ABIDE_fs-6.0.0/0051105/scripts/recon-all.log

Sat Oct  7 17:43:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051105 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051105/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051105
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-967 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:      66074836   46479388   19595448    1741576          0   41844320
-/+ buffers/cache:    4635068   61439768
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: 2017/10/07-15:43:51-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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: 2017/10/07-15:43:52-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-967  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-6.0.0/0051105

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051105/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051105/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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/0051105/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-6.0.0/0051105/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 17:43:54 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 17:44:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-967 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 17:44:04 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.27250
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27250/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27250/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.27250/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:44:06 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.27250/nu0.mnc ./tmp.mri_nu_correct.mni.27250/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27250/0/ -iterations 1000 -distance 50
[ntraut@tars-967:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/] [2017-10-07 17:44:06] 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.27250/0/ ./tmp.mri_nu_correct.mni.27250/nu0.mnc ./tmp.mri_nu_correct.mni.27250/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
Number of iterations: 49 
CV of field change: 0.000983605
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.27250/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.27250/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.27250/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 17:45:21 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 17:45:21 CEST 2017
Ended   at Sat Oct  7 17:45:59 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 17:46:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5587, 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-6.0.0/0051105/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/talairach_avi.log 

TalAviQA: 0.97790
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 17:46:02 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-6.0.0/0051105/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-967 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 17:46:02 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.28125
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28125/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28125/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.28125/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:46:04 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.28125/nu0.mnc ./tmp.mri_nu_correct.mni.28125/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28125/0/
[ntraut@tars-967:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/] [2017-10-07 17:46:04] 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.28125/0/ ./tmp.mri_nu_correct.mni.28125/nu0.mnc ./tmp.mri_nu_correct.mni.28125/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: 0.000947781
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 17:46:58 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.28125/nu1.mnc ./tmp.mri_nu_correct.mni.28125/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.28125/1/
[ntraut@tars-967:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/] [2017-10-07 17:46:58] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.28125/1/ ./tmp.mri_nu_correct.mni.28125/nu1.mnc ./tmp.mri_nu_correct.mni.28125/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
Number of iterations: 25 
CV of field change: 0.000985244
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28125/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-6.0.0/0051105/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28125/ones.mgz 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.28125/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.28125/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.28125/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/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.28125/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/input.mean.dat 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.28125/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.28125/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28125/ones.mgz --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/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.28125/ones.mgz --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/output.mean.dat 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.28125/ones.mgz
Loading ./tmp.mri_nu_correct.mni.28125/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.28125/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.28125/nu2.mnc ./tmp.mri_nu_correct.mni.28125/nu2.mnc mul .95629133082067140491
Saving result to './tmp.mri_nu_correct.mni.28125/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.28125/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.28125/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.28125/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 ( 9, 152) to ( 3, 110)
 
 
Sat Oct  7 17:48:14 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 17:48:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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
 1.05304  -0.01733  -0.04726  -2.73104;
 0.01785   1.01882   0.45608  -13.62891;
 0.04319  -0.46862   1.08004  -16.75069;
 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 = 16
Starting OpenSpline(): npoints = 16
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 64 (64), valley at 25 (25)
csf peak at 32, setting threshold to 53
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 63 (63), valley at 25 (25)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 4 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 17:50:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = (41, 35, 26) --> (206, 189, 220)
using (96, 86, 123) as brain centroid...
mean wm in atlas = 108, using box (76,67,99) --> (116, 104,146) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 5.5
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.349
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.351659 @ (0.000, 0.000, 0.000)
max log p =    -4.236966 @ (4.545, 4.545, -13.636)
max log p =    -4.194746 @ (-2.273, 6.818, -6.818)
max log p =    -4.160437 @ (-1.136, -7.955, 3.409)
max log p =    -4.160437 @ (0.000, 0.000, 0.000)
max log p =    -4.160437 @ (0.000, 0.000, 0.000)
Found translation: (1.1, 3.4, -17.0): log p = -4.160
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.759, old_max_log_p =-4.160 (thresh=-4.2)
 1.06375   0.00000   0.00000  -6.75199;
 0.00000   1.14215   0.47309  -60.86976;
 0.00000  -0.44009   1.06246   34.07212;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.759, old_max_log_p =-3.759 (thresh=-3.8)
 1.06375   0.00000   0.00000  -6.75199;
 0.00000   1.14215   0.47309  -60.86976;
 0.00000  -0.44009   1.06246   34.07212;
 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=-3.637, old_max_log_p =-3.759 (thresh=-3.8)
 1.06244  -0.05118   0.02491  -3.48107;
 0.02985   1.11097   0.42465  -58.21355;
-0.03378  -0.38228   1.01610   38.65500;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.637 (thresh=-3.6)
 1.04252  -0.05022   0.02444  -1.07439;
 0.02926   1.11846   0.46625  -62.39538;
-0.03473  -0.41842   1.00166   45.25020;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.633 (thresh=-3.6)
 1.04252  -0.05022   0.02444  -1.07439;
 0.02926   1.11846   0.46625  -62.39538;
-0.03473  -0.41842   1.00166   45.25020;
 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=-3.617, old_max_log_p =-3.633 (thresh=-3.6)
 1.04426  -0.05690   0.04105  -2.48448;
 0.02976   1.12252   0.44874  -61.75409;
-0.05124  -0.39872   1.00744   43.12392;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.617, old_max_log_p =-3.617 (thresh=-3.6)
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 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
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.617 (old=-4.349)
transform before final EM align:
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 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
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.1  tol 0.000000
final transform:
 1.04569  -0.04779   0.04484  -4.30427;
 0.02082   1.12096   0.45715  -61.02280;
-0.05142  -0.40741   1.00256   44.87205;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1264.968695
mri_em_register stimesec    1.334797
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   157572
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    81
mri_em_register ru_nivcsw   3655
registration took 11 minutes and 3 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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=123 y=104 z=117 r=68
      first estimation of the main basin volume: 1373919 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        17 found in the rest of the brain 
      global maximum in x=147, y=101, z=84, 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=9366995510 voxels, voxel volume =1.000 
                     = 9366995510 mmm3 = 9366995.968 cm3
done.
PostAnalyze...Basin Prior
 137 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=124,y=113, z=111, r=9455 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 43407
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1033560618
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1051113528
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 1080018188
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 1067824956
    OTHER      CSF_MIN=0, CSF_intensity=11, CSF_MAX=36 , nb = 1080265950
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    35,      35,        35,   56
  after  analyzing :    27,      35,        35,   40
   RIGHT_CER   
  before analyzing :    20,      26,        36,   62
  after  analyzing :    20,      32,        36,   39
   LEFT_CER    
  before analyzing :    20,      22,        28,   62
  after  analyzing :    20,      26,        28,   35
  RIGHT_BRAIN  
  before analyzing :    35,      34,        34,   56
  after  analyzing :    26,      34,        34,   39
  LEFT_BRAIN   
  before analyzing :    36,      34,        33,   56
  after  analyzing :    26,      34,        34,   39
     OTHER     
  before analyzing :    36,      65,        81,   94
  after  analyzing :    36,      75,        81,   79
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...74 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 67.605, std = 7.157

