12 negative triangles
273: dt=0.8488, 10 negative triangles
274: dt=0.8488, 15 negative triangles
275: dt=0.8488, 10 negative triangles
276: dt=0.8488, 12 negative triangles
277: dt=0.8488, 8 negative triangles
278: dt=0.8488, 12 negative triangles
279: dt=0.8488, 10 negative triangles
280: dt=0.8488, 9 negative triangles
281: dt=0.8488, 8 negative triangles
282: dt=0.8488, 10 negative triangles
283: dt=0.8488, 9 negative triangles
284: dt=0.8488, 11 negative triangles
285: dt=0.8488, 8 negative triangles
286: dt=0.8488, 9 negative triangles
287: dt=0.8064, 11 negative triangles
288: dt=0.8064, 9 negative triangles
289: dt=0.8064, 10 negative triangles
290: dt=0.8064, 9 negative triangles
291: dt=0.8064, 9 negative triangles
292: dt=0.8064, 11 negative triangles
293: dt=0.8064, 9 negative triangles
294: dt=0.8064, 9 negative triangles
295: dt=0.8064, 9 negative triangles
296: dt=0.8064, 9 negative triangles
297: dt=0.7660, 10 negative triangles
298: dt=0.7660, 8 negative triangles
299: dt=0.7660, 7 negative triangles
300: dt=0.7660, 6 negative triangles
301: dt=0.7660, 6 negative triangles
302: dt=0.7660, 7 negative triangles
303: dt=0.7660, 7 negative triangles
304: dt=0.7660, 6 negative triangles
305: dt=0.7660, 6 negative triangles
306: dt=0.7660, 4 negative triangles
307: dt=0.7660, 6 negative triangles
308: dt=0.7660, 5 negative triangles
309: dt=0.7660, 5 negative triangles
310: dt=0.7660, 5 negative triangles
311: dt=0.7660, 2 negative triangles
312: dt=0.7660, 4 negative triangles
313: dt=0.7660, 1 negative triangles
314: dt=0.7660, 3 negative triangles
315: dt=0.7660, 1 negative triangles
316: dt=0.7660, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.11 hours
mris_sphere utimesec    4042.976374
mris_sphere stimesec    1.056839
mris_sphere ru_maxrss   316148
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55733
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10936
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    143839
mris_sphere ru_nivcsw   320326
FSRUNTIME@ mris_sphere  1.1147 hours 1 threads
PIDs (13181 13185) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sat Oct  7 23:06:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sat Oct  7 23:06:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 

Waiting for PID 16072 of (16072 16075) to complete...
Waiting for PID 16075 of (16072 16075) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg

using smoothwm curvature for final alignment

cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

0 inflated.H
1 sulc
2 smoothwm (computed)
$Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading surface from ../surf/lh.sphere...
reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0

tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
curvature mean = -0.000, std = 5.587
curvature mean = 0.026, std = 0.815
curvature mean = 0.020, std = 0.847
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, 0.00, -16.00) sse = 363448.8, tmin=1.1895
  d=32.00 min @ (0.00, -8.00, 8.00) sse = 268727.1, tmin=2.4051
  d=16.00 min @ (4.00, 4.00, 0.00) sse = 231352.7, tmin=3.6365
  d=8.00 min @ (-2.00, 0.00, -2.00) sse = 215689.5, tmin=4.8891
  d=4.00 min @ (1.00, 1.00, 0.00) sse = 213149.1, tmin=6.1524
  d=2.00 min @ (-0.50, -0.50, 0.50) sse = 212497.0, tmin=7.4213
  d=1.00 min @ (0.25, 0.00, 0.00) sse = 212365.1, tmin=8.6778
  d=0.50 min @ (0.00, 0.12, -0.12) sse = 212301.4, tmin=9.9393
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.94 min
curvature mean = -0.018, std = 0.828
curvature mean = 0.008, std = 0.939
curvature mean = -0.024, std = 0.837
curvature mean = 0.003, std = 0.975
curvature mean = -0.026, std = 0.839
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.029, std = 0.313
curvature mean = 0.034, std = 0.245
curvature mean = 0.067, std = 0.305
curvature mean = 0.030, std = 0.302
curvature mean = 0.038, std = 0.482
curvature mean = 0.030, std = 0.327
curvature mean = 0.023, std = 0.613
curvature mean = 0.030, std = 0.339
curvature mean = 0.008, std = 0.718
MRISregister() return, current seed 0
-01: dt=0.0000, 33 negative triangles
123: dt=0.9900, 33 negative triangles
expanding nbhd size to 1
124: dt=0.9900, 47 negative triangles
125: dt=0.9900, 33 negative triangles
126: dt=0.9900, 38 negative triangles
127: dt=0.9900, 39 negative triangles
128: dt=0.9900, 34 negative triangles
129: dt=0.9900, 25 negative triangles
130: dt=0.9900, 27 negative triangles
131: dt=0.9900, 25 negative triangles
132: dt=0.9900, 28 negative triangles
133: dt=0.9900, 24 negative triangles
134: dt=0.9900, 16 negative triangles
135: dt=0.9900, 18 negative triangles
136: dt=0.9900, 15 negative triangles
137: dt=0.9900, 11 negative triangles
138: dt=0.9900, 13 negative triangles
139: dt=0.9900, 11 negative triangles
140: dt=0.9900, 11 negative triangles
141: dt=0.9900, 13 negative triangles
142: dt=0.9900, 11 negative triangles
143: dt=0.9900, 11 negative triangles
144: dt=0.9900, 13 negative triangles
145: dt=0.9900, 11 negative triangles
146: dt=0.9900, 11 negative triangles
147: dt=0.9900, 10 negative triangles
148: dt=0.9900, 9 negative triangles
149: dt=0.9900, 9 negative triangles
150: dt=0.9900, 10 negative triangles
151: dt=0.9900, 8 negative triangles
152: dt=0.9900, 8 negative triangles
153: dt=0.9900, 8 negative triangles
154: dt=0.9900, 6 negative triangles
155: dt=0.9900, 6 negative triangles
156: dt=0.9900, 8 negative triangles
157: dt=0.9900, 6 negative triangles
158: dt=0.9900, 6 negative triangles
159: dt=0.9900, 5 negative triangles
160: dt=0.9900, 3 negative triangles
161: dt=0.9900, 3 negative triangles
162: dt=0.9900, 3 negative triangles
163: dt=0.9900, 7 negative triangles
164: dt=0.9900, 5 negative triangles
165: dt=0.9900, 3 negative triangles
166: dt=0.9900, 5 negative triangles
167: dt=0.9900, 2 negative triangles
168: dt=0.9900, 2 negative triangles
169: dt=0.9900, 1 negative triangles
170: dt=0.9900, 4 negative triangles
171: dt=0.9900, 1 negative triangles
172: dt=0.9900, 1 negative triangles
173: dt=0.9900, 1 negative triangles
174: dt=0.9900, 3 negative triangles
175: dt=0.9900, 1 negative triangles
176: dt=0.9900, 1 negative triangles
177: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.16 hours
mris_register utimesec    4185.182755
mris_register stimesec    2.024692
mris_register ru_maxrss   280516
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   41627
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  10928
mris_register ru_oublock  11032
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    286530
mris_register ru_nivcsw   200349
FSRUNTIME@ mris_register  1.1627 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg

using smoothwm curvature for final alignment

cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 

0 inflated.H
1 sulc
2 smoothwm (computed)
$Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading surface from ../surf/rh.sphere...
reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 1
randomSeed 0

tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading rh.sulc
curvature mean = 0.000, std = 5.609
curvature mean = 0.013, std = 0.813
curvature mean = 0.018, std = 0.852
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 409367.8, tmin=1.1770
  d=32.00 min @ (-8.00, -8.00, -8.00) sse = 242232.1, tmin=2.3802
  d=8.00 min @ (0.00, 2.00, 2.00) sse = 226017.7, tmin=4.8307
  d=2.00 min @ (0.00, 0.00, -0.50) sse = 225757.7, tmin=7.2843
  d=1.00 min @ (0.00, -0.25, 0.25) sse = 225598.1, tmin=8.5238
  d=0.50 min @ (0.12, 0.12, -0.12) sse = 225553.8, tmin=9.7855
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.79 min
curvature mean = -0.013, std = 0.819
curvature mean = 0.008, std = 0.943
curvature mean = -0.019, std = 0.825
curvature mean = 0.003, std = 0.977
curvature mean = -0.020, std = 0.826
curvature mean = 0.001, std = 0.991
2 Reading smoothwm
curvature mean = -0.027, std = 0.292
curvature mean = 0.030, std = 0.240
curvature mean = 0.066, std = 0.333
curvature mean = 0.028, std = 0.297
curvature mean = 0.038, std = 0.521
curvature mean = 0.027, std = 0.322
curvature mean = 0.022, std = 0.663
curvature mean = 0.027, std = 0.334
curvature mean = 0.007, std = 0.774
MRISregister() return, current seed 0
-01: dt=0.0000, 51 negative triangles
116: dt=0.9900, 51 negative triangles
expanding nbhd size to 1
117: dt=0.9900, 71 negative triangles
118: dt=0.9900, 51 negative triangles
119: dt=0.9900, 55 negative triangles
120: dt=0.9405, 53 negative triangles
121: dt=0.9405, 46 negative triangles
122: dt=0.9405, 49 negative triangles
123: dt=0.9405, 51 negative triangles
124: dt=0.9405, 49 negative triangles
125: dt=0.9405, 42 negative triangles
126: dt=0.9405, 41 negative triangles
127: dt=0.9405, 40 negative triangles
128: dt=0.9405, 36 negative triangles
129: dt=0.9405, 34 negative triangles
130: dt=0.9405, 31 negative triangles
131: dt=0.9405, 32 negative triangles
132: dt=0.9405, 30 negative triangles
133: dt=0.9405, 28 negative triangles
134: dt=0.9405, 25 negative triangles
135: dt=0.9405, 26 negative triangles
136: dt=0.9405, 27 negative triangles
137: dt=0.9405, 21 negative triangles
138: dt=0.9405, 21 negative triangles
139: dt=0.9405, 23 negative triangles
140: dt=0.9405, 20 negative triangles
141: dt=0.9405, 18 negative triangles
142: dt=0.9405, 16 negative triangles
143: dt=0.9405, 20 negative triangles
144: dt=0.9405, 20 negative triangles
145: dt=0.9405, 16 negative triangles
146: dt=0.9405, 17 negative triangles
147: dt=0.9405, 13 negative triangles
148: dt=0.9405, 9 negative triangles
149: dt=0.9405, 7 negative triangles
150: dt=0.9405, 7 negative triangles
151: dt=0.9405, 5 negative triangles
152: dt=0.9405, 8 negative triangles
153: dt=0.9405, 8 negative triangles
154: dt=0.9405, 6 negative triangles
155: dt=0.9405, 3 negative triangles
156: dt=0.9405, 3 negative triangles
157: dt=0.9405, 2 negative triangles
158: dt=0.9405, 2 negative triangles
159: dt=0.9405, 2 negative triangles
160: dt=0.9405, 1 negative triangles
161: dt=0.9405, 1 negative triangles
162: dt=0.9405, 4 negative triangles
163: dt=0.9405, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.23 hours
mris_register utimesec    4573.610705
mris_register stimesec    2.038690
mris_register ru_maxrss   278608
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39760
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10904
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    316317
mris_register ru_nivcsw   191615
FSRUNTIME@ mris_register  1.2300 hours 1 threads
PIDs (16072 16075) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 00:20:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 00:20:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

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

Waiting for PID 18883 of (18883 18886) to complete...
Waiting for PID 18886 of (18883 18886) to complete...

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

reading surface from ../surf/lh.white.preaparc...
writing curvature file ../surf/lh.jacobian_white

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

reading surface from ../surf/rh.white.preaparc...
writing curvature file ../surf/rh.jacobian_white
PIDs (18883 18886) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 00:20:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv 

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 00:20:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv 

Waiting for PID 18929 of (18929 18932) to complete...
Waiting for PID 18932 of (18929 18932) to complete...

 mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv

averaging curvature patterns 5 times...
reading surface from ../surf/lh.sphere.reg...
reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
writing curvature file to ../surf/lh.avg_curv...

 mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv

averaging curvature patterns 5 times...
reading surface from ../surf/rh.sphere.reg...
reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
writing curvature file to ../surf/rh.avg_curv...
PIDs (18929 18932) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 00:20:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 00:20:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot 

Waiting for PID 18979 of (18979 18982) to complete...
Waiting for PID 18982 of (18979 18982) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.8   using min determinant for regularization = 0.006
0 singular and 342 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1292 labels changed using aseg
relabeling using gibbs priors...
000:   3268 changed, 155300 examined...
001:    784 changed, 14001 examined...
002:    178 changed, 4325 examined...
003:     61 changed, 1077 examined...
004:     20 changed, 375 examined...
005:      9 changed, 118 examined...
006:      6 changed, 57 examined...
007:      2 changed, 33 examined...
008:      1 changed, 18 examined...
009:      0 changed, 6 examined...
250 labels changed using aseg
000: 142 total segments, 94 labels (323 vertices) changed
001: 52 total segments, 3 labels (13 vertices) changed
002: 48 total segments, 2 labels (3 vertices) changed
003: 46 total segments, 0 labels (0 vertices) changed
9 filter iterations complete (10 requested, 0 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2005 vertices marked for relabeling...
2005 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.7   using min determinant for regularization = 0.004
0 singular and 309 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1323 labels changed using aseg
relabeling using gibbs priors...
000:   2924 changed, 153799 examined...
001:    690 changed, 12665 examined...
002:    159 changed, 3921 examined...
003:     63 changed, 966 examined...
004:     23 changed, 373 examined...
005:      6 changed, 148 examined...
006:      1 changed, 43 examined...
007:      1 changed, 5 examined...
008:      0 changed, 7 examined...
173 labels changed using aseg
000: 89 total segments, 51 labels (229 vertices) changed
001: 41 total segments, 4 labels (4 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1789 vertices marked for relabeling...
1789 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 15 seconds.
PIDs (18979 18982) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 00:20:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 00:20:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 rh 

Waiting for PID 19040 of (19040 19043) to complete...
Waiting for PID 19043 of (19040 19043) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 lh

using white.preaparc starting white location...
using white.preaparc starting pial locations...
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
26893 bright wm thresholded.
2956 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig...
computing class statistics...
border white:    289174 voxels (1.72%)
border gray      336461 voxels (2.01%)
WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0]
GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70)
setting MAX_BORDER_WHITE to 112.4 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 41.4 (was 40)
setting MAX_GRAY to 93.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-7.8,    GM=62+-7.8
mean inside = 92.0, mean outside = 71.1
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.04-->6.58) (max @ vno 36261 --> 154244)
face area 0.33 +- 0.16 (0.00-->4.18)
mean absolute distance = 0.51 +- 0.74
3842 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 3 with 51 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 259 points - only 0.00% unknown
deleting segment 6 with 29 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
mean border=76.1, 95 (95) missing vertices, mean dist 0.3 [0.5 (%16.3)->0.5 (%83.7))]
%78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.08-->6.58) (max @ vno 36261 --> 154244)
face area 0.33 +- 0.16 (0.00-->4.03)
mean absolute distance = 0.32 +- 0.52
3850 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2804627.2, rms=8.317
001: dt: 0.5000, sse=1517290.5, rms=5.087 (38.839%)
002: dt: 0.5000, sse=1222872.0, rms=4.029 (20.802%)
003: dt: 0.5000, sse=1179258.8, rms=3.823 (5.103%)
004: dt: 0.5000, sse=1135155.0, rms=3.632 (4.999%)
rms = 3.71, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=930379.7, rms=2.490 (31.437%)
006: dt: 0.2500, sse=859760.2, rms=1.943 (21.956%)
007: dt: 0.2500, sse=839704.8, rms=1.744 (10.262%)
008: dt: 0.2500, sse=833168.4, rms=1.681 (3.604%)
rms = 1.64, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=831559.8, rms=1.638 (2.539%)
010: dt: 0.1250, sse=822879.6, rms=1.565 (4.475%)
rms = 1.56, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=822383.4, rms=1.555 (0.635%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 41 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 112 points - only 0.00% unknown
deleting segment 6 with 21 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
mean border=79.7, 89 (35) missing vertices, mean dist -0.2 [0.3 (%75.5)->0.2 (%24.5))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.10-->6.48) (max @ vno 36261 --> 154244)
face area 0.36 +- 0.17 (0.00-->4.59)
mean absolute distance = 0.24 +- 0.38
3610 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1507966.9, rms=4.872
012: dt: 0.5000, sse=1117570.0, rms=3.239 (33.513%)
rms = 3.53, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=964327.4, rms=2.336 (27.895%)
014: dt: 0.2500, sse=895519.9, rms=1.772 (24.145%)
015: dt: 0.2500, sse=870471.1, rms=1.508 (14.860%)
016: dt: 0.2500, sse=862148.3, rms=1.418 (5.975%)
017: dt: 0.2500, sse=857755.9, rms=1.364 (3.796%)
rms = 1.34, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=855856.8, rms=1.340 (1.824%)
019: dt: 0.1250, sse=849833.5, rms=1.265 (5.595%)
rms = 1.26, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=849464.0, rms=1.262 (0.193%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 15 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 41 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
deleting segment 4 with 115 points - only 0.00% unknown
deleting segment 5 with 23 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
mean border=81.7, 82 (24) missing vertices, mean dist -0.1 [0.3 (%65.8)->0.2 (%34.2))]
%89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.07-->6.33) (max @ vno 36261 --> 154244)
face area 0.34 +- 0.17 (0.00-->4.36)
mean absolute distance = 0.22 +- 0.32
3286 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1025113.4, rms=2.928
021: dt: 0.5000, sse=1018467.2, rms=2.858 (2.403%)
rms = 3.32, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=873522.2, rms=1.838 (35.672%)
023: dt: 0.2500, sse=829900.0, rms=1.398 (23.951%)
024: dt: 0.2500, sse=819919.3, rms=1.275 (8.810%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=817518.3, rms=1.259 (1.257%)
026: dt: 0.1250, sse=809938.1, rms=1.154 (8.310%)
rms = 1.15, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=809446.3, rms=1.152 (0.220%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 41 points - only 0.00% unknown
deleting segment 3 with 14 points - only 0.00% unknown
deleting segment 4 with 113 points - only 0.00% unknown
deleting segment 5 with 23 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
mean border=82.4, 76 (19) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=832280.7, rms=1.578
rms = 1.92, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=793440.0, rms=1.082 (31.397%)
029: dt: 0.2500, sse=781115.5, rms=0.865 (20.123%)
rms = 0.87, time step reduction 2 of 3 to 0.125...
rms = 0.86, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=779869.8, rms=0.859 (0.653%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 7714 vertices
erasing segment 1 (vno[0] = 109207)
erasing segment 2 (vno[0] = 110460)
erasing segment 3 (vno[0] = 113599)
erasing segment 4 (vno[0] = 113647)
erasing segment 5 (vno[0] = 113687)
erasing segment 6 (vno[0] = 114813)
erasing segment 7 (vno[0] = 115908)
erasing segment 8 (vno[0] = 116914)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.area
vertex spacing 0.89 +- 0.26 (0.04-->6.31) (max @ vno 36261 --> 154244)
face area 0.34 +- 0.16 (0.00-->4.39)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=50.4, 115 (115) missing vertices, mean dist 1.5 [0.6 (%0.0)->3.1 (%100.0))]
%11 local maxima, %34 large gradients and %50 min vals, 579 gradients ignored
perforing initial smooth deformation to move away from white surface
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=32446480.0, rms=32.650
001: dt: 0.0500, sse=28340256.0, rms=30.462 (6.702%)
002: dt: 0.0500, sse=25419706.0, rms=28.804 (5.441%)
003: dt: 0.0500, sse=23199350.0, rms=27.477 (4.607%)
004: dt: 0.0500, sse=21418316.0, rms=26.365 (4.050%)
005: dt: 0.0500, sse=19933022.0, rms=25.399 (3.662%)
006: dt: 0.0500, sse=18658330.0, rms=24.540 (3.381%)
007: dt: 0.0500, sse=17542114.0, rms=23.763 (3.169%)
008: dt: 0.0500, sse=16549367.0, rms=23.049 (3.003%)
009: dt: 0.0500, sse=15655907.0, rms=22.387 (2.871%)
010: dt: 0.0500, sse=14844162.0, rms=21.769 (2.764%)
positioning took 1.1 minutes
mean border=50.2, 101 (72) missing vertices, mean dist 1.3 [0.2 (%0.0)->2.6 (%100.0))]
%12 local maxima, %34 large gradients and %49 min vals, 546 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=15607909.0, rms=22.353
011: dt: 0.0500, sse=14861106.0, rms=21.783 (2.547%)
012: dt: 0.0500, sse=14174959.0, rms=21.247 (2.464%)
013: dt: 0.0500, sse=13542039.0, rms=20.739 (2.388%)
014: dt: 0.0500, sse=12957204.0, rms=20.259 (2.316%)
015: dt: 0.0500, sse=12415446.0, rms=19.804 (2.248%)
016: dt: 0.0500, sse=11913827.0, rms=19.372 (2.178%)
017: dt: 0.0500, sse=11447261.0, rms=18.962 (2.116%)
018: dt: 0.0500, sse=11014040.0, rms=18.574 (2.051%)
019: dt: 0.0500, sse=10610629.0, rms=18.204 (1.990%)
020: dt: 0.0500, sse=10235223.0, rms=17.853 (1.928%)
positioning took 1.1 minutes
mean border=50.2, 116 (64) missing vertices, mean dist 1.1 [0.1 (%0.5)->2.3 (%99.5))]
%13 local maxima, %34 large gradients and %49 min vals, 550 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=10335192.0, rms=17.953
021: dt: 0.0500, sse=9981051.0, rms=17.618 (1.870%)
022: dt: 0.0500, sse=9651309.0, rms=17.299 (1.808%)
023: dt: 0.0500, sse=9342591.0, rms=16.995 (1.756%)
024: dt: 0.0500, sse=9054039.0, rms=16.706 (1.700%)
025: dt: 0.0500, sse=8783382.0, rms=16.431 (1.651%)
026: dt: 0.0500, sse=8529487.0, rms=16.168 (1.601%)
027: dt: 0.0500, sse=8290122.0, rms=15.915 (1.559%)
028: dt: 0.0500, sse=8063184.5, rms=15.673 (1.526%)
029: dt: 0.0500, sse=7847435.0, rms=15.438 (1.496%)
030: dt: 0.0500, sse=7642155.5, rms=15.212 (1.468%)
positioning took 1.1 minutes
mean border=50.1, 135 (55) missing vertices, mean dist 1.0 [0.1 (%4.8)->2.1 (%95.2))]
%13 local maxima, %34 large gradients and %48 min vals, 513 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7712222.0, rms=15.290
031: dt: 0.5000, sse=6280224.5, rms=13.614 (10.962%)
032: dt: 0.5000, sse=5251889.5, rms=12.262 (9.928%)
033: dt: 0.5000, sse=4447532.0, rms=11.089 (9.564%)
034: dt: 0.5000, sse=3803668.5, rms=10.048 (9.391%)
035: dt: 0.5000, sse=3282773.2, rms=9.120 (9.238%)
036: dt: 0.5000, sse=2861233.2, rms=8.291 (9.088%)
037: dt: 0.5000, sse=2506599.5, rms=7.528 (9.197%)
038: dt: 0.5000, sse=2226631.2, rms=6.865 (8.817%)
039: dt: 0.5000, sse=2012917.4, rms=6.314 (8.027%)
040: dt: 0.5000, sse=1859373.9, rms=5.885 (6.794%)
041: dt: 0.5000, sse=1755381.9, rms=5.576 (5.250%)
042: dt: 0.5000, sse=1689512.6, rms=5.369 (3.711%)
043: dt: 0.5000, sse=1650396.1, rms=5.245 (2.312%)
044: dt: 0.5000, sse=1626033.6, rms=5.162 (1.571%)
045: dt: 0.5000, sse=1607965.0, rms=5.102 (1.164%)
rms = 5.06, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1596598.0, rms=5.063 (0.777%)
047: dt: 0.2500, sse=1518227.2, rms=4.749 (6.195%)
048: dt: 0.2500, sse=1495523.6, rms=4.666 (1.746%)
rms = 4.66, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1495134.9, rms=4.661 (0.100%)
050: dt: 0.1250, sse=1481604.4, rms=4.606 (1.186%)
rms = 4.60, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1479875.8, rms=4.599 (0.147%)
positioning took 3.1 minutes
mean border=49.5, 3703 (21) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.6 (%50.5))]
%20 local maxima, %30 large gradients and %43 min vals, 308 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1677294.9, rms=4.511
052: dt: 0.5000, sse=1617266.9, rms=4.291 (4.893%)
rms = 4.28, time step reduction 1 of 3 to 0.250...
053: dt: 0.5000, sse=1605399.6, rms=4.275 (0.363%)
054: dt: 0.2500, sse=1535103.0, rms=3.926 (8.171%)
055: dt: 0.2500, sse=1520959.6, rms=3.866 (1.520%)
rms = 3.89, time step reduction 2 of 3 to 0.125...
rms = 3.84, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1515180.9, rms=3.837 (0.762%)
positioning took 1.0 minutes
mean border=49.1, 4110 (17) missing vertices, mean dist 0.1 [0.2 (%50.6)->0.5 (%49.4))]
%28 local maxima, %23 large gradients and %42 min vals, 314 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1551520.6, rms=3.982
rms = 4.29, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1526417.2, rms=3.866 (2.917%)
rms = 3.88, time step reduction 2 of 3 to 0.125...
rms = 3.85, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1523831.4, rms=3.853 (0.339%)
positioning took 0.6 minutes
mean border=48.7, 7515 (17) missing vertices, mean dist 0.1 [0.2 (%48.8)->0.4 (%51.2))]
%32 local maxima, %18 large gradients and %41 min vals, 316 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing pial surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1552112.0, rms=3.981
059: dt: 0.5000, sse=1527515.9, rms=3.920 (1.535%)
rms = 4.05, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1472687.6, rms=3.662 (6.580%)
061: dt: 0.2500, sse=1442396.9, rms=3.531 (3.577%)
062: dt: 0.2500, sse=1430081.0, rms=3.477 (1.538%)
rms = 3.44, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1420828.9, rms=3.439 (1.078%)
064: dt: 0.1250, sse=1404028.5, rms=3.348 (2.652%)
rms = 3.33, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1399164.6, rms=3.327 (0.631%)
positioning took 1.5 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.area.pial
vertex spacing 1.03 +- 0.46 (0.03-->7.33) (max @ vno 11185 --> 154107)
face area 0.41 +- 0.33 (0.00-->7.77)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 155300 vertices processed
25000 of 155300 vertices processed
50000 of 155300 vertices processed
75000 of 155300 vertices processed
100000 of 155300 vertices processed
125000 of 155300 vertices processed
150000 of 155300 vertices processed
0 of 155300 vertices processed
25000 of 155300 vertices processed
50000 of 155300 vertices processed
75000 of 155300 vertices processed
100000 of 155300 vertices processed
125000 of 155300 vertices processed
150000 of 155300 vertices processed
thickness calculation complete, 536:1288 truncations.
29393 vertices at 0 distance
102165 vertices at 1 distance
97217 vertices at 2 distance
45032 vertices at 3 distance
15665 vertices at 4 distance
5017 vertices at 5 distance
1751 vertices at 6 distance
569 vertices at 7 distance
255 vertices at 8 distance
126 vertices at 9 distance
84 vertices at 10 distance
56 vertices at 11 distance
41 vertices at 12 distance
42 vertices at 13 distance
48 vertices at 14 distance
22 vertices at 15 distance
11 vertices at 16 distance
16 vertices at 17 distance
20 vertices at 18 distance
19 vertices at 19 distance
15 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.thickness
positioning took 17.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051026 rh