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.51, sigma = 6.02
      after  rotation: sse = 4.51, sigma = 6.02
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  5.06, its var is  6.98   
      before Erosion-Dilatation  1.99% of inacurate vertices
      after  Erosion-Dilatation  1.92% 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...35 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1496715 voxels, voxel volume = 1.000 mm3
           = 1496715 mmm3 = 1496.715 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    24.273309
mri_watershed stimesec    0.423935
mri_watershed ru_maxrss   825752
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213776
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2440
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1625
mri_watershed ru_nivcsw   93
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:01:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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, 52, 44) --> (192, 188, 191)
using (103, 97, 118) as brain centroid...
mean wm in atlas = 107, using box (87,80,100) --> (119, 113,136) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 5.8
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.171
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.992748 @ (9.091, 9.091, -9.091)
max log p =    -3.828710 @ (-4.545, -4.545, -4.545)
max log p =    -3.828710 @ (0.000, 0.000, 0.000)
max log p =    -3.797133 @ (1.136, 3.409, 1.136)
max log p =    -3.788119 @ (-0.568, -0.568, 0.568)
max log p =    -3.785866 @ (-0.284, 0.284, 0.852)
Found translation: (4.8, 7.7, -11.1): log p = -3.786
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.429, old_max_log_p =-3.786 (thresh=-3.8)
 1.07500   0.00000   0.00000  -4.31354;
 0.00000   1.06753   0.42117  -48.94395;
 0.00000  -0.43171   0.98772   46.03884;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.429, old_max_log_p =-3.429 (thresh=-3.4)
 1.07500   0.00000   0.00000  -4.31354;
 0.00000   1.06753   0.42117  -48.94395;
 0.00000  -0.43171   0.98772   46.03884;
 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=-3.227, old_max_log_p =-3.429 (thresh=-3.4)
 1.03415  -0.04082  -0.01630   5.25701;
 0.03773   1.11140   0.36428  -50.53644;
-0.00253  -0.36516   1.03299   31.64216;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.211, old_max_log_p =-3.227 (thresh=-3.2)
 1.03415  -0.01795   0.03010  -2.47598;
 0.00373   1.07941   0.38966  -45.57224;
-0.03759  -0.39978   1.02050   41.24948;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.211, old_max_log_p =-3.211 (thresh=-3.2)
 1.03415  -0.01795   0.03010  -2.47598;
 0.00373   1.07941   0.38966  -45.57224;
-0.03759  -0.39978   1.02050   41.24948;
 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=-3.174, old_max_log_p =-3.211 (thresh=-3.2)
 1.03273  -0.03557   0.02370   0.38734;
 0.02036   1.07693   0.39888  -48.83958;
-0.03772  -0.40814   1.01608   43.63070;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.173, old_max_log_p =-3.174 (thresh=-3.2)
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 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
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.173 (old=-4.171)
transform before final EM align:
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 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
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.7  tol 0.000000
final transform:
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1104.946022
mri_em_register stimesec    1.396787
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   158953
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    94
mri_em_register ru_nivcsw   3317
registration took 9 minutes and 31 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:11:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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, 52, 44) --> (192, 188, 191)
using (103, 97, 118) as brain centroid...
mean wm in atlas = 107, using box (87,80,100) --> (119, 113,136) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 5.8
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
 1.03374  -0.04445   0.02053   1.61643;
 0.02912   1.07990   0.39074  -49.35633;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 55, 44) --> (188, 161, 193)
Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0
0 of 375 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (61, 55, 43) --> (124, 155, 192)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 304 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 137, 75) --> (174, 174, 124)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
7 of 7 (100.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (83, 138, 71) --> (125, 174, 124)
Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0
0 of 9 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 122, 104) --> (142, 183, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 27 (0.0%) samples deleted
using 722 total control points for intensity normalization...
bias field = 0.954 +- 0.052
7 of 715 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 55, 44) --> (188, 161, 193)
Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 494 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (61, 55, 43) --> (124, 155, 192)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
0 of 465 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 137, 75) --> (174, 174, 124)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
6 of 53 (11.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (83, 138, 71) --> (125, 174, 124)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
6 of 48 (12.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 122, 104) --> (142, 183, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
53 of 98 (54.1%) samples deleted
using 1158 total control points for intensity normalization...
bias field = 1.009 +- 0.056
4 of 1071 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 55, 44) --> (188, 161, 193)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 584 (0.3%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (61, 55, 43) --> (124, 155, 192)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 551 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 137, 75) --> (174, 174, 124)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
13 of 79 (16.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (83, 138, 71) --> (125, 174, 124)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
44 of 89 (49.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 122, 104) --> (142, 183, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
152 of 188 (80.9%) samples deleted
using 1491 total control points for intensity normalization...
bias field = 1.008 +- 0.048
4 of 1242 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 46 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:13:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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) = 1.30 (predicted orig area = 6.1)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.770, neg=0, invalid=762
0001: dt=208.753927, rms=0.725 (5.918%), neg=0, invalid=762
0002: dt=218.378378, rms=0.711 (1.883%), neg=0, invalid=762
0003: dt=162.796117, rms=0.705 (0.851%), neg=0, invalid=762
0004: dt=443.904000, rms=0.697 (1.214%), neg=0, invalid=762
0005: dt=110.976000, rms=0.693 (0.588%), neg=0, invalid=762
0006: dt=1479.680000, rms=0.681 (1.677%), neg=0, invalid=762
0007: dt=129.472000, rms=0.679 (0.322%), neg=0, invalid=762
0008: dt=295.936000, rms=0.677 (0.185%), neg=0, invalid=762
0009: dt=295.936000, rms=0.677 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.678, neg=0, invalid=762
0010: dt=129.472000, rms=0.676 (0.276%), neg=0, invalid=762
0011: dt=1183.744000, rms=0.673 (0.542%), neg=0, invalid=762
0012: dt=221.952000, rms=0.670 (0.315%), neg=0, invalid=762
0013: dt=129.472000, rms=0.670 (0.044%), neg=0, invalid=762
0014: dt=129.472000, rms=0.670 (0.044%), neg=0, invalid=762
0015: dt=129.472000, rms=0.669 (0.076%), neg=0, invalid=762
0016: dt=129.472000, rms=0.669 (0.105%), neg=0, invalid=762
0017: dt=129.472000, rms=0.668 (0.127%), neg=0, invalid=762
0018: dt=129.472000, rms=0.667 (0.152%), neg=0, invalid=762
0019: dt=129.472000, rms=0.666 (0.169%), neg=0, invalid=762
0020: dt=129.472000, rms=0.664 (0.176%), neg=0, invalid=762
0021: dt=129.472000, rms=0.663 (0.159%), neg=0, invalid=762
0022: dt=129.472000, rms=0.662 (0.149%), neg=0, invalid=762
0023: dt=129.472000, rms=0.661 (0.149%), neg=0, invalid=762
0024: dt=129.472000, rms=0.660 (0.148%), neg=0, invalid=762
0025: dt=129.472000, rms=0.660 (0.141%), neg=0, invalid=762
0026: dt=129.472000, rms=0.659 (0.137%), neg=0, invalid=762
0027: dt=129.472000, rms=0.658 (0.128%), neg=0, invalid=762
0028: dt=129.472000, rms=0.657 (0.118%), neg=0, invalid=762
0029: dt=129.472000, rms=0.656 (0.112%), neg=0, invalid=762
0030: dt=1479.680000, rms=0.656 (0.095%), neg=0, invalid=762
0031: dt=1479.680000, rms=0.656 (-5.418%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.659, neg=0, invalid=762
0032: dt=145.152000, rms=0.652 (1.181%), neg=0, invalid=762
0033: dt=121.379310, rms=0.646 (0.875%), neg=0, invalid=762
0034: dt=79.029024, rms=0.641 (0.724%), neg=0, invalid=762
0035: dt=111.304348, rms=0.638 (0.449%), neg=0, invalid=762
0036: dt=89.132420, rms=0.635 (0.541%), neg=0, invalid=762
0037: dt=78.940767, rms=0.633 (0.308%), neg=0, invalid=762
0038: dt=141.241379, rms=0.630 (0.461%), neg=0, invalid=762
0039: dt=36.288000, rms=0.628 (0.252%), neg=0, invalid=762
0040: dt=145.152000, rms=0.626 (0.334%), neg=0, invalid=762
0041: dt=94.986425, rms=0.624 (0.317%), neg=0, invalid=762
0042: dt=64.876712, rms=0.623 (0.160%), neg=0, invalid=762
0043: dt=64.876712, rms=0.622 (0.202%), neg=0, invalid=762
0044: dt=64.876712, rms=0.620 (0.271%), neg=0, invalid=762
0045: dt=64.876712, rms=0.618 (0.360%), neg=0, invalid=762
0046: dt=64.876712, rms=0.616 (0.400%), neg=0, invalid=762
0047: dt=64.876712, rms=0.613 (0.477%), neg=0, invalid=762
0048: dt=64.876712, rms=0.610 (0.472%), neg=0, invalid=762
0049: dt=64.876712, rms=0.607 (0.429%), neg=0, invalid=762
0050: dt=64.876712, rms=0.605 (0.390%), neg=0, invalid=762
0051: dt=64.876712, rms=0.603 (0.356%), neg=0, invalid=762
0052: dt=64.876712, rms=0.601 (0.320%), neg=0, invalid=762
0053: dt=64.876712, rms=0.599 (0.257%), neg=0, invalid=762
0054: dt=64.876712, rms=0.598 (0.209%), neg=0, invalid=762
0055: dt=64.876712, rms=0.597 (0.170%), neg=0, invalid=762
0056: dt=64.876712, rms=0.596 (0.172%), neg=0, invalid=762
0057: dt=64.876712, rms=0.595 (0.135%), neg=0, invalid=762
0058: dt=64.876712, rms=0.595 (0.106%), neg=0, invalid=762
0059: dt=64.876712, rms=0.594 (0.088%), neg=0, invalid=762
0060: dt=145.152000, rms=0.594 (0.044%), neg=0, invalid=762
0061: dt=145.152000, rms=0.594 (-0.103%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.594, neg=0, invalid=762
0062: dt=67.537688, rms=0.593 (0.258%), neg=0, invalid=762
0063: dt=145.152000, rms=0.592 (0.200%), neg=0, invalid=762
0064: dt=145.152000, rms=0.592 (-0.533%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0065: dt=2.800000, rms=0.612 (0.118%), neg=0, invalid=762
0066: dt=1.600000, rms=0.612 (0.005%), neg=0, invalid=762
0067: dt=1.600000, rms=0.612 (0.001%), neg=0, invalid=762
0068: dt=1.600000, rms=0.612 (-0.021%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0069: dt=0.700000, rms=0.612 (0.093%), neg=0, invalid=762
0070: dt=0.125000, rms=0.612 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.670, neg=0, invalid=762
0071: dt=5.568493, rms=0.652 (2.665%), neg=0, invalid=762
0072: dt=2.160000, rms=0.652 (0.081%), neg=0, invalid=762
0073: dt=2.160000, rms=0.652 (-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
0074: dt=0.000000, rms=0.652 (0.076%), neg=0, invalid=762
0075: dt=0.000000, rms=0.652 (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=0.705, neg=0, invalid=762
0076: dt=1.280000, rms=0.701 (0.575%), neg=0, invalid=762
0077: dt=2.043478, rms=0.696 (0.763%), neg=0, invalid=762
0078: dt=0.320000, rms=0.696 (0.017%), neg=0, invalid=762
0079: dt=0.320000, rms=0.696 (0.016%), neg=0, invalid=762
0080: dt=0.320000, rms=0.696 (0.015%), neg=0, invalid=762
0081: dt=0.320000, rms=0.696 (0.001%), neg=0, invalid=762
0082: dt=1.792000, rms=0.695 (0.165%), neg=0, invalid=762
0083: dt=0.000000, rms=0.695 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.695, neg=0, invalid=762
0084: dt=0.768000, rms=0.694 (0.143%), neg=0, invalid=762
0085: dt=1.536000, rms=0.694 (0.041%), neg=0, invalid=762
0086: dt=1.536000, rms=0.694 (-0.040%), 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=0.666, neg=0, invalid=762
0087: dt=0.855208, rms=0.647 (2.819%), neg=0, invalid=762
0088: dt=0.080000, rms=0.646 (0.147%), neg=0, invalid=762
0089: dt=0.080000, rms=0.646 (-0.089%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.647, neg=0, invalid=762
0090: dt=0.028000, rms=0.646 (0.097%), neg=0, invalid=762
0091: dt=0.007000, rms=0.646 (0.001%), neg=0, invalid=762
0092: dt=0.007000, rms=0.646 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.13839 (10)
Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (517 voxels, overlap=0.005)
Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (517 voxels, peak =  8), gca=8.1
gca peak = 0.15565 (16)
mri peak = 0.07958 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (423 voxels, overlap=0.119)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (423 voxels, peak =  8), gca=8.2
gca peak = 0.26829 (96)
mri peak = 0.07753 (84)
Right_Pallidum (52): linear fit = 0.90 x + 0.0 (683 voxels, overlap=0.109)
Right_Pallidum (52): linear fit = 0.90 x + 0.0 (683 voxels, peak = 87), gca=86.9
gca peak = 0.20183 (93)
mri peak = 0.06283 (83)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (513 voxels, overlap=0.599)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (513 voxels, peak = 85), gca=85.1
gca peak = 0.21683 (55)
mri peak = 0.09181 (54)
Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (556 voxels, overlap=0.989)
Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (556 voxels, peak = 53), gca=53.1
gca peak = 0.30730 (58)
mri peak = 0.09663 (55)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (591 voxels, overlap=0.963)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (591 voxels, peak = 54), gca=54.2
gca peak = 0.11430 (101)
mri peak = 0.09126 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (54149 voxels, overlap=0.748)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (54149 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.09353 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54013 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54013 voxels, peak = 107), gca=106.6
gca peak = 0.14995 (59)
mri peak = 0.04425 (58)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (18643 voxels, overlap=0.988)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (18643 voxels, peak = 56), gca=55.8
gca peak = 0.15082 (58)
mri peak = 0.04959 (51)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (18062 voxels, overlap=0.981)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (18062 voxels, peak = 53), gca=53.1
gca peak = 0.14161 (67)
mri peak = 0.08290 (67)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (875 voxels, overlap=0.988)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (875 voxels, peak = 66), gca=66.0
gca peak = 0.15243 (71)
mri peak = 0.08190 (69)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (762 voxels, overlap=0.858)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (762 voxels, peak = 66), gca=66.4
gca peak = 0.13336 (57)
mri peak = 0.04368 (55)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (16574 voxels, overlap=0.976)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (16574 voxels, peak = 57), gca=57.0
gca peak = 0.13252 (56)
mri peak = 0.04346 (51)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (20106 voxels, overlap=0.994)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (20106 voxels, peak = 53), gca=52.9
gca peak = 0.18181 (84)
mri peak = 0.06300 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6214 voxels, overlap=0.634)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6214 voxels, peak = 92), gca=92.0
gca peak = 0.20573 (83)
mri peak = 0.07176 (85)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5738 voxels, overlap=0.924)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5738 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.09351 (57)
Left_Amygdala (18): linear fit = 0.94 x + 0.0 (378 voxels, overlap=0.977)
Left_Amygdala (18): linear fit = 0.94 x + 0.0 (378 voxels, peak = 54), gca=53.9
gca peak = 0.39313 (56)
mri peak = 0.10663 (54)
Right_Amygdala (54): linear fit = 0.94 x + 0.0 (448 voxels, overlap=1.003)
Right_Amygdala (54): linear fit = 0.94 x + 0.0 (448 voxels, peak = 53), gca=52.9
gca peak = 0.14181 (85)
mri peak = 0.05894 (84)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4976 voxels, overlap=0.969)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4976 voxels, peak = 83), gca=82.9
gca peak = 0.11978 (83)
mri peak = 0.07145 (83)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4273 voxels, overlap=0.928)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4273 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.07639 (73)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (2030 voxels, overlap=0.845)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (2030 voxels, peak = 76), gca=76.2
gca peak = 0.14159 (79)
mri peak = 0.07807 (72)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (2035 voxels, overlap=0.886)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (2035 voxels, peak = 76), gca=76.2
gca peak = 0.10025 (80)
mri peak = 0.12785 (80)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (9743 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (9743 voxels, peak = 85), gca=85.2
gca peak = 0.13281 (86)
mri peak = 0.09188 (86)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (804 voxels, overlap=0.719)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (804 voxels, peak = 87), gca=87.3
gca peak = 0.12801 (89)
mri peak = 0.08987 (87)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (823 voxels, overlap=0.834)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (823 voxels, peak = 89), gca=88.6
gca peak = 0.20494 (23)
mri peak = 0.10264 (38)
gca peak = 0.15061 (21)
mri peak = 0.13416 (10)
Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (206 voxels, overlap=0.285)
Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (206 voxels, peak =  9), gca=9.1
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 0.94 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.46 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=0.674, neg=0, invalid=762
0093: dt=147.744681, rms=0.669 (0.751%), neg=0, invalid=762
0094: dt=295.936000, rms=0.665 (0.585%), neg=0, invalid=762
0095: dt=92.480000, rms=0.663 (0.216%), neg=0, invalid=762
0096: dt=443.904000, rms=0.661 (0.378%), neg=0, invalid=762
0097: dt=73.984000, rms=0.660 (0.146%), neg=0, invalid=762
0098: dt=1183.744000, rms=0.658 (0.362%), neg=0, invalid=762
0099: dt=110.976000, rms=0.657 (0.149%), neg=0, invalid=762
0100: dt=110.976000, rms=0.656 (0.032%), neg=0, invalid=762
0101: dt=110.976000, rms=0.656 (0.039%), neg=0, invalid=762
0102: dt=110.976000, rms=0.656 (0.055%), neg=0, invalid=762
0103: dt=110.976000, rms=0.655 (0.067%), neg=0, invalid=762
0104: dt=110.976000, rms=0.655 (0.074%), neg=0, invalid=762
0105: dt=110.976000, rms=0.654 (0.089%), neg=0, invalid=762
0106: dt=110.976000, rms=0.654 (0.088%), neg=0, invalid=762
0107: dt=110.976000, rms=0.653 (0.081%), neg=0, invalid=762
0108: dt=110.976000, rms=0.653 (0.077%), neg=0, invalid=762
0109: dt=110.976000, rms=0.652 (0.083%), neg=0, invalid=762
0110: dt=110.976000, rms=0.652 (0.083%), neg=0, invalid=762
0111: dt=110.976000, rms=0.651 (0.077%), neg=0, invalid=762
0112: dt=110.976000, rms=0.651 (0.068%), neg=0, invalid=762
0113: dt=110.976000, rms=0.650 (0.065%), neg=0, invalid=762
0114: dt=110.976000, rms=0.650 (0.065%), neg=0, invalid=762
0115: dt=110.976000, rms=0.649 (0.065%), neg=0, invalid=762
0116: dt=110.976000, rms=0.649 (0.065%), neg=0, invalid=762
0117: dt=110.976000, rms=0.648 (0.064%), neg=0, invalid=762
0118: dt=110.976000, rms=0.648 (0.063%), neg=0, invalid=762
0119: dt=110.976000, rms=0.648 (0.064%), neg=0, invalid=762
0120: dt=110.976000, rms=0.647 (0.061%), neg=0, invalid=762
0121: dt=110.976000, rms=0.647 (0.055%), neg=0, invalid=762
0122: dt=110.976000, rms=0.647 (0.054%), neg=0, invalid=762
0123: dt=110.976000, rms=0.646 (0.054%), neg=0, invalid=762
0124: dt=110.976000, rms=0.646 (0.055%), neg=0, invalid=762
0125: dt=110.976000, rms=0.646 (0.052%), neg=0, invalid=762
0126: dt=110.976000, rms=0.645 (0.049%), neg=0, invalid=762
0127: dt=110.976000, rms=0.645 (0.047%), neg=0, invalid=762
0128: dt=110.976000, rms=0.645 (0.046%), neg=0, invalid=762
0129: dt=110.976000, rms=0.644 (0.042%), neg=0, invalid=762
0130: dt=110.976000, rms=0.644 (0.041%), neg=0, invalid=762
0131: dt=110.976000, rms=0.644 (0.041%), neg=0, invalid=762
0132: dt=110.976000, rms=0.644 (0.039%), neg=0, invalid=762
0133: dt=110.976000, rms=0.643 (0.039%), neg=0, invalid=762
0134: dt=110.976000, rms=0.643 (0.033%), neg=0, invalid=762
0135: dt=110.976000, rms=0.643 (0.033%), neg=0, invalid=762
0136: dt=110.976000, rms=0.643 (0.036%), neg=0, invalid=762
0137: dt=110.976000, rms=0.642 (0.034%), neg=0, invalid=762
0138: dt=110.976000, rms=0.642 (0.030%), neg=0, invalid=762
0139: dt=110.976000, rms=0.642 (0.030%), neg=0, invalid=762
0140: dt=110.976000, rms=0.642 (0.032%), neg=0, invalid=762
0141: dt=110.976000, rms=0.642 (0.032%), neg=0, invalid=762
0142: dt=110.976000, rms=0.641 (0.029%), neg=0, invalid=762
0143: dt=110.976000, rms=0.641 (0.025%), neg=0, invalid=762
0144: dt=110.976000, rms=0.641 (0.024%), neg=0, invalid=762
0145: dt=2071.552000, rms=0.641 (0.053%), neg=0, invalid=762
0146: dt=32.368000, rms=0.641 (0.008%), neg=0, invalid=762
0147: dt=32.368000, rms=0.641 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.641, neg=0, invalid=762
0148: dt=110.976000, rms=0.640 (0.159%), neg=0, invalid=762
0149: dt=517.888000, rms=0.640 (0.130%), neg=0, invalid=762
0150: dt=32.368000, rms=0.640 (0.008%), neg=0, invalid=762
0151: dt=32.368000, rms=0.639 (0.002%), neg=0, invalid=762
0152: dt=32.368000, rms=0.640 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.641, neg=0, invalid=762
0153: dt=103.239344, rms=0.637 (0.630%), neg=0, invalid=762
0154: dt=98.114537, rms=0.633 (0.664%), neg=0, invalid=762
0155: dt=61.333333, rms=0.630 (0.405%), neg=0, invalid=762
0156: dt=103.680000, rms=0.627 (0.447%), neg=0, invalid=762
0157: dt=36.288000, rms=0.625 (0.315%), neg=0, invalid=762
0158: dt=580.608000, rms=0.617 (1.354%), neg=0, invalid=762
0159: dt=69.500000, rms=0.613 (0.603%), neg=0, invalid=762
0160: dt=36.288000, rms=0.612 (0.151%), neg=0, invalid=762
0161: dt=497.664000, rms=0.610 (0.392%), neg=0, invalid=762
0162: dt=62.923077, rms=0.606 (0.575%), neg=0, invalid=762
0163: dt=36.288000, rms=0.606 (0.061%), neg=0, invalid=762
0164: dt=580.608000, rms=0.603 (0.400%), neg=0, invalid=762
0165: dt=64.458781, rms=0.601 (0.388%), neg=0, invalid=762
0166: dt=36.288000, rms=0.601 (0.040%), neg=0, invalid=762
0167: dt=36.288000, rms=0.601 (0.030%), neg=0, invalid=762
0168: dt=36.288000, rms=0.600 (0.057%), neg=0, invalid=762
0169: dt=36.288000, rms=0.600 (0.085%), neg=0, invalid=762
0170: dt=36.288000, rms=0.599 (0.112%), neg=0, invalid=762
0171: dt=36.288000, rms=0.598 (0.132%), neg=0, invalid=762
0172: dt=36.288000, rms=0.598 (0.149%), neg=0, invalid=762
0173: dt=36.288000, rms=0.597 (0.145%), neg=0, invalid=762
0174: dt=36.288000, rms=0.596 (0.151%), neg=0, invalid=762
0175: dt=36.288000, rms=0.595 (0.148%), neg=0, invalid=762
0176: dt=36.288000, rms=0.594 (0.156%), neg=0, invalid=762
0177: dt=36.288000, rms=0.593 (0.152%), neg=0, invalid=762
0178: dt=36.288000, rms=0.592 (0.146%), neg=0, invalid=762
0179: dt=36.288000, rms=0.591 (0.135%), neg=0, invalid=762
0180: dt=36.288000, rms=0.591 (0.014%), neg=0, invalid=762
0181: dt=36.288000, rms=0.591 (0.025%), neg=0, invalid=762
0182: dt=36.288000, rms=0.591 (0.042%), neg=0, invalid=762
0183: dt=36.288000, rms=0.591 (0.050%), neg=0, invalid=762
0184: dt=36.288000, rms=0.590 (0.062%), neg=0, invalid=762
0185: dt=36.288000, rms=0.590 (0.066%), neg=0, invalid=762
0186: dt=36.288000, rms=0.589 (0.071%), neg=0, invalid=762
0187: dt=36.288000, rms=0.589 (0.074%), neg=0, invalid=762
0188: dt=36.288000, rms=0.589 (0.017%), neg=0, invalid=762
0189: dt=18.144000, rms=0.589 (0.006%), neg=0, invalid=762
0190: dt=9.072000, rms=0.589 (0.004%), neg=0, invalid=762
0191: dt=2.268000, rms=0.589 (0.001%), neg=0, invalid=762
0192: dt=0.070875, rms=0.589 (0.000%), neg=0, invalid=762
0193: dt=0.004430, rms=0.589 (0.001%), neg=0, invalid=762
0194: dt=0.002215, rms=0.589 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.590, neg=0, invalid=762
0195: dt=84.317460, rms=0.587 (0.407%), neg=0, invalid=762
0196: dt=82.944000, rms=0.586 (0.201%), neg=0, invalid=762
0197: dt=36.288000, rms=0.585 (0.082%), neg=0, invalid=762
0198: dt=580.608000, rms=0.583 (0.423%), neg=0, invalid=762
0199: dt=36.288000, rms=0.582 (0.114%), neg=0, invalid=762
0200: dt=145.152000, rms=0.582 (0.091%), neg=0, invalid=762
0201: dt=36.288000, rms=0.582 (0.010%), neg=0, invalid=762
0202: dt=36.288000, rms=0.582 (0.018%), neg=0, invalid=762
0203: dt=36.288000, rms=0.581 (0.033%), neg=0, invalid=762
0204: dt=36.288000, rms=0.581 (0.041%), neg=0, invalid=762
0205: dt=36.288000, rms=0.581 (0.054%), neg=0, invalid=762
0206: dt=36.288000, rms=0.581 (0.060%), neg=0, invalid=762
0207: dt=36.288000, rms=0.580 (0.066%), neg=0, invalid=762
0208: dt=36.288000, rms=0.580 (0.070%), neg=0, invalid=762
0209: dt=36.288000, rms=0.579 (0.075%), neg=0, invalid=762
0210: dt=36.288000, rms=0.579 (0.080%), neg=0, invalid=762
0211: dt=36.288000, rms=0.578 (0.086%), neg=0, invalid=762
0212: dt=36.288000, rms=0.578 (0.084%), neg=0, invalid=762
0213: dt=36.288000, rms=0.577 (0.087%), neg=0, invalid=762
0214: dt=36.288000, rms=0.577 (0.087%), neg=0, invalid=762
0215: dt=36.288000, rms=0.576 (0.084%), neg=0, invalid=762
0216: dt=36.288000, rms=0.576 (0.083%), neg=0, invalid=762
0217: dt=36.288000, rms=0.575 (0.080%), neg=0, invalid=762
0218: dt=36.288000, rms=0.575 (0.079%), neg=0, invalid=762
0219: dt=36.288000, rms=0.575 (0.075%), neg=0, invalid=762
0220: dt=36.288000, rms=0.574 (0.075%), neg=0, invalid=762
0221: dt=36.288000, rms=0.574 (0.076%), neg=0, invalid=762
0222: dt=36.288000, rms=0.573 (0.073%), neg=0, invalid=762
0223: dt=36.288000, rms=0.573 (0.069%), neg=0, invalid=762
0224: dt=36.288000, rms=0.572 (0.070%), neg=0, invalid=762
0225: dt=36.288000, rms=0.572 (0.067%), neg=0, invalid=762
0226: dt=36.288000, rms=0.572 (0.071%), neg=0, invalid=762
0227: dt=36.288000, rms=0.571 (0.068%), neg=0, invalid=762
0228: dt=36.288000, rms=0.571 (0.065%), neg=0, invalid=762
0229: dt=36.288000, rms=0.571 (0.065%), neg=0, invalid=762
0230: dt=36.288000, rms=0.570 (0.062%), neg=0, invalid=762
0231: dt=36.288000, rms=0.570 (0.060%), neg=0, invalid=762
0232: dt=36.288000, rms=0.570 (0.060%), neg=0, invalid=762
0233: dt=36.288000, rms=0.569 (0.059%), neg=0, invalid=762
0234: dt=36.288000, rms=0.569 (0.056%), neg=0, invalid=762
0235: dt=36.288000, rms=0.569 (0.056%), neg=0, invalid=762
0236: dt=36.288000, rms=0.568 (0.056%), neg=0, invalid=762
0237: dt=36.288000, rms=0.568 (0.054%), neg=0, invalid=762
0238: dt=36.288000, rms=0.568 (0.057%), neg=0, invalid=762
0239: dt=36.288000, rms=0.567 (0.054%), neg=0, invalid=762
0240: dt=36.288000, rms=0.567 (0.051%), neg=0, invalid=762
0241: dt=36.288000, rms=0.567 (0.051%), neg=0, invalid=762
0242: dt=36.288000, rms=0.566 (0.049%), neg=0, invalid=762
0243: dt=36.288000, rms=0.566 (0.048%), neg=0, invalid=762
0244: dt=36.288000, rms=0.566 (0.046%), neg=0, invalid=762
0245: dt=36.288000, rms=0.566 (0.046%), neg=0, invalid=762
0246: dt=36.288000, rms=0.565 (0.047%), neg=0, invalid=762
0247: dt=36.288000, rms=0.565 (0.044%), neg=0, invalid=762
0248: dt=36.288000, rms=0.565 (0.044%), neg=0, invalid=762
0249: dt=36.288000, rms=0.565 (0.040%), neg=0, invalid=762
0250: dt=36.288000, rms=0.564 (0.040%), neg=0, invalid=762
0251: dt=36.288000, rms=0.564 (0.037%), neg=0, invalid=762
0252: dt=36.288000, rms=0.564 (0.038%), neg=0, invalid=762
0253: dt=36.288000, rms=0.564 (0.036%), neg=0, invalid=762
0254: dt=36.288000, rms=0.564 (0.037%), neg=0, invalid=762
0255: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762
0256: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762
0257: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762
0258: dt=36.288000, rms=0.563 (0.036%), neg=0, invalid=762
0259: dt=36.288000, rms=0.563 (0.038%), neg=0, invalid=762
0260: dt=36.288000, rms=0.562 (0.035%), neg=0, invalid=762
0261: dt=36.288000, rms=0.562 (0.031%), neg=0, invalid=762
0262: dt=36.288000, rms=0.562 (0.032%), neg=0, invalid=762
0263: dt=36.288000, rms=0.562 (0.027%), neg=0, invalid=762
0264: dt=36.288000, rms=0.562 (0.032%), neg=0, invalid=762
0265: dt=36.288000, rms=0.562 (0.031%), neg=0, invalid=762
0266: dt=36.288000, rms=0.561 (0.028%), neg=0, invalid=762
0267: dt=36.288000, rms=0.561 (0.027%), neg=0, invalid=762
0268: dt=36.288000, rms=0.561 (0.028%), neg=0, invalid=762
0269: dt=36.288000, rms=0.561 (0.029%), neg=0, invalid=762
0270: dt=36.288000, rms=0.561 (0.026%), neg=0, invalid=762
0271: dt=36.288000, rms=0.561 (0.023%), neg=0, invalid=762
0272: dt=36.288000, rms=0.561 (0.026%), neg=0, invalid=762
0273: dt=36.288000, rms=0.560 (0.024%), neg=0, invalid=762
0274: dt=36.288000, rms=0.560 (0.028%), neg=0, invalid=762
0275: dt=36.288000, rms=0.560 (0.026%), neg=0, invalid=762
0276: dt=36.288000, rms=0.560 (0.022%), neg=0, invalid=762
0277: dt=36.288000, rms=0.560 (0.023%), neg=0, invalid=762
0278: dt=36.288000, rms=0.560 (0.023%), neg=0, invalid=762
0279: dt=36.288000, rms=0.560 (0.023%), neg=0, invalid=762
0280: dt=145.152000, rms=0.560 (0.003%), neg=0, invalid=762
0281: dt=145.152000, rms=0.559 (0.013%), neg=0, invalid=762
0282: dt=145.152000, rms=0.559 (-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=0.567, neg=0, invalid=762
0283: dt=22.787879, rms=0.565 (0.377%), neg=0, invalid=762
0284: dt=77.195876, rms=0.561 (0.622%), neg=0, invalid=762
0285: dt=11.200000, rms=0.559 (0.313%), neg=0, invalid=762
0286: dt=11.200000, rms=0.558 (0.182%), neg=0, invalid=762
0287: dt=11.200000, rms=0.557 (0.164%), neg=0, invalid=762
0288: dt=2.800000, rms=0.557 (0.040%), neg=0, invalid=762
0289: dt=1.400000, rms=0.557 (0.020%), neg=0, invalid=762
0290: dt=0.700000, rms=0.557 (0.009%), neg=0, invalid=762
0291: dt=0.350000, rms=0.557 (0.005%), neg=0, invalid=762
0292: dt=0.175000, rms=0.557 (0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.558, neg=0, invalid=762
0293: dt=38.004751, rms=0.553 (0.862%), neg=0, invalid=762
0294: dt=24.016360, rms=0.550 (0.459%), neg=0, invalid=762
0295: dt=25.600000, rms=0.549 (0.260%), neg=0, invalid=762
0296: dt=31.695238, rms=0.547 (0.280%), neg=0, invalid=762
0297: dt=11.200000, rms=0.546 (0.191%), neg=0, invalid=762
0298: dt=153.600000, rms=0.543 (0.673%), neg=0, invalid=762
0299: dt=18.541176, rms=0.540 (0.531%), neg=0, invalid=762
0300: dt=25.600000, rms=0.539 (0.127%), neg=0, invalid=762
0301: dt=25.600000, rms=0.538 (0.140%), neg=0, invalid=762
0302: dt=19.200000, rms=0.538 (0.117%), neg=0, invalid=762
0303: dt=38.400000, rms=0.537 (0.141%), neg=0, invalid=762
0304: dt=11.200000, rms=0.536 (0.106%), neg=0, invalid=762
0305: dt=179.200000, rms=0.533 (0.561%), neg=0, invalid=762
0306: dt=11.200000, rms=0.532 (0.221%), neg=0, invalid=762
0307: dt=38.400000, rms=0.532 (0.082%), neg=0, invalid=762
0308: dt=11.200000, rms=0.532 (0.064%), neg=0, invalid=762
0309: dt=179.200000, rms=0.530 (0.310%), neg=0, invalid=762
0310: dt=11.200000, rms=0.529 (0.183%), neg=0, invalid=762
0311: dt=25.600000, rms=0.528 (0.091%), neg=0, invalid=762
0312: dt=32.000000, rms=0.528 (0.081%), neg=0, invalid=762
0313: dt=11.200000, rms=0.528 (0.037%), neg=0, invalid=762
0314: dt=11.200000, rms=0.528 (0.027%), neg=0, invalid=762
0315: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=762
0316: dt=11.200000, rms=0.527 (0.066%), neg=0, invalid=762
0317: dt=11.200000, rms=0.527 (0.078%), neg=0, invalid=762
0318: dt=11.200000, rms=0.526 (0.097%), neg=0, invalid=762
0319: dt=11.200000, rms=0.526 (0.103%), neg=0, invalid=762
0320: dt=11.200000, rms=0.525 (0.108%), neg=0, invalid=762
0321: dt=11.200000, rms=0.524 (0.120%), neg=0, invalid=762
0322: dt=11.200000, rms=0.524 (0.125%), neg=0, invalid=762
0323: dt=11.200000, rms=0.523 (0.125%), neg=0, invalid=762
0324: dt=11.200000, rms=0.522 (0.132%), neg=0, invalid=762
0325: dt=11.200000, rms=0.522 (0.128%), neg=0, invalid=762
0326: dt=11.200000, rms=0.521 (0.129%), neg=0, invalid=762
0327: dt=11.200000, rms=0.520 (0.129%), neg=0, invalid=762
0328: dt=11.200000, rms=0.520 (0.122%), neg=0, invalid=762
0329: dt=11.200000, rms=0.519 (0.121%), neg=0, invalid=762
0330: dt=11.200000, rms=0.519 (0.116%), neg=0, invalid=762
0331: dt=11.200000, rms=0.518 (0.107%), neg=0, invalid=762
0332: dt=11.200000, rms=0.517 (0.108%), neg=0, invalid=762
0333: dt=11.200000, rms=0.517 (0.099%), neg=0, invalid=762
0334: dt=11.200000, rms=0.516 (0.093%), neg=0, invalid=762
0335: dt=11.200000, rms=0.516 (0.089%), neg=0, invalid=762
0336: dt=11.200000, rms=0.516 (0.086%), neg=0, invalid=762
0337: dt=11.200000, rms=0.515 (0.084%), neg=0, invalid=762
0338: dt=11.200000, rms=0.515 (0.072%), neg=0, invalid=762
0339: dt=11.200000, rms=0.514 (0.072%), neg=0, invalid=762
0340: dt=11.200000, rms=0.514 (0.068%), neg=0, invalid=762
0341: dt=11.200000, rms=0.514 (0.066%), neg=0, invalid=762
0342: dt=11.200000, rms=0.513 (0.059%), neg=0, invalid=762
0343: dt=11.200000, rms=0.513 (0.055%), neg=0, invalid=762
0344: dt=11.200000, rms=0.513 (0.055%), neg=0, invalid=762
0345: dt=11.200000, rms=0.513 (0.050%), neg=0, invalid=762
0346: dt=11.200000, rms=0.512 (0.045%), neg=0, invalid=762
0347: dt=11.200000, rms=0.512 (0.042%), neg=0, invalid=762
0348: dt=11.200000, rms=0.512 (0.048%), neg=0, invalid=762
0349: dt=11.200000, rms=0.512 (0.041%), neg=0, invalid=762
0350: dt=11.200000, rms=0.511 (0.036%), neg=0, invalid=762
0351: dt=11.200000, rms=0.511 (0.038%), neg=0, invalid=762
0352: dt=11.200000, rms=0.511 (0.038%), neg=0, invalid=762
0353: dt=11.200000, rms=0.511 (0.037%), neg=0, invalid=762
0354: dt=11.200000, rms=0.511 (0.035%), neg=0, invalid=762
0355: dt=11.200000, rms=0.511 (0.032%), neg=0, invalid=762
0356: dt=11.200000, rms=0.510 (0.034%), neg=0, invalid=762
0357: dt=11.200000, rms=0.510 (0.036%), neg=0, invalid=762
0358: dt=11.200000, rms=0.510 (0.033%), neg=0, invalid=762
0359: dt=11.200000, rms=0.510 (0.031%), neg=0, invalid=762
0360: dt=11.200000, rms=0.510 (0.035%), neg=0, invalid=762
0361: dt=11.200000, rms=0.510 (0.028%), neg=0, invalid=762
0362: dt=11.200000, rms=0.509 (0.029%), neg=0, invalid=762
0363: dt=11.200000, rms=0.509 (0.032%), neg=0, invalid=762
0364: dt=11.200000, rms=0.509 (0.024%), neg=0, invalid=762
0365: dt=11.200000, rms=0.509 (0.024%), neg=0, invalid=762
0366: dt=32.000000, rms=0.509 (0.007%), neg=0, invalid=762
0367: dt=32.000000, rms=0.509 (-0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0368: dt=0.000000, rms=0.527 (0.145%), neg=0, invalid=762
0369: dt=0.000000, rms=0.527 (0.000%), neg=0, invalid=762
0370: dt=0.150000, rms=0.527 (-0.023%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0371: dt=0.000000, rms=0.527 (0.145%), neg=0, invalid=762
0372: dt=0.000000, rms=0.527 (0.000%), neg=0, invalid=762
0373: dt=0.150000, rms=0.527 (-0.022%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.564, neg=0, invalid=762
0374: dt=0.448000, rms=0.562 (0.289%), neg=0, invalid=762
0375: dt=0.320000, rms=0.562 (0.033%), neg=0, invalid=762
0376: dt=0.320000, rms=0.562 (-0.015%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.563, neg=0, invalid=762
0377: dt=0.448000, rms=0.562 (0.203%), neg=0, invalid=762
0378: dt=0.192000, rms=0.562 (0.010%), neg=0, invalid=762
0379: dt=0.192000, rms=0.562 (-0.004%), 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=0.514, neg=0, invalid=762
0380: dt=0.448000, rms=0.500 (2.827%), neg=0, invalid=762
0381: dt=0.448000, rms=0.497 (0.570%), neg=0, invalid=762
0382: dt=0.448000, rms=0.495 (0.305%), neg=0, invalid=762
0383: dt=0.448000, rms=0.495 (0.175%), neg=0, invalid=762
0384: dt=0.448000, rms=0.494 (0.122%), neg=0, invalid=762
0385: dt=0.448000, rms=0.494 (0.090%), neg=0, invalid=762
0386: dt=0.448000, rms=0.493 (0.070%), neg=0, invalid=762
0387: dt=0.448000, rms=0.493 (0.051%), neg=0, invalid=762
0388: dt=0.448000, rms=0.493 (0.045%), neg=0, invalid=762
0389: dt=0.448000, rms=0.493 (0.033%), neg=0, invalid=762
0390: dt=0.448000, rms=0.492 (0.060%), neg=0, invalid=762
0391: dt=0.448000, rms=0.492 (0.072%), neg=0, invalid=762
0392: dt=0.448000, rms=0.492 (0.065%), neg=0, invalid=762
0393: dt=0.448000, rms=0.492 (-0.005%), neg=0, invalid=762
0394: dt=0.112000, rms=0.492 (0.001%), neg=0, invalid=762
0395: dt=0.256000, rms=0.492 (0.005%), neg=0, invalid=762
0396: dt=0.448000, rms=0.492 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0397: dt=0.384000, rms=0.486 (1.203%), neg=0, invalid=762
0398: dt=0.384000, rms=0.485 (0.278%), neg=0, invalid=762
0399: dt=0.384000, rms=0.485 (0.097%), neg=0, invalid=762
0400: dt=0.448000, rms=0.484 (0.045%), neg=0, invalid=762
0401: dt=0.448000, rms=0.484 (0.010%), neg=0, invalid=762
0402: dt=0.448000, rms=0.484 (0.019%), neg=0, invalid=762
0403: dt=0.448000, rms=0.484 (-0.001%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0404: dt=0.000000, rms=0.482 (0.175%), neg=0, invalid=762
0405: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0406: dt=129.472000, rms=0.482 (0.193%), neg=0, invalid=762
0407: dt=129.472000, rms=0.482 (0.021%), neg=0, invalid=762
0408: dt=129.472000, rms=0.482 (-0.031%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0409: dt=9.072000, rms=0.482 (0.187%), neg=0, invalid=762
0410: dt=6.480000, rms=0.482 (0.004%), neg=0, invalid=762
0411: dt=6.480000, rms=0.482 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0412: dt=82.944000, rms=0.481 (0.350%), neg=0, invalid=762
0413: dt=36.288000, rms=0.481 (0.089%), neg=0, invalid=762
0414: dt=36.288000, rms=0.481 (0.047%), neg=0, invalid=762
0415: dt=36.288000, rms=0.480 (0.076%), neg=0, invalid=762
0416: dt=36.288000, rms=0.480 (0.088%), neg=0, invalid=762
0417: dt=36.288000, rms=0.479 (0.077%), neg=0, invalid=762
0418: dt=36.288000, rms=0.479 (0.073%), neg=0, invalid=762
0419: dt=124.416000, rms=0.479 (0.046%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.480, neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0420: dt=11.200000, rms=0.478 (0.363%), neg=0, invalid=762
0421: dt=11.200000, rms=0.478 (0.092%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0422: dt=11.200000, rms=0.477 (0.063%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0423: dt=11.200000, rms=0.477 (0.039%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0424: dt=11.200000, rms=0.477 (-0.049%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.478, neg=0, invalid=762
0425: dt=30.740984, rms=0.473 (0.979%), neg=0, invalid=762
0426: dt=11.200000, rms=0.472 (0.262%), neg=0, invalid=762
0427: dt=92.207407, rms=0.470 (0.524%), neg=0, invalid=762
0428: dt=11.200000, rms=0.468 (0.309%), neg=0, invalid=762
0429: dt=44.800000, rms=0.467 (0.181%), neg=0, invalid=762
0430: dt=44.800000, rms=0.467 (-0.322%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.470, neg=0, invalid=762
0431: dt=9.022556, rms=0.467 (0.713%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0432: dt=14.989474, rms=0.465 (0.279%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0433: dt=13.824000, rms=0.465 (0.197%), neg=0, invalid=762
0434: dt=13.824000, rms=0.464 (0.181%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0435: dt=13.824000, rms=0.463 (0.230%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0436: dt=13.824000, rms=0.462 (0.153%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0437: dt=13.824000, rms=0.461 (0.197%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0438: dt=13.824000, rms=0.460 (0.149%), neg=0, invalid=762
0439: dt=13.824000, rms=0.460 (0.085%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0440: dt=13.824000, rms=0.460 (0.045%), neg=0, invalid=762
0441: dt=10.222222, rms=0.459 (0.095%), neg=0, invalid=762
0442: dt=5.000000, rms=0.459 (0.030%), neg=0, invalid=762
0443: dt=5.000000, rms=0.459 (0.015%), neg=0, invalid=762
0444: dt=5.000000, rms=0.459 (0.005%), neg=0, invalid=762
0445: dt=5.000000, rms=0.459 (0.016%), neg=0, invalid=762
0446: dt=5.000000, rms=0.459 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0447: dt=14.185075, rms=0.455 (1.003%), neg=0, invalid=762
0448: dt=9.801047, rms=0.454 (0.245%), neg=0, invalid=762
0449: dt=9.801047, rms=0.453 (0.172%), neg=0, invalid=762
0450: dt=9.801047, rms=0.452 (0.189%), neg=0, invalid=762
0451: dt=9.801047, rms=0.452 (0.133%), neg=0, invalid=762
0452: dt=9.801047, rms=0.452 (0.036%), neg=0, invalid=762
0453: dt=9.801047, rms=0.451 (0.099%), neg=0, invalid=762
0454: dt=9.801047, rms=0.451 (0.129%), neg=0, invalid=762
0455: dt=9.801047, rms=0.450 (0.130%), neg=0, invalid=762
0456: dt=9.801047, rms=0.450 (0.094%), neg=0, invalid=762
0457: dt=9.801047, rms=0.449 (0.111%), neg=0, invalid=762
0458: dt=9.801047, rms=0.449 (0.093%), neg=0, invalid=762
0459: dt=6.400000, rms=0.449 (0.057%), neg=0, invalid=762
0460: dt=6.400000, rms=0.448 (0.023%), neg=0, invalid=762
0461: dt=6.400000, rms=0.448 (0.022%), neg=0, invalid=762
0462: dt=6.400000, rms=0.448 (0.014%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.454, neg=0, invalid=762
0463: dt=0.000000, rms=0.453 (0.190%), neg=0, invalid=762
0464: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.454, neg=0, invalid=762
0465: dt=0.000000, rms=0.453 (0.190%), neg=0, invalid=762
0466: dt=0.000000, rms=0.453 (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=0.446, neg=0, invalid=762
iter 0, gcam->neg = 747
after 12 iterations, nbhd size=1, neg = 0
0467: dt=1.995590, rms=0.420 (5.868%), neg=0, invalid=762
0468: dt=0.024000, rms=0.420 (0.006%), neg=0, invalid=762
0469: dt=0.024000, rms=0.420 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0470: dt=0.096000, rms=0.419 (0.329%), neg=0, invalid=762
0471: dt=0.007000, rms=0.419 (0.001%), neg=0, invalid=762
0472: dt=0.007000, rms=0.419 (0.000%), neg=0, invalid=762
0473: dt=0.007000, rms=0.419 (-0.001%), 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=0.408, neg=0, invalid=762
0474: dt=4.624000, rms=0.408 (0.001%), neg=0, invalid=762
0475: dt=0.361250, rms=0.408 (0.000%), neg=0, invalid=762
0476: dt=0.361250, 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
0477: dt=27.744000, rms=0.408 (0.005%), neg=0, invalid=762
0478: dt=8.092000, rms=0.408 (0.000%), neg=0, invalid=762
0479: dt=8.092000, rms=0.408 (0.000%), neg=0, invalid=762
0480: dt=8.092000, rms=0.408 (-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=0.409, neg=0, invalid=762
0481: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0482: dt=36.288000, rms=0.408 (0.035%), neg=0, invalid=762
0483: dt=103.680000, rms=0.408 (0.036%), neg=0, invalid=762
0484: dt=124.416000, rms=0.408 (0.025%), neg=0, invalid=762
0485: dt=124.416000, rms=0.408 (-0.018%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0486: dt=2.800000, rms=0.409 (0.019%), neg=0, invalid=762
0487: dt=2.800000, rms=0.409 (0.006%), neg=0, invalid=762
0488: dt=2.800000, rms=0.409 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0489: dt=86.502283, rms=0.406 (0.557%), neg=0, invalid=762
0490: dt=22.970297, rms=0.406 (0.178%), neg=0, invalid=762
0491: dt=22.970297, rms=0.405 (0.073%), neg=0, invalid=762
0492: dt=22.970297, rms=0.405 (0.092%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0493: dt=22.970297, rms=0.404 (0.133%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0494: dt=22.970297, rms=0.404 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0495: dt=22.970297, rms=0.403 (0.150%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0496: dt=22.970297, rms=0.403 (0.123%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0497: dt=22.970297, rms=0.402 (0.107%), neg=0, invalid=762
0498: dt=25.600000, rms=0.402 (0.011%), neg=0, invalid=762
0499: dt=25.600000, rms=0.402 (0.015%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0500: dt=25.600000, rms=0.402 (0.021%), neg=0, invalid=762
0501: dt=25.600000, rms=0.402 (0.027%), neg=0, invalid=762
0502: dt=25.600000, rms=0.402 (0.030%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0503: dt=25.600000, rms=0.402 (0.039%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0504: dt=25.600000, rms=0.402 (0.043%), neg=0, invalid=762
0505: dt=25.600000, rms=0.401 (0.053%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0506: dt=25.600000, rms=0.401 (0.053%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0507: dt=25.600000, rms=0.401 (0.050%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=0, neg = 0
0508: dt=25.600000, rms=0.401 (0.042%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.404, neg=0, invalid=762
0509: dt=0.000135, rms=0.404 (0.000%), neg=0, invalid=762
0510: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.404, neg=0, invalid=762
0511: dt=8.450704, rms=0.404 (0.073%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0512: dt=15.652174, rms=0.403 (0.081%), neg=0, invalid=762
iter 0, gcam->neg = 50
after 13 iterations, nbhd size=1, neg = 0
0513: dt=58.448980, rms=0.402 (0.230%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 3 iterations, nbhd size=0, neg = 0
0514: dt=19.000000, rms=0.402 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 22
after 5 iterations, nbhd size=0, neg = 0
0515: dt=19.000000, rms=0.402 (0.016%), neg=0, invalid=762
iter 0, gcam->neg = 27
after 11 iterations, nbhd size=1, neg = 0
0516: dt=19.000000, rms=0.401 (0.089%), neg=0, invalid=762
iter 0, gcam->neg = 45
after 20 iterations, nbhd size=1, neg = 0
0517: dt=19.000000, rms=0.401 (0.018%), neg=0, invalid=762
iter 0, gcam->neg = 93
after 16 iterations, nbhd size=1, neg = 0
0518: dt=19.000000, rms=0.401 (0.060%), neg=0, invalid=762
iter 0, gcam->neg = 81
after 15 iterations, nbhd size=1, neg = 0
0519: dt=19.000000, rms=0.401 (0.036%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
0520: dt=0.000050, rms=0.406 (0.000%), neg=0, invalid=762
0521: dt=0.000000, rms=0.406 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
0522: dt=0.000000, rms=0.406 (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=0.397, neg=0, invalid=762
iter 0, gcam->neg = 650
after 13 iterations, nbhd size=1, neg = 0
0523: dt=1.280000, rms=0.389 (2.016%), neg=0, invalid=762
0524: dt=0.000015, rms=0.389 (0.000%), neg=0, invalid=762
0525: dt=0.000015, rms=0.389 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.389, neg=0, invalid=762
0526: dt=0.112000, rms=0.389 (0.093%), neg=0, invalid=762
0527: dt=0.112000, rms=0.389 (0.035%), neg=0, invalid=762
0528: dt=0.112000, rms=0.389 (0.020%), neg=0, invalid=762
0529: dt=0.112000, rms=0.389 (-0.029%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 30 minutes and 30 seconds.
mri_ca_register utimesec    9954.389702
mri_ca_register stimesec    8.388724
mri_ca_register ru_maxrss   1342628
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   3579157
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63368
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3436
mri_ca_register ru_nivcsw   27757
FSRUNTIME@ mri_ca_register  2.5083 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 20:43:33 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-967
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-6.0.0/0051105/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.14
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 = 0.12842 (10)
Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (402 voxels, overlap=0.005)
Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (402 voxels, peak =  9), gca=8.9
gca peak = 0.17677 (13)
mri peak = 0.09407 (10)
Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (250 voxels, overlap=0.422)
Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (250 voxels, peak =  7), gca=7.2
gca peak = 0.28129 (95)
mri peak = 0.09944 (87)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (618 voxels, overlap=0.079)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (618 voxels, peak = 87), gca=86.9
gca peak = 0.16930 (96)
mri peak = 0.09299 (89)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (603 voxels, overlap=0.535)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (603 voxels, peak = 88), gca=87.8
gca peak = 0.24553 (55)
mri peak = 0.11855 (58)
Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (575 voxels, overlap=1.004)
Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (575 voxels, peak = 52), gca=52.0
gca peak = 0.30264 (59)
mri peak = 0.08911 (54)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (668 voxels, overlap=1.010)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (668 voxels, peak = 56), gca=55.8
gca peak = 0.07580 (103)
mri peak = 0.09635 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38679 voxels, overlap=0.693)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38679 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.09987 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (37237 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (37237 voxels, peak = 106), gca=105.6
gca peak = 0.09712 (58)
mri peak = 0.04919 (55)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (24608 voxels, overlap=0.948)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (24608 voxels, peak = 55), gca=54.8
gca peak = 0.11620 (58)
mri peak = 0.05033 (51)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (24622 voxels, overlap=0.918)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (24622 voxels, peak = 53), gca=53.1
gca peak = 0.30970 (66)
mri peak = 0.09891 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, overlap=1.003)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, peak = 66), gca=66.0
gca peak = 0.15280 (69)
mri peak = 0.10693 (69)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (849 voxels, overlap=0.512)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (849 voxels, peak = 64), gca=63.8
gca peak = 0.13902 (56)
mri peak = 0.05194 (55)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15876 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15876 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.04853 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (17828 voxels, overlap=0.997)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (17828 voxels, peak = 52), gca=52.0
gca peak = 0.16765 (84)
mri peak = 0.08307 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4383 voxels, overlap=0.730)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4383 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.08716 (85)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4335 voxels, overlap=0.911)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4335 voxels, peak = 87), gca=86.9
gca peak = 0.29869 (57)
mri peak = 0.10345 (56)
Left_Amygdala (18): linear fit = 0.96 x + 0.0 (415 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 0.96 x + 0.0 (415 voxels, peak = 55), gca=55.0
gca peak = 0.33601 (57)
mri peak = 0.10768 (55)
Right_Amygdala (54): linear fit = 0.94 x + 0.0 (428 voxels, overlap=1.014)
Right_Amygdala (54): linear fit = 0.94 x + 0.0 (428 voxels, peak = 54), gca=53.9
gca peak = 0.11131 (90)
mri peak = 0.07890 (82)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3879 voxels, overlap=0.804)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3879 voxels, peak = 86), gca=85.9
gca peak = 0.11793 (83)
mri peak = 0.08773 (83)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3993 voxels, overlap=0.974)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3993 voxels, peak = 82), gca=81.8
gca peak = 0.08324 (81)
mri peak = 0.09324 (76)
Left_Putamen (12): linear fit = 0.94 x + 0.0 (2146 voxels, overlap=0.712)
Left_Putamen (12): linear fit = 0.94 x + 0.0 (2146 voxels, peak = 77), gca=76.5
gca peak = 0.10360 (77)
mri peak = 0.07948 (72)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (2223 voxels, overlap=0.772)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (2223 voxels, peak = 72), gca=72.0
gca peak = 0.08424 (78)
mri peak = 0.13054 (80)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11036 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11036 voxels, peak = 81), gca=80.7
gca peak = 0.12631 (89)
mri peak = 0.08984 (87)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1297 voxels, overlap=0.823)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1297 voxels, peak = 87), gca=86.8
gca peak = 0.14500 (87)
mri peak = 0.08968 (86)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1408 voxels, overlap=0.913)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1408 voxels, peak = 85), gca=84.8
gca peak = 0.14975 (24)
mri peak = 0.04717 ( 4)
gca peak = 0.19357 (14)
mri peak = 0.09621 (10)
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 0.94 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 0.50 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.29485 ( 9)
mri peak = 0.12842 (10)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (402 voxels, overlap=0.959)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (402 voxels, peak =  9), gca=9.5
gca peak = 0.25357 ( 7)
mri peak = 0.09407 (10)
Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (250 voxels, overlap=0.936)
Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (250 voxels, peak =  8), gca=7.5
gca peak = 0.26667 (87)
mri peak = 0.09944 (87)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (618 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (618 voxels, peak = 86), gca=85.7
gca peak = 0.17947 (88)
mri peak = 0.09299 (89)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (603 voxels, overlap=1.006)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (603 voxels, peak = 88), gca=87.6
gca peak = 0.27769 (52)
mri peak = 0.11855 (58)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (575 voxels, overlap=1.005)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (575 voxels, peak = 53), gca=52.8
gca peak = 0.30423 (53)
mri peak = 0.08911 (54)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (668 voxels, overlap=1.010)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (668 voxels, peak = 55), gca=55.4
gca peak = 0.07771 (104)
mri peak = 0.09635 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38679 voxels, overlap=0.753)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38679 voxels, peak = 104), gca=104.0
gca peak = 0.07820 (106)
mri peak = 0.09987 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37237 voxels, overlap=0.679)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37237 voxels, peak = 106), gca=106.0
gca peak = 0.10313 (55)
mri peak = 0.04919 (55)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24608 voxels, overlap=0.996)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24608 voxels, peak = 54), gca=54.2
gca peak = 0.12643 (53)
mri peak = 0.05033 (51)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (24622 voxels, overlap=0.986)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (24622 voxels, peak = 53), gca=53.0
gca peak = 0.30965 (66)
mri peak = 0.09891 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, overlap=1.003)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, peak = 66), gca=66.0
gca peak = 0.13200 (64)
mri peak = 0.10693 (69)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (849 voxels, overlap=0.990)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (849 voxels, peak = 63), gca=63.0
gca peak = 0.13344 (57)
mri peak = 0.05194 (55)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (15876 voxels, overlap=0.993)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (15876 voxels, peak = 55), gca=55.0
gca peak = 0.15539 (52)
mri peak = 0.04853 (55)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17828 voxels, overlap=0.996)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17828 voxels, peak = 54), gca=54.3
gca peak = 0.15873 (90)
mri peak = 0.08307 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4383 voxels, overlap=0.958)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4383 voxels, peak = 91), gca=91.3
gca peak = 0.18381 (87)
mri peak = 0.08716 (85)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4335 voxels, overlap=0.980)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4335 voxels, peak = 86), gca=85.7
gca peak = 0.29815 (55)
mri peak = 0.10345 (56)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (415 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (415 voxels, peak = 55), gca=55.0
gca peak = 0.41931 (54)
mri peak = 0.10768 (55)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (428 voxels, overlap=1.014)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (428 voxels, peak = 54), gca=54.0
gca peak = 0.11467 (86)
mri peak = 0.07890 (82)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3879 voxels, overlap=0.957)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3879 voxels, peak = 85), gca=84.7
gca peak = 0.10564 (79)
mri peak = 0.08773 (83)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3993 voxels, overlap=0.943)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3993 voxels, peak = 80), gca=80.2
gca peak = 0.09401 (78)
mri peak = 0.09324 (76)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2146 voxels, overlap=0.912)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2146 voxels, peak = 78), gca=78.0
gca peak = 0.09691 (72)
mri peak = 0.07948 (72)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2223 voxels, overlap=0.994)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2223 voxels, peak = 73), gca=73.1
gca peak = 0.08837 (81)
mri peak = 0.13054 (80)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11036 voxels, overlap=0.621)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11036 voxels, peak = 82), gca=82.2
gca peak = 0.13258 (87)
mri peak = 0.08984 (87)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1297 voxels, overlap=0.791)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1297 voxels, peak = 87), gca=86.6
gca peak = 0.14341 (83)
mri peak = 0.08968 (86)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1408 voxels, overlap=0.877)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1408 voxels, peak = 83), gca=82.6
gca peak = 0.29623 (13)
mri peak = 0.04717 ( 4)
gca peak = 0.31719 ( 7)
mri peak = 0.09621 (10)
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18199 (30)
gca peak Left_Thalamus = 1.00000 (89)
gca peak Third_Ventricle = 0.29623 (13)
gca peak Fourth_Ventricle = 0.31719 ( 7)
gca peak CSF = 0.39966 (18)
gca peak Left_Accumbens_area = 0.54630 (57)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.76046 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.26998 (22)
gca peak Right_Accumbens_area = 0.42997 (65)
gca peak Right_vessel = 0.82280 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.89470 (16)
gca peak WM_hypointensities = 0.07201 (78)
gca peak non_WM_hypointensities = 0.09744 (44)
gca peak Optic_Chiasm = 0.71107 (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 1.07 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
55681 voxels changed in iteration 0 of unlikely voxel relabeling
108 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
27832 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels)
346 hippocampal voxels changed.
2 amygdala voxels changed.
pass 1: 63045 changed. image ll: -2.093, PF=0.500
pass 2: 17237 changed. image ll: -2.092, PF=0.500
pass 3: 5368 changed.
pass 4: 1904 changed.
31194 voxels changed in iteration 0 of unlikely voxel relabeling
162 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
4996 voxels changed in iteration 0 of unlikely voxel relabeling
45 voxels changed in iteration 1 of unlikely voxel relabeling
7 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4814 voxels changed in iteration 0 of unlikely voxel relabeling
47 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
3848 voxels changed in iteration 0 of unlikely voxel relabeling
17 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    3103.937129
mri_ca_label stimesec    1.551764
mri_ca_label ru_maxrss   2103344
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   649072
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63360
mri_ca_label ru_oublock  448
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    282
mri_ca_label ru_nivcsw   6638
auto-labeling took 51 minutes and 4 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/cc_up.lta 0051105 