using white.preaparc starting white location...
using white.preaparc starting pial locations...
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
26893 bright wm thresholded.
2956 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig...
computing class statistics...
border white:    289174 voxels (1.72%)
border gray      336461 voxels (2.01%)
WM (97.0): 96.9 +- 9.4 [70.0 --> 110.0]
GM (67.0) : 66.6 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.7 (was 70)
setting MAX_BORDER_WHITE to 111.4 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 41.4 (was 40)
setting MAX_GRAY to 92.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-7.0,    GM=62+-7.0
mean inside = 91.6, mean outside = 70.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.03-->3.78) (max @ vno 153384 --> 153404)
face area 0.33 +- 0.15 (0.00-->3.64)
mean absolute distance = 0.51 +- 0.74
3427 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 1 with 22 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 178 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
mean border=75.8, 97 (97) missing vertices, mean dist 0.3 [0.5 (%16.3)->0.5 (%83.7))]
%76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.25 (0.09-->3.84) (max @ vno 90569 --> 91721)
face area 0.33 +- 0.16 (0.00-->3.65)
mean absolute distance = 0.31 +- 0.52
3973 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2717593.0, rms=8.181
001: dt: 0.5000, sse=1461957.8, rms=4.948 (39.517%)
002: dt: 0.5000, sse=1194039.1, rms=3.948 (20.201%)
003: dt: 0.5000, sse=1158211.2, rms=3.803 (3.676%)
004: dt: 0.5000, sse=1116598.8, rms=3.617 (4.892%)
rms = 3.72, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=918173.1, rms=2.463 (31.909%)
006: dt: 0.2500, sse=850478.4, rms=1.919 (22.094%)
007: dt: 0.2500, sse=832364.1, rms=1.735 (9.578%)
rms = 1.69, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=829141.9, rms=1.689 (2.673%)
009: dt: 0.1250, sse=819302.7, rms=1.595 (5.549%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=818189.0, rms=1.583 (0.732%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 44 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 5 with 44 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
mean border=79.4, 76 (24) missing vertices, mean dist -0.2 [0.3 (%75.4)->0.2 (%24.6))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.11-->4.05) (max @ vno 90569 --> 91721)
face area 0.36 +- 0.17 (0.00-->4.24)
mean absolute distance = 0.23 +- 0.38
3499 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1478565.1, rms=4.816
011: dt: 0.5000, sse=1114181.1, rms=3.229 (32.962%)
rms = 3.56, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=952384.8, rms=2.308 (28.505%)
013: dt: 0.2500, sse=898221.5, rms=1.761 (23.694%)
014: dt: 0.2500, sse=863294.2, rms=1.515 (14.013%)
015: dt: 0.2500, sse=858010.1, rms=1.433 (5.376%)
016: dt: 0.2500, sse=852204.7, rms=1.383 (3.494%)
rms = 1.36, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=852572.5, rms=1.364 (1.386%)
018: dt: 0.1250, sse=844609.9, rms=1.287 (5.641%)
rms = 1.29, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=844554.6, rms=1.286 (0.097%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 21 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 37 points - only 0.00% unknown
deleting segment 4 with 85 points - only 0.00% unknown
deleting segment 5 with 15 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
mean border=81.3, 59 (17) missing vertices, mean dist -0.1 [0.3 (%65.7)->0.2 (%34.3))]
%88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.06-->4.16) (max @ vno 90569 --> 91721)
face area 0.34 +- 0.16 (0.00-->4.20)
mean absolute distance = 0.22 +- 0.32
3048 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1016447.4, rms=2.918
rms = 2.89, time step reduction 1 of 3 to 0.250...
020: dt: 0.5000, sse=1033967.8, rms=2.891 (0.937%)
021: dt: 0.2500, sse=855048.0, rms=1.666 (42.360%)
022: dt: 0.2500, sse=821322.5, rms=1.363 (18.195%)
rms = 1.34, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=820083.2, rms=1.341 (1.645%)
024: dt: 0.1250, sse=807183.8, rms=1.177 (12.213%)
rms = 1.17, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=806095.6, rms=1.165 (0.997%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 21 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 133 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 15 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
mean border=82.1, 71 (12) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=827677.5, rms=1.587
rms = 1.96, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=789056.9, rms=1.099 (30.748%)
027: dt: 0.2500, sse=777278.4, rms=0.884 (19.581%)
rms = 0.89, time step reduction 2 of 3 to 0.125...
rms = 0.88, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=776287.9, rms=0.879 (0.610%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7533 vertices
erasing segment 1 (vno[0] = 108009)
erasing segment 2 (vno[0] = 108012)
erasing segment 3 (vno[0] = 110042)
erasing segment 4 (vno[0] = 110085)
erasing segment 5 (vno[0] = 111126)
erasing segment 6 (vno[0] = 112181)
erasing segment 7 (vno[0] = 113450)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.area
vertex spacing 0.90 +- 0.26 (0.03-->4.26) (max @ vno 113447 --> 114521)
face area 0.34 +- 0.16 (0.00-->4.18)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=50.2, 117 (117) missing vertices, mean dist 1.5 [0.0 (%0.0)->3.1 (%100.0))]
%12 local maxima, %35 large gradients and %49 min vals, 711 gradients ignored
perforing initial smooth deformation to move away from white surface
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=31763528.0, rms=32.441
001: dt: 0.0500, sse=27735550.0, rms=30.262 (6.718%)
002: dt: 0.0500, sse=24869992.0, rms=28.610 (5.458%)
003: dt: 0.0500, sse=22688598.0, rms=27.286 (4.629%)
004: dt: 0.0500, sse=20937348.0, rms=26.174 (4.075%)
005: dt: 0.0500, sse=19476524.0, rms=25.209 (3.687%)
006: dt: 0.0500, sse=18223022.0, rms=24.350 (3.406%)
007: dt: 0.0500, sse=17124914.0, rms=23.572 (3.194%)
008: dt: 0.0500, sse=16147654.0, rms=22.858 (3.031%)
009: dt: 0.0500, sse=15267504.0, rms=22.195 (2.902%)
010: dt: 0.0500, sse=14469053.0, rms=21.575 (2.791%)
positioning took 1.0 minutes
mean border=50.0, 109 (63) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.6 (%100.0))]
%13 local maxima, %35 large gradients and %48 min vals, 673 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=15220140.0, rms=22.160
011: dt: 0.0500, sse=14485679.0, rms=21.590 (2.572%)
012: dt: 0.0500, sse=13811562.0, rms=21.054 (2.486%)
013: dt: 0.0500, sse=13189933.0, rms=20.546 (2.410%)
014: dt: 0.0500, sse=12615611.0, rms=20.066 (2.337%)
015: dt: 0.0500, sse=12084454.0, rms=19.611 (2.266%)
016: dt: 0.0500, sse=11592709.0, rms=19.181 (2.196%)
017: dt: 0.0500, sse=11136938.0, rms=18.773 (2.128%)
018: dt: 0.0500, sse=10714167.0, rms=18.386 (2.060%)
019: dt: 0.0500, sse=10321429.0, rms=18.019 (1.995%)
020: dt: 0.0500, sse=9956381.0, rms=17.671 (1.930%)
positioning took 1.0 minutes
mean border=49.9, 122 (56) missing vertices, mean dist 1.1 [0.1 (%0.5)->2.3 (%99.5))]
%13 local maxima, %36 large gradients and %47 min vals, 650 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=10045566.0, rms=17.764
021: dt: 0.0500, sse=9701816.0, rms=17.432 (1.870%)
022: dt: 0.0500, sse=9381526.0, rms=17.116 (1.810%)
023: dt: 0.0500, sse=9081780.0, rms=16.816 (1.757%)
024: dt: 0.0500, sse=8801807.0, rms=16.530 (1.700%)
025: dt: 0.0500, sse=8539536.0, rms=16.257 (1.648%)
026: dt: 0.0500, sse=8293519.0, rms=15.998 (1.598%)
027: dt: 0.0500, sse=8061346.5, rms=15.748 (1.558%)
028: dt: 0.0500, sse=7841141.0, rms=15.508 (1.525%)
029: dt: 0.0500, sse=7632145.5, rms=15.276 (1.493%)
030: dt: 0.0500, sse=7433009.0, rms=15.052 (1.467%)
positioning took 1.1 minutes
mean border=49.9, 146 (51) missing vertices, mean dist 1.0 [0.1 (%4.6)->2.0 (%95.4))]
%14 local maxima, %36 large gradients and %47 min vals, 638 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7501263.0, rms=15.131
031: dt: 0.5000, sse=6091755.5, rms=13.448 (11.123%)
032: dt: 0.5000, sse=5066842.0, rms=12.071 (10.241%)
033: dt: 0.5000, sse=4263149.0, rms=10.868 (9.965%)
034: dt: 0.5000, sse=3621523.8, rms=9.798 (9.847%)
035: dt: 0.5000, sse=3115775.5, rms=8.863 (9.534%)
036: dt: 0.5000, sse=2709225.0, rms=8.032 (9.379%)
037: dt: 0.5000, sse=2380262.5, rms=7.293 (9.205%)
038: dt: 0.5000, sse=2126635.8, rms=6.666 (8.599%)
039: dt: 0.5000, sse=1938475.8, rms=6.162 (7.556%)
040: dt: 0.5000, sse=1810340.8, rms=5.792 (6.012%)
041: dt: 0.5000, sse=1722856.1, rms=5.525 (4.598%)
042: dt: 0.5000, sse=1669737.0, rms=5.355 (3.082%)
043: dt: 0.5000, sse=1628962.1, rms=5.223 (2.468%)
044: dt: 0.5000, sse=1602386.1, rms=5.132 (1.734%)
045: dt: 0.5000, sse=1580629.1, rms=5.059 (1.422%)
rms = 5.01, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1567357.0, rms=5.012 (0.942%)
047: dt: 0.2500, sse=1480014.8, rms=4.660 (7.017%)
048: dt: 0.2500, sse=1453969.6, rms=4.562 (2.095%)
rms = 4.56, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1452807.1, rms=4.555 (0.159%)
050: dt: 0.1250, sse=1436481.2, rms=4.487 (1.491%)
rms = 4.48, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1434122.2, rms=4.478 (0.206%)
positioning took 3.1 minutes
mean border=49.2, 3403 (22) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.6 (%52.2))]
%22 local maxima, %30 large gradients and %42 min vals, 319 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1651825.0, rms=4.466
052: dt: 0.5000, sse=1598728.1, rms=4.264 (4.527%)
rms = 4.25, time step reduction 1 of 3 to 0.250...
053: dt: 0.5000, sse=1588748.8, rms=4.254 (0.227%)
054: dt: 0.2500, sse=1505262.2, rms=3.843 (9.669%)
055: dt: 0.2500, sse=1488773.5, rms=3.770 (1.903%)
rms = 3.79, time step reduction 2 of 3 to 0.125...
rms = 3.73, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1481424.2, rms=3.732 (0.997%)
positioning took 1.0 minutes
mean border=48.7, 3758 (15) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))]
%31 local maxima, %22 large gradients and %41 min vals, 328 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1529620.0, rms=3.931
rms = 4.29, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1499080.8, rms=3.787 (3.665%)
rms = 3.79, time step reduction 2 of 3 to 0.125...
rms = 3.77, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1495744.2, rms=3.770 (0.445%)
positioning took 0.6 minutes
mean border=48.3, 7191 (14) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.4 (%51.7))]
%34 local maxima, %18 large gradients and %40 min vals, 355 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing pial surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1526884.8, rms=3.915
rms = 3.89, time step reduction 1 of 3 to 0.250...
059: dt: 0.5000, sse=1511662.8, rms=3.889 (0.670%)
060: dt: 0.2500, sse=1442113.8, rms=3.570 (8.208%)
061: dt: 0.2500, sse=1412040.2, rms=3.433 (3.826%)
rms = 3.41, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1405689.6, rms=3.407 (0.757%)
063: dt: 0.1250, sse=1376256.1, rms=3.250 (4.625%)
rms = 3.22, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1369910.2, rms=3.220 (0.912%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.area.pial
vertex spacing 1.03 +- 0.46 (0.06-->7.88) (max @ vno 69901 --> 69884)
face area 0.41 +- 0.33 (0.00-->7.75)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 153799 vertices processed
25000 of 153799 vertices processed
50000 of 153799 vertices processed
75000 of 153799 vertices processed
100000 of 153799 vertices processed
125000 of 153799 vertices processed
150000 of 153799 vertices processed
0 of 153799 vertices processed
25000 of 153799 vertices processed
50000 of 153799 vertices processed
75000 of 153799 vertices processed
100000 of 153799 vertices processed
125000 of 153799 vertices processed
150000 of 153799 vertices processed
thickness calculation complete, 392:1318 truncations.
28689 vertices at 0 distance
99785 vertices at 1 distance
97782 vertices at 2 distance
45158 vertices at 3 distance
15448 vertices at 4 distance
4987 vertices at 5 distance
1722 vertices at 6 distance
641 vertices at 7 distance
234 vertices at 8 distance
129 vertices at 9 distance
79 vertices at 10 distance
87 vertices at 11 distance
55 vertices at 12 distance
34 vertices at 13 distance
37 vertices at 14 distance
18 vertices at 15 distance
21 vertices at 16 distance
17 vertices at 17 distance
20 vertices at 18 distance
14 vertices at 19 distance
13 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.thickness
positioning took 16.8 minutes
PIDs (19040 19043) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 00:38:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf
mris_calc -o lh.area.mid lh.area add lh.area.pial
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_calc -o lh.area.mid lh.area.mid div 2
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_convert --volume 0051026 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label
Total face volume 307875
Total vertex volume 304615 (mask=0)
#@# 0051026 lh 304615
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 00:38:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf
mris_calc -o rh.area.mid rh.area add rh.area.pial
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_calc -o rh.area.mid rh.area.mid div 2
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_convert --volume 0051026 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label
Total face volume 306008
Total vertex volume 302421 (mask=0)
#@# 0051026 rh 302421
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 00:38:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

 mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 0051026 

SUBJECTS_DIR is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
loading input data...
computing distance to left white surface 
computing distance to left pial surface 
computing distance to right white surface 
computing distance to right pial surface 
 hemi masks overlap voxels = 261
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz
mris_volmask took 13.01 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 00:51:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051026 lh white 


 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051026 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 00:51:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051026 rh white 


 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051026 rh pial 

Waiting for PID 20180 of (20180 20183 20186 20189) to complete...
Waiting for PID 20183 of (20180 20183 20186 20189) to complete...
Waiting for PID 20186 of (20180 20183 20186 20189) to complete...
Waiting for PID 20189 of (20180 20183 20186 20189) to complete...

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051026 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 307875
Total vertex volume 304615 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1654   1135   3040  2.799 0.525     0.106     0.023       13     1.5  bankssts
  743    497   1259  2.609 0.492     0.131     0.018       10     0.5  caudalanteriorcingulate
 3714   2485   7194  2.714 0.516     0.109     0.023       33     3.2  caudalmiddlefrontal
 2403   1649   3062  1.801 0.410     0.149     0.045       36     4.1  cuneus
  695    501   2252  3.503 0.970     0.148     0.035       22     1.2  entorhinal
 4906   3375  10733  2.781 0.626     0.134     0.030       67     6.0  fusiform
 7404   4933  14612  2.672 0.551     0.128     0.028       93     8.4  inferiorparietal
 5854   4031  13796  2.766 0.646     0.119     0.028       84     6.5  inferiortemporal
 1747   1137   3261  2.349 0.896     0.127     0.032       25     2.0  isthmuscingulate
 9175   6017  16600  2.308 0.615     0.146     0.045      135    17.0  lateraloccipital
 4870   3270  11272  3.228 0.639     0.126     0.030       61     5.7  lateralorbitofrontal
 3672   2627   6564  2.247 0.639     0.138     0.037       49     5.4  lingual
 3130   2194   6482  2.715 0.585     0.115     0.029       46     3.4  medialorbitofrontal
 5746   3871  14916  3.049 0.676     0.124     0.028       84     6.5  middletemporal
  944    678   2289  2.892 0.659     0.116     0.023        8     0.9  parahippocampal
 2339   1481   4354  2.665 0.574     0.100     0.026       16     2.1  paracentral
 2384   1672   5592  3.017 0.478     0.111     0.022       23     1.9  parsopercularis
 1339    868   3394  3.072 0.558     0.132     0.027       20     1.5  parsorbitalis
 2328   1632   5517  2.997 0.633     0.121     0.025       28     2.2  parstriangularis
 1880   1372   2235  1.784 0.411     0.131     0.036       21     2.8  pericalcarine
 7341   4639  12390  2.314 0.712     0.113     0.029       84     9.0  postcentral
 1787   1192   3483  2.662 0.752     0.122     0.019       24     1.3  posteriorcingulate
 9624   6143  18603  2.749 0.607     0.109     0.028       95    11.1  precentral
 7182   4867  13465  2.541 0.556     0.130     0.029       90     8.2  precuneus
 1554   1018   3338  2.875 0.654     0.119     0.026       19     1.8  rostralanteriorcingulate
 9010   6214  18914  2.631 0.566     0.138     0.035      132    12.4  rostralmiddlefrontal
13084   8991  33058  3.187 0.600     0.126     0.032      142    16.3  superiorfrontal
11067   7183  18829  2.361 0.563     0.121     0.027      121    11.6  superiorparietal
 6725   4484  16554  3.131 0.688     0.111     0.024       73     6.5  superiortemporal
 6986   4697  14861  2.795 0.581     0.128     0.029       90     8.0  supramarginal
  496    321   1346  3.118 0.610     0.171     0.055       12     1.2  frontalpole
  701    514   2361  3.492 0.915     0.140     0.040       13     1.2  temporalpole
  700    430   1293  2.671 0.538     0.134     0.041        9     1.1  transversetemporal
 3812   2551   7693  3.144 0.701     0.122     0.035       42     5.2  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051026 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 307875
Total vertex volume 304615 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1654   1029   3040  2.799 0.525     0.135     0.041       32     2.9  bankssts
  743    532   1259  2.609 0.492     0.136     0.029       24     1.0  caudalanteriorcingulate
 3714   2783   7194  2.714 0.516     0.127     0.029       47     4.7  caudalmiddlefrontal
 2403   1818   3062  1.801 0.410     0.152     0.042       37     4.4  cuneus
  695    770   2252  3.503 0.970     0.196     0.048       13     1.6  entorhinal
 4906   4362  10733  2.781 0.626     0.167     0.043       92    10.5  fusiform
 7404   5943  14612  2.672 0.551     0.150     0.039      110    12.9  inferiorparietal
 5854   5696  13796  2.766 0.646     0.169     0.041       82    11.6  inferiortemporal
 1747   1530   3261  2.349 0.896     0.165     0.047       25     3.7  isthmuscingulate
 9175   7923  16600  2.308 0.615     0.160     0.045      159    18.7  lateraloccipital
 4870   3764  11272  3.228 0.639     0.146     0.042       99     9.0  lateralorbitofrontal
 3672   3323   6564  2.247 0.639     0.175     0.075      246    16.3  lingual
 3130   2767   6482  2.715 0.585     0.168     0.044       65     6.2  medialorbitofrontal
 5746   5665  14916  3.049 0.676     0.162     0.035       83     9.6  middletemporal
  944    939   2289  2.892 0.659     0.187     0.050       13     2.3  parahippocampal
 2339   1806   4354  2.665 0.574     0.134     0.031       31     3.3  paracentral
 2384   2055   5592  3.017 0.478     0.159     0.037       38     4.0  parsopercularis
 1339   1344   3394  3.072 0.558     0.163     0.034       18     2.2  parsorbitalis
 2328   1986   5517  2.997 0.633     0.164     0.037       37     4.1  parstriangularis
 1880   1249   2235  1.784 0.411     0.127     0.038       33     2.8  pericalcarine
 7341   5986  12390  2.314 0.712     0.136     0.034       96    11.7  postcentral
 1787   1425   3483  2.662 0.752     0.160     0.043       49     3.5  posteriorcingulate
 9624   7253  18603  2.749 0.607     0.125     0.029      152    12.8  precentral
 7182   5646  13465  2.541 0.556     0.150     0.041      117    13.7  precuneus
 1554   1377   3338  2.875 0.654     0.170     0.047       30     3.3  rostralanteriorcingulate
 9010   7926  18914  2.631 0.566     0.164     0.037      139    16.1  rostralmiddlefrontal
13084  11434  33058  3.187 0.600     0.151     0.038      178    22.1  superiorfrontal
11067   8548  18829  2.361 0.563     0.136     0.031      138    14.8  superiorparietal
 6725   6000  16554  3.131 0.688     0.163     0.043      110    13.8  superiortemporal
 6986   5898  14861  2.795 0.581     0.163     0.040      113    12.9  supramarginal
  496    528   1346  3.118 0.610     0.205     0.042        9     1.0  frontalpole
  701    871   2361  3.492 0.915     0.210     0.053       14     1.7  temporalpole
  700    608   1293  2.671 0.538     0.176     0.055        9     1.9  transversetemporal
 3812   2406   7693  3.144 0.701     0.164     0.052       94     9.4  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051026 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 306008
Total vertex volume 302421 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1578   1083   3223  2.747 0.430     0.128     0.035       20     2.5  bankssts
 1368    971   2856  2.479 0.831     0.132     0.023       20     1.2  caudalanteriorcingulate
 3337   2299   6792  2.661 0.528     0.121     0.025       36     3.5  caudalmiddlefrontal
 2622   1690   4290  2.142 0.579     0.137     0.040       37     4.0  cuneus
  554    415   1872  3.543 0.734     0.143     0.027        6     0.6  entorhinal
 5350   3662  12204  2.888 0.595     0.128     0.029       77     6.3  fusiform
 7979   5325  15855  2.647 0.523     0.122     0.028      102     9.0  inferiorparietal
 5185   3558  12840  2.945 0.692     0.127     0.032       75     6.7  inferiortemporal
 1650   1084   3375  2.594 0.922     0.131     0.033       24     1.7  isthmuscingulate
 8874   6119  16211  2.312 0.583     0.142     0.039      124    14.1  lateraloccipital
 4438   2991  10075  3.115 0.667     0.130     0.033       67     5.6  lateralorbitofrontal
 4507   3196   8575  2.359 0.666     0.151     0.051       71     9.4  lingual
 3625   2398   6931  2.618 0.693     0.114     0.028       53     4.0  medialorbitofrontal
 5521   3821  14437  3.018 0.665     0.125     0.027       78     5.8  middletemporal
  874    624   2023  2.698 0.791     0.103     0.017        6     0.5  parahippocampal
 2473   1546   4267  2.597 0.502     0.105     0.026       19     2.4  paracentral
 2134   1462   4728  2.916 0.488     0.119     0.026       25     2.2  parsopercularis
 1764   1190   4602  3.111 0.690     0.126     0.028       24     1.9  parsorbitalis
 3064   2149   7146  2.949 0.536     0.145     0.037       46     4.6  parstriangularis
 2092   1414   2676  2.061 0.453     0.126     0.033       18     2.9  pericalcarine
 6922   4372  11711  2.367 0.712     0.112     0.025       65     6.8  postcentral
 2408   1564   4948  2.771 0.732     0.139     0.032       40     3.0  posteriorcingulate
 8858   5548  16837  2.784 0.596     0.107     0.024       94     8.9  precentral
 6608   4480  12389  2.584 0.567     0.136     0.034       88     8.8  precuneus
 1170    792   2642  2.846 0.743     0.122     0.029       15     1.3  rostralanteriorcingulate
 9372   6417  19257  2.600 0.589     0.135     0.032      126    12.5  rostralmiddlefrontal
12498   8513  30062  3.054 0.625     0.124     0.030      131    14.2  superiorfrontal
10676   6898  17908  2.352 0.475     0.124     0.028      124    11.4  superiorparietal
 6345   4276  15346  3.133 0.684     0.110     0.026       78     7.3  superiortemporal
 6190   4156  13382  2.801 0.563     0.118     0.025       68     6.2  supramarginal
  492    342   1556  3.221 0.568     0.161     0.037        9     0.8  frontalpole
  720    515   2813  3.702 0.631     0.126     0.029       10     0.9  temporalpole
  542    338   1140  2.887 0.545     0.111     0.038        5     0.7  transversetemporal
 3926   2629   7420  2.925 0.675     0.120     0.036       55     5.0  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051026 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 306008
Total vertex volume 302421 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1578   1222   3223  2.747 0.430     0.149     0.038       23     2.5  bankssts
 1368   1234   2856  2.479 0.831     0.171     0.044       31     2.7  caudalanteriorcingulate
 3337   2758   6792  2.661 0.528     0.139     0.028       48     4.3  caudalmiddlefrontal
 2622   2261   4290  2.142 0.579     0.159     0.039       38     4.9  cuneus
  554    621   1872  3.543 0.734     0.198     0.046       11     1.1  entorhinal
 5350   4699  12204  2.888 0.595     0.163     0.046      120    10.8  fusiform
 7979   6462  15855  2.647 0.523     0.143     0.034      107    12.5  inferiorparietal
 5185   5060  12840  2.945 0.692     0.174     0.044       82    10.6  inferiortemporal
 1650   1423   3375  2.594 0.922     0.161     0.045       27     3.1  isthmuscingulate
 8874   7884  16211  2.312 0.583     0.159     0.040      143    16.8  lateraloccipital
 4438   3573  10075  3.115 0.667     0.161     0.044      102     9.3  lateralorbitofrontal
 4507   4027   8575  2.359 0.666     0.175     0.049       89    10.9  lingual
 3625   3029   6931  2.618 0.693     0.164     0.044       64     7.5  medialorbitofrontal
 5521   5498  14437  3.018 0.665     0.162     0.037       76     9.6  middletemporal
  874    860   2023  2.698 0.791     0.202     0.055       17     2.4  parahippocampal
 2473   1724   4267  2.597 0.502     0.119     0.028       33     3.1  paracentral
 2134   1828   4728  2.916 0.488     0.154     0.037       27     3.7  parsopercularis
 1764   1707   4602  3.111 0.690     0.158     0.033       26     2.7  parsorbitalis
 3064   2696   7146  2.949 0.536     0.164     0.043       45     5.9  parstriangularis
 2092   1256   2676  2.061 0.453     0.116     0.030       29     2.7  pericalcarine
 6922   5470  11711  2.367 0.712     0.129     0.029       65     8.9  postcentral
 2408   2042   4948  2.771 0.732     0.175     0.049      110     4.9  posteriorcingulate
 8858   6350  16837  2.784 0.596     0.113     0.029      180    11.9  precentral
 6608   5011  12389  2.584 0.567     0.145     0.038       91    11.6  precuneus
 1170   1044   2642  2.846 0.743     0.178     0.050       30     2.4  rostralanteriorcingulate
 9372   8055  19257  2.600 0.589     0.161     0.039      147    16.9  rostralmiddlefrontal
12498  10832  30062  3.054 0.625     0.155     0.039      185    22.1  superiorfrontal
10676   8193  17908  2.352 0.475     0.131     0.030      133    13.3  superiorparietal
 6345   5681  15346  3.133 0.684     0.169     0.044      105    13.6  superiortemporal
 6190   5147  13382  2.801 0.563     0.155     0.038       97    11.3  supramarginal
  492    615   1556  3.221 0.568     0.216     0.044        7     1.1  frontalpole
  720    997   2813  3.702 0.631     0.230     0.054       11     1.8  temporalpole
  542    447   1140  2.887 0.545     0.155     0.044        7     1.1  transversetemporal
 3926   2576   7420  2.925 0.675     0.167     0.056      101     9.7  insula
PIDs (20180 20183 20186 20189) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 00:53:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 00:53:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot 