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-6.0.0/0051105/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/norm.mgz
50632 voxels in left wm, 33313 in right wm, xrange [120, 130]
searching rotation angles z=[-4 10], y=[-6  8]

searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.8  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.3  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.8  
searching scale 1 Z rot 9.1  
searching scale 1 Z rot 9.3  
searching scale 1 Z rot 9.6  global minimum found at slice 123.6, rotations (1.27, 2.80)
final transformation (x=123.6, yr=1.265, zr=2.804):
 0.99856  -0.04892   0.02206   6.94757;
 0.04891   0.99880   0.00108   23.95334;
-0.02209   0.00000   0.99976   19.75628;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 127
cc center is found at 127 98 111
eigenvectors:
 0.00005  -0.00418   0.99999;
-0.20966  -0.97777  -0.00407;
 0.97777  -0.20966  -0.00093;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.9 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 21:35:29 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 21:35:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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...
1100 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 60 (60), valley at 20 (20)
csf peak at 30, 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 19 (19)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 12 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 21:38:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1459687 voxels in mask (pct=  8.70)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 21:38:44 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): 106.4 +- 5.3 [79.0 --> 125.0]
GM (68.0) : 66.6 +- 9.6 [30.0 --> 95.0]
setting bottom of white matter range to 76.2
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...
6852 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5292 filled
3265 bright non-wm voxels segmented.
3056 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 0.52 minutes
reading wm segmentation from wm.seg.mgz...
88 voxels added to wm to prevent paths from MTL structures to cortex
2320 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 36336 voxels turned on, 33511 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 116   new 116
115,126,128 old 116   new 116
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  19 found -  19 modified     |    TOTAL:  19
pass   2 (xy+):   0 found -  19 modified     |    TOTAL:  19
pass   1 (xy-):  24 found -  24 modified     |    TOTAL:  43
pass   2 (xy-):   0 found -  24 modified     |    TOTAL:  43
pass   1 (yz+):  28 found -  28 modified     |    TOTAL:  71
pass   2 (yz+):   0 found -  28 modified     |    TOTAL:  71
pass   1 (yz-):  24 found -  24 modified     |    TOTAL:  95
pass   2 (yz-):   0 found -  24 modified     |    TOTAL:  95
pass   1 (xz+):  26 found -  26 modified     |    TOTAL: 121
pass   2 (xz+):   0 found -  26 modified     |    TOTAL: 121
pass   1 (xz-):  18 found -  18 modified     |    TOTAL: 139
pass   2 (xz-):   0 found -  18 modified     |    TOTAL: 139
Iteration Number : 1
pass   1 (+++):  19 found -  19 modified     |    TOTAL:  19
pass   2 (+++):   0 found -  19 modified     |    TOTAL:  19
pass   1 (+++):  34 found -  34 modified     |    TOTAL:  53
pass   2 (+++):   0 found -  34 modified     |    TOTAL:  53
pass   1 (+++):  26 found -  26 modified     |    TOTAL:  79
pass   2 (+++):   0 found -  26 modified     |    TOTAL:  79
pass   1 (+++):  11 found -  11 modified     |    TOTAL:  90
pass   2 (+++):   0 found -  11 modified     |    TOTAL:  90
Iteration Number : 1
pass   1 (++): 129 found - 129 modified     |    TOTAL: 129
pass   2 (++):   0 found - 129 modified     |    TOTAL: 129
pass   1 (+-): 120 found - 120 modified     |    TOTAL: 249
pass   2 (+-):   0 found - 120 modified     |    TOTAL: 249
pass   1 (--): 134 found - 134 modified     |    TOTAL: 383
pass   2 (--):   0 found - 134 modified     |    TOTAL: 383
pass   1 (-+): 115 found - 115 modified     |    TOTAL: 498
pass   2 (-+):   0 found - 115 modified     |    TOTAL: 498
Iteration Number : 2
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   8
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  10
pass   1 (xz+):   9 found -   9 modified     |    TOTAL:  19
pass   2 (xz+):   0 found -   9 modified     |    TOTAL:  19
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  26
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  26
Iteration Number : 2
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   7
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   4
pass   1 (--):   2 found -   2 modified     |    TOTAL:   6
pass   2 (--):   0 found -   2 modified     |    TOTAL:   6
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   8
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-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 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

Total Number of Modified Voxels = 768 (out of 504614: 0.152196)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 21:40:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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
 1.03374  -0.04445   0.02053   1.61642;
 0.02912   1.07990   0.39074  -49.35634;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.03374  -0.04445   0.02053   1.61642;
 0.02912   1.07990   0.39074  -49.35634;
-0.03759  -0.39978   1.02050   41.71447;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1309 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75)
no need to search
using seed (126, 124, 151), TAL = (2.0, 23.0, 4.0)
talairach voxel to voxel transform
 0.96546   0.02851  -0.03034   1.11210;
-0.03407   0.81004  -0.30947   52.94506;
 0.02222   0.31838   0.85756  -20.09424;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  124,  151) --> (2.0, 23.0, 4.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (2.00, 23.00, 4.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 23.00, 4.00) SRC: (104.34, 102.98, 151.28)
search lh wm seed point around talairach space (-16.00, 23.00, 4.00), SRC: (139.09, 101.75, 152.08)
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 21:41:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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


Iteration Number : 1
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   6
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   7
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   8
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   9
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   9
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  12
pass   2 (xz-):   0 found -   3 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 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 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
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 17 (out of 242126: 0.007021)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 1238 vertices, 1351 faces
slice 60: 9362 vertices, 9770 faces
slice 70: 22016 vertices, 22452 faces
slice 80: 34953 vertices, 35432 faces
slice 90: 48745 vertices, 49218 faces
slice 100: 61229 vertices, 61689 faces
slice 110: 73470 vertices, 73883 faces
slice 120: 85099 vertices, 85558 faces
slice 130: 95678 vertices, 96099 faces
slice 140: 106091 vertices, 106478 faces
slice 150: 115147 vertices, 115478 faces
slice 160: 123658 vertices, 123997 faces
slice 170: 129909 vertices, 130174 faces
slice 180: 134975 vertices, 135213 faces
slice 190: 138369 vertices, 138512 faces
slice 200: 138684 vertices, 138762 faces
slice 210: 138684 vertices, 138762 faces
slice 220: 138684 vertices, 138762 faces
slice 230: 138684 vertices, 138762 faces
slice 240: 138684 vertices, 138762 faces
slice 250: 138684 vertices, 138762 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...
   138684 voxel in cpt #1: X=-78 [v=138684,e=416286,f=277524] located at (-23.815098, -19.036688, 21.929897)
For the whole surface: X=-78 [v=138684,e=416286,f=277524]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 21:41:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   6
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   7
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   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 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 11 (out of 241850: 0.004548)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 1068 vertices, 1192 faces
slice 60: 8981 vertices, 9368 faces
slice 70: 21165 vertices, 21643 faces
slice 80: 35222 vertices, 35746 faces
slice 90: 48699 vertices, 49160 faces
slice 100: 60819 vertices, 61255 faces
slice 110: 72468 vertices, 72869 faces
slice 120: 84202 vertices, 84618 faces
slice 130: 94838 vertices, 95257 faces
slice 140: 104834 vertices, 105199 faces
slice 150: 114025 vertices, 114368 faces
slice 160: 122577 vertices, 122889 faces
slice 170: 128745 vertices, 129017 faces
slice 180: 134369 vertices, 134593 faces
slice 190: 137582 vertices, 137674 faces
slice 200: 137638 vertices, 137700 faces
slice 210: 137638 vertices, 137700 faces
slice 220: 137638 vertices, 137700 faces
slice 230: 137638 vertices, 137700 faces
slice 240: 137638 vertices, 137700 faces
slice 250: 137638 vertices, 137700 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...
   137638 voxel in cpt #1: X=-62 [v=137638,e=413100,f=275400] located at (31.852715, -18.958689, 20.307655)
For the whole surface: X=-62 [v=137638,e=413100,f=275400]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 21:41:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 21:41:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

Waiting for PID 6099 of (6099 6102) to complete...
Waiting for PID 6102 of (6099 6102) 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 (6099 6102) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 21:41:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 21:41:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

Waiting for PID 6145 of (6145 6148) to complete...
Waiting for PID 6148 of (6145 6148) 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 = 45.3 mm, total surface area = 71767 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.7 minutes

step 000: RMS=0.160 (target=0.015)   
step 005: RMS=0.122 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.059 (target=0.015)   
step 030: RMS=0.053 (target=0.015)   
step 035: RMS=0.048 (target=0.015)   
step 040: RMS=0.046 (target=0.015)   
step 045: RMS=0.044 (target=0.015)   
step 050: RMS=0.042 (target=0.015)   
step 055: RMS=0.041 (target=0.015)   
step 060: RMS=0.041 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    42.777496
mris_inflate stimesec    0.106983
mris_inflate ru_maxrss   202956
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29724
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  9776
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2165
mris_inflate ru_nivcsw   3521

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 45.1 mm, total surface area = 71194 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.7 minutes

step 000: RMS=0.161 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.061 (target=0.015)   
step 030: RMS=0.055 (target=0.015)   
step 035: RMS=0.050 (target=0.015)   
step 040: RMS=0.048 (target=0.015)   
step 045: RMS=0.046 (target=0.015)   
step 050: RMS=0.045 (target=0.015)   
step 055: RMS=0.044 (target=0.015)   
step 060: RMS=0.044 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    42.528534
mris_inflate stimesec    0.103984
mris_inflate ru_maxrss   201304
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29310
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  9704
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2143
mris_inflate ru_nivcsw   3269
PIDs (6145 6148) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 21:42:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 21:42:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