Waiting for PID 20292 of (20292 20295) to complete...
Waiting for PID 20295 of (20292 20295) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 2.9   using min determinant for regularization = 0.086
0 singular and 762 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
133 labels changed using aseg
relabeling using gibbs priors...
000:  10185 changed, 155300 examined...
001:   2465 changed, 39863 examined...
002:    717 changed, 12853 examined...
003:    303 changed, 4019 examined...
004:    142 changed, 1713 examined...
005:     81 changed, 796 examined...
006:     30 changed, 432 examined...
007:     22 changed, 184 examined...
008:      8 changed, 120 examined...
009:      1 changed, 47 examined...
010:      0 changed, 6 examined...
22 labels changed using aseg
000: 302 total segments, 217 labels (2779 vertices) changed
001: 96 total segments, 12 labels (35 vertices) changed
002: 85 total segments, 1 labels (2 vertices) changed
003: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 38 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1170 vertices marked for relabeling...
1170 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 719 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
16 labels changed using aseg
relabeling using gibbs priors...
000:   9951 changed, 153799 examined...
001:   2349 changed, 38804 examined...
002:    672 changed, 12208 examined...
003:    285 changed, 3781 examined...
004:    119 changed, 1559 examined...
005:     72 changed, 671 examined...
006:     48 changed, 412 examined...
007:     21 changed, 254 examined...
008:      7 changed, 141 examined...
009:      1 changed, 35 examined...
010:      1 changed, 7 examined...
011:      0 changed, 7 examined...
1 labels changed using aseg
000: 290 total segments, 206 labels (3279 vertices) changed
001: 96 total segments, 13 labels (92 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 43 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1284 vertices marked for relabeling...
1284 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (20292 20295) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 00:53:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051026 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 00:53:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051026 rh white 

Waiting for PID 20339 of (20339 20342) to complete...
Waiting for PID 20342 of (20339 20342) to complete...