Waiting for PID 6215 of (6215 6218) to complete...
Waiting for PID 6218 of (6215 6218) 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 0.98 +- 0.59 (0.00-->8.45) (max @ vno 103620 --> 103638)
face area 0.03 +- 0.04 (-0.40-->0.78)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.336...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=174.987, avgs=0
005/300: dt: 0.9000, rms radial error=174.731, avgs=0
010/300: dt: 0.9000, rms radial error=174.181, avgs=0
015/300: dt: 0.9000, rms radial error=173.459, avgs=0
020/300: dt: 0.9000, rms radial error=172.636, avgs=0
025/300: dt: 0.9000, rms radial error=171.754, avgs=0
030/300: dt: 0.9000, rms radial error=170.840, avgs=0
035/300: dt: 0.9000, rms radial error=169.908, avgs=0
040/300: dt: 0.9000, rms radial error=168.967, avgs=0
045/300: dt: 0.9000, rms radial error=168.022, avgs=0
050/300: dt: 0.9000, rms radial error=167.077, avgs=0
055/300: dt: 0.9000, rms radial error=166.134, avgs=0
060/300: dt: 0.9000, rms radial error=165.193, avgs=0
065/300: dt: 0.9000, rms radial error=164.257, avgs=0
070/300: dt: 0.9000, rms radial error=163.324, avgs=0
075/300: dt: 0.9000, rms radial error=162.397, avgs=0
080/300: dt: 0.9000, rms radial error=161.477, avgs=0
085/300: dt: 0.9000, rms radial error=160.565, avgs=0
090/300: dt: 0.9000, rms radial error=159.659, avgs=0
095/300: dt: 0.9000, rms radial error=158.758, avgs=0
100/300: dt: 0.9000, rms radial error=157.862, avgs=0
105/300: dt: 0.9000, rms radial error=156.971, avgs=0
110/300: dt: 0.9000, rms radial error=156.085, avgs=0
115/300: dt: 0.9000, rms radial error=155.203, avgs=0
120/300: dt: 0.9000, rms radial error=154.328, avgs=0
125/300: dt: 0.9000, rms radial error=153.458, avgs=0
130/300: dt: 0.9000, rms radial error=152.592, avgs=0
135/300: dt: 0.9000, rms radial error=151.731, avgs=0
140/300: dt: 0.9000, rms radial error=150.874, avgs=0
145/300: dt: 0.9000, rms radial error=150.023, avgs=0
150/300: dt: 0.9000, rms radial error=149.177, avgs=0
155/300: dt: 0.9000, rms radial error=148.335, avgs=0
160/300: dt: 0.9000, rms radial error=147.498, avgs=0
165/300: dt: 0.9000, rms radial error=146.665, avgs=0
170/300: dt: 0.9000, rms radial error=145.837, avgs=0
175/300: dt: 0.9000, rms radial error=145.015, avgs=0
180/300: dt: 0.9000, rms radial error=144.197, avgs=0
185/300: dt: 0.9000, rms radial error=143.385, avgs=0
190/300: dt: 0.9000, rms radial error=142.576, avgs=0
195/300: dt: 0.9000, rms radial error=141.772, avgs=0
200/300: dt: 0.9000, rms radial error=140.973, avgs=0
205/300: dt: 0.9000, rms radial error=140.178, avgs=0
210/300: dt: 0.9000, rms radial error=139.387, avgs=0
215/300: dt: 0.9000, rms radial error=138.601, avgs=0
220/300: dt: 0.9000, rms radial error=137.819, avgs=0
225/300: dt: 0.9000, rms radial error=137.041, avgs=0
230/300: dt: 0.9000, rms radial error=136.268, avgs=0
235/300: dt: 0.9000, rms radial error=135.499, avgs=0
240/300: dt: 0.9000, rms radial error=134.735, avgs=0
245/300: dt: 0.9000, rms radial error=133.975, avgs=0
250/300: dt: 0.9000, rms radial error=133.218, avgs=0
255/300: dt: 0.9000, rms radial error=132.467, avgs=0
260/300: dt: 0.9000, rms radial error=131.719, avgs=0
265/300: dt: 0.9000, rms radial error=130.975, avgs=0
270/300: dt: 0.9000, rms radial error=130.236, avgs=0
275/300: dt: 0.9000, rms radial error=129.501, avgs=0
280/300: dt: 0.9000, rms radial error=128.770, avgs=0
285/300: dt: 0.9000, rms radial error=128.044, avgs=0
290/300: dt: 0.9000, rms radial error=127.319, avgs=0
295/300: dt: 0.9000, rms radial error=126.601, avgs=0
300/300: dt: 0.9000, rms radial error=125.888, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15913.47
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 = 2600.95
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 3 (K=160.0), pass 1, starting sse = 246.64
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00178
epoch 4 (K=640.0), pass 1, starting sse = 17.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00302
final distance error %26.28
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    238.110801
mris_sphere stimesec    0.176973
mris_sphere ru_maxrss   203164
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   29263
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9800
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    10207
mris_sphere ru_nivcsw   17488
FSRUNTIME@ mris_sphere  0.0662 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 0.99 +- 0.59 (0.00-->8.37) (max @ vno 101870 --> 101871)
face area 0.03 +- 0.04 (-0.25-->0.68)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.341...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=174.740, avgs=0
005/300: dt: 0.9000, rms radial error=174.483, avgs=0
010/300: dt: 0.9000, rms radial error=173.931, avgs=0
015/300: dt: 0.9000, rms radial error=173.211, avgs=0
020/300: dt: 0.9000, rms radial error=172.390, avgs=0
025/300: dt: 0.9000, rms radial error=171.512, avgs=0
030/300: dt: 0.9000, rms radial error=170.601, avgs=0
035/300: dt: 0.9000, rms radial error=169.673, avgs=0
040/300: dt: 0.9000, rms radial error=168.736, avgs=0
045/300: dt: 0.9000, rms radial error=167.797, avgs=0
050/300: dt: 0.9000, rms radial error=166.857, avgs=0
055/300: dt: 0.9000, rms radial error=165.918, avgs=0
060/300: dt: 0.9000, rms radial error=164.982, avgs=0
065/300: dt: 0.9000, rms radial error=164.050, avgs=0
070/300: dt: 0.9000, rms radial error=163.129, avgs=0
075/300: dt: 0.9000, rms radial error=162.213, avgs=0
080/300: dt: 0.9000, rms radial error=161.302, avgs=0
085/300: dt: 0.9000, rms radial error=160.396, avgs=0
090/300: dt: 0.9000, rms radial error=159.496, avgs=0
095/300: dt: 0.9000, rms radial error=158.603, avgs=0
100/300: dt: 0.9000, rms radial error=157.715, avgs=0
105/300: dt: 0.9000, rms radial error=156.831, avgs=0
110/300: dt: 0.9000, rms radial error=155.952, avgs=0
115/300: dt: 0.9000, rms radial error=155.078, avgs=0
120/300: dt: 0.9000, rms radial error=154.208, avgs=0
125/300: dt: 0.9000, rms radial error=153.343, avgs=0
130/300: dt: 0.9000, rms radial error=152.483, avgs=0
135/300: dt: 0.9000, rms radial error=151.629, avgs=0
140/300: dt: 0.9000, rms radial error=150.780, avgs=0
145/300: dt: 0.9000, rms radial error=149.935, avgs=0
150/300: dt: 0.9000, rms radial error=149.095, avgs=0
155/300: dt: 0.9000, rms radial error=148.259, avgs=0
160/300: dt: 0.9000, rms radial error=147.428, avgs=0
165/300: dt: 0.9000, rms radial error=146.601, avgs=0
170/300: dt: 0.9000, rms radial error=145.779, avgs=0
175/300: dt: 0.9000, rms radial error=144.961, avgs=0
180/300: dt: 0.9000, rms radial error=144.148, avgs=0
185/300: dt: 0.9000, rms radial error=143.339, avgs=0
190/300: dt: 0.9000, rms radial error=142.535, avgs=0
195/300: dt: 0.9000, rms radial error=141.735, avgs=0
200/300: dt: 0.9000, rms radial error=140.939, avgs=0
205/300: dt: 0.9000, rms radial error=140.147, avgs=0
210/300: dt: 0.9000, rms radial error=139.360, avgs=0
215/300: dt: 0.9000, rms radial error=138.577, avgs=0
220/300: dt: 0.9000, rms radial error=137.799, avgs=0
225/300: dt: 0.9000, rms radial error=137.025, avgs=0
230/300: dt: 0.9000, rms radial error=136.256, avgs=0
235/300: dt: 0.9000, rms radial error=135.491, avgs=0
240/300: dt: 0.9000, rms radial error=134.730, avgs=0
245/300: dt: 0.9000, rms radial error=133.973, avgs=0
250/300: dt: 0.9000, rms radial error=133.221, avgs=0
255/300: dt: 0.9000, rms radial error=132.473, avgs=0
260/300: dt: 0.9000, rms radial error=131.730, avgs=0
265/300: dt: 0.9000, rms radial error=130.990, avgs=0
270/300: dt: 0.9000, rms radial error=130.255, avgs=0
275/300: dt: 0.9000, rms radial error=129.524, avgs=0
280/300: dt: 0.9000, rms radial error=128.796, avgs=0
285/300: dt: 0.9000, rms radial error=128.073, avgs=0
290/300: dt: 0.9000, rms radial error=127.354, avgs=0
295/300: dt: 0.9000, rms radial error=126.639, avgs=0
300/300: dt: 0.9000, rms radial error=125.927, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15691.36
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 2 (K=40.0), pass 1, starting sse = 2517.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 3 (K=160.0), pass 1, starting sse = 233.97
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00207
epoch 4 (K=640.0), pass 1, starting sse = 16.03
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00253
final distance error %25.81
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    237.648871
mris_sphere stimesec    0.198969
mris_sphere ru_maxrss   201500
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   29364
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9728
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    7734
mris_sphere ru_nivcsw   19187
FSRUNTIME@ mris_sphere  0.0661 hours 1 threads
PIDs (6215 6218) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 21:46:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 21:46:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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


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

#@# Fix Topology lh Sat Oct  7 21:46:29 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 lh 

#@# Fix Topology rh Sat Oct  7 21:46:29 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 rh 

Waiting for PID 6397 of (6397 6400) to complete...
Waiting for PID 6400 of (6397 6400) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 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=-78 (nv=138684, nf=277524, ne=416286, g=40)
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 13 iterations
marking ambiguous vertices...
4846 ambiguous faces found in tessellation
segmenting defects...
44 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 41 into 40
43 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5727  (-4.7863)
      -vertex     loglikelihood: -6.5155  (-3.2577)
      -normal dot loglikelihood: -3.6289  (-3.6289)
      -quad curv  loglikelihood: -6.6108  (-3.3054)
      Total Loglikelihood : -26.3279

CORRECTING DEFECT 0 (vertices=46, convex hull=76, v0=497)
After retessellation of defect 0 (v0=497), euler #=-41 (135635,405446,269770) : difference with theory (-40) = 1 

CORRECTING DEFECT 1 (vertices=45, convex hull=98, v0=1730)
After retessellation of defect 1 (v0=1730), euler #=-40 (135659,405557,269858) : difference with theory (-39) = 1 

CORRECTING DEFECT 2 (vertices=241, convex hull=205, v0=2156)
After retessellation of defect 2 (v0=2156), euler #=-39 (135754,405941,270148) : difference with theory (-38) = 1 

CORRECTING DEFECT 3 (vertices=92, convex hull=129, v0=12686)
After retessellation of defect 3 (v0=12686), euler #=-38 (135815,406179,270326) : difference with theory (-37) = 1 

CORRECTING DEFECT 4 (vertices=58, convex hull=114, v0=14162)
After retessellation of defect 4 (v0=14162), euler #=-37 (135844,406319,270438) : difference with theory (-36) = 1 

CORRECTING DEFECT 5 (vertices=25, convex hull=45, v0=36340)
After retessellation of defect 5 (v0=36340), euler #=-36 (135859,406380,270485) : difference with theory (-35) = 1 

CORRECTING DEFECT 6 (vertices=33, convex hull=68, v0=37580)
After retessellation of defect 6 (v0=37580), euler #=-35 (135873,406449,270541) : difference with theory (-34) = 1 

CORRECTING DEFECT 7 (vertices=68, convex hull=103, v0=44028)
After retessellation of defect 7 (v0=44028), euler #=-34 (135906,406592,270652) : difference with theory (-33) = 1 

CORRECTING DEFECT 8 (vertices=9, convex hull=39, v0=46769)
After retessellation of defect 8 (v0=46769), euler #=-33 (135907,406606,270666) : difference with theory (-32) = 1 

CORRECTING DEFECT 9 (vertices=47, convex hull=69, v0=47480)
After retessellation of defect 9 (v0=47480), euler #=-32 (135924,406686,270730) : difference with theory (-31) = 1 

CORRECTING DEFECT 10 (vertices=97, convex hull=87, v0=49502)
After retessellation of defect 10 (v0=49502), euler #=-31 (135933,406749,270785) : difference with theory (-30) = 1 

CORRECTING DEFECT 11 (vertices=66, convex hull=100, v0=61027)
After retessellation of defect 11 (v0=61027), euler #=-30 (135978,406929,270921) : difference with theory (-29) = 1 

CORRECTING DEFECT 12 (vertices=97, convex hull=86, v0=61858)
After retessellation of defect 12 (v0=61858), euler #=-29 (135995,407017,270993) : difference with theory (-28) = 1 

CORRECTING DEFECT 13 (vertices=87, convex hull=63, v0=61887)
After retessellation of defect 13 (v0=61887), euler #=-28 (136004,407068,271036) : difference with theory (-27) = 1 

CORRECTING DEFECT 14 (vertices=290, convex hull=347, v0=67015)
After retessellation of defect 14 (v0=67015), euler #=-27 (136160,407708,271521) : difference with theory (-26) = 1 

CORRECTING DEFECT 15 (vertices=32, convex hull=61, v0=75228)
After retessellation of defect 15 (v0=75228), euler #=-26 (136176,407781,271579) : difference with theory (-25) = 1 

CORRECTING DEFECT 16 (vertices=34, convex hull=40, v0=79035)
After retessellation of defect 16 (v0=79035), euler #=-25 (136181,407810,271604) : difference with theory (-24) = 1 

CORRECTING DEFECT 17 (vertices=110, convex hull=65, v0=81174)
After retessellation of defect 17 (v0=81174), euler #=-24 (136206,407918,271688) : difference with theory (-23) = 1 

CORRECTING DEFECT 18 (vertices=9, convex hull=26, v0=86008)
After retessellation of defect 18 (v0=86008), euler #=-23 (136208,407935,271704) : difference with theory (-22) = 1 

CORRECTING DEFECT 19 (vertices=29, convex hull=22, v0=93331)
After retessellation of defect 19 (v0=93331), euler #=-22 (136211,407951,271718) : difference with theory (-21) = 1 

CORRECTING DEFECT 20 (vertices=32, convex hull=32, v0=101354)
After retessellation of defect 20 (v0=101354), euler #=-21 (136215,407974,271738) : difference with theory (-20) = 1 

CORRECTING DEFECT 21 (vertices=31, convex hull=49, v0=102544)
After retessellation of defect 21 (v0=102544), euler #=-20 (136227,408029,271782) : difference with theory (-19) = 1 

CORRECTING DEFECT 22 (vertices=93, convex hull=78, v0=103701)
After retessellation of defect 22 (v0=103701), euler #=-19 (136231,408085,271835) : difference with theory (-18) = 1 

CORRECTING DEFECT 23 (vertices=213, convex hull=217, v0=105800)
After retessellation of defect 23 (v0=105800), euler #=-18 (136296,408381,272067) : difference with theory (-17) = 1 

CORRECTING DEFECT 24 (vertices=14, convex hull=18, v0=107650)
After retessellation of defect 24 (v0=107650), euler #=-17 (136298,408392,272077) : difference with theory (-16) = 1 

CORRECTING DEFECT 25 (vertices=16, convex hull=31, v0=108724)
After retessellation of defect 25 (v0=108724), euler #=-16 (136299,408402,272087) : difference with theory (-15) = 1 

CORRECTING DEFECT 26 (vertices=16, convex hull=32, v0=111448)
After retessellation of defect 26 (v0=111448), euler #=-15 (136300,408417,272102) : difference with theory (-14) = 1 

CORRECTING DEFECT 27 (vertices=43, convex hull=101, v0=112443)
After retessellation of defect 27 (v0=112443), euler #=-14 (136320,408524,272190) : difference with theory (-13) = 1 

CORRECTING DEFECT 28 (vertices=11, convex hull=19, v0=113114)
After retessellation of defect 28 (v0=113114), euler #=-13 (136321,408535,272201) : difference with theory (-12) = 1 

CORRECTING DEFECT 29 (vertices=8, convex hull=24, v0=114683)
After retessellation of defect 29 (v0=114683), euler #=-12 (136323,408548,272213) : difference with theory (-11) = 1 

CORRECTING DEFECT 30 (vertices=25, convex hull=47, v0=115537)
After retessellation of defect 30 (v0=115537), euler #=-11 (136333,408596,272252) : difference with theory (-10) = 1 

CORRECTING DEFECT 31 (vertices=450, convex hull=116, v0=116379)
After retessellation of defect 31 (v0=116379), euler #=-10 (136354,408709,272345) : difference with theory (-9) = 1 

CORRECTING DEFECT 32 (vertices=31, convex hull=72, v0=117738)
After retessellation of defect 32 (v0=117738), euler #=-9 (136376,408804,272419) : difference with theory (-8) = 1 

CORRECTING DEFECT 33 (vertices=81, convex hull=63, v0=118055)
After retessellation of defect 33 (v0=118055), euler #=-8 (136392,408874,272474) : difference with theory (-7) = 1 

CORRECTING DEFECT 34 (vertices=194, convex hull=193, v0=118285)
normal vector of length zero at vertex 138286 with 3 faces
normal vector of length zero at vertex 138286 with 3 faces
normal vector of length zero at vertex 138286 with 3 faces
normal vector of length zero at vertex 138286 with 3 faces
normal vector of length zero at vertex 138286 with 3 faces
After retessellation of defect 34 (v0=118285), euler #=-7 (136466,409191,272718) : difference with theory (-6) = 1 

CORRECTING DEFECT 35 (vertices=50, convex hull=99, v0=118608)
After retessellation of defect 35 (v0=118608), euler #=-6 (136491,409309,272812) : difference with theory (-5) = 1 

CORRECTING DEFECT 36 (vertices=34, convex hull=59, v0=119337)
After retessellation of defect 36 (v0=119337), euler #=-5 (136500,409358,272853) : difference with theory (-4) = 1 

CORRECTING DEFECT 37 (vertices=66, convex hull=88, v0=121052)
After retessellation of defect 37 (v0=121052), euler #=-4 (136519,409452,272929) : difference with theory (-3) = 1 

CORRECTING DEFECT 38 (vertices=16, convex hull=21, v0=121517)
After retessellation of defect 38 (v0=121517), euler #=-3 (136522,409468,272943) : difference with theory (-2) = 1 

CORRECTING DEFECT 39 (vertices=5, convex hull=26, v0=122815)
After retessellation of defect 39 (v0=122815), euler #=-2 (136523,409477,272952) : difference with theory (-1) = 1 

CORRECTING DEFECT 40 (vertices=80, convex hull=106, v0=133541)
After retessellation of defect 40 (v0=133541), euler #=0 (136542,409582,273040) : difference with theory (0) = 0 

CORRECTING DEFECT 41 (vertices=12, convex hull=25, v0=136303)
After retessellation of defect 41 (v0=136303), euler #=1 (136544,409597,273054) : difference with theory (1) = 0 

CORRECTING DEFECT 42 (vertices=39, convex hull=73, v0=137655)
After retessellation of defect 42 (v0=137655), euler #=2 (136564,409686,273124) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.03-->7.96) (max @ vno 70942 --> 74415)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.03-->7.96) (max @ vno 70942 --> 74415)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
155 mutations (34.0%), 301 crossovers (66.0%), 245 vertices were eliminated
building final representation...
2120 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=136564, nf=273124, ne=409686, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 26.6 minutes
0 defective edges
removing intersecting faces
000: 329 intersecting
001: 17 intersecting
mris_fix_topology utimesec    1595.232487
mris_fix_topology stimesec    0.311952
mris_fix_topology ru_maxrss   436208
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   55082
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  9760
mris_fix_topology ru_oublock  13104
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    497
mris_fix_topology ru_nivcsw   4681
FSRUNTIME@ mris_fix_topology lh  0.4431 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 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=-62 (nv=137638, nf=275400, ne=413100, g=32)
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 8 iterations
marking ambiguous vertices...
4605 ambiguous faces found in tessellation
segmenting defects...
44 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 14 into 16
      -merging segment 28 into 26
42 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.6102  (-4.8051)
      -vertex     loglikelihood: -6.5262  (-3.2631)
      -normal dot loglikelihood: -3.6026  (-3.6026)
      -quad curv  loglikelihood: -6.6157  (-3.3078)
      Total Loglikelihood : -26.3547

CORRECTING DEFECT 0 (vertices=159, convex hull=152, v0=2016)
After retessellation of defect 0 (v0=2016), euler #=-39 (134820,403252,268393) : difference with theory (-39) = 0 

CORRECTING DEFECT 1 (vertices=60, convex hull=98, v0=4183)
After retessellation of defect 1 (v0=4183), euler #=-38 (134854,403398,268506) : difference with theory (-38) = 0 

CORRECTING DEFECT 2 (vertices=15, convex hull=69, v0=5121)
After retessellation of defect 2 (v0=5121), euler #=-37 (134861,403443,268545) : difference with theory (-37) = 0 

CORRECTING DEFECT 3 (vertices=7, convex hull=22, v0=12108)
After retessellation of defect 3 (v0=12108), euler #=-36 (134862,403452,268554) : difference with theory (-36) = 0 

CORRECTING DEFECT 4 (vertices=46, convex hull=101, v0=14822)
After retessellation of defect 4 (v0=14822), euler #=-35 (134889,403577,268653) : difference with theory (-35) = 0 

CORRECTING DEFECT 5 (vertices=28, convex hull=64, v0=15776)
After retessellation of defect 5 (v0=15776), euler #=-34 (134900,403632,268698) : difference with theory (-34) = 0 

CORRECTING DEFECT 6 (vertices=236, convex hull=168, v0=18443)
After retessellation of defect 6 (v0=18443), euler #=-33 (134959,403892,268900) : difference with theory (-33) = 0 

CORRECTING DEFECT 7 (vertices=28, convex hull=61, v0=29150)
After retessellation of defect 7 (v0=29150), euler #=-32 (134971,403951,268948) : difference with theory (-32) = 0 

CORRECTING DEFECT 8 (vertices=50, convex hull=24, v0=33624)
After retessellation of defect 8 (v0=33624), euler #=-31 (134980,403985,268974) : difference with theory (-31) = 0 

CORRECTING DEFECT 9 (vertices=37, convex hull=72, v0=38034)
After retessellation of defect 9 (v0=38034), euler #=-30 (134996,404065,269039) : difference with theory (-30) = 0 

CORRECTING DEFECT 10 (vertices=39, convex hull=74, v0=39026)
After retessellation of defect 10 (v0=39026), euler #=-29 (135017,404158,269112) : difference with theory (-29) = 0 

CORRECTING DEFECT 11 (vertices=50, convex hull=72, v0=39500)
After retessellation of defect 11 (v0=39500), euler #=-28 (135036,404247,269183) : difference with theory (-28) = 0 

CORRECTING DEFECT 12 (vertices=35, convex hull=65, v0=43096)
After retessellation of defect 12 (v0=43096), euler #=-27 (135052,404326,269247) : difference with theory (-27) = 0 

CORRECTING DEFECT 13 (vertices=18, convex hull=22, v0=53503)
After retessellation of defect 13 (v0=53503), euler #=-26 (135054,404341,269261) : difference with theory (-26) = 0 

CORRECTING DEFECT 14 (vertices=67, convex hull=80, v0=62594)
After retessellation of defect 14 (v0=62594), euler #=-25 (135078,404446,269343) : difference with theory (-25) = 0 

CORRECTING DEFECT 15 (vertices=216, convex hull=137, v0=63563)
After retessellation of defect 15 (v0=63563), euler #=-23 (135118,404631,269490) : difference with theory (-24) = -1 

CORRECTING DEFECT 16 (vertices=9, convex hull=26, v0=63829)
After retessellation of defect 16 (v0=63829), euler #=-22 (135120,404645,269503) : difference with theory (-23) = -1 

CORRECTING DEFECT 17 (vertices=90, convex hull=31, v0=65502)
After retessellation of defect 17 (v0=65502), euler #=-21 (135127,404675,269527) : difference with theory (-22) = -1 

CORRECTING DEFECT 18 (vertices=76, convex hull=41, v0=67111)
After retessellation of defect 18 (v0=67111), euler #=-20 (135142,404736,269574) : difference with theory (-21) = -1 

CORRECTING DEFECT 19 (vertices=442, convex hull=378, v0=71122)
normal vector of length zero at vertex 136208 with 3 faces
After retessellation of defect 19 (v0=71122), euler #=-21 (135389,405678,270268) : difference with theory (-20) = 1 

CORRECTING DEFECT 20 (vertices=83, convex hull=49, v0=73053)
After retessellation of defect 20 (v0=73053), euler #=-20 (135399,405728,270309) : difference with theory (-19) = 1 

CORRECTING DEFECT 21 (vertices=294, convex hull=56, v0=76580)
After retessellation of defect 21 (v0=76580), euler #=-19 (135413,405800,270368) : difference with theory (-18) = 1 

CORRECTING DEFECT 22 (vertices=22, convex hull=42, v0=81964)
After retessellation of defect 22 (v0=81964), euler #=-18 (135421,405841,270402) : difference with theory (-17) = 1 

CORRECTING DEFECT 23 (vertices=74, convex hull=42, v0=96175)
After retessellation of defect 23 (v0=96175), euler #=-17 (135431,405886,270438) : difference with theory (-16) = 1 

CORRECTING DEFECT 24 (vertices=11, convex hull=15, v0=98733)
After retessellation of defect 24 (v0=98733), euler #=-16 (135434,405898,270448) : difference with theory (-15) = 1 

CORRECTING DEFECT 25 (vertices=161, convex hull=142, v0=100971)
After retessellation of defect 25 (v0=100971), euler #=-14 (135505,406182,270663) : difference with theory (-14) = 0 

CORRECTING DEFECT 26 (vertices=7, convex hull=16, v0=102772)
After retessellation of defect 26 (v0=102772), euler #=-13 (135507,406192,270672) : difference with theory (-13) = 0 

CORRECTING DEFECT 27 (vertices=25, convex hull=30, v0=105680)
After retessellation of defect 27 (v0=105680), euler #=-12 (135511,406217,270694) : difference with theory (-12) = 0 

CORRECTING DEFECT 28 (vertices=18, convex hull=35, v0=107135)
After retessellation of defect 28 (v0=107135), euler #=-11 (135512,406232,270709) : difference with theory (-11) = 0 

CORRECTING DEFECT 29 (vertices=20, convex hull=31, v0=107332)
After retessellation of defect 29 (v0=107332), euler #=-10 (135515,406250,270725) : difference with theory (-10) = 0 

CORRECTING DEFECT 30 (vertices=8, convex hull=27, v0=109431)
After retessellation of defect 30 (v0=109431), euler #=-9 (135516,406257,270732) : difference with theory (-9) = 0 

CORRECTING DEFECT 31 (vertices=33, convex hull=62, v0=110023)
After retessellation of defect 31 (v0=110023), euler #=-8 (135536,406341,270797) : difference with theory (-8) = 0 

CORRECTING DEFECT 32 (vertices=20, convex hull=44, v0=113347)
After retessellation of defect 32 (v0=113347), euler #=-7 (135545,406382,270830) : difference with theory (-7) = 0 

CORRECTING DEFECT 33 (vertices=37, convex hull=72, v0=116330)
After retessellation of defect 33 (v0=116330), euler #=-6 (135561,406456,270889) : difference with theory (-6) = 0 