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051026 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 307875
Total vertex volume 304615 (mask=0)
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1450    976   2923  2.719 0.565     0.137     0.033       20     2.0  G&S_frontomargin
 1856   1243   4146  2.493 0.793     0.141     0.048       26     3.5  G&S_occipital_inf
 2028   1152   3539  2.598 0.620     0.109     0.034       19     2.4  G&S_paracentral
 1851   1236   4261  2.909 0.529     0.122     0.025       20     1.9  G&S_subcentral
  999    661   2530  2.931 0.626     0.147     0.040       20     1.4  G&S_transv_frontopol
 2692   1802   5907  3.018 0.518     0.114     0.023       27     2.6  G&S_cingul-Ant
 1367    953   2556  2.775 0.484     0.110     0.019        9     1.0  G&S_cingul-Mid-Ant
 1181    849   2344  2.733 0.427     0.097     0.016        8     0.7  G&S_cingul-Mid-Post
  725    477   2201  3.341 0.661     0.145     0.029       13     0.8  G_cingul-Post-dorsal
  330    212    804  2.772 0.957     0.155     0.049        8     0.5  G_cingul-Post-ventral
 2223   1559   3239  1.820 0.510     0.153     0.048       37     4.0  G_cuneus
 1323    892   3642  3.026 0.506     0.117     0.027       18     1.3  G_front_inf-Opercular
  548    346   1693  3.232 0.596     0.153     0.033       11     0.7  G_front_inf-Orbital
 1368    946   3949  3.239 0.645     0.142     0.035       25     1.7  G_front_inf-Triangul
 5074   3474  12578  2.788 0.577     0.140     0.037       83     7.3  G_front_middle
 9066   6092  25282  3.301 0.619     0.138     0.039      135    14.6  G_front_sup
  900    587   1831  3.140 0.693     0.137     0.048       14     1.6  G_Ins_lg&S_cent_ins
  783    506   2360  3.576 0.742     0.133     0.040       12     1.1  G_insular_short
 2864   1834   5969  2.549 0.618     0.141     0.040       44     4.4  G_occipital_middle
 2313   1431   3836  2.213 0.588     0.132     0.042       29     3.4  G_occipital_sup
 1959   1297   4956  2.852 0.612     0.144     0.036       33     2.8  G_oc-temp_lat-fusifor
 2465   1733   4721  2.245 0.675     0.152     0.044       40     4.4  G_oc-temp_med-Lingual
 1388    983   4275  3.278 0.885     0.139     0.032       30     2.0  G_oc-temp_med-Parahip
 3155   2020   8523  3.134 0.650     0.133     0.036       53     4.5  G_orbital
 3056   1995   7144  2.722 0.551     0.146     0.037       57     4.3  G_pariet_inf-Angular
 3736   2455   9130  2.949 0.622     0.135     0.032       58     4.7  G_pariet_inf-Supramar
 4464   2796   8998  2.509 0.629     0.124     0.029       58     5.0  G_parietal_sup
 2754   1593   5172  2.447 0.704     0.119     0.041       46     4.7  G_postcentral
 3740   2297   8584  2.936 0.663     0.116     0.033       39     4.7  G_precentral
 3270   2215   7686  2.685 0.535     0.140     0.032       54     4.1  G_precuneus
 1195    898   3244  2.655 0.608     0.149     0.038       27     2.0  G_rectus
  713    457   1289  2.663 0.913     0.110     0.056       15     1.4  G_subcallosal
  566    347   1131  2.647 0.548     0.127     0.040        7     1.0  G_temp_sup-G_T_transv
 2516   1645   8023  3.310 0.757     0.139     0.035       49     3.3  G_temp_sup-Lateral
  920    625   2683  3.681 0.795     0.085     0.026        6     1.0  G_temp_sup-Plan_polar
 1060    709   2323  2.809 0.501     0.100     0.018        9     0.9  G_temp_sup-Plan_tempo
 3317   2268   8962  2.801 0.718     0.136     0.037       68     5.0  G_temporal_inf
 3141   2098  10268  3.286 0.659     0.134     0.034       60     4.2  G_temporal_middle
  411    286    667  2.834 0.424     0.089     0.013        2     0.2  Lat_Fis-ant-Horizont
  390    302    687  2.918 0.534     0.101     0.010        2     0.2  Lat_Fis-ant-Vertical
 1137    770   1713  2.781 0.408     0.112     0.026        8     1.2  Lat_Fis-post
 2526   1723   4972  2.247 0.654     0.169     0.058       51     6.3  Pole_occipital
 1700   1180   5321  3.091 0.735     0.153     0.045       38     3.1  Pole_temporal
 2241   1665   3045  2.031 0.557     0.139     0.036       27     3.3  S_calcarine
 3643   2459   4340  1.974 0.523     0.108     0.021       23     3.2  S_central
 1438   1007   2210  2.370 0.464     0.104     0.018        9     1.1  S_cingul-Marginalis
  678    455   1242  3.436 0.362     0.102     0.018        3     0.5  S_circular_insula_ant
 1649   1108   3024  3.287 0.626     0.090     0.017        7     1.1  S_circular_insula_inf
 1820   1278   2902  2.877 0.433     0.106     0.019        9     1.5  S_circular_insula_sup
 1080    764   1882  2.725 0.601     0.108     0.016        8     0.8  S_collat_transv_ant
  724    459    867  2.251 0.373     0.127     0.033        6     1.0  S_collat_transv_post
 2081   1463   3663  2.466 0.478     0.117     0.026       18     2.1  S_front_inf
 1503   1071   2644  2.408 0.492     0.125     0.029       17     1.7  S_front_middle
 3482   2439   6230  2.739 0.428     0.100     0.019       20     2.7  S_front_sup
  397    292    648  2.425 0.425     0.123     0.019        3     0.4  S_interm_prim-Jensen
 3386   2350   4599  2.216 0.419     0.108     0.018       24     2.6  S_intrapariet&P_trans
 1105    746   1376  2.135 0.402     0.114     0.024        7     1.1  S_oc_middle&Lunatus
 1715   1128   2410  2.188 0.452     0.121     0.026       17     1.8  S_oc_sup&transversal
  546    365    730  2.581 0.384     0.151     0.037        6     0.9  S_occipital_ant
 1055    753   1876  2.670 0.418     0.101     0.017        6     0.6  S_oc-temp_lat
 2091   1497   3517  2.507 0.678     0.115     0.022       17     1.9  S_oc-temp_med&Lingual
  442    293    618  2.533 0.494     0.121     0.020        3     0.4  S_orbital_lateral
  745    546   1216  2.721 0.593     0.113     0.016        5     0.4  S_orbital_med-olfact
 1810   1235   3855  3.373 0.571     0.121     0.028       18     2.0  S_orbital-H_Shaped
 2955   1931   4209  2.354 0.568     0.121     0.027       28     3.2  S_parieto_occipital
 1363    805   1237  1.920 0.751     0.117     0.018       21     0.8  S_pericallosal
 3353   2262   4924  2.390 0.461     0.111     0.022       25     2.7  S_postcentral
 1837   1257   3188  2.784 0.374     0.094     0.015       11     1.1  S_precentral-inf-part
 2055   1405   3245  2.655 0.398     0.105     0.021       14     1.6  S_precentral-sup-part
  727    496   1174  2.867 0.405     0.095     0.013        3     0.4  S_suborbital
 1351    940   2126  2.430 0.492     0.111     0.020        8     1.2  S_subparietal
 2078   1397   3168  2.638 0.416     0.104     0.018       14     1.4  S_temporal_inf
 6751   4626  11820  2.770 0.501     0.109     0.020       50     5.7  S_temporal_sup
  374    258    569  2.425 0.408     0.133     0.026        4     0.4  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051026 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 306008
Total vertex volume 302421 (mask=0)
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1060    748   2247  2.638 0.613     0.144     0.039       20     1.6  G&S_frontomargin
 1514   1125   3172  2.344 0.696     0.157     0.045       27     2.7  G&S_occipital_inf
 1669    943   2701  2.468 0.556     0.108     0.032       17     2.2  G&S_paracentral
 1503   1012   3420  2.997 0.546     0.136     0.031       19     1.8  G&S_subcentral
 1179    821   3044  2.751 0.618     0.170     0.048       25     2.6  G&S_transv_frontopol
 3582   2438   7435  2.888 0.609     0.111     0.023       33     3.3  G&S_cingul-Ant
 1794   1249   3759  2.863 0.558     0.121     0.023       21     1.6  G&S_cingul-Mid-Ant
 2000   1347   4031  2.910 0.551     0.123     0.029       21     2.3  G&S_cingul-Mid-Post
  682    454   2022  3.318 0.546     0.153     0.040       13     1.0  G_cingul-Post-dorsal
  317    208    914  3.183 0.594     0.148     0.049        8     0.4  G_cingul-Post-ventral
 2453   1569   4222  2.146 0.582     0.143     0.041       38     4.0  G_cuneus
 1516   1027   4137  3.002 0.539     0.135     0.034       26     1.9  G_front_inf-Opercular
  542    357   1760  3.188 0.527     0.154     0.040       11     0.9  G_front_inf-Orbital
 1277    922   3718  3.088 0.558     0.173     0.053       29     2.5  G_front_inf-Triangul
 4221   2889  11375  2.837 0.611     0.146     0.037       70     6.5  G_front_middle
 8158   5430  22509  3.212 0.602     0.134     0.035      108    10.8  G_front_sup
  742    500   1534  2.852 0.696     0.126     0.038       12     1.1  G_Ins_lg&S_cent_ins
 1170    752   2456  2.909 0.823     0.145     0.056       30     2.1  G_insular_short
 2230   1426   5378  2.794 0.535     0.139     0.037       41     3.0  G_occipital_middle
 2395   1443   3983  2.346 0.462     0.130     0.038       30     3.3  G_occipital_sup
 2482   1646   6003  2.944 0.564     0.134     0.036       46     3.5  G_oc-temp_lat-fusifor
 2770   1928   5731  2.307 0.718     0.163     0.061       53     6.9  G_oc-temp_med-Lingual
 1275    898   4237  3.333 0.781     0.145     0.032       19     1.7  G_oc-temp_med-Parahip
 3518   2361  10028  3.154 0.680     0.142     0.043       78     5.9  G_orbital
 3342   2173   8620  2.839 0.603     0.141     0.038       64     5.1  G_pariet_inf-Angular
 2985   2001   7342  2.892 0.554     0.126     0.027       39     3.4  G_pariet_inf-Supramar
 3921   2493   7494  2.444 0.520     0.124     0.026       50     3.8  G_parietal_sup
 2755   1626   5314  2.511 0.691     0.110     0.026       28     2.9  G_postcentral
 3308   1966   7900  3.008 0.549     0.110     0.029       56     3.7  G_precentral
 2974   1943   6962  2.749 0.530     0.150     0.041       55     4.8  G_precuneus
  868    595   2297  2.651 0.696     0.135     0.039       18     1.3  G_rectus
  484    310    853  2.491 0.965     0.122     0.056       13     0.9  G_subcallosal
  405    247    987  2.908 0.621     0.101     0.039        4     0.6  G_temp_sup-G_T_transv
 2434   1609   7226  3.257 0.654     0.145     0.040       44     4.3  G_temp_sup-Lateral
  804    571   2489  3.765 0.623     0.101     0.018        6     0.7  G_temp_sup-Plan_polar
  871    572   1927  2.809 0.616     0.099     0.051       23     2.5  G_temp_sup-Plan_tempo
 2797   1910   8161  3.094 0.670     0.142     0.040       55     4.1  G_temporal_inf
 3229   2222  10217  3.146 0.701     0.135     0.035       57     4.4  G_temporal_middle
  582    388    936  2.872 0.423     0.102     0.015        3     0.4  Lat_Fis-ant-Horizont
  328    226    564  2.837 0.423     0.105     0.016        2     0.3  Lat_Fis-ant-Vertical
 1380    961   2223  2.825 0.438     0.091     0.016        5     0.8  Lat_Fis-post
 3975   2835   7176  2.090 0.546     0.163     0.052       67     8.6  Pole_occipital
 1835   1285   6218  3.254 0.851     0.144     0.030       33     2.4  Pole_temporal
 2359   1656   3531  2.484 0.622     0.131     0.034       23     3.4  S_calcarine
 3648   2371   4208  2.070 0.587     0.104     0.022       22     3.5  S_central
 1280    894   2058  2.453 0.444     0.093     0.017        8     0.8  S_cingul-Marginalis
  841    566   1342  2.970 0.869     0.097     0.017        3     0.6  S_circular_insula_ant
 1436    957   2366  2.971 0.691     0.088     0.016        6     1.0  S_circular_insula_inf
 1491   1024   2621  3.092 0.428     0.108     0.019        7     1.2  S_circular_insula_sup
 1292    904   2538  3.020 0.598     0.090     0.012        5     0.7  S_collat_transv_ant
  365    250    394  1.962 0.363     0.131     0.022        3     0.4  S_collat_transv_post
 2332   1630   3684  2.407 0.400     0.106     0.019       16     2.0  S_front_inf
 2486   1677   4265  2.466 0.557     0.126     0.027       25     2.6  S_front_middle
 2979   2064   5016  2.574 0.498     0.104     0.020       18     2.3  S_front_sup
  601    413    885  2.390 0.388     0.100     0.013        3     0.4  S_interm_prim-Jensen
 4041   2735   5659  2.265 0.393     0.110     0.021       30     3.2  S_intrapariet&P_trans
  913    632   1301  2.300 0.479     0.094     0.015        5     0.6  S_oc_middle&Lunatus
 1606   1072   2315  2.381 0.400     0.121     0.027       15     1.9  S_oc_sup&transversal
  835    574   1215  2.466 0.343     0.117     0.024        7     0.8  S_occipital_ant
 1129    795   1945  2.691 0.464     0.113     0.026        8     1.2  S_oc-temp_lat
 2247   1608   3784  2.447 0.508     0.099     0.017       14     1.6  S_oc-temp_med&Lingual
  704    486   1037  2.536 0.420     0.130     0.026        6     0.9  S_orbital_lateral
  764    533   1250  2.837 0.832     0.105     0.014        5     0.4  S_orbital_med-olfact
 1655   1133   3185  3.042 0.588     0.119     0.021       14     1.3  S_orbital-H_Shaped
 2698   1832   3798  2.271 0.562     0.132     0.035       29     3.5  S_parieto_occipital
 1829   1135   1707  1.868 0.677     0.119     0.020       26     1.1  S_pericallosal
 2680   1776   3866  2.402 0.436     0.111     0.020       22     2.1  S_postcentral
 1901   1274   2976  2.752 0.444     0.104     0.018       12     1.5  S_precentral-inf-part
 1862   1250   2948  2.578 0.570     0.103     0.018       11     1.4  S_precentral-sup-part
  569    389    807  2.500 0.454     0.113     0.015        4     0.3  S_suborbital
 1601   1110   2724  2.597 0.461     0.118     0.024       12     1.7  S_subparietal
 1459   1004   2258  2.578 0.522     0.114     0.019       12     1.3  S_temporal_inf
 6496   4470  11427  2.765 0.482     0.105     0.019       45     5.0  S_temporal_sup
  305    213    586  3.037 0.459     0.116     0.020        2     0.2  S_temporal_transverse
PIDs (20339 20342) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 00:54:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 00:54:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot 

Waiting for PID 20412 of (20412 20415) to complete...
Waiting for PID 20415 of (20412 20415) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 383 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1479 labels changed using aseg
relabeling using gibbs priors...
000:   2147 changed, 155300 examined...
001:    472 changed, 9831 examined...
002:    132 changed, 2765 examined...
003:     55 changed, 802 examined...
004:     25 changed, 336 examined...
005:     21 changed, 134 examined...
006:     13 changed, 117 examined...
007:      7 changed, 61 examined...
008:      7 changed, 44 examined...
009:      8 changed, 37 examined...
010:      5 changed, 45 examined...
011:      2 changed, 27 examined...
012:      2 changed, 14 examined...
013:      1 changed, 11 examined...
014:      0 changed, 7 examined...
248 labels changed using aseg
000: 78 total segments, 45 labels (349 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
871 vertices marked for relabeling...
871 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051026 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.009
0 singular and 325 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1237 labels changed using aseg
relabeling using gibbs priors...
000:   2183 changed, 153799 examined...
001:    507 changed, 10042 examined...
002:    125 changed, 2811 examined...
003:     48 changed, 803 examined...
004:     18 changed, 287 examined...
005:      8 changed, 115 examined...
006:      4 changed, 45 examined...
007:      2 changed, 22 examined...
008:      1 changed, 15 examined...
009:      1 changed, 7 examined...
010:      0 changed, 8 examined...
111 labels changed using aseg
000: 59 total segments, 26 labels (292 vertices) changed
001: 35 total segments, 2 labels (4 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1072 vertices marked for relabeling...
1072 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (20412 20415) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 00:54:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0051026 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 00:54:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0051026 rh white 

Waiting for PID 20464 of (20464 20467) to complete...
Waiting for PID 20467 of (20464 20467) to complete...