CORRECTING DEFECT 34 (vertices=35, convex hull=75, v0=118166)
After retessellation of defect 34 (v0=118166), euler #=-5 (135576,406532,270951) : difference with theory (-5) = 0 

CORRECTING DEFECT 35 (vertices=25, convex hull=58, v0=132499)
After retessellation of defect 35 (v0=132499), euler #=-4 (135585,406582,270993) : difference with theory (-4) = 0 

CORRECTING DEFECT 36 (vertices=27, convex hull=68, v0=132886)
After retessellation of defect 36 (v0=132886), euler #=-3 (135602,406662,271057) : difference with theory (-3) = 0 

CORRECTING DEFECT 37 (vertices=42, convex hull=63, v0=133364)
After retessellation of defect 37 (v0=133364), euler #=-2 (135623,406750,271125) : difference with theory (-2) = 0 

CORRECTING DEFECT 38 (vertices=34, convex hull=60, v0=134390)
After retessellation of defect 38 (v0=134390), euler #=-1 (135640,406825,271184) : difference with theory (-1) = 0 

CORRECTING DEFECT 39 (vertices=129, convex hull=67, v0=134779)
After retessellation of defect 39 (v0=134779), euler #=0 (135663,406923,271260) : difference with theory (0) = 0 

CORRECTING DEFECT 40 (vertices=29, convex hull=63, v0=134947)
After retessellation of defect 40 (v0=134947), euler #=1 (135677,406990,271314) : difference with theory (1) = 0 

CORRECTING DEFECT 41 (vertices=37, convex hull=84, v0=135957)
After retessellation of defect 41 (v0=135957), euler #=2 (135698,407088,271392) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.08-->13.44) (max @ vno 55647 --> 60516)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.08-->13.44) (max @ vno 55647 --> 60516)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
125 mutations (36.1%), 221 crossovers (63.9%), 64 vertices were eliminated
building final representation...
1940 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=135698, nf=271392, ne=407088, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 19.5 minutes
0 defective edges
removing intersecting faces
000: 265 intersecting
001: 12 intersecting
mris_fix_topology utimesec    1171.905843
mris_fix_topology stimesec    0.394939
mris_fix_topology ru_maxrss   429948
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   54861
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  12992
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    365
mris_fix_topology ru_nivcsw   4020
FSRUNTIME@ mris_fix_topology rh  0.3256 hours 1 threads
PIDs (6397 6400) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 136564 - 409686 + 273124 = 2 --> 0 holes
      F =2V-4:          273124 = 273128-4 (0)
      2E=3F:            819372 = 819372 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 135698 - 407088 + 271392 = 2 --> 0 holes
      F =2V-4:          271392 = 271396-4 (0)
      2E=3F:            814176 = 814176 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 48 intersecting
001: 14 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 50 intersecting
001: 8 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 22:13:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 22:13:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 rh 

Waiting for PID 7870 of (7870 7873) to complete...
Waiting for PID 7873 of (7870 7873) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
23920 bright wm thresholded.
3496 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.orig...
computing class statistics...
border white:    249299 voxels (1.49%)
border gray      297398 voxels (1.77%)
WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0]
GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 50.5 (was 70)
setting MAX_BORDER_WHITE to 112.5 (was 105)
setting MIN_BORDER_WHITE to 61.0 (was 85)
setting MAX_CSF to 39.9 (was 40)
setting MAX_GRAY to 93.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 29.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.01-->3.63) (max @ vno 115332 --> 116189)
face area 0.27 +- 0.12 (0.00-->3.18)
mean absolute distance = 0.63 +- 0.74
4116 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=61+-7.8
mean inside = 91.7, mean outside = 70.4
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=75.7, 59 (59) missing vertices, mean dist 0.3 [0.5 (%36.0)->0.7 (%64.0))]
%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 +- 0.25 (0.11-->3.82) (max @ vno 115332 --> 116189)
face area 0.27 +- 0.13 (0.00-->2.66)
mean absolute distance = 0.31 +- 0.49
3020 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4118089.0, rms=11.674
001: dt: 0.5000, sse=2274381.8, rms=8.173 (29.989%)
002: dt: 0.5000, sse=1532191.5, rms=6.204 (24.088%)
003: dt: 0.5000, sse=1199868.9, rms=5.090 (17.965%)
004: dt: 0.5000, sse=1048864.0, rms=4.467 (12.230%)
005: dt: 0.5000, sse=982180.4, rms=4.182 (6.381%)
006: dt: 0.5000, sse=957553.6, rms=4.049 (3.187%)
007: dt: 0.5000, sse=944733.2, rms=3.994 (1.357%)
rms = 3.95, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=934191.0, rms=3.948 (1.153%)
009: dt: 0.2500, sse=712399.4, rms=2.565 (35.019%)
010: dt: 0.2500, sse=663023.4, rms=2.151 (16.164%)
011: dt: 0.2500, sse=651300.8, rms=2.038 (5.248%)
012: dt: 0.2500, sse=645632.5, rms=1.983 (2.671%)
rms = 1.94, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=641662.8, rms=1.942 (2.066%)
014: dt: 0.1250, sse=630543.9, rms=1.827 (5.924%)
rms = 1.81, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=629182.4, rms=1.810 (0.945%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.0, 65 (19) missing vertices, mean dist -0.2 [0.3 (%73.0)->0.2 (%27.0))]
%83 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 0.90 +- 0.25 (0.12-->4.18) (max @ vno 108799 --> 107907)
face area 0.35 +- 0.16 (0.00-->3.37)
mean absolute distance = 0.23 +- 0.36
2932 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1344469.5, rms=5.022
016: dt: 0.5000, sse=982940.6, rms=3.372 (32.846%)
rms = 3.75, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=839373.9, rms=2.423 (28.159%)
018: dt: 0.2500, sse=782857.2, rms=1.909 (21.212%)
019: dt: 0.2500, sse=763263.6, rms=1.695 (11.192%)
020: dt: 0.2500, sse=756913.1, rms=1.621 (4.346%)
rms = 1.58, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=752598.4, rms=1.579 (2.613%)
022: dt: 0.1250, sse=745808.8, rms=1.477 (6.467%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=743511.8, rms=1.462 (1.037%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.2, 54 (9) missing vertices, mean dist -0.1 [0.3 (%67.1)->0.2 (%32.9))]
%87 local maxima, % 8 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 (0.05-->4.39) (max @ vno 108799 --> 107907)
face area 0.34 +- 0.16 (0.00-->3.31)
mean absolute distance = 0.22 +- 0.32
2816 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=929087.4, rms=3.169
rms = 3.15, time step reduction 1 of 3 to 0.250...
024: dt: 0.5000, sse=931729.7, rms=3.153 (0.486%)
025: dt: 0.2500, sse=757017.4, rms=1.841 (41.627%)
026: dt: 0.2500, sse=727541.6, rms=1.509 (18.027%)
rms = 1.48, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=724687.8, rms=1.484 (1.642%)
028: dt: 0.1250, sse=711280.2, rms=1.295 (12.726%)
rms = 1.28, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=710446.1, rms=1.279 (1.282%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=82.0, 60 (4) missing vertices, mean dist -0.0 [0.2 (%55.7)->0.2 (%44.3))]
%89 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-6.0.0/0051105/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=732282.2, rms=1.693
rms = 2.17, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=696679.4, rms=1.158 (31.581%)
031: dt: 0.2500, sse=682944.9, rms=0.958 (17.302%)
rms = 0.98, time step reduction 2 of 3 to 0.125...
rms = 0.95, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=681152.0, rms=0.952 (0.577%)
positioning took 0.4 minutes
generating cortex label...
6 non-cortical segments detected
only using segment with 7076 vertices
erasing segment 1 (vno[0] = 67299)
erasing segment 2 (vno[0] = 100962)
erasing segment 3 (vno[0] = 101069)
erasing segment 4 (vno[0] = 105965)
erasing segment 5 (vno[0] = 109610)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.01-->4.41) (max @ vno 107907 --> 108799)
face area 0.33 +- 0.16 (0.00-->3.32)
refinement took 5.3 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
23920 bright wm thresholded.
3496 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.orig...
computing class statistics...
border white:    249299 voxels (1.49%)
border gray      297398 voxels (1.77%)
WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0]
GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.5 (was 70)
setting MAX_BORDER_WHITE to 111.5 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 40.9 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 30.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.01-->5.42) (max @ vno 55647 --> 60516)
face area 0.27 +- 0.12 (0.00-->3.93)
mean absolute distance = 0.64 +- 0.75
4054 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+-7.8
mean inside = 91.5, mean outside = 70.4
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=76.0, 53 (53) missing vertices, mean dist 0.3 [0.5 (%37.7)->0.7 (%62.3))]
%75 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 0.92 +- 0.25 (0.13-->5.06) (max @ vno 55647 --> 60516)
face area 0.27 +- 0.13 (0.00-->2.90)
mean absolute distance = 0.31 +- 0.50
3082 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3969590.0, rms=11.490
001: dt: 0.5000, sse=2178555.5, rms=7.990 (30.465%)
002: dt: 0.5000, sse=1466748.1, rms=6.039 (24.412%)
003: dt: 0.5000, sse=1145249.5, rms=4.919 (18.547%)
004: dt: 0.5000, sse=1007150.8, rms=4.340 (11.769%)
005: dt: 0.5000, sse=963890.9, rms=4.070 (6.228%)
006: dt: 0.5000, sse=925727.3, rms=3.957 (2.783%)
007: dt: 0.5000, sse=916690.8, rms=3.903 (1.350%)
rms = 3.88, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=911521.9, rms=3.876 (0.692%)
009: dt: 0.2500, sse=692211.3, rms=2.473 (36.206%)
010: dt: 0.2500, sse=645961.0, rms=2.062 (16.622%)
011: dt: 0.2500, sse=635521.1, rms=1.961 (4.879%)
012: dt: 0.2500, sse=630563.8, rms=1.886 (3.837%)
rms = 1.86, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=626312.6, rms=1.859 (1.415%)
014: dt: 0.1250, sse=615245.8, rms=1.721 (7.419%)
rms = 1.71, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=612738.2, rms=1.706 (0.890%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=79.2, 58 (17) missing vertices, mean dist -0.2 [0.3 (%72.0)->0.2 (%28.0))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.08-->4.90) (max @ vno 55647 --> 60516)
face area 0.35 +- 0.16 (0.00-->3.31)
mean absolute distance = 0.23 +- 0.37
2824 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1295973.8, rms=4.877
016: dt: 0.5000, sse=975937.0, rms=3.371 (30.892%)
rms = 3.73, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=833973.0, rms=2.433 (27.827%)
018: dt: 0.2500, sse=778558.4, rms=1.935 (20.477%)
019: dt: 0.2500, sse=757235.8, rms=1.711 (11.535%)
020: dt: 0.2500, sse=750094.4, rms=1.636 (4.429%)
021: dt: 0.2500, sse=745283.4, rms=1.568 (4.121%)
rms = 1.54, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=742279.2, rms=1.538 (1.928%)
023: dt: 0.1250, sse=734379.1, rms=1.440 (6.389%)
rms = 1.43, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=733666.0, rms=1.429 (0.756%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=81.3, 47 (9) missing vertices, mean dist -0.1 [0.3 (%66.1)->0.2 (%33.9))]
%86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.04-->4.84) (max @ vno 55647 --> 60516)
face area 0.34 +- 0.16 (0.00-->3.01)
mean absolute distance = 0.22 +- 0.32
2663 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=894831.4, rms=3.003
rms = 3.09, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=778272.4, rms=2.109 (29.765%)
026: dt: 0.2500, sse=721058.1, rms=1.454 (31.080%)
027: dt: 0.2500, sse=711154.8, rms=1.358 (6.550%)
rms = 1.33, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=710539.4, rms=1.332 (1.929%)
029: dt: 0.1250, sse=704820.5, rms=1.253 (5.937%)
rms = 1.25, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=703658.8, rms=1.254 (-0.039%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=82.0, 55 (9) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))]
%88 local maxima, % 7 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-6.0.0/0051105/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=726628.0, rms=1.662
rms = 2.14, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=687874.9, rms=1.142 (31.298%)
032: dt: 0.2500, sse=677089.9, rms=0.939 (17.752%)
rms = 0.95, time step reduction 2 of 3 to 0.125...
rms = 0.93, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=676474.2, rms=0.933 (0.677%)
positioning took 0.4 minutes
generating cortex label...
17 non-cortical segments detected
only using segment with 7102 vertices
erasing segment 0 (vno[0] = 48875)
erasing segment 1 (vno[0] = 48924)
erasing segment 3 (vno[0] = 66100)
erasing segment 4 (vno[0] = 72686)
erasing segment 5 (vno[0] = 74955)
erasing segment 6 (vno[0] = 77311)
erasing segment 7 (vno[0] = 79385)
erasing segment 8 (vno[0] = 79404)
erasing segment 9 (vno[0] = 81512)
erasing segment 10 (vno[0] = 96586)
erasing segment 11 (vno[0] = 100480)
erasing segment 12 (vno[0] = 101352)
erasing segment 13 (vno[0] = 103130)
erasing segment 14 (vno[0] = 104099)
erasing segment 15 (vno[0] = 108701)
erasing segment 16 (vno[0] = 119686)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.01-->4.82) (max @ vno 55647 --> 60516)
face area 0.33 +- 0.16 (0.00-->3.00)
refinement took 5.5 minutes
PIDs (7870 7873) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 22:18:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 22:18:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

Waiting for PID 8056 of (8056 8059) to complete...
Waiting for PID 8059 of (8056 8059) 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 (8056 8059) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 22:18:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 22:18:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 8101 of (8101 8104) to complete...
Waiting for PID 8104 of (8101 8104) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 45.5 mm, total surface area = 82185 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.182 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.095 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.054 (target=0.015)   
step 030: RMS=0.045 (target=0.015)   
step 035: RMS=0.038 (target=0.015)   
step 040: RMS=0.033 (target=0.015)   
step 045: RMS=0.029 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    44.504234
mris_inflate stimesec    0.111982
mris_inflate ru_maxrss   200012
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29117
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10696
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2236
mris_inflate ru_nivcsw   3389

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 45.3 mm, total surface area = 81800 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.184 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.080 (target=0.015)   
step 020: RMS=0.066 (target=0.015)   
step 025: RMS=0.056 (target=0.015)   
step 030: RMS=0.046 (target=0.015)   
step 035: RMS=0.040 (target=0.015)   
step 040: RMS=0.035 (target=0.015)   
step 045: RMS=0.031 (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 0.7 minutes
mris_inflate utimesec    44.185282
mris_inflate stimesec    0.106983
mris_inflate ru_maxrss   198608
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   28765
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10632
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2175
mris_inflate ru_nivcsw   3378
PIDs (8101 8104) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 22:19:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 22:19:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 8201 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8204 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8207 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8210 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8213 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8216 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8219 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8222 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8225 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8229 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8232 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...
Waiting for PID 8235 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 9.810*4pi (123.271) --> -9 handles
ICI = 190.1, FI = 1871.4, variation=29721.109
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
167 vertices thresholded to be in k1 ~ [-0.38 0.73], k2 ~ [-0.22 0.14]
total integrated curvature = 0.594*4pi (7.462) --> 0 handles
ICI = 1.5, FI = 7.5, variation=138.071
122 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
72 vertices thresholded to be in [-0.12 0.16]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.020
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 2.007*4pi (25.216) --> -1 handles
ICI = 185.7, FI = 1854.1, variation=29716.497
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
162 vertices thresholded to be in k1 ~ [-0.21 0.71], k2 ~ [-0.30 0.09]
total integrated curvature = 0.520*4pi (6.535) --> 0 handles
ICI = 1.5, FI = 8.5, variation=149.025
158 vertices thresholded to be in [-0.10 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
96 vertices thresholded to be in [-0.12 0.21]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022
done.
PIDs (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 22:20:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051105 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      [ 0051105/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                      [ 267 ]
Gb_filter = 0

WARN:    S lookup   min:                          -1.542588
WARN:    S explicit min:                          0.000000	vertex = 1229

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 22:21:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051105 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      [ 0051105/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                      [ 250 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.239601
WARN:    S explicit min:                          0.000000	vertex = 1528
#--------------------------------------------
#@# Sphere lh Sat Oct  7 22:21:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 22:21:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 8390 of (8390 8393) to complete...
Waiting for PID 8393 of (8390 8393) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0.312...
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 %20.23
pass 1: epoch 2 of 3 starting distance error %20.21
unfolding complete - removing small folds...
starting distance error %20.08
removing remaining folds...
final distance error %20.11
MRISunfold() return, current seed 1234
-01: dt=0.0000, 211 negative triangles
198: dt=0.9900, 211 negative triangles
199: dt=0.9900, 103 negative triangles
200: dt=0.9900, 80 negative triangles
201: dt=0.9900, 68 negative triangles
202: dt=0.9900, 69 negative triangles
203: dt=0.9900, 61 negative triangles
204: dt=0.9900, 62 negative triangles
205: dt=0.9900, 58 negative triangles
206: dt=0.9900, 53 negative triangles
207: dt=0.9900, 48 negative triangles
208: dt=0.9900, 44 negative triangles
209: dt=0.9900, 46 negative triangles
210: dt=0.9900, 41 negative triangles
211: dt=0.9900, 44 negative triangles
212: dt=0.9900, 42 negative triangles
213: dt=0.9900, 47 negative triangles
214: dt=0.9900, 36 negative triangles
215: dt=0.9900, 35 negative triangles
216: dt=0.9900, 38 negative triangles
217: dt=0.9900, 39 negative triangles
218: dt=0.9900, 36 negative triangles
219: dt=0.9900, 36 negative triangles
220: dt=0.9900, 34 negative triangles
221: dt=0.9900, 35 negative triangles
222: dt=0.9900, 34 negative triangles
223: dt=0.9900, 28 negative triangles
224: dt=0.9900, 29 negative triangles
225: dt=0.9900, 32 negative triangles
226: dt=0.9900, 28 negative triangles
227: dt=0.9900, 22 negative triangles
228: dt=0.9900, 22 negative triangles
229: dt=0.9900, 28 negative triangles
230: dt=0.9900, 22 negative triangles
231: dt=0.9900, 14 negative triangles
232: dt=0.9900, 16 negative triangles
233: dt=0.9900, 21 negative triangles
234: dt=0.9900, 17 negative triangles
235: dt=0.9900, 15 negative triangles
236: dt=0.9900, 15 negative triangles
237: dt=0.9900, 15 negative triangles
238: dt=0.9900, 15 negative triangles
239: dt=0.9900, 12 negative triangles
240: dt=0.9900, 10 negative triangles
241: dt=0.9900, 12 negative triangles
242: dt=0.9900, 13 negative triangles
243: dt=0.9900, 9 negative triangles
244: dt=0.9900, 6 negative triangles
245: dt=0.9900, 9 negative triangles
246: dt=0.9900, 8 negative triangles
247: dt=0.9900, 10 negative triangles
248: dt=0.9900, 9 negative triangles
249: dt=0.9900, 6 negative triangles
250: dt=0.9900, 8 negative triangles
251: dt=0.9900, 7 negative triangles
252: dt=0.9900, 8 negative triangles
253: dt=0.9900, 10 negative triangles
254: dt=0.9405, 8 negative triangles
255: dt=0.9405, 6 negative triangles
256: dt=0.9405, 8 negative triangles
257: dt=0.9405, 6 negative triangles
258: dt=0.9405, 8 negative triangles
259: dt=0.9405, 10 negative triangles
260: dt=0.9405, 8 negative triangles
261: dt=0.9405, 6 negative triangles
262: dt=0.9405, 8 negative triangles
263: dt=0.9405, 6 negative triangles
264: dt=0.8935, 8 negative triangles
265: dt=0.8935, 10 negative triangles
266: dt=0.8935, 8 negative triangles
267: dt=0.8935, 5 negative triangles
268: dt=0.8935, 7 negative triangles
269: dt=0.8935, 4 negative triangles
270: dt=0.8935, 6 negative triangles
271: dt=0.8935, 4 negative triangles
272: dt=0.8935, 6 negative triangles
273: dt=0.8935, 5 negative triangles
274: dt=0.8935, 7 negative triangles
275: dt=0.8935, 5 negative triangles
276: dt=0.8935, 1 negative triangles
277: dt=0.8935, 1 negative triangles
278: dt=0.8935, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.03 hours
mris_sphere utimesec    3716.487008
mris_sphere stimesec    2.055687
mris_sphere ru_maxrss   281280
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   49580
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9688
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    146436
mris_sphere ru_nivcsw   315771
FSRUNTIME@ mris_sphere  1.0320 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0.316...
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 %20.21
pass 1: epoch 2 of 3 starting distance error %20.18
unfolding complete - removing small folds...
starting distance error %20.09
removing remaining folds...
final distance error %20.11
MRISunfold() return, current seed 1234
-01: dt=0.0000, 179 negative triangles
212: dt=0.9900, 179 negative triangles
213: dt=0.9900, 84 negative triangles
214: dt=0.9900, 59 negative triangles
215: dt=0.9900, 49 negative triangles
216: dt=0.9900, 32 negative triangles
217: dt=0.9900, 33 negative triangles
218: dt=0.9900, 29 negative triangles
219: dt=0.9900, 17 negative triangles
220: dt=0.9900, 14 negative triangles
221: dt=0.9900, 11 negative triangles
222: dt=0.9900, 12 negative triangles
223: dt=0.9900, 11 negative triangles
224: dt=0.9900, 7 negative triangles
225: dt=0.9900, 3 negative triangles
226: dt=0.9900, 11 negative triangles
227: dt=0.9900, 5 negative triangles
228: dt=0.9900, 3 negative triangles
229: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.05 hours
mris_sphere utimesec    3806.646301
mris_sphere stimesec    1.799726
mris_sphere ru_maxrss   279364
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   49089
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9576
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    154467
mris_sphere ru_nivcsw   312096
FSRUNTIME@ mris_sphere  1.0470 hours 1 threads
PIDs (8390 8393) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sat Oct  7 23:23:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 23:23:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 10683 of (10683 10686) to complete...
Waiting for PID 10686 of (10683 10686) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 5.622
curvature mean = 0.026, std = 0.813
curvature mean = 0.018, std = 0.861
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (8.00, 0.00, -8.00) sse = 257169.6, tmin=2.1614
  d=16.00 min @ (-4.00, -4.00, 0.00) sse = 237371.9, tmin=3.3282
  d=8.00 min @ (0.00, 2.00, 2.00) sse = 228214.8, tmin=4.5179
  d=4.00 min @ (-1.00, -1.00, 0.00) sse = 226869.7, tmin=5.7004
  d=2.00 min @ (0.50, 0.50, -0.50) sse = 226211.0, tmin=6.8737
  d=1.00 min @ (-0.25, 0.00, 0.00) sse = 226111.8, tmin=8.0357
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 226063.6, tmin=9.2013
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   9.20 min
curvature mean = -0.003, std = 0.826
curvature mean = 0.005, std = 0.943
curvature mean = -0.004, std = 0.837
curvature mean = 0.002, std = 0.977
curvature mean = -0.005, std = 0.840
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.031, std = 0.682
curvature mean = 0.040, std = 0.248
curvature mean = 0.031, std = 0.151
curvature mean = 0.035, std = 0.307
curvature mean = 0.020, std = 0.236
curvature mean = 0.034, std = 0.333
curvature mean = 0.012, std = 0.306
curvature mean = 0.034, std = 0.345
curvature mean = 0.004, std = 0.381
MRISregister() return, current seed 0
-01: dt=0.0000, 81 negative triangles
115: dt=0.9900, 81 negative triangles
expanding nbhd size to 1
116: dt=0.9900, 102 negative triangles
117: dt=0.9900, 76 negative triangles
118: dt=0.9900, 76 negative triangles
119: dt=0.9900, 84 negative triangles
120: dt=0.9900, 84 negative triangles
121: dt=0.9900, 82 negative triangles
122: dt=0.9900, 86 negative triangles
123: dt=0.9900, 78 negative triangles
124: dt=0.9900, 85 negative triangles
125: dt=0.9900, 80 negative triangles
126: dt=0.9900, 75 negative triangles
127: dt=0.9900, 85 negative triangles
128: dt=0.9900, 71 negative triangles
129: dt=0.9900, 75 negative triangles
130: dt=0.9900, 70 negative triangles
131: dt=0.9900, 71 negative triangles
132: dt=0.9900, 71 negative triangles
133: dt=0.9900, 67 negative triangles
134: dt=0.9900, 67 negative triangles
135: dt=0.9900, 67 negative triangles
136: dt=0.9900, 68 negative triangles
137: dt=0.9900, 65 negative triangles
138: dt=0.9900, 57 negative triangles
139: dt=0.9900, 54 negative triangles
140: dt=0.9900, 54 negative triangles
141: dt=0.9900, 58 negative triangles
142: dt=0.9900, 51 negative triangles
143: dt=0.9900, 47 negative triangles
144: dt=0.9900, 43 negative triangles
145: dt=0.9900, 35 negative triangles
146: dt=0.9900, 38 negative triangles
147: dt=0.9900, 29 negative triangles
148: dt=0.9900, 32 negative triangles
149: dt=0.9900, 34 negative triangles
150: dt=0.9900, 25 negative triangles
151: dt=0.9900, 26 negative triangles
152: dt=0.9900, 18 negative triangles
153: dt=0.9900, 18 negative triangles
154: dt=0.9900, 12 negative triangles
155: dt=0.9900, 9 negative triangles
156: dt=0.9900, 14 negative triangles
157: dt=0.9900, 10 negative triangles
158: dt=0.9900, 9 negative triangles
159: dt=0.9900, 8 negative triangles
160: dt=0.9900, 6 negative triangles
161: dt=0.9900, 5 negative triangles
162: dt=0.9900, 4 negative triangles
163: dt=0.9900, 5 negative triangles
164: dt=0.9900, 5 negative triangles
165: dt=0.9900, 3 negative triangles
166: dt=0.9900, 3 negative triangles
167: dt=0.9900, 2 negative triangles
168: dt=0.9900, 3 negative triangles
169: dt=0.9900, 3 negative triangles
170: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.58 hours
mris_register utimesec    5675.695163
mris_register stimesec    6.955942
mris_register ru_maxrss   255116
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   35166
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  9712
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    391579
mris_register ru_nivcsw   262835
FSRUNTIME@ mris_register  1.5785 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 5.535
curvature mean = 0.032, std = 0.818
curvature mean = 0.018, std = 0.859
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 344245.8, tmin=1.0366
  d=32.00 min @ (0.00, 8.00, -8.00) sse = 232640.5, tmin=2.1623
  d=16.00 min @ (4.00, 0.00, 4.00) sse = 224522.1, tmin=3.3291
  d=8.00 min @ (-2.00, 0.00, -2.00) sse = 211512.3, tmin=4.5188
  d=2.00 min @ (0.50, -0.50, 0.00) sse = 210704.9, tmin=6.8586
  d=1.00 min @ (0.00, 0.25, 0.00) sse = 210680.2, tmin=8.0140
  d=0.50 min @ (-0.12, -0.12, -0.12) sse = 210635.5, tmin=9.1740
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   9.17 min
curvature mean = 0.010, std = 0.828
curvature mean = 0.007, std = 0.945
curvature mean = 0.007, std = 0.837
curvature mean = 0.003, std = 0.978
curvature mean = 0.006, std = 0.839
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.028, std = 0.317
curvature mean = 0.036, std = 0.241
curvature mean = 0.064, std = 0.324
curvature mean = 0.030, std = 0.300
curvature mean = 0.039, std = 0.502
curvature mean = 0.028, std = 0.328
curvature mean = 0.022, std = 0.640
curvature mean = 0.028, std = 0.339
curvature mean = 0.008, std = 0.753
MRISregister() return, current seed 0
-01: dt=0.0000, 100 negative triangles
113: dt=0.9900, 100 negative triangles
expanding nbhd size to 1
114: dt=0.9900, 109 negative triangles
115: dt=0.9900, 99 negative triangles
116: dt=0.9900, 96 negative triangles
117: dt=0.9900, 101 negative triangles
118: dt=0.9900, 89 negative triangles
119: dt=0.9900, 92 negative triangles
120: dt=0.9900, 81 negative triangles
121: dt=0.9900, 82 negative triangles
122: dt=0.9900, 78 negative triangles
123: dt=0.9900, 76 negative triangles
124: dt=0.9900, 75 negative triangles
125: dt=0.9900, 69 negative triangles
126: dt=0.9900, 66 negative triangles
127: dt=0.9900, 66 negative triangles
128: dt=0.9900, 64 negative triangles
129: dt=0.9900, 63 negative triangles
130: dt=0.9900, 58 negative triangles
131: dt=0.9900, 55 negative triangles
132: dt=0.9900, 55 negative triangles
133: dt=0.9900, 51 negative triangles
134: dt=0.9900, 52 negative triangles
135: dt=0.9900, 47 negative triangles
136: dt=0.9900, 49 negative triangles
137: dt=0.9900, 48 negative triangles
138: dt=0.9900, 45 negative triangles
139: dt=0.9900, 47 negative triangles
140: dt=0.9900, 49 negative triangles
141: dt=0.9900, 48 negative triangles
142: dt=0.9900, 47 negative triangles
143: dt=0.9900, 45 negative triangles
144: dt=0.9900, 41 negative triangles
145: dt=0.9900, 41 negative triangles
146: dt=0.9900, 43 negative triangles
147: dt=0.9900, 39 negative triangles
148: dt=0.9900, 38 negative triangles
149: dt=0.9900, 40 negative triangles
150: dt=0.9900, 38 negative triangles
151: dt=0.9900, 37 negative triangles
152: dt=0.9900, 33 negative triangles
153: dt=0.9900, 29 negative triangles
154: dt=0.9900, 29 negative triangles
155: dt=0.9900, 32 negative triangles
156: dt=0.9900, 27 negative triangles
157: dt=0.9900, 28 negative triangles
158: dt=0.9900, 25 negative triangles
159: dt=0.9900, 25 negative triangles
160: dt=0.9900, 26 negative triangles
161: dt=0.9900, 29 negative triangles
162: dt=0.9900, 21 negative triangles
163: dt=0.9900, 22 negative triangles
164: dt=0.9900, 22 negative triangles
165: dt=0.9900, 20 negative triangles
166: dt=0.9900, 17 negative triangles
167: dt=0.9900, 17 negative triangles
168: dt=0.9900, 16 negative triangles
169: dt=0.9900, 11 negative triangles
170: dt=0.9900, 10 negative triangles
171: dt=0.9900, 10 negative triangles
172: dt=0.9900, 10 negative triangles
173: dt=0.9900, 7 negative triangles
174: dt=0.9900, 6 negative triangles
175: dt=0.9900, 5 negative triangles
176: dt=0.9900, 3 negative triangles
177: dt=0.9900, 3 negative triangles
178: dt=0.9900, 2 negative triangles
179: dt=0.9900, 2 negative triangles
180: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.58 hours
mris_register utimesec    5679.435594
mris_register stimesec    5.474167
mris_register ru_maxrss   254276
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   37233
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  9552
mris_register ru_oublock  9648
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    398441
mris_register ru_nivcsw   251270
FSRUNTIME@ mris_register  1.5787 hours 1 threads
PIDs (10683 10686) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 00:58:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 00:58:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