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0051026 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 307875
Total vertex volume 304615 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1656   1124   3500  2.871 0.624     0.122     0.022       20     1.3  caudalanteriorcingulate
 3982   2674   7755  2.713 0.506     0.111     0.023       36     3.5  caudalmiddlefrontal
 3505   2364   4916  1.935 0.526     0.138     0.041       46     5.4  cuneus
  613    447   2126  3.663 0.924     0.145     0.035       20     1.0  entorhinal
 4672   3200   9880  2.760 0.625     0.131     0.028       57     5.5  fusiform
 7252   4853  14346  2.662 0.554     0.130     0.029       93     8.5  inferiorparietal
 5940   4093  14290  2.758 0.657     0.125     0.032       96     7.7  inferiortemporal
 1710   1119   3218  2.373 0.884     0.128     0.032       25     2.0  isthmuscingulate
 9164   6001  16666  2.306 0.622     0.146     0.045      135    16.6  lateraloccipital
 5329   3538  12487  3.188 0.665     0.127     0.034       71     6.7  lateralorbitofrontal
 3842   2726   6859  2.257 0.632     0.139     0.038       54     5.9  lingual
 2595   1839   5728  2.731 0.608     0.119     0.032       43     3.5  medialorbitofrontal
 7459   5049  17983  2.977 0.647     0.121     0.027       99     8.0  middletemporal
  969    691   2342  2.881 0.680     0.116     0.022        8     0.9  parahippocampal
 2840   1806   5254  2.657 0.582     0.105     0.033       34     3.8  paracentral
 2153   1513   4918  3.004 0.470     0.110     0.021       20     1.6  parsopercularis
 1312    877   3290  3.199 0.543     0.124     0.023       15     1.2  parsorbitalis
 2734   1927   6447  2.950 0.653     0.126     0.028       36     2.8  parstriangularis
 1819   1327   2151  1.795 0.409     0.131     0.035       20     2.7  pericalcarine
 8287   5277  13881  2.330 0.696     0.114     0.029       91    10.1  postcentral
 1981   1318   3753  2.635 0.751     0.121     0.019       26     1.5  posteriorcingulate
 9369   6006  18283  2.763 0.603     0.108     0.026       80     9.5  precentral
 7097   4812  13442  2.548 0.551     0.133     0.029       92     8.2  precuneus
 2218   1464   4676  2.893 0.658     0.124     0.030       28     2.9  rostralanteriorcingulate
 6726   4600  14260  2.631 0.552     0.138     0.034      101     9.3  rostralmiddlefrontal
13777   9450  34038  3.120 0.620     0.129     0.033      159    17.5  superiorfrontal
 8878   5780  15109  2.363 0.556     0.118     0.026       93     8.7  superiorparietal
 8625   5814  21241  3.141 0.718     0.113     0.026       96     9.2  superiortemporal
 6613   4431  13953  2.802 0.583     0.128     0.029       84     7.4  supramarginal
  682    417   1254  2.673 0.535     0.136     0.041        9     1.1  transversetemporal
 3196   2135   6570  3.162 0.675     0.116     0.029       31     3.7  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0051026 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 306008
Total vertex volume 302421 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1523   1072   3126  2.461 0.848     0.132     0.023       22     1.3  caudalanteriorcingulate
 3415   2360   6905  2.669 0.521     0.120     0.025       36     3.4  caudalmiddlefrontal
 3164   2055   5115  2.125 0.554     0.136     0.039       44     4.8  cuneus
  483    367   1679  3.516 0.663     0.140     0.025        5     0.5  entorhinal
 5072   3464  11268  2.870 0.569     0.127     0.030       72     6.4  fusiform
 8090   5402  16249  2.665 0.533     0.124     0.028      105     9.3  inferiorparietal
 5527   3803  13835  2.965 0.705     0.128     0.031       79     6.8  inferiortemporal
 1635   1078   3319  2.592 0.893     0.130     0.032       23     1.7  isthmuscingulate
 8873   6113  16157  2.305 0.570     0.142     0.039      124    13.9  lateraloccipital
 5112   3485  12038  3.134 0.667     0.139     0.039      100     7.5  lateralorbitofrontal
 4410   3130   8358  2.340 0.653     0.152     0.051       70     9.4  lingual
 2321   1563   4837  2.584 0.722     0.122     0.036       40     3.0  medialorbitofrontal
 6571   4536  16443  2.968 0.645     0.123     0.027       88     6.7  middletemporal
 1000    704   2328  2.754 0.829     0.108     0.020        8     0.7  parahippocampal
 2611   1639   4585  2.611 0.503     0.105     0.026       20     2.5  paracentral
 2573   1768   5662  2.902 0.494     0.123     0.027       31     2.8  parsopercularis
 1513   1019   3863  3.059 0.674     0.117     0.027       18     1.5  parsorbitalis
 2946   2049   6615  2.932 0.538     0.145     0.037       44     4.5  parstriangularis
 2109   1426   2722  2.062 0.453     0.126     0.033       19     2.9  pericalcarine
 7733   4906  12842  2.351 0.696     0.112     0.025       73     7.7  postcentral
 2467   1611   5127  2.805 0.716     0.137     0.031       39     3.1  posteriorcingulate
 8397   5253  16150  2.795 0.588     0.108     0.025       92     8.5  precentral
 6814   4608  12949  2.592 0.559     0.135     0.034       91     9.0  precuneus
 1696   1119   3304  2.782 0.748     0.116     0.026       20     1.8  rostralanteriorcingulate
 6963   4745  14294  2.605 0.586     0.128     0.030       82     8.4  rostralmiddlefrontal
15917  10791  37083  2.967 0.649     0.126     0.029      177    18.7  superiorfrontal
 8989   5790  15183  2.368 0.478     0.124     0.028      104     9.3  superiorparietal
 8326   5633  20727  3.129 0.701     0.115     0.029      107    10.8  superiortemporal
 5590   3767  12081  2.794 0.569     0.115     0.024       59     5.5  supramarginal
  559    346   1172  2.928 0.569     0.114     0.037        5     0.8  transversetemporal
 3331   2250   6406  2.911 0.653     0.117     0.031       37     3.8  insula
PIDs (20464 20467) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 00:55:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 pctsurfcon --s 0051026 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 00:55:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts

 pctsurfcon --s 0051026 --rh-only 

Waiting for PID 20539 of (20539 20551) to complete...
Waiting for PID 20551 of (20539 20551) to complete...

 pctsurfcon --s 0051026 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts/pctsurfcon.log
Sun Oct  8 00:55:07 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $
Linux tars-609 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.wm.mgh --regheader 0051026 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 75940
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.wm.mgh
Dim: 155300 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.gm.mgh --projfrac 0.3 --regheader 0051026 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 91157
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.gm.mgh
Dim: 155300 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20539/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.w-g.pct.mgh --annot 0051026 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/stats/lh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.w-g.pct.mgh --annot 0051026 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 1000
Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.w-g.pct.mgh
Vertex Area is 0.669866 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation

Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up

 pctsurfcon --s 0051026 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts/pctsurfcon.log
Sun Oct  8 00:55:07 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/scripts
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $
Linux tars-609 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.wm.mgh --regheader 0051026 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 75225
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.wm.mgh
Dim: 153799 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.gm.mgh --projfrac 0.3 --regheader 0051026 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 90234
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.gm.mgh
Dim: 153799 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/tmp.pctsurfcon.20551/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.w-g.pct.mgh --annot 0051026 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/stats/rh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.w-g.pct.mgh --annot 0051026 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 2000
Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.w-g.pct.mgh
Vertex Area is 0.670808 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation

Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
PIDs (20539 20551) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 00:55:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1172 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1668 voxels changed to hypointensity...
2855 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 00:55:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_aparc2aseg --s 0051026 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 00:55:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_aparc2aseg --s 0051026 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 00:55:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_aparc2aseg --s 0051026 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz 

Waiting for PID 20719 of (20719 20722 20725) to complete...
Waiting for PID 20722 of (20719 20722 20725) to complete...
Waiting for PID 20725 of (20719 20722 20725) to complete...

 mri_aparc2aseg --s 0051026 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
subject 0051026
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.38
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 54
rescaling Left_Lateral_Ventricle from 13 -->  9
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 48
rescaling Left_Thalamus from 94 --> 93
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 64
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 89
rescaling Third_Ventricle from 25 --> 14
rescaling Fourth_Ventricle from 22 -->  9
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 57
rescaling Left_Amygdala from 56 --> 59
rescaling CSF from 32 --> 20
rescaling Left_Accumbens_area from 62 --> 57
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 55
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 23
rescaling Right_Cerebellum_White_Matter from 87 --> 85
rescaling Right_Cerebellum_Cortex from 59 --> 49
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 72
rescaling Right_Pallidum from 97 --> 88
rescaling Right_Hippocampus from 53 --> 54
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 91
rescaling Fifth_Ventricle from 40 --> 18
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 601104
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 419 changed.
pass 2: 70 changed.
pass 3: 8 changed.
pass 4: 4 changed.
pass 5: 2 changed.
pass 6: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051026 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
subject 0051026
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)

Reading rh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.38
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 54
rescaling Left_Lateral_Ventricle from 13 -->  9
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 48
rescaling Left_Thalamus from 94 --> 93
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 64
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 89
rescaling Third_Ventricle from 25 --> 14
rescaling Fourth_Ventricle from 22 -->  9
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 57
rescaling Left_Amygdala from 56 --> 59
rescaling CSF from 32 --> 20
rescaling Left_Accumbens_area from 62 --> 57
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 55
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 23
rescaling Right_Cerebellum_White_Matter from 87 --> 85
rescaling Right_Cerebellum_Cortex from 59 --> 49
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 72
rescaling Right_Pallidum from 97 --> 88
rescaling Right_Hippocampus from 53 --> 54
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 91
rescaling Fifth_Ventricle from 40 --> 18
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 601124
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 419 changed.
pass 2: 70 changed.
pass 3: 8 changed.
pass 4: 4 changed.
pass 5: 2 changed.
pass 6: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051026 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
subject 0051026
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.aparc.DKTatlas.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.aparc.DKTatlas.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.38
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 54
rescaling Left_Lateral_Ventricle from 13 -->  9
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 48
rescaling Left_Thalamus from 94 --> 93
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 64
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 89
rescaling Third_Ventricle from 25 --> 14
rescaling Fourth_Ventricle from 22 -->  9
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 57
rescaling Left_Amygdala from 56 --> 59
rescaling CSF from 32 --> 20
rescaling Left_Accumbens_area from 62 --> 57
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 55
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 23
rescaling Right_Cerebellum_White_Matter from 87 --> 85
rescaling Right_Cerebellum_Cortex from 59 --> 49
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 72
rescaling Right_Pallidum from 97 --> 88
rescaling Right_Hippocampus from 53 --> 54
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 91
rescaling Fifth_Ventricle from 40 --> 18
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 601124
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 419 changed.
pass 2: 70 changed.
pass 3: 8 changed.
pass 4: 4 changed.
pass 5: 2 changed.
pass 6: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (20719 20722 20725) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 01:03:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri

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

Sun Oct  8 01:03:46 CEST 2017

setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
$Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $
Linux tars-609 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri
cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 01:03:46 CEST 2017 
Ended   at Sun Oct  8 01:03:52 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 01:03:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0051026 


$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0051026 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
Computing euler number
orig.nofix lheno =  -92, rheno = -72
orig.nofix lhholes =   47, rhholes = 37
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 01:05:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026

 mri_aparc2aseg --s 0051026 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 

SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
subject 0051026
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8304 vertices from left hemi
Ripped 8083 vertices from right hemi

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/aparc+aseg.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1130085
Used brute-force search on 60 voxels
Fixing Parahip LH WM
  Found 9 clusters
     0 k 2.000000
     1 k 1.000000
     2 k 40.000000
     3 k 1.000000
     4 k 1410.000000
     5 k 3.000000
     6 k 23.000000
     7 k 1.000000
     8 k 1.000000
Fixing Parahip RH WM
  Found 11 clusters
     0 k 3.000000
     1 k 1.000000
     2 k 3.000000
     3 k 1.000000
     4 k 2.000000
     5 k 1443.000000
     6 k 4.000000
     7 k 5.000000
     8 k 1.000000
     9 k 1.000000
     10 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0051026 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 


$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0051026 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 390 segmentations
Computing statistics for each segmentation

Reporting on  70 segmentations
Using PrintSegStat
mri_segstats done
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 01:14:25 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22405 of (22405 22411 22417 22423 22429) to complete...
Waiting for PID 22411 of (22405 22411 22417 22423 22429) to complete...
Waiting for PID 22417 of (22405 22411 22417 22423 22429) to complete...
Waiting for PID 22423 of (22405 22411 22417 22423 22429) to complete...
Waiting for PID 22429 of (22405 22411 22417 22423 22429) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA1_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4129 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 526
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4655
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA2_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7909 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 840
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8749
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA3a_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4077 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 153
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4230
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA3b_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5983 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 510
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6493
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA4a_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5784 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 995
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6779
mri_label2label: Done

PIDs (22405 22411 22417 22423 22429) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22505 of (22505 22511 22517 22521) to complete...
Waiting for PID 22511 of (22505 22511 22517 22521) to complete...
Waiting for PID 22517 of (22505 22511 22517 22521) to complete...
Waiting for PID 22521 of (22505 22511 22517 22521) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA4p_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4070 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 475
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4545
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA6_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  13589 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 2712
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16301
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA44_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4181 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 334
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4515
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0051026 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA45_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3422 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 877
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4299
mri_label2label: Done

PIDs (22505 22511 22517 22521) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0051026 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0051026 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0051026 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0051026 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0051026 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22627 of (22627 22633 22639 22645 22651) to complete...
Waiting for PID 22633 of (22627 22633 22639 22645 22651) to complete...
Waiting for PID 22639 of (22627 22633 22639 22645 22651) to complete...
Waiting for PID 22645 of (22627 22633 22639 22645 22651) to complete...
Waiting for PID 22651 of (22627 22633 22639 22645 22651) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0051026 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.V1_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4641 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 1351
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5992
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0051026 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.V2_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8114 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 3486
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11600
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0051026 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.MT_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2018 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 459
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2477
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0051026 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.entorhinal_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1290 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1290 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 106
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1396
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0051026 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.perirhinal_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1199 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 147
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1346
mri_label2label: Done

PIDs (22627 22633 22639 22645 22651) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 23163 of (23163 23169 23175 23182 23188) to complete...
Waiting for PID 23169 of (23163 23169 23175 23182 23188) to complete...
Waiting for PID 23175 of (23163 23169 23175 23182 23188) to complete...
Waiting for PID 23182 of (23163 23169 23175 23182 23188) to complete...
Waiting for PID 23188 of (23163 23169 23175 23182 23188) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA1_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1014 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 171
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1185
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA2_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2092 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 220
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2312
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA3a_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1504 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 42
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1546
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA3b_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1996 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 190
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2186
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA4a_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2319 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 405
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2724
mri_label2label: Done

PIDs (23163 23169 23175 23182 23188) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 23350 of (23350 23356 23362 23367) to complete...
Waiting for PID 23356 of (23350 23356 23362 23367) to complete...
Waiting for PID 23362 of (23350 23356 23362 23367) to complete...
Waiting for PID 23367 of (23350 23356 23362 23367) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA4p_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1549 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 128
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1677
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA6_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7035 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 1275
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8310
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA44_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1912 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 108
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2020
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.BA45_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1151 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 346
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1497
mri_label2label: Done

PIDs (23350 23356 23362 23367) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 23636 of (23636 23642 23648 23654 23659) to complete...
Waiting for PID 23642 of (23636 23642 23648 23654 23659) to complete...
Waiting for PID 23648 of (23636 23642 23648 23654 23659) to complete...
Waiting for PID 23654 of (23636 23642 23648 23654 23659) to complete...
Waiting for PID 23659 of (23636 23642 23648 23654 23659) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.V1_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3405 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 850
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4255
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.V2_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3334 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 1600
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4934
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.MT_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  513 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 114
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 627
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.entorhinal_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 470 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  470 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 37
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 507
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./lh.perirhinal_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 450 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  450 nlabel points
Performing mapping from target back to the source label 155300
Number of reverse mapping hits = 70
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 520
mri_label2label: Done

PIDs (23636 23642 23648 23654 23659) completed and logs appended.

 mris_label2annot --s 0051026 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 

Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label
cmdline mris_label2annot --s 0051026 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut

subject 0051026
hemi    lh
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
AnnotName  BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 108317 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051026 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 

Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label
cmdline mris_label2annot --s 0051026 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut

subject 0051026
hemi    lh
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
AnnotName  BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 127772 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/lh.BA_exvivo.thresh.annot

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 0051026 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 307875
Total vertex volume 304615 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1334    762   2514  2.510 0.673     0.126     0.038       17     1.8  BA1_exvivo
 4498   2921   7837  2.504 0.541     0.111     0.025       41     4.1  BA2_exvivo
 1091    743   1065  1.835 0.370     0.136     0.030       10     1.1  BA3a_exvivo
 2675   1726   4031  2.029 0.744     0.111     0.032       38     3.9  BA3b_exvivo
 2207   1213   4026  2.849 0.557     0.098     0.028       17     2.6  BA4a_exvivo
 1496   1029   2188  2.272 0.485     0.113     0.024        9     1.7  BA4p_exvivo
12251   8101  28854  3.039 0.603     0.115     0.029      127    13.6  BA6_exvivo
 2263   1560   5085  2.944 0.460     0.102     0.020       21     1.7  BA44_exvivo
 3439   2424   8353  2.921 0.664     0.134     0.031       48     4.1  BA45_exvivo
 3323   2460   5236  1.961 0.577     0.151     0.047       55     6.3  V1_exvivo
 9003   6005  14076  2.093 0.579     0.147     0.045      130    15.9  V2_exvivo
 2139   1415   4507  2.662 0.585     0.141     0.033       27     2.8  MT_exvivo
  516    366   1884  3.602 0.880     0.125     0.025        5     0.4  perirhinal_exvivo
  748    563   1761  3.011 0.744     0.150     0.030       11     0.8  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051026 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 307875
Total vertex volume 304615 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.thresh.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
  884    463   1697  2.566 0.645     0.130     0.064       24     2.6  BA1_exvivo
 1767   1127   3150  2.496 0.589     0.104     0.024       15     1.6  BA2_exvivo
  931    629    860  1.794 0.322     0.139     0.032        9     1.0  BA3a_exvivo
 1684   1109   1893  1.657 0.415     0.104     0.022       13     1.6  BA3b_exvivo
 2157   1236   3918  2.781 0.573     0.100     0.028       15     2.5  BA4a_exvivo
 1234    853   1770  2.229 0.461     0.110     0.023        8     1.3  BA4p_exvivo
 6818   4416  15548  3.014 0.597     0.115     0.031       78     8.2  BA6_exvivo
 1416    986   3318  3.011 0.419     0.108     0.021       15     1.1  BA44_exvivo
 1366    974   3877  3.153 0.698     0.138     0.033       23     1.6  BA45_exvivo
 3503   2605   5583  1.965 0.565     0.151     0.046       56     6.5  V1_exvivo
 4521   3052   7026  1.999 0.549     0.158     0.051       76     9.4  V2_exvivo
  569    389   1156  2.614 0.448     0.161     0.036        9     0.9  MT_exvivo
  260    182    939  3.680 0.688     0.135     0.024        3     0.3  perirhinal_exvivo
  418    298    949  3.010 0.607     0.137     0.024        6     0.4  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 01:17:46 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 23938 of (23938 23944 23950 23956 23962) to complete...
Waiting for PID 23944 of (23938 23944 23950 23956 23962) to complete...
Waiting for PID 23950 of (23938 23944 23950 23956 23962) to complete...
Waiting for PID 23956 of (23938 23944 23950 23956 23962) to complete...
Waiting for PID 23962 of (23938 23944 23950 23956 23962) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA1_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3962 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 520
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4482
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA2_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6687 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 591
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7278
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA3a_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3980 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 301
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4281
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA3b_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4522 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 478
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5000
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA4a_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5747 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 896
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6643
mri_label2label: Done

PIDs (23938 23944 23950 23956 23962) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 24008 of (24008 24014 24020 24026) to complete...
Waiting for PID 24014 of (24008 24014 24020 24026) to complete...
Waiting for PID 24020 of (24008 24014 24020 24026) to complete...
Waiting for PID 24026 of (24008 24014 24020 24026) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA4p_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4473 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 512
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4985
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA6_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  12256 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 1807
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14063
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA44_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6912 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 1016
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7928
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0051026 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA45_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5355 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 1811
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7166
mri_label2label: Done

PIDs (24008 24014 24020 24026) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0051026 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0051026 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0051026 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0051026 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0051026 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 24085 of (24085 24091 24097 24103 24109) to complete...
Waiting for PID 24091 of (24085 24091 24097 24103 24109) to complete...
Waiting for PID 24097 of (24085 24091 24097 24103 24109) to complete...
Waiting for PID 24103 of (24085 24091 24097 24103 24109) to complete...
Waiting for PID 24109 of (24085 24091 24097 24103 24109) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0051026 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.V1_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4727 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 1616
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6343
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0051026 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.V2_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8016 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 3524
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11540
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0051026 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.MT_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1932 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 429
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2361
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0051026 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.entorhinal_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1038 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1038 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 144
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1182
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0051026 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.perirhinal_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  752 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 134
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 886
mri_label2label: Done

PIDs (24085 24091 24097 24103 24109) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 24158 of (24158 24164 24170 24175 24182) to complete...
Waiting for PID 24164 of (24158 24164 24170 24175 24182) to complete...
Waiting for PID 24170 of (24158 24164 24170 24175 24182) to complete...
Waiting for PID 24175 of (24158 24164 24170 24175 24182) to complete...
Waiting for PID 24182 of (24158 24164 24170 24175 24182) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA1_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  876 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 123
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 999
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA2_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2688 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 185
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2873
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA3a_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1698 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 72
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1770
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA3b_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2183 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 277
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2460
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA4a_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1388 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 265
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1653
mri_label2label: Done

PIDs (24158 24164 24170 24175 24182) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 24225 of (24225 24231 24237 24243) to complete...
Waiting for PID 24231 of (24225 24231 24237 24243) to complete...
Waiting for PID 24237 of (24225 24231 24237 24243) to complete...
Waiting for PID 24243 of (24225 24231 24237 24243) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA4p_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1489 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 182
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1671
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA6_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6959 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 1078
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8037
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA44_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1012 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 189
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1201
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.BA45_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1178 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 336
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1514
mri_label2label: Done

PIDs (24225 24231 24237 24243) completed and logs appended.

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface 


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 24334 of (24334 24341 24347 24353 24358) to complete...
Waiting for PID 24341 of (24334 24341 24347 24353 24358) to complete...
Waiting for PID 24347 of (24334 24341 24347 24353 24358) to complete...
Waiting for PID 24353 of (24334 24341 24347 24353 24358) to complete...
Waiting for PID 24358 of (24334 24341 24347 24353 24358) to complete...

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.V1_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3232 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 945
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4177
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.V2_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3437 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 1592
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5029
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.MT_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  268 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 69
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 337
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.entorhinal_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 694 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  694 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 89
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 783
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0051026 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface


srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = 0051026
trglabel = ./rh.perirhinal_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0
Loading source label.
Found 291 points in source label.
Starting surface-based mapping
Reading source registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  291 nlabel points
Performing mapping from target back to the source label 153799
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 362
mri_label2label: Done

PIDs (24334 24341 24347 24353 24358) completed and logs appended.

 mris_label2annot --s 0051026 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 

Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label
cmdline mris_label2annot --s 0051026 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut

subject 0051026
hemi    rh
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
AnnotName  BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 107098 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051026 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 

Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label
cmdline mris_label2annot --s 0051026 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname tars-609
machine  x86_64
user     ntraut

subject 0051026
hemi    rh
SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt
AnnotName  BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 127356 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/label/rh.BA_exvivo.thresh.annot

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 0051026 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 306008
Total vertex volume 302421 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
 1047    598   2280  2.649 0.573     0.128     0.036       15     1.3  BA1_exvivo
 3540   2289   6088  2.510 0.551     0.108     0.020       30     2.9  BA2_exvivo
 1147    799   1147  1.860 0.462     0.127     0.030        9     1.4  BA3a_exvivo
 2387   1473   3163  1.924 0.617     0.105     0.024       21     2.3  BA3b_exvivo
 2042   1110   3646  2.791 0.441     0.100     0.030       39     2.6  BA4a_exvivo
 1525    922   2306  2.620 0.484     0.098     0.025       10     1.5  BA4p_exvivo
 9760   6397  22705  3.011 0.634     0.113     0.026       88     9.5  BA6_exvivo
 3751   2539   7767  2.902 0.503     0.112     0.023       35     3.4  BA44_exvivo
 5544   3842  12860  2.888 0.577     0.138     0.033       79     7.5  BA45_exvivo
 3824   2744   6769  2.130 0.593     0.157     0.051       62     8.3  V1_exvivo
 8982   6003  15315  2.238 0.576     0.145     0.044      128    15.2  V2_exvivo
 2049   1377   3464  2.498 0.496     0.121     0.026       21     2.1  MT_exvivo
  657    491   2283  3.559 0.746     0.140     0.024        7     0.6  perirhinal_exvivo
  446    290   1532  3.379 0.752     0.148     0.040        9     0.8  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051026 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051026/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 306008
Total vertex volume 302421 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.thresh.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1690943 mm^3    (det: 1.152082 )
lhCtxGM: 302187.450 301335.000  diff=  852.5  pctdiff= 0.282
rhCtxGM: 300149.670 299367.000  diff=  782.7  pctdiff= 0.261
lhCtxWM: 267570.720 267576.500  diff=   -5.8  pctdiff=-0.002
rhCtxWM: 263312.855 264187.500  diff= -874.6  pctdiff=-0.332
SubCortGMVol  63995.000
SupraTentVol  1211677.695 (1207443.000) diff=4234.695 pctdiff=0.349
SupraTentVolNotVent  1200714.695 (1196480.000) diff=4234.695 pctdiff=0.353
BrainSegVol  1370123.000 (1367777.000) diff=2346.000 pctdiff=0.171
BrainSegVolNotVent  1356048.000 (1356662.695) diff=-614.695 pctdiff=-0.045
BrainSegVolNotVent  1356048.000
CerebellumVol 159428.000
VentChorVol   10963.000
3rd4th5thCSF   3112.000
CSFVol   766.000, OptChiasmVol   140.000
MaskVol 1826083.000
  751    423   1637  2.655 0.565     0.122     0.032        9     0.8  BA1_exvivo
 2022   1288   3801  2.612 0.540     0.103     0.020       16     1.6  BA2_exvivo
 1023    702    907  1.838 0.408     0.131     0.029        8     1.2  BA3a_exvivo
 1895   1214   2096  1.717 0.432     0.099     0.020       13     1.6  BA3b_exvivo
 1308    641   2237  2.927 0.446     0.102     0.035       13     1.7  BA4a_exvivo
 1295    800   1921  2.612 0.482     0.098     0.026        7     1.4  BA4p_exvivo
 6491   4211  15174  2.991 0.649     0.113     0.026       82     6.6  BA6_exvivo
  996    677   2368  3.039 0.512     0.120     0.028       12     1.1  BA44_exvivo
 1385    998   3817  3.111 0.514     0.161     0.049       27     2.6  BA45_exvivo
 3599   2578   6138  2.119 0.583     0.155     0.049       57     7.6  V1_exvivo
 4658   3186   8133  2.182 0.563     0.155     0.048       74     8.9  V2_exvivo
  313    198    735  2.834 0.446     0.122     0.026        4     0.3  MT_exvivo
  381    291   1494  3.708 0.681     0.135     0.021        4     0.3  perirhinal_exvivo
  326    226    917  3.346 0.665     0.154     0.041        5     0.7  entorhinal_exvivo

Started at Sat Oct 7 17:21:27 CEST 2017 
Ended   at Sun Oct 8 01:21:01 CEST 2017
#@#%# recon-all-run-time-hours 7.993
recon-all -s 0051026 finished without error at Sun Oct  8 01:21:01 CEST 2017