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

Waiting for PID 17579 of (17579 17582) to complete...
Waiting for PID 17582 of (17579 17582) 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 (17579 17582) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 00:58:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 00:58:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 17624 of (17624 17627) to complete...
Waiting for PID 17627 of (17624 17627) 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 (17624 17627) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 00:58:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 00:58:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 17675 of (17675 17678) to complete...
Waiting for PID 17678 of (17675 17678) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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...
1176 labels changed using aseg
relabeling using gibbs priors...
000:   3171 changed, 136564 examined...
001:    775 changed, 13440 examined...
002:    204 changed, 4260 examined...
003:     59 changed, 1228 examined...
004:     20 changed, 341 examined...
005:      4 changed, 113 examined...
006:      2 changed, 30 examined...
007:      2 changed, 10 examined...
008:      1 changed, 11 examined...
009:      0 changed, 7 examined...
260 labels changed using aseg
000: 125 total segments, 74 labels (318 vertices) changed
001: 52 total segments, 1 labels (1 vertices) changed
002: 51 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 16 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1341 vertices marked for relabeling...
1341 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 15 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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...
960 labels changed using aseg
relabeling using gibbs priors...
000:   2740 changed, 135698 examined...
001:    634 changed, 11920 examined...
002:    179 changed, 3502 examined...
003:     51 changed, 1087 examined...
004:     18 changed, 302 examined...
005:     11 changed, 112 examined...
006:      8 changed, 61 examined...
007:      2 changed, 38 examined...
008:      1 changed, 14 examined...
009:      2 changed, 8 examined...
010:      4 changed, 11 examined...
011:      3 changed, 12 examined...
012:      1 changed, 14 examined...
013:      0 changed, 6 examined...
139 labels changed using aseg
000: 85 total segments, 42 labels (167 vertices) changed
001: 43 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1280 vertices marked for relabeling...
1280 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 14 seconds.
PIDs (17675 17678) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 00:58:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 00:58:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 rh 

Waiting for PID 17723 of (17723 17726) to complete...
Waiting for PID 17726 of (17723 17726) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
23920 bright wm thresholded.
3496 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.orig...
computing class statistics...
border white:    249299 voxels (1.49%)
border gray      297398 voxels (1.77%)
WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0]
GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 50.5 (was 70)
setting MAX_BORDER_WHITE to 112.5 (was 105)
setting MIN_BORDER_WHITE to 61.0 (was 85)
setting MAX_CSF to 39.9 (was 40)
setting MAX_GRAY to 93.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 29.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-7.8,    GM=61+-7.8
mean inside = 91.7, mean outside = 70.4
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.01-->4.41) (max @ vno 107907 --> 108799)
face area 0.33 +- 0.16 (0.00-->3.30)
mean absolute distance = 0.53 +- 0.74
2966 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 107 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 5 with 218 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 76 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
mean border=75.2, 79 (77) missing vertices, mean dist 0.3 [0.6 (%16.0)->0.5 (%84.0))]
%75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.10-->4.60) (max @ vno 108799 --> 107907)
face area 0.33 +- 0.16 (0.00-->3.12)
mean absolute distance = 0.32 +- 0.51
3177 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2700460.2, rms=8.853
001: dt: 0.5000, sse=1383195.8, rms=5.277 (40.391%)
002: dt: 0.5000, sse=1086298.4, rms=4.101 (22.291%)
003: dt: 0.5000, sse=1048583.6, rms=3.925 (4.294%)
004: dt: 0.5000, sse=1007907.1, rms=3.727 (5.025%)
rms = 3.83, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=830177.3, rms=2.612 (29.936%)
006: dt: 0.2500, sse=781010.3, rms=2.108 (19.300%)
007: dt: 0.2500, sse=753680.6, rms=1.926 (8.611%)
008: dt: 0.2500, sse=747226.1, rms=1.869 (2.979%)
rms = 1.82, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=743816.6, rms=1.820 (2.618%)
010: dt: 0.1250, sse=735167.1, rms=1.732 (4.848%)
rms = 1.72, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=734046.4, rms=1.717 (0.816%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 92 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 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 155 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 9 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 12 with 15 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 16 with 4 points - only 0.00% unknown
mean border=78.8, 81 (17) missing vertices, mean dist -0.2 [0.4 (%74.1)->0.2 (%25.9))]
%83 local maxima, %13 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 (0.06-->4.26) (max @ vno 108799 --> 107907)
face area 0.36 +- 0.17 (0.00-->3.53)
mean absolute distance = 0.24 +- 0.38
3074 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1371763.1, rms=5.061
012: dt: 0.5000, sse=1001176.1, rms=3.325 (34.312%)
rms = 3.65, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=852238.9, rms=2.371 (28.688%)
014: dt: 0.2500, sse=790474.9, rms=1.819 (23.255%)
015: dt: 0.2500, sse=770429.6, rms=1.585 (12.884%)
016: dt: 0.2500, sse=766275.6, rms=1.518 (4.204%)
rms = 1.49, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=762311.8, rms=1.486 (2.116%)
018: dt: 0.1250, sse=758721.0, rms=1.379 (7.231%)
rms = 1.39, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=754637.3, rms=1.389 (-0.705%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 100 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 167 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 42 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
mean border=81.1, 69 (8) missing vertices, mean dist -0.1 [0.3 (%67.5)->0.2 (%32.5))]
%87 local maxima, % 8 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-->4.15) (max @ vno 108804 --> 107913)
face area 0.34 +- 0.17 (0.00-->3.38)
mean absolute distance = 0.22 +- 0.32
2814 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=945537.9, rms=3.178
rms = 3.15, time step reduction 1 of 3 to 0.250...
020: dt: 0.5000, sse=944300.2, rms=3.146 (1.006%)
021: dt: 0.2500, sse=763459.4, rms=1.803 (42.701%)
022: dt: 0.2500, sse=739061.2, rms=1.467 (18.634%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=741841.8, rms=1.457 (0.657%)
024: dt: 0.1250, sse=719198.1, rms=1.259 (13.611%)
rms = 1.24, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=717631.1, rms=1.239 (1.612%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 108 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 146 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 74 points - only 0.00% unknown
deleting segment 9 with 21 points - only 0.00% unknown
deleting segment 10 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
mean border=82.0, 75 (4) missing vertices, mean dist -0.0 [0.2 (%56.1)->0.2 (%43.9))]
%89 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-6.0.0/0051105/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=739799.3, rms=1.684
rms = 2.17, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=699913.6, rms=1.133 (32.743%)
027: dt: 0.2500, sse=691625.2, rms=0.927 (18.129%)
rms = 0.94, time step reduction 2 of 3 to 0.125...
rms = 0.92, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=688307.7, rms=0.923 (0.490%)
positioning took 0.4 minutes
generating cortex label...
7 non-cortical segments detected
only using segment with 7082 vertices
erasing segment 1 (vno[0] = 67299)
erasing segment 2 (vno[0] = 86396)
erasing segment 3 (vno[0] = 100962)
erasing segment 4 (vno[0] = 105965)
erasing segment 5 (vno[0] = 109610)
erasing segment 6 (vno[0] = 115208)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.area
vertex spacing 0.89 +- 0.26 (0.01-->4.19) (max @ vno 107907 --> 108799)
face area 0.34 +- 0.16 (0.00-->3.32)
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 3 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=49.4, 78 (78) missing vertices, mean dist 1.5 [1.0 (%0.0)->2.9 (%100.0))]
%10 local maxima, %38 large gradients and %48 min vals, 290 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=29457250.0, rms=33.199
001: dt: 0.0500, sse=25732182.0, rms=30.978 (6.691%)
002: dt: 0.0500, sse=23073256.0, rms=29.289 (5.451%)
003: dt: 0.0500, sse=21049010.0, rms=27.935 (4.623%)
004: dt: 0.0500, sse=19425520.0, rms=26.799 (4.065%)
005: dt: 0.0500, sse=18070298.0, rms=25.813 (3.680%)
006: dt: 0.0500, sse=16907554.0, rms=24.936 (3.399%)
007: dt: 0.0500, sse=15887370.0, rms=24.140 (3.192%)
008: dt: 0.0500, sse=14979127.0, rms=23.408 (3.030%)
009: dt: 0.0500, sse=14161459.0, rms=22.730 (2.900%)
010: dt: 0.0500, sse=13418458.0, rms=22.095 (2.794%)
positioning took 0.9 minutes
mean border=49.1, 72 (37) missing vertices, mean dist 1.2 [0.3 (%0.0)->2.4 (%100.0))]
%11 local maxima, %38 large gradients and %47 min vals, 282 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=14182640.0, rms=22.749
011: dt: 0.0500, sse=13496971.0, rms=22.164 (2.570%)
012: dt: 0.0500, sse=12866909.0, rms=21.613 (2.487%)
013: dt: 0.0500, sse=12285422.0, rms=21.091 (2.414%)
014: dt: 0.0500, sse=11747881.0, rms=20.597 (2.342%)
015: dt: 0.0500, sse=11249788.0, rms=20.128 (2.275%)
016: dt: 0.0500, sse=10787875.0, rms=19.684 (2.209%)
017: dt: 0.0500, sse=10358975.0, rms=19.261 (2.145%)
018: dt: 0.0500, sse=9960533.0, rms=18.861 (2.081%)
019: dt: 0.0500, sse=9589504.0, rms=18.480 (2.021%)
020: dt: 0.0500, sse=9244067.0, rms=18.117 (1.960%)
positioning took 0.9 minutes
mean border=49.1, 92 (25) missing vertices, mean dist 1.1 [0.1 (%0.6)->2.1 (%99.4))]
%12 local maxima, %38 large gradients and %46 min vals, 286 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=9304085.0, rms=18.187
021: dt: 0.0500, sse=8977817.0, rms=17.840 (1.911%)
022: dt: 0.0500, sse=8673485.0, rms=17.509 (1.852%)
023: dt: 0.0500, sse=8388229.0, rms=17.194 (1.802%)
024: dt: 0.0500, sse=8122213.5, rms=16.894 (1.743%)
025: dt: 0.0500, sse=7873471.5, rms=16.609 (1.688%)
026: dt: 0.0500, sse=7640297.5, rms=16.337 (1.638%)
027: dt: 0.0500, sse=7420511.5, rms=16.076 (1.596%)
028: dt: 0.0500, sse=7211945.5, rms=15.825 (1.564%)
029: dt: 0.0500, sse=7013544.5, rms=15.581 (1.536%)
030: dt: 0.0500, sse=6824939.5, rms=15.347 (1.506%)
positioning took 0.9 minutes
mean border=49.0, 119 (21) missing vertices, mean dist 0.9 [0.1 (%5.7)->1.9 (%94.3))]
%12 local maxima, %38 large gradients and %46 min vals, 240 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=6900011.5, rms=15.441
031: dt: 0.5000, sse=5562625.5, rms=13.674 (11.445%)
032: dt: 0.5000, sse=4612672.5, rms=12.258 (10.355%)
033: dt: 0.5000, sse=3869610.8, rms=11.025 (10.058%)
034: dt: 0.5000, sse=3272932.0, rms=9.920 (10.027%)
035: dt: 0.5000, sse=2796849.5, rms=8.942 (9.852%)
036: dt: 0.5000, sse=2412269.5, rms=8.066 (9.805%)
037: dt: 0.5000, sse=2117754.0, rms=7.325 (9.178%)
038: dt: 0.5000, sse=1902859.5, rms=6.733 (8.086%)
039: dt: 0.5000, sse=1757109.5, rms=6.300 (6.428%)
040: dt: 0.5000, sse=1655969.1, rms=5.981 (5.074%)
041: dt: 0.5000, sse=1586954.0, rms=5.753 (3.805%)
042: dt: 0.5000, sse=1541940.9, rms=5.596 (2.733%)
043: dt: 0.5000, sse=1511292.1, rms=5.490 (1.894%)
044: dt: 0.5000, sse=1493130.4, rms=5.422 (1.230%)
rms = 5.37, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1479781.1, rms=5.375 (0.878%)
046: dt: 0.2500, sse=1399895.0, rms=5.034 (6.335%)
047: dt: 0.2500, sse=1374823.1, rms=4.937 (1.940%)
rms = 4.94, time step reduction 2 of 3 to 0.125...
048: dt: 0.2500, sse=1375597.5, rms=4.935 (0.030%)
049: dt: 0.1250, sse=1362483.8, rms=4.878 (1.153%)
rms = 4.87, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1360345.1, rms=4.869 (0.189%)
positioning took 2.6 minutes
mean border=48.4, 3092 (6) missing vertices, mean dist 0.1 [0.2 (%49.6)->0.6 (%50.4))]
%19 local maxima, %32 large gradients and %42 min vals, 155 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=1535858.6, rms=4.783
051: dt: 0.5000, sse=1479482.8, rms=4.565 (4.568%)
rms = 4.55, time step reduction 1 of 3 to 0.250...
052: dt: 0.5000, sse=1467996.2, rms=4.551 (0.312%)
053: dt: 0.2500, sse=1384189.5, rms=4.116 (9.549%)
054: dt: 0.2500, sse=1362109.9, rms=4.012 (2.532%)
rms = 4.01, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1361182.6, rms=4.005 (0.167%)
056: dt: 0.1250, sse=1345501.2, rms=3.921 (2.104%)
rms = 3.91, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1342467.1, rms=3.907 (0.363%)
positioning took 1.2 minutes
mean border=47.9, 3479 (2) missing vertices, mean dist 0.1 [0.2 (%51.8)->0.5 (%48.2))]
%29 local maxima, %24 large gradients and %41 min vals, 160 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=1375968.9, rms=4.047
rms = 4.29, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1357135.5, rms=3.951 (2.356%)
rms = 3.95, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1355118.9, rms=3.947 (0.114%)
rms = 3.91, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1347846.5, rms=3.907 (1.009%)
positioning took 0.6 minutes
mean border=47.4, 6549 (2) missing vertices, mean dist 0.1 [0.2 (%50.3)->0.4 (%49.7))]
%33 local maxima, %19 large gradients and %39 min vals, 172 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-6.0.0/0051105/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1369792.0, rms=4.012
rms = 4.09, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1348569.9, rms=3.909 (2.571%)
062: dt: 0.2500, sse=1324266.9, rms=3.806 (2.622%)
063: dt: 0.2500, sse=1311486.8, rms=3.750 (1.477%)
064: dt: 0.2500, sse=1295362.9, rms=3.679 (1.890%)
rms = 3.65, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1288992.9, rms=3.651 (0.749%)
066: dt: 0.1250, sse=1272366.6, rms=3.557 (2.579%)
rms = 3.53, time step reduction 3 of 3 to 0.062...
067: dt: 0.1250, sse=1267563.1, rms=3.534 (0.653%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.area.pial
vertex spacing 1.03 +- 0.45 (0.03-->7.85) (max @ vno 96965 --> 95990)
face area 0.41 +- 0.33 (0.00-->8.74)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 136564 vertices processed
25000 of 136564 vertices processed
50000 of 136564 vertices processed
75000 of 136564 vertices processed
100000 of 136564 vertices processed
125000 of 136564 vertices processed
0 of 136564 vertices processed
25000 of 136564 vertices processed
50000 of 136564 vertices processed
75000 of 136564 vertices processed
100000 of 136564 vertices processed
125000 of 136564 vertices processed
thickness calculation complete, 353:957 truncations.
27258 vertices at 0 distance
91515 vertices at 1 distance
85707 vertices at 2 distance
38117 vertices at 3 distance
12634 vertices at 4 distance
3944 vertices at 5 distance
1199 vertices at 6 distance
412 vertices at 7 distance
191 vertices at 8 distance
96 vertices at 9 distance
65 vertices at 10 distance
65 vertices at 11 distance
56 vertices at 12 distance
47 vertices at 13 distance
37 vertices at 14 distance
15 vertices at 15 distance
25 vertices at 16 distance
15 vertices at 17 distance
17 vertices at 18 distance
17 vertices at 19 distance
16 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.thickness
positioning took 15.6 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
23920 bright wm thresholded.
3496 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.orig...
computing class statistics...
border white:    249299 voxels (1.49%)
border gray      297398 voxels (1.77%)
WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0]
GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.5 (was 70)
setting MAX_BORDER_WHITE to 111.5 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 40.9 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 30.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-7.0,    GM=62+-7.8
mean inside = 91.5, mean outside = 70.4
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.01-->4.82) (max @ vno 55647 --> 60516)
face area 0.33 +- 0.15 (0.00-->2.99)
mean absolute distance = 0.52 +- 0.75
3129 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 54 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 310 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 27 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
deleting segment 11 with 54 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 9 points - only 0.00% unknown
deleting segment 14 with 7 points - only 0.00% unknown
mean border=75.6, 74 (72) missing vertices, mean dist 0.3 [0.6 (%16.9)->0.5 (%83.1))]
%72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.04-->4.67) (max @ vno 55647 --> 60516)
face area 0.33 +- 0.16 (0.00-->3.25)
mean absolute distance = 0.31 +- 0.51
3164 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2471972.0, rms=8.379
001: dt: 0.5000, sse=1300944.5, rms=5.013 (40.173%)
002: dt: 0.5000, sse=1048867.8, rms=3.952 (21.168%)
003: dt: 0.5000, sse=1027928.8, rms=3.861 (2.295%)
004: dt: 0.5000, sse=987943.6, rms=3.650 (5.458%)
rms = 3.80, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=811869.3, rms=2.513 (31.153%)
006: dt: 0.2500, sse=754158.6, rms=2.002 (20.352%)
007: dt: 0.2500, sse=737967.4, rms=1.829 (8.649%)
rms = 1.78, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=734779.9, rms=1.784 (2.411%)
009: dt: 0.1250, sse=727528.2, rms=1.681 (5.824%)
rms = 1.67, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=724518.6, rms=1.668 (0.763%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 53 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 203 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 45 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 9 points - only 11.11% unknown
deleting segment 12 with 6 points - only 0.00% unknown
mean border=79.0, 71 (19) missing vertices, mean dist -0.2 [0.3 (%73.2)->0.2 (%26.8))]
%81 local maxima, %14 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-->4.60) (max @ vno 55647 --> 60516)
face area 0.35 +- 0.17 (0.00-->3.43)
mean absolute distance = 0.23 +- 0.37
2857 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1309219.0, rms=4.865
011: dt: 0.5000, sse=984835.6, rms=3.323 (31.693%)
rms = 3.64, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=845579.6, rms=2.393 (28.004%)
013: dt: 0.2500, sse=787174.4, rms=1.860 (22.257%)
014: dt: 0.2500, sse=765525.8, rms=1.625 (12.628%)
015: dt: 0.2500, sse=758600.6, rms=1.544 (5.012%)
016: dt: 0.2500, sse=754683.2, rms=1.489 (3.579%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=752813.2, rms=1.464 (1.620%)
018: dt: 0.1250, sse=745664.3, rms=1.368 (6.572%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=744962.4, rms=1.362 (0.456%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 55 points - only 0.00% unknown
deleting segment 2 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 238 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 50 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
deleting segment 12 with 7 points - only 0.00% unknown
mean border=81.2, 73 (16) missing vertices, mean dist -0.1 [0.3 (%66.6)->0.2 (%33.4))]
%86 local maxima, % 9 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-->4.58) (max @ vno 55647 --> 60516)
face area 0.34 +- 0.16 (0.00-->3.04)
mean absolute distance = 0.22 +- 0.32
2689 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=902626.7, rms=2.990
rms = 3.08, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=783815.1, rms=2.080 (30.451%)
021: dt: 0.2500, sse=728011.9, rms=1.410 (32.217%)
022: dt: 0.2500, sse=718554.3, rms=1.314 (6.827%)
rms = 1.29, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=716124.9, rms=1.293 (1.540%)
024: dt: 0.1250, sse=710596.0, rms=1.217 (5.927%)
rms = 1.22, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=710292.1, rms=1.217 (-0.054%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
deleting segment 1 with 55 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
deleting segment 4 with 245 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 48 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
deleting segment 12 with 7 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
mean border=81.9, 78 (16) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))]
%88 local maxima, % 7 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-6.0.0/0051105/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=733035.6, rms=1.653
rms = 2.12, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=694949.3, rms=1.122 (32.117%)
027: dt: 0.2500, sse=685699.2, rms=0.911 (18.780%)
rms = 0.93, time step reduction 2 of 3 to 0.125...
rms = 0.91, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=683681.3, rms=0.905 (0.658%)
positioning took 0.4 minutes
generating cortex label...
16 non-cortical segments detected
only using segment with 7064 vertices
erasing segment 0 (vno[0] = 47676)
erasing segment 2 (vno[0] = 66100)
erasing segment 3 (vno[0] = 72686)
erasing segment 4 (vno[0] = 74955)
erasing segment 5 (vno[0] = 77311)
erasing segment 6 (vno[0] = 79385)
erasing segment 7 (vno[0] = 79404)
erasing segment 8 (vno[0] = 81512)
erasing segment 9 (vno[0] = 88058)
erasing segment 10 (vno[0] = 100480)
erasing segment 11 (vno[0] = 101352)
erasing segment 12 (vno[0] = 103130)
erasing segment 13 (vno[0] = 104099)
erasing segment 14 (vno[0] = 108701)
erasing segment 15 (vno[0] = 135431)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.area
vertex spacing 0.89 +- 0.26 (0.01-->4.56) (max @ vno 55647 --> 60516)
face area 0.34 +- 0.16 (0.00-->3.04)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 8 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=50.0, 81 (81) missing vertices, mean dist 1.5 [3.8 (%0.0)->2.9 (%100.0))]
%11 local maxima, %39 large gradients and %45 min vals, 463 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=28113704.0, rms=32.540
001: dt: 0.0500, sse=24545696.0, rms=30.353 (6.723%)
002: dt: 0.0500, sse=21995768.0, rms=28.687 (5.488%)
003: dt: 0.0500, sse=20056470.0, rms=27.353 (4.653%)
004: dt: 0.0500, sse=18499802.0, rms=26.232 (4.097%)
005: dt: 0.0500, sse=17202020.0, rms=25.260 (3.706%)
006: dt: 0.0500, sse=16088886.0, rms=24.395 (3.424%)
007: dt: 0.0500, sse=15114726.0, rms=23.612 (3.209%)
008: dt: 0.0500, sse=14248342.0, rms=22.893 (3.044%)
009: dt: 0.0500, sse=13468190.0, rms=22.226 (2.915%)
010: dt: 0.0500, sse=12760814.0, rms=21.603 (2.803%)
positioning took 0.9 minutes
mean border=49.8, 82 (39) missing vertices, mean dist 1.3 [2.0 (%0.0)->2.4 (%100.0))]
%12 local maxima, %39 large gradients and %44 min vals, 441 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=13484645.0, rms=22.242
011: dt: 0.0500, sse=12832335.0, rms=21.669 (2.577%)
012: dt: 0.0500, sse=12233040.0, rms=21.129 (2.494%)
013: dt: 0.0500, sse=11681176.0, rms=20.618 (2.415%)
014: dt: 0.0500, sse=11171509.0, rms=20.136 (2.341%)
015: dt: 0.0500, sse=10700127.0, rms=19.678 (2.270%)
016: dt: 0.0500, sse=10263281.0, rms=19.245 (2.202%)
017: dt: 0.0500, sse=9858479.0, rms=18.834 (2.134%)
018: dt: 0.0500, sse=9482811.0, rms=18.445 (2.067%)
019: dt: 0.0500, sse=9133861.0, rms=18.076 (2.002%)
020: dt: 0.0500, sse=8809371.0, rms=17.725 (1.938%)
positioning took 0.9 minutes
mean border=49.7, 108 (34) missing vertices, mean dist 1.1 [0.1 (%0.7)->2.1 (%99.3))]
%13 local maxima, %39 large gradients and %43 min vals, 406 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=8895193.0, rms=17.826
021: dt: 0.0500, sse=8588383.0, rms=17.491 (1.884%)
022: dt: 0.0500, sse=8302878.5, rms=17.172 (1.821%)
023: dt: 0.0500, sse=8035737.0, rms=16.868 (1.768%)
024: dt: 0.0500, sse=7786686.5, rms=16.580 (1.708%)
025: dt: 0.0500, sse=7554331.5, rms=16.307 (1.650%)
026: dt: 0.0500, sse=7336978.5, rms=16.047 (1.595%)
027: dt: 0.0500, sse=7132343.5, rms=15.798 (1.552%)
028: dt: 0.0500, sse=6938094.5, rms=15.557 (1.520%)
029: dt: 0.0500, sse=6753533.0, rms=15.326 (1.489%)
030: dt: 0.0500, sse=6578100.0, rms=15.102 (1.459%)
positioning took 0.9 minutes
mean border=49.6, 147 (26) missing vertices, mean dist 1.0 [0.1 (%6.8)->1.9 (%93.2))]
%13 local maxima, %39 large gradients and %43 min vals, 370 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=6663554.5, rms=15.212
031: dt: 0.5000, sse=5403962.5, rms=13.512 (11.175%)
032: dt: 0.5000, sse=4523226.0, rms=12.176 (9.888%)
033: dt: 0.5000, sse=3826992.0, rms=11.006 (9.609%)
034: dt: 0.5000, sse=3261253.0, rms=9.950 (9.596%)
035: dt: 0.5000, sse=2789420.8, rms=8.975 (9.796%)
036: dt: 0.5000, sse=2411856.2, rms=8.110 (9.639%)
037: dt: 0.5000, sse=2105441.5, rms=7.335 (9.558%)
038: dt: 0.5000, sse=1876122.8, rms=6.695 (8.715%)
039: dt: 0.5000, sse=1705520.4, rms=6.179 (7.720%)
040: dt: 0.5000, sse=1598984.1, rms=5.830 (5.634%)
041: dt: 0.5000, sse=1525796.2, rms=5.581 (4.280%)
042: dt: 0.5000, sse=1483706.2, rms=5.430 (2.700%)
043: dt: 0.5000, sse=1454016.1, rms=5.322 (1.989%)
044: dt: 0.5000, sse=1437111.9, rms=5.258 (1.201%)
rms = 5.22, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1425933.8, rms=5.217 (0.784%)
046: dt: 0.2500, sse=1346972.9, rms=4.869 (6.668%)
047: dt: 0.2500, sse=1323018.0, rms=4.772 (2.001%)
rms = 4.78, time step reduction 2 of 3 to 0.125...
rms = 4.75, time step reduction 3 of 3 to 0.062...
048: dt: 0.1250, sse=1317350.4, rms=4.746 (0.539%)
positioning took 2.4 minutes
mean border=48.9, 3213 (13) missing vertices, mean dist 0.1 [0.2 (%50.8)->0.6 (%49.2))]
%20 local maxima, %34 large gradients and %39 min vals, 186 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=1521424.4, rms=4.759
049: dt: 0.5000, sse=1458198.1, rms=4.506 (5.326%)
rms = 4.48, time step reduction 1 of 3 to 0.250...
050: dt: 0.5000, sse=1445987.6, rms=4.480 (0.580%)
051: dt: 0.2500, sse=1377156.9, rms=4.108 (8.306%)
052: dt: 0.2500, sse=1364301.4, rms=4.046 (1.501%)
rms = 4.05, time step reduction 2 of 3 to 0.125...
rms = 4.01, time step reduction 3 of 3 to 0.062...
053: dt: 0.1250, sse=1357532.2, rms=4.009 (0.909%)
positioning took 0.9 minutes
mean border=48.5, 3399 (12) missing vertices, mean dist 0.1 [0.2 (%51.9)->0.4 (%48.1))]
%30 local maxima, %25 large gradients and %38 min vals, 206 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=1395583.9, rms=4.170
rms = 4.51, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1369332.5, rms=4.038 (3.183%)
rms = 4.05, time step reduction 2 of 3 to 0.125...
rms = 4.02, time step reduction 3 of 3 to 0.062...
055: dt: 0.1250, sse=1366586.8, rms=4.023 (0.369%)
positioning took 0.5 minutes
mean border=48.0, 6106 (11) missing vertices, mean dist 0.1 [0.2 (%49.0)->0.4 (%51.0))]
%35 local maxima, %20 large gradients and %36 min vals, 217 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-6.0.0/0051105/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1399840.4, rms=4.188
rms = 4.16, time step reduction 1 of 3 to 0.250...
056: dt: 0.5000, sse=1386044.1, rms=4.160 (0.670%)
057: dt: 0.2500, sse=1313505.6, rms=3.807 (8.478%)
058: dt: 0.2500, sse=1281807.2, rms=3.653 (4.061%)
rms = 3.63, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1277070.1, rms=3.631 (0.598%)
060: dt: 0.1250, sse=1250325.8, rms=3.479 (4.192%)
rms = 3.44, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1243304.8, rms=3.443 (1.021%)
positioning took 1.0 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.area.pial
vertex spacing 1.03 +- 0.45 (0.05-->8.08) (max @ vno 93389 --> 92316)
face area 0.41 +- 0.33 (0.00-->4.83)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 135698 vertices processed
25000 of 135698 vertices processed
50000 of 135698 vertices processed
75000 of 135698 vertices processed
100000 of 135698 vertices processed
125000 of 135698 vertices processed
0 of 135698 vertices processed
25000 of 135698 vertices processed
50000 of 135698 vertices processed
75000 of 135698 vertices processed
100000 of 135698 vertices processed
125000 of 135698 vertices processed
thickness calculation complete, 99:590 truncations.
27587 vertices at 0 distance
93341 vertices at 1 distance
84964 vertices at 2 distance
36452 vertices at 3 distance
11683 vertices at 4 distance
3418 vertices at 5 distance
1119 vertices at 6 distance
396 vertices at 7 distance
158 vertices at 8 distance
83 vertices at 9 distance
67 vertices at 10 distance
56 vertices at 11 distance
46 vertices at 12 distance
28 vertices at 13 distance
18 vertices at 14 distance
24 vertices at 15 distance
14 vertices at 16 distance
14 vertices at 17 distance
9 vertices at 18 distance
9 vertices at 19 distance
6 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.thickness
positioning took 14.6 minutes
PIDs (17723 17726) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 01:14:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label
Total face volume 256923
Total vertex volume 252720 (mask=0)
#@# 0051105 lh 252720
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 01:14:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label
Total face volume 253688
Total vertex volume 250027 (mask=0)
#@# 0051105 rh 250027
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 01:14:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 

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 = 112
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/ribbon.mgz
mris_volmask took 12.08 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 01:26:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 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 0051105 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 01:26:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 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 0051105 rh pial 

Waiting for PID 19028 of (19028 19031 19034 19037) to complete...
Waiting for PID 19031 of (19028 19031 19034 19037) to complete...
Waiting for PID 19034 of (19028 19031 19034 19037) to complete...
Waiting for PID 19037 of (19028 19031 19034 19037) 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 0051105 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923
Total vertex volume 252720 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1360    960   2364  2.566 0.482     0.115     0.022       11     1.3  bankssts
  898    597   1491  2.324 0.696     0.129     0.023       15     0.8  caudalanteriorcingulate
 3647   2465   7878  2.833 0.500     0.116     0.027       36     3.6  caudalmiddlefrontal
 2302   1556   3125  1.950 0.552     0.162     0.045       40     4.6  cuneus
  434    292   1622  3.684 0.955     0.106     0.024        4     0.4  entorhinal
 4723   3209  10068  2.754 0.666     0.134     0.031       66     6.0  fusiform
 7667   5132  14825  2.578 0.511     0.127     0.028       99     8.5  inferiorparietal
 5354   3586  11981  2.794 0.613     0.136     0.034       85     7.6  inferiortemporal
 1558   1022   3047  2.557 0.815     0.133     0.034       23     2.1  isthmuscingulate
 8151   5333  12202  2.079 0.547     0.146     0.042      123    13.4  lateraloccipital
 3756   2485   7380  2.795 0.613     0.133     0.032       51     4.8  lateralorbitofrontal
 4073   2776   6111  2.049 0.625     0.153     0.044       68     7.3  lingual
 2325   1615   5107  2.653 0.666     0.129     0.033       38     3.0  medialorbitofrontal
 4371   3015  11420  3.051 0.679     0.131     0.027       65     5.0  middletemporal
  851    602   1754  2.541 0.596     0.092     0.021        5     0.7  parahippocampal
 2733   1679   5068  2.784 0.572     0.115     0.027       29     2.7  paracentral
 2287   1555   5022  2.799 0.543     0.125     0.029       26     2.8  parsopercularis
 1071    715   2901  2.998 0.706     0.161     0.051       22     2.3  parsorbitalis
 1833   1244   3996  2.725 0.537     0.116     0.025       21     1.8  parstriangularis
 1996   1352   2142  1.770 0.451     0.148     0.044       26     3.4  pericalcarine
 7126   4640  11191  2.108 0.642     0.116     0.026       78     7.1  postcentral
 1931   1266   3777  2.556 0.804     0.131     0.031       31     2.4  posteriorcingulate
 7702   4850  14581  2.629 0.682     0.114     0.028       78     9.3  precentral
 5136   3501   9228  2.463 0.525     0.125     0.028       63     6.1  precuneus
 1054    698   2410  2.984 0.784     0.153     0.047       30     1.7  rostralanteriorcingulate
 9184   6424  19015  2.520 0.566     0.133     0.035      140    13.3  rostralmiddlefrontal
 9722   6569  22806  2.974 0.579     0.126     0.028      111    10.9  superiorfrontal
 7800   5189  12758  2.218 0.535     0.126     0.029       95     8.6  superiorparietal
 6317   4234  13786  2.854 0.651     0.119     0.024       69     6.3  superiortemporal
 6231   4189  12377  2.678 0.530     0.128     0.029       83     7.1  supramarginal
  345    218    989  2.977 0.533     0.154     0.038        8     0.5  frontalpole
  584    451   2487  3.948 0.843     0.139     0.035        8     0.8  temporalpole
  763    481   1119  2.085 0.512     0.117     0.033        8     0.9  transversetemporal
 3371   2234   6683  3.055 0.721     0.118     0.035       38     4.3  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051105 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923
Total vertex volume 252720 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1360    916   2364  2.566 0.482     0.127     0.037       27     2.2  bankssts
  898    699   1491  2.324 0.696     0.175     0.045       39     1.7  caudalanteriorcingulate
 3647   2987   7878  2.833 0.500     0.142     0.034       48     5.6  caudalmiddlefrontal
 2302   1828   3125  1.950 0.552     0.164     0.043       37     4.6  cuneus
  434    613   1622  3.684 0.955     0.198     0.035        4     0.8  entorhinal
 4723   4049  10068  2.754 0.666     0.172     0.045       92     9.8  fusiform
 7667   6290  14825  2.578 0.511     0.151     0.033      110    11.7  inferiorparietal
 5354   4868  11981  2.794 0.613     0.164     0.038       79     9.5  inferiortemporal
 1558   1346   3047  2.557 0.815     0.182     0.050       41     3.6  isthmuscingulate
 8151   6459  12202  2.079 0.547     0.145     0.036      110    12.9  lateraloccipital
 3756   2939   7380  2.795 0.613     0.152     0.044       64     6.8  lateralorbitofrontal
 4073   3401   6111  2.049 0.625     0.170     0.049       74     9.1  lingual
 2325   2286   5107  2.653 0.666     0.184     0.045       42     5.0  medialorbitofrontal
 4371   4259  11420  3.051 0.679     0.156     0.034       53     6.6  middletemporal
  851    793   1754  2.541 0.596     0.140     0.034        6     1.3  parahippocampal
 2733   2009   5068  2.784 0.572     0.138     0.036       45     4.4  paracentral
 2287   2049   5022  2.799 0.543     0.165     0.043       43     4.4  parsopercularis
 1071   1212   2901  2.998 0.706     0.211     0.052       22     2.6  parsorbitalis
 1833   1639   3996  2.725 0.537     0.168     0.041       29     3.6  parstriangularis
 1996   1163   2142  1.770 0.451     0.130     0.036       32     3.3  pericalcarine
 7126   6054  11191  2.108 0.642     0.142     0.030       75    10.2  postcentral
 1931   1565   3777  2.556 0.804     0.151     0.041       30     3.6  posteriorcingulate
 7702   5978  14581  2.629 0.682     0.126     0.029       91    10.4  precentral
 5136   4016   9228  2.463 0.525     0.150     0.038       86     8.7  precuneus
 1054    947   2410  2.984 0.784     0.209     0.059       23     3.0  rostralanteriorcingulate
 9184   8513  19015  2.520 0.566     0.178     0.042      157    18.9  rostralmiddlefrontal
 9722   8501  22806  2.974 0.579     0.158     0.039      148    17.7  superiorfrontal
 7800   6192  12758  2.218 0.535     0.143     0.031      107    11.2  superiorparietal
 6317   5287  13786  2.854 0.651     0.160     0.041      113    12.2  superiortemporal
 6231   5021  12377  2.678 0.530     0.146     0.036       97     9.9  supramarginal
  345    427    989  2.977 0.533     0.219     0.046        5     0.9  frontalpole
  584    833   2487  3.948 0.843     0.204     0.037        6     1.2  temporalpole
  763    637   1119  2.085 0.512     0.156     0.042       10     1.5  transversetemporal
 3371   2241   6683  3.055 0.721     0.170     0.057       76     8.9  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 0051105 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688
Total vertex volume 250027 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1135    800   1950  2.547 0.385     0.114     0.020        9     1.0  bankssts
  959    659   1925  2.576 0.711     0.139     0.029       17     0.9  caudalanteriorcingulate
 3129   2065   6528  2.771 0.550     0.103     0.023       24     2.7  caudalmiddlefrontal
 2396   1567   3483  1.969 0.523     0.157     0.048       39     4.6  cuneus
  481    365   1571  3.133 0.792     0.125     0.036        4     0.7  entorhinal
 4086   2739   8893  2.710 0.659     0.133     0.031       56     5.0  fusiform
 8711   5860  16753  2.534 0.555     0.124     0.029      114     9.9  inferiorparietal
 4703   3137  10921  2.886 0.694     0.126     0.030       58     5.7  inferiortemporal
 1505    979   3063  2.517 0.795     0.126     0.037       21     1.9  isthmuscingulate
 7475   4920  11394  2.093 0.566     0.150     0.048      126    15.7  lateraloccipital
 3240   2230   6247  2.531 0.669     0.147     0.040       59     5.1  lateralorbitofrontal
 4596   3166   7470  2.153 0.577     0.157     0.047       76     8.5  lingual
 2803   1906   5585  2.545 0.727     0.132     0.039       52     3.9  medialorbitofrontal
 4560   3215  11211  2.837 0.647     0.130     0.027       69     5.1  middletemporal
  801    548   1623  2.532 0.615     0.111     0.035        9     0.9  parahippocampal
 2425   1585   4382  2.593 0.605     0.113     0.027       22     2.5  paracentral
 2137   1496   4791  2.809 0.592     0.116     0.026       21     2.4  parsopercularis
 1194    835   3214  2.860 0.596     0.165     0.046       23     2.2  parsorbitalis
 2419   1693   4842  2.649 0.547     0.134     0.033       35     3.0  parstriangularis
 2420   1595   2658  1.744 0.427     0.147     0.047       33     4.4  pericalcarine
 6491   4203   9691  2.037 0.641     0.118     0.030       70     7.3  postcentral
 1668   1095   3403  2.605 0.767     0.129     0.031       26     1.9  posteriorcingulate
 7370   4611  14605  2.807 0.666     0.112     0.033       70    10.2  precentral
 5955   4097  10801  2.442 0.592     0.133     0.029       75     7.0  precuneus
  736    481   1634  2.934 0.549     0.154     0.039       18     1.1  rostralanteriorcingulate
 9949   6900  19892  2.452 0.589     0.136     0.035      144    14.0  rostralmiddlefrontal
 9922   6745  22562  2.857 0.588     0.126     0.030      113    11.5  superiorfrontal
 7726   5032  13459  2.331 0.552     0.129     0.032       97     9.4  superiorparietal
 5335   3545  11374  2.817 0.587     0.113     0.022       53     4.8  superiortemporal
 6233   4211  12356  2.549 0.581     0.123     0.028       78     6.5  supramarginal
  503    330   1300  2.962 0.592     0.177     0.059       12     1.5  frontalpole
  649    461   2737  3.817 0.636     0.133     0.035        9     0.9  temporalpole
  652    426   1040  2.182 0.563     0.169     0.060       14     1.7  transversetemporal
 3441   2274   6616  2.921 0.758     0.121     0.037       44     4.5  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 0051105 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688
Total vertex volume 250027 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1135    744   1950  2.547 0.385     0.148     0.045       28     2.4  bankssts
  959    825   1925  2.576 0.711     0.171     0.043       27     1.8  caudalanteriorcingulate
 3129   2556   6528  2.771 0.550     0.128     0.033       29     4.5  caudalmiddlefrontal
 2396   2014   3483  1.969 0.523     0.170     0.048       35     5.1  cuneus
  481    583   1571  3.133 0.792     0.220     0.051        9     1.3  entorhinal
 4086   3687   8893  2.710 0.659     0.166     0.044       65     8.3  fusiform
 8711   7264  16753  2.534 0.555     0.149     0.035      117    13.7  inferiorparietal
 4703   4269  10921  2.886 0.694     0.163     0.039       63     8.8  inferiortemporal
 1505   1345   3063  2.517 0.795     0.180     0.048       31     3.2  isthmuscingulate
 7475   5921  11394  2.093 0.566     0.148     0.039      121    12.7  lateraloccipital
 3240   2764   6247  2.531 0.669     0.188     0.052       76     7.8  lateralorbitofrontal
 4596   3813   7470  2.153 0.577     0.171     0.049       84    10.6  lingual
 2803   2498   5585  2.545 0.727     0.175     0.052       74     6.9  medialorbitofrontal
 4560   4608  11211  2.837 0.647     0.167     0.037       62     7.8  middletemporal
  801    715   1623  2.532 0.615     0.166     0.044       13     1.7  parahippocampal
 2425   1762   4382  2.593 0.605     0.134     0.034       32     3.6  paracentral
 2137   1997   4791  2.809 0.592     0.169     0.043       33     4.3  parsopercularis
 1194   1425   3214  2.860 0.596     0.213     0.045       24     2.7  parsorbitalis
 2419   2082   4842  2.649 0.547     0.176     0.045       52     5.4  parstriangularis
 2420   1485   2658  1.744 0.427     0.130     0.035       46     3.9  pericalcarine
 6491   5332   9691  2.037 0.641     0.144     0.033       68    10.0  postcentral
 1668   1379   3403  2.605 0.767     0.160     0.040       35     3.0  posteriorcingulate
 7370   5494  14605  2.807 0.666     0.119     0.027       78     9.0  precentral
 5955   4677  10801  2.442 0.592     0.148     0.039       83    10.1  precuneus
  736    663   1634  2.934 0.549     0.189     0.048       13     1.8  rostralanteriorcingulate
 9949   9108  19892  2.452 0.589     0.175     0.040      158    18.5  rostralmiddlefrontal
 9922   8734  22562  2.857 0.588     0.161     0.041      157    18.8  superiorfrontal
 7726   6292  13459  2.331 0.552     0.150     0.036      110    12.4  superiorparietal
 5335   4552  11374  2.817 0.587     0.164     0.044       98    11.0  superiortemporal
 6233   5342  12356  2.549 0.581     0.159     0.038       89    11.3  supramarginal
  503    509   1300  2.962 0.592     0.189     0.040       14     0.9  frontalpole
  649    956   2737  3.817 0.636     0.236     0.048       10     1.7  temporalpole
  652    524   1040  2.182 0.563     0.167     0.057       11     1.6  transversetemporal
 3441   2196   6616  2.921 0.758     0.162     0.061       85     9.2  insula
PIDs (19028 19031 19034 19037) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 01:28:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 01:28:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 19121 of (19121 19124) to complete...
Waiting for PID 19124 of (19121 19124) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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...
89 labels changed using aseg
relabeling using gibbs priors...
000:   9220 changed, 136564 examined...
001:   2186 changed, 35994 examined...
002:    678 changed, 11492 examined...
003:    290 changed, 3759 examined...
004:    132 changed, 1663 examined...
005:     61 changed, 759 examined...
006:     23 changed, 303 examined...
007:     11 changed, 136 examined...
008:      8 changed, 72 examined...
009:      6 changed, 42 examined...
010:      1 changed, 30 examined...
011:      0 changed, 7 examined...
5 labels changed using aseg
000: 288 total segments, 201 labels (2339 vertices) changed
001: 94 total segments, 7 labels (70 vertices) changed
002: 87 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 45 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
833 vertices marked for relabeling...
833 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 19 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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...
45 labels changed using aseg
relabeling using gibbs priors...
000:   8807 changed, 135698 examined...
001:   1981 changed, 34813 examined...
002:    565 changed, 10406 examined...
003:    243 changed, 3221 examined...
004:    121 changed, 1363 examined...
005:     50 changed, 699 examined...
006:     27 changed, 320 examined...
007:      9 changed, 139 examined...
008:      6 changed, 58 examined...
009:      3 changed, 37 examined...
010:      2 changed, 16 examined...
011:      2 changed, 13 examined...
012:      1 changed, 15 examined...
013:      0 changed, 5 examined...
14 labels changed using aseg
000: 244 total segments, 158 labels (2304 vertices) changed
001: 92 total segments, 8 labels (25 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 34 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
905 vertices marked for relabeling...
905 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 19 seconds.
PIDs (19121 19124) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 01:28:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 01:28:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh white 

Waiting for PID 19172 of (19172 19175) to complete...
Waiting for PID 19175 of (19172 19175) 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 0051105 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923
Total vertex volume 252720 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1312    899   2715  2.658 0.499     0.136     0.033       25     1.8  G&S_frontomargin
 1506   1010   2607  2.213 0.637     0.145     0.041       21     2.3  G&S_occipital_inf
 2145   1229   3828  2.600 0.601     0.117     0.034       28     3.1  G&S_paracentral
 1736   1161   3773  2.738 0.582     0.143     0.031       27     2.1  G&S_subcentral
  693    471   1769  2.715 0.523     0.153     0.037       16     0.9  G&S_transv_frontopol
 1924   1350   4105  2.918 0.602     0.130     0.033       35     2.2  G&S_cingul-Ant
 1217    859   2350  2.746 0.455     0.122     0.025       15     1.2  G&S_cingul-Mid-Ant
 1535   1048   3226  2.850 0.513     0.125     0.032       19     1.9  G&S_cingul-Mid-Post
  733    493   1966  2.994 0.492     0.157     0.039       14     1.1  G_cingul-Post-dorsal
  415    282   1205  3.032 0.839     0.158     0.049        7     0.8  G_cingul-Post-ventral
 2018   1381   2772  1.811 0.523     0.162     0.044       35     3.8  G_cuneus
 1393    938   3883  2.942 0.555     0.132     0.032       20     2.0  G_front_inf-Opercular
  484    301   1228  2.968 0.503     0.140     0.040        9     0.8  G_front_inf-Orbital
 1124    749   2852  2.845 0.478     0.132     0.036       19     1.4  G_front_inf-Triangul
 4921   3398  13040  2.820 0.606     0.145     0.043       94     8.7  G_front_middle
 6716   4403  18328  3.178 0.553     0.134     0.032       91     8.3  G_front_sup
  783    497   1500  2.867 0.771     0.131     0.058       15     1.5  G_Ins_lg&S_cent_ins
  677    437   1932  3.420 0.748     0.124     0.033       10     0.8  G_insular_short
 2719   1733   5756  2.571 0.568     0.149     0.042       52     4.2  G_occipital_middle
 1461    983   2256  1.962 0.525     0.150     0.044       23     2.5  G_occipital_sup
 1972   1266   4867  3.017 0.652     0.146     0.037       37     2.7  G_oc-temp_lat-fusifor
 2790   1865   4380  2.016 0.671     0.175     0.057       62     6.3  G_oc-temp_med-Lingual
  993    659   2875  3.098 0.925     0.102     0.030        9     1.2  G_oc-temp_med-Parahip
 2494   1626   6064  2.786 0.748     0.148     0.043       48     4.4  G_orbital
 2835   1888   6945  2.803 0.501     0.142     0.035       50     4.0  G_pariet_inf-Angular
 3069   2015   6946  2.761 0.570     0.137     0.033       49     3.9  G_pariet_inf-Supramar
 2938   1922   5849  2.447 0.533     0.134     0.033       45     3.5  G_parietal_sup
 2875   1766   4962  2.209 0.584     0.120     0.034       38     3.5  G_postcentral
 3071   1804   6830  2.862 0.688     0.111     0.031       34     4.2  G_precentral
 2465   1676   5768  2.653 0.560     0.142     0.036       46     3.6  G_precuneus
  997    677   2830  2.861 0.679     0.144     0.050       24     2.0  G_rectus
  160    106    345  2.993 0.796     0.102     0.036        2     0.1  G_subcallosal
  541    345    953  2.166 0.545     0.111     0.036        6     0.7  G_temp_sup-G_T_transv
 2131   1399   6336  3.118 0.573     0.140     0.035       38     3.1  G_temp_sup-Lateral
  720    524   2076  3.323 0.934     0.100     0.023        4     0.6  G_temp_sup-Plan_polar
 1178    804   2574  2.900 0.514     0.108     0.018       11     0.7  G_temp_sup-Plan_tempo
 2977   1941   7918  2.979 0.615     0.148     0.043       64     5.4  G_temporal_inf
 2256   1559   7181  3.270 0.605     0.145     0.034       43     3.0  G_temporal_middle
  264    177    435  2.604 0.598     0.078     0.012        1     0.1  Lat_Fis-ant-Horizont
  322    223    490  2.508 0.464     0.100     0.013        2     0.2  Lat_Fis-ant-Vertical
 1274    861   1788  2.701 0.529     0.134     0.030       18     1.6  Lat_Fis-post
 2478   1615   3292  1.829 0.458     0.162     0.055       48     5.6  Pole_occipital
 1519   1105   5622  3.519 0.806     0.142     0.032       23     2.1  Pole_temporal
 2654   1784   2914  1.877 0.485     0.133     0.036       29     4.0  S_calcarine
 2889   1982   3051  1.734 0.547     0.116     0.022       21     2.7  S_central
 1251    849   1940  2.534 0.450     0.114     0.022       13     1.2  S_cingul-Marginalis
  482    340    834  2.990 0.346     0.114     0.025        4     0.5  S_circular_insula_ant
 1242    866   2071  2.922 0.741     0.099     0.017        6     0.9  S_circular_insula_inf
 1792   1212   2867  2.876 0.556     0.102     0.018        9     1.3  S_circular_insula_sup
 1023    701   1708  2.536 0.464     0.122     0.026       13     1.1  S_collat_transv_ant
  422    298    438  1.810 0.366     0.135     0.029        4     0.5  S_collat_transv_post
 2356   1639   3673  2.315 0.428     0.110     0.020       16     1.9  S_front_inf
 1979   1423   3245  2.362 0.436     0.125     0.033       18     2.6  S_front_middle
 2775   1901   4624  2.561 0.465     0.107     0.022       17     2.5  S_front_sup
  425    310    703  2.504 0.387     0.127     0.022        3     0.5  S_interm_prim-Jensen
 2563   1742   3421  2.112 0.399     0.110     0.019       21     2.2  S_intrapariet&P_trans
 1438    957   1660  1.996 0.398     0.125     0.031       12     1.8  S_oc_middle&Lunatus
 1567   1068   2085  2.167 0.379     0.119     0.020       15     1.2  S_oc_sup&transversal
  656    465   1069  2.281 0.389     0.116     0.021        6     0.6  S_occipital_ant
 1118    775   1700  2.252 0.490     0.121     0.026       11     1.3  S_oc-temp_lat
 2021   1429   3118  2.452 0.487     0.109     0.019       12     1.6  S_oc-temp_med&Lingual
  356    251    572  2.445 0.520     0.139     0.029        3     0.5  S_orbital_lateral
  688    460    928  2.414 0.588     0.111     0.017        5     0.4  S_orbital_med-olfact
 1295    871   2498  3.001 0.494     0.129     0.028       14     1.4  S_orbital-H_Shaped
 2112   1417   2953  2.309 0.452     0.108     0.022       15     2.1  S_parieto_occipital
 1418    801   1215  1.808 0.745     0.119     0.024       25     1.2  S_pericallosal
 3517   2357   4746  2.164 0.481     0.108     0.020       25     2.9  S_postcentral
 1455    989   2366  2.632 0.424     0.110     0.021       10     1.1  S_precentral-inf-part
 1525   1043   2537  2.523 0.443     0.101     0.021        9     1.3  S_precentral-sup-part
  581    425    809  2.284 0.403     0.128     0.021        6     0.5  S_suborbital
  812    570   1232  2.481 0.355     0.111     0.024        6     0.7  S_subparietal
 1657   1161   2575  2.647 0.531     0.118     0.020       12     1.4  S_temporal_inf
 6262   4264  10173  2.536 0.456     0.110     0.021       51     5.2  S_temporal_sup
  501    343    577  2.067 0.417     0.125     0.017        5     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 0051105 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688
Total vertex volume 250027 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
  801    549   1692  2.664 0.624     0.152     0.048       14     1.7  G&S_frontomargin
 1263    821   2186  2.341 0.565     0.129     0.031       15     1.5  G&S_occipital_inf
 1579    967   2792  2.365 0.591     0.130     0.044       24     2.7  G&S_paracentral
 1549   1055   3238  2.543 0.698     0.140     0.034       21     2.0  G&S_subcentral
 1272    901   3108  2.765 0.636     0.165     0.043       28     2.1  G&S_transv_frontopol
 2731   1875   5565  2.839 0.568     0.140     0.034       49     3.4  G&S_cingul-Ant
 1125    796   2358  2.778 0.471     0.106     0.022        9     0.9  G&S_cingul-Mid-Ant
 1421    974   2925  2.828 0.552     0.123     0.029       15     1.7  G&S_cingul-Mid-Post
  560    374   1738  3.129 0.564     0.154     0.054       12     1.1  G_cingul-Post-dorsal
  386    277   1215  2.985 0.660     0.157     0.056        8     0.8  G_cingul-Post-ventral
 2215   1456   3094  1.856 0.469     0.157     0.048       36     4.2  G_cuneus
 1392    955   4030  3.024 0.621     0.130     0.031       20     1.9  G_front_inf-Opercular
  483    333   1367  2.911 0.536     0.151     0.043       10     0.6  G_front_inf-Orbital
 1065    754   2484  2.596 0.506     0.149     0.042       23     1.6  G_front_inf-Triangul
 4830   3283  12632  2.768 0.605     0.147     0.042       89     8.0  G_front_middle
 6783   4498  17193  2.936 0.578     0.133     0.034       93     8.8  G_front_sup
  593    428   1304  2.828 0.866     0.138     0.041       11     0.8  G_Ins_lg&S_cent_ins
  798    481   2007  3.047 1.038     0.132     0.056       16     1.5  G_insular_short
 2699   1755   5581  2.578 0.659     0.154     0.043       53     4.1  G_occipital_middle
 1552    964   2842  2.263 0.551     0.143     0.042       23     2.4  G_occipital_sup
 1826   1155   4558  2.886 0.573     0.151     0.041       36     2.9  G_oc-temp_lat-fusifor
 2964   2027   5450  2.196 0.613     0.168     0.055       57     6.6  G_oc-temp_med-Lingual
 1088    773   3170  2.970 0.780     0.123     0.044       12     1.5  G_oc-temp_med-Parahip
 2553   1734   6454  2.676 0.757     0.164     0.051       63     5.4  G_orbital
 3360   2215   7791  2.643 0.552     0.139     0.037       62     4.8  G_pariet_inf-Angular
 2904   1961   6795  2.739 0.591     0.139     0.035       50     3.9  G_pariet_inf-Supramar
 2387   1562   5146  2.547 0.601     0.140     0.037       38     3.1  G_parietal_sup
 2370   1442   3855  2.091 0.565     0.125     0.038       32     3.3  G_postcentral
 2745   1537   6952  3.218 0.514     0.112     0.043       32     4.9  G_precentral
 2600   1740   6020  2.706 0.569     0.154     0.039       49     4.0  G_precuneus
  711    484   1853  2.446 0.847     0.153     0.065       19     1.7  G_rectus
  393    246    691  2.632 0.931     0.092     0.036        6     0.4  G_subcallosal
  459    294    903  2.318 0.716     0.162     0.058       10     0.9  G_temp_sup-G_T_transv
 1725   1102   4718  3.041 0.545     0.129     0.026       25     1.9  G_temp_sup-Lateral
  881    607   2134  3.091 0.763     0.080     0.021        5     0.6  G_temp_sup-Plan_polar
  879    600   1852  2.704 0.572     0.104     0.022        7     0.8  G_temp_sup-Plan_tempo
 2430   1654   7329  3.155 0.650     0.143     0.039       45     3.8  G_temporal_inf
 2610   1809   7573  2.960 0.645     0.144     0.034       56     3.7  G_temporal_middle
  315    229    481  2.804 0.367     0.103     0.016        1     0.2  Lat_Fis-ant-Horizont
  279    187    468  2.771 0.614     0.099     0.024        1     0.2  Lat_Fis-ant-Vertical
 1502   1003   2134  2.532 0.467     0.116     0.025       12     1.8  Lat_Fis-post
 3293   2218   5125  1.996 0.587     0.169     0.054       64     7.0  Pole_occipital
 1796   1176   6153  3.419 0.697     0.131     0.031       24     2.3  Pole_temporal
 2744   1857   2917  1.822 0.459     0.146     0.041       37     4.6  S_calcarine
 2960   1986   3211  1.871 0.616     0.109     0.023       19     3.0  S_central
 1345    965   2125  2.423 0.530     0.096     0.015        6     0.8  S_cingul-Marginalis
  542    368    868  2.820 0.618     0.117     0.024        3     0.6  S_circular_insula_ant
 1069    730   1647  2.790 0.647     0.095     0.017        5     0.8  S_circular_insula_inf
 1501   1003   2267  2.812 0.510     0.103     0.021        8     1.4  S_circular_insula_sup
 1108    760   1737  2.466 0.517     0.098     0.015        6     0.7  S_collat_transv_ant
  256    189    360  2.450 0.599     0.151     0.030        2     0.3  S_collat_transv_post
 2516   1742   4197  2.327 0.511     0.111     0.022       23     2.4  S_front_inf
 2487   1710   3463  2.198 0.451     0.110     0.022       16     2.2  S_front_middle
 2509   1719   4156  2.496 0.541     0.105     0.025       16     2.4  S_front_sup
  636    428    825  2.291 0.480     0.102     0.017        3     0.6  S_interm_prim-Jensen
 3359   2244   4740  2.162 0.454     0.115     0.024       29     3.1  S_intrapariet&P_trans
  979    668   1048  1.824 0.435     0.134     0.078       16     4.7  S_oc_middle&Lunatus
 1407    934   1681  2.015 0.386     0.122     0.027       14     1.6  S_oc_sup&transversal
  645    439    915  2.084 0.403     0.116     0.027        6     0.7  S_occipital_ant
 1157    794   1671  2.255 0.433     0.111     0.020        9     0.9  S_oc-temp_lat
 1694   1195   2446  2.383 0.470     0.111     0.019       12     1.3  S_oc-temp_med&Lingual
  615    429    872  2.287 0.473     0.139     0.034        7     0.8  S_orbital_lateral
  559    395    879  2.580 0.656     0.098     0.017        3     0.3  S_orbital_med-olfact
 1161    825   2086  2.530 0.532     0.144     0.033       14     1.5  S_orbital-H_Shaped
 2447   1622   3498  2.261 0.546     0.115     0.024       20     2.5  S_parieto_occipital
 1281    775   1073  1.785 0.580     0.127     0.018       21     0.8  S_pericallosal
 3186   2095   4815  2.287 0.516     0.108     0.021       25     2.7  S_postcentral
 1740   1200   2870  2.711 0.502     0.096     0.017        9     1.2  S_precentral-inf-part
 1506   1026   2302  2.546 0.537     0.102     0.017        7     1.2  S_precentral-sup-part
  347    243    582  2.710 0.694     0.152     0.026        4     0.4  S_suborbital
 1216    842   1915  2.428 0.458     0.112     0.020        8     1.0  S_subparietal
 1342    940   1986  2.523 0.508     0.124     0.025       10     1.4  S_temporal_inf
 5938   4127   9416  2.489 0.460     0.109     0.019       45     4.7  S_temporal_sup
  387    273    506  2.343 0.633     0.151     0.025        4     0.4  S_temporal_transverse
PIDs (19172 19175) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 01:29:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 01:29:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 19235 of (19235 19238) to complete...
Waiting for PID 19238 of (19235 19238) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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...
1240 labels changed using aseg
relabeling using gibbs priors...
000:   1979 changed, 136564 examined...
001:    456 changed, 9305 examined...
002:    124 changed, 2675 examined...
003:     49 changed, 755 examined...
004:     29 changed, 273 examined...
005:     15 changed, 170 examined...
006:      7 changed, 82 examined...
007:      4 changed, 49 examined...
008:      4 changed, 26 examined...
009:      2 changed, 24 examined...
010:      2 changed, 12 examined...
011:      1 changed, 10 examined...
012:      1 changed, 7 examined...
013:      0 changed, 7 examined...
203 labels changed using aseg
000: 57 total segments, 24 labels (176 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 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...
742 vertices marked for relabeling...
742 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 15 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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...
1360 labels changed using aseg
relabeling using gibbs priors...
000:   1943 changed, 135698 examined...
001:    451 changed, 9077 examined...
002:    129 changed, 2550 examined...
003:     56 changed, 780 examined...
004:     28 changed, 342 examined...
005:     20 changed, 165 examined...
006:     17 changed, 101 examined...
007:      7 changed, 95 examined...
008:      6 changed, 43 examined...
009:      4 changed, 31 examined...
010:      2 changed, 24 examined...
011:      1 changed, 14 examined...
012:      0 changed, 9 examined...
184 labels changed using aseg
000: 52 total segments, 19 labels (64 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
692 vertices marked for relabeling...
692 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 15 seconds.
PIDs (19235 19238) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 01:29:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 01:29:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh white 

Waiting for PID 19285 of (19285 19288) to complete...
Waiting for PID 19288 of (19285 19288) 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 0051105 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923
Total vertex volume 252720 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1463    978   2473  2.480 0.636     0.126     0.023       22     1.4  caudalanteriorcingulate
 3916   2648   8515  2.846 0.496     0.117     0.027       39     3.9  caudalmiddlefrontal
 3014   2041   4269  2.027 0.550     0.145     0.038       43     5.1  cuneus
  452    300   1627  3.617 0.979     0.104     0.024        4     0.4  entorhinal
 4240   2870   8640  2.721 0.648     0.134     0.032       61     5.4  fusiform
 7704   5172  14890  2.596 0.514     0.127     0.028       98     8.4  inferiorparietal
 5336   3610  12642  2.831 0.643     0.134     0.033       81     7.1  inferiortemporal
 1558   1024   3042  2.567 0.809     0.133     0.035       22     2.1  isthmuscingulate
 8209   5361  12313  2.074 0.556     0.145     0.042      123    13.4  lateraloccipital
 4111   2682   8461  2.815 0.635     0.132     0.033       62     5.3  lateralorbitofrontal
 4196   2855   6198  2.042 0.619     0.153     0.044       71     7.4  lingual
 1835   1271   4078  2.632 0.689     0.125     0.033       29     2.4  medialorbitofrontal
 5804   3983  13688  2.910 0.659     0.128     0.028       82     6.8  middletemporal
  907    637   1848  2.532 0.594     0.091     0.021        5     0.8  parahippocampal
 3095   1910   6018  2.829 0.567     0.117     0.027       33     3.2  paracentral
 2074   1411   4506  2.810 0.549     0.127     0.030       24     2.6  parsopercularis
  990    674   2583  3.163 0.607     0.141     0.038       15     1.5  parsorbitalis
 2341   1584   4808  2.663 0.506     0.115     0.025       28     2.3  parstriangularis
 2048   1392   2283  1.783 0.458     0.152     0.047       28     3.9  pericalcarine
 8110   5291  12596  2.143 0.638     0.120     0.027       91     8.4  postcentral
 2181   1424   4330  2.591 0.767     0.131     0.031       35     2.7  posteriorcingulate
 7709   4821  14563  2.635 0.682     0.113     0.029       78     9.4  precentral
 5024   3437   9247  2.446 0.551     0.127     0.029       65     6.0  precuneus
 1383    924   3000  2.939 0.737     0.149     0.042       33     2.0  rostralanteriorcingulate
 7067   4969  15148  2.502 0.590     0.139     0.039      114    11.6  rostralmiddlefrontal
10553   7201  24271  2.892 0.608     0.128     0.029      126    12.0  superiorfrontal
 6095   4047  10040  2.230 0.517     0.124     0.028       75     6.6  superiorparietal
 8043   5457  18573  2.906 0.733     0.123     0.027       94     9.1  superiortemporal
 5607   3781  11109  2.677 0.531     0.126     0.028       74     6.2  supramarginal
  799    504   1151  2.081 0.506     0.119     0.032        8     0.9  transversetemporal
 2799   1876   5810  3.123 0.680     0.114     0.029       28     2.9  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 0051105 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688
Total vertex volume 250027 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1004    692   1985  2.555 0.712     0.139     0.029       17     1.0  caudalanteriorcingulate
 3309   2196   6786  2.751 0.554     0.104     0.022       25     2.8  caudalmiddlefrontal
 2835   1856   4063  1.962 0.512     0.147     0.044       41     5.0  cuneus
  442    343   1415  3.098 0.798     0.128     0.038        4     0.6  entorhinal
 3672   2479   7635  2.660 0.589     0.131     0.031       48     4.5  fusiform
 8728   5848  16748  2.529 0.556     0.125     0.030      114    10.1  inferiorparietal
 5156   3429  12513  2.904 0.739     0.128     0.029       68     6.2  inferiortemporal
 1478    961   2979  2.527 0.786     0.123     0.034       19     1.7  isthmuscingulate
 7485   4917  11396  2.094 0.573     0.150     0.048      123    15.7  lateraloccipital
 3703   2522   7439  2.500 0.680     0.150     0.047       77     6.5  lateralorbitofrontal
 4548   3133   7390  2.158 0.577     0.158     0.047       76     8.5  lingual
 2012   1350   4327  2.581 0.761     0.137     0.048       42     3.6  medialorbitofrontal
 5477   3854  12751  2.800 0.619     0.129     0.027       79     6.1  middletemporal
  875    600   1747  2.527 0.594     0.112     0.034       10     1.0  parahippocampal
 2569   1672   4665  2.588 0.601     0.114     0.027       24     2.8  paracentral
 2443   1716   5369  2.763 0.601     0.117     0.027       26     2.8  parsopercularis
 1009    698   2588  2.951 0.558     0.144     0.032       14     1.3  parsorbitalis
 2624   1803   5107  2.629 0.511     0.132     0.033       38     3.2  parstriangularis
 2377   1561   2646  1.759 0.440     0.147     0.047       33     4.4  pericalcarine
 7115   4609  10852  2.072 0.650     0.117     0.029       75     7.9  postcentral
 1784   1168   3628  2.602 0.755     0.130     0.031       28     2.1  posteriorcingulate
 7115   4458  14201  2.818 0.660     0.112     0.033       68     9.8  precentral
 6133   4243  11348  2.447 0.581     0.136     0.030       83     7.5  precuneus
 1074    717   2208  2.853 0.658     0.145     0.034       23     1.4  rostralanteriorcingulate
 7260   5020  14496  2.443 0.593     0.140     0.036      106    11.0  rostralmiddlefrontal
12745   8718  28382  2.783 0.612     0.129     0.031      158    15.4  superiorfrontal
 6396   4152  11045  2.332 0.552     0.130     0.032       82     7.7  superiorparietal
 6818   4590  15587  2.878 0.664     0.115     0.024       68     6.6  superiortemporal
 5947   4015  11748  2.560 0.585     0.124     0.028       74     6.3  supramarginal
  659    427   1063  2.202 0.574     0.164     0.058       14     1.7  transversetemporal
 3014   2026   5921  2.974 0.740     0.118     0.029       31     3.4  insula
PIDs (19285 19288) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 01:29:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 pctsurfcon --s 0051105 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 01:29:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts

 pctsurfcon --s 0051105 --rh-only 

Waiting for PID 19350 of (19350 19362) to complete...
Waiting for PID 19362 of (19350 19362) to complete...

 pctsurfcon --s 0051105 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts/pctsurfcon.log
Sun Oct  8 01:29:54 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-6.0.0/0051105/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-967 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-6.0.0/0051105/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.wm.mgh --regheader 0051105 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 65062
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.wm.mgh
Dim: 136564 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.gm.mgh --projfrac 0.3 --regheader 0051105 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 80207
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.gm.mgh
Dim: 136564 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.w-g.pct.mgh --annot 0051105 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/lh.w-g.pct.mgh --annot 0051105 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/lh.w-g.pct.mgh
Vertex Area is 0.667487 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 0051105 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts/pctsurfcon.log
Sun Oct  8 01:29:54 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-6.0.0/0051105/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-967 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-6.0.0/0051105/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.wm.mgh --regheader 0051105 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 64817
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.wm.mgh
Dim: 135698 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.gm.mgh --projfrac 0.3 --regheader 0051105 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 80080
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.gm.mgh
Dim: 135698 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.w-g.pct.mgh --annot 0051105 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.w-g.pct.mgh --annot 0051105 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.w-g.pct.mgh
Vertex Area is 0.669006 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 (19350 19362) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 01:30:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
735 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
643 voxels changed to hypointensity...
1529 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 01:30:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105

 mri_aparc2aseg --s 0051105 --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 01:30:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105

 mri_aparc2aseg --s 0051105 --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 01:30:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105

 mri_aparc2aseg --s 0051105 --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 19543 of (19543 19546 19549) to complete...
Waiting for PID 19546 of (19543 19546 19549) to complete...
Waiting for PID 19549 of (19543 19546 19549) to complete...

 mri_aparc2aseg --s 0051105 --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 0051105
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.14
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 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 55
rescaling Left_Thalamus from 94 --> 90
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 63
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 88
rescaling Third_Ventricle from 25 --> 14
rescaling Fourth_Ventricle from 22 -->  7
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 55
rescaling Left_Amygdala from 56 --> 55
rescaling CSF from 32 --> 19
rescaling Left_Accumbens_area from 62 --> 56
rescaling Left_VentralDC from 87 --> 83
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 53
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 22
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 54
rescaling Right_Thalamus_Proper from 85 --> 80
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 73
rescaling Right_Pallidum from 97 --> 86
rescaling Right_Hippocampus from 53 --> 53
rescaling Right_Amygdala from 55 --> 54
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 17
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 = 498595
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 191 changed.
pass 2: 9 changed.
pass 3: 2 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051105 --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 0051105
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.14
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 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 55
rescaling Left_Thalamus from 94 --> 90
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 63
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 88
rescaling Third_Ventricle from 25 --> 14
rescaling Fourth_Ventricle from 22 -->  7
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 55
rescaling Left_Amygdala from 56 --> 55
rescaling CSF from 32 --> 19
rescaling Left_Accumbens_area from 62 --> 56
rescaling Left_VentralDC from 87 --> 83
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 53
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 22
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 54
rescaling Right_Thalamus_Proper from 85 --> 80
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 73
rescaling Right_Pallidum from 97 --> 86
rescaling Right_Hippocampus from 53 --> 53
rescaling Right_Amygdala from 55 --> 54
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 17
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 = 498605
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 191 changed.
pass 2: 9 changed.
pass 3: 2 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051105 --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 0051105
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.14
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 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 55
rescaling Left_Thalamus from 94 --> 90
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 63
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 88
rescaling Third_Ventricle from 25 --> 14
rescaling Fourth_Ventricle from 22 -->  7
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 55
rescaling Left_Amygdala from 56 --> 55
rescaling CSF from 32 --> 19
rescaling Left_Accumbens_area from 62 --> 56
rescaling Left_VentralDC from 87 --> 83
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 53
rescaling Right_Lateral_Ventricle from 13 -->  8
rescaling Right_Inf_Lat_Vent from 25 --> 22
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 54
rescaling Right_Thalamus_Proper from 85 --> 80
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 73
rescaling Right_Pallidum from 97 --> 86
rescaling Right_Hippocampus from 53 --> 53
rescaling Right_Amygdala from 55 --> 54
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 17
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 = 498605
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 191 changed.
pass 2: 9 changed.
pass 3: 2 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (19543 19546 19549) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 01:37:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri

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

Sun Oct  8 01:37:43 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-6.0.0/0051105/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-967 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-6.0.0/0051105/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-967
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 01:37:43 CEST 2017 
Ended   at Sun Oct  8 01:37:50 CEST 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 01:37:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105

 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 0051105 


$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 0051105 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1405286 mm^3    (det: 1.386270 )
Computing euler number
orig.nofix lheno =  -78, rheno = -62
orig.nofix lhholes =   40, rhholes = 32
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
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 01:39:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105

 mri_aparc2aseg --s 0051105 --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 0051105
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-6.0.0/0051105/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7908 vertices from left hemi
Ripped 7893 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-6.0.0/0051105/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 920498
Used brute-force search on 303 voxels
Fixing Parahip LH WM
  Found 16 clusters
     0 k 2.000000
     1 k 88.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1092.000000
     5 k 1.000000
     6 k 5.000000
     7 k 1.000000
     8 k 1.000000
     9 k 1.000000
     10 k 25.000000
     11 k 1.000000
     12 k 2.000000
     13 k 1.000000
     14 k 1.000000
     15 k 1.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 3.000000
     1 k 5.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1102.000000
     5 k 7.000000
     6 k 1.000000
     7 k 2.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0051105 --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 0051105 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-967
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1405286 mm^3    (det: 1.386270 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
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-6.0.0/0051105/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 01:48:41 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 20686 of (20686 20692 20698 20704 20708) to complete...
Waiting for PID 20692 of (20686 20692 20698 20704 20708) to complete...
Waiting for PID 20698 of (20686 20692 20698 20704 20708) to complete...
Waiting for PID 20704 of (20686 20692 20698 20704 20708) to complete...
Waiting for PID 20708 of (20686 20692 20698 20704 20708) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 576
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4705
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 952
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8861
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 183
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4260
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 415
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6398
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 748
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6532
mri_label2label: Done

PIDs (20686 20692 20698 20704 20708) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 20756 of (20756 20762 20768 20773) to complete...
Waiting for PID 20762 of (20756 20762 20768 20773) to complete...
Waiting for PID 20768 of (20756 20762 20768 20773) to complete...
Waiting for PID 20773 of (20756 20762 20768 20773) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 365
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4435
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 1175
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14764
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 238
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4419
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 642
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4064
mri_label2label: Done

PIDs (20756 20762 20768 20773) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 20831 of (20831 20837 20843 20848 20854) to complete...
Waiting for PID 20837 of (20831 20837 20843 20848 20854) to complete...
Waiting for PID 20843 of (20831 20837 20843 20848 20854) to complete...
Waiting for PID 20848 of (20831 20837 20843 20848 20854) to complete...
Waiting for PID 20854 of (20831 20837 20843 20848 20854) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 1560
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6201
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 2755
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10869
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 471
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2489
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 34
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1324
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 24
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1223
mri_label2label: Done

PIDs (20831 20837 20843 20848 20854) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 20903 of (20903 20909 20915 20921 20927) to complete...
Waiting for PID 20909 of (20903 20909 20915 20921 20927) to complete...
Waiting for PID 20915 of (20903 20909 20915 20921 20927) to complete...
Waiting for PID 20921 of (20903 20909 20915 20921 20927) to complete...
Waiting for PID 20927 of (20903 20909 20915 20921 20927) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1154
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 389
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2481
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 55
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1559
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 95
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2091
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 395
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2714
mri_label2label: Done

PIDs (20903 20909 20915 20921 20927) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 21002 of (21002 21008 21014 21020) to complete...
Waiting for PID 21008 of (21002 21008 21014 21020) to complete...
Waiting for PID 21014 of (21002 21008 21014 21020) to complete...
Waiting for PID 21020 of (21002 21008 21014 21020) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 84
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1633
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 467
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7502
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 130
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2042
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 249
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1400
mri_label2label: Done

PIDs (21002 21008 21014 21020) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 21064 of (21064 21070 21076 21082 21088) to complete...
Waiting for PID 21070 of (21064 21070 21076 21082 21088) to complete...
Waiting for PID 21076 of (21064 21070 21076 21082 21088) to complete...
Waiting for PID 21082 of (21064 21070 21076 21082 21088) to complete...
Waiting for PID 21088 of (21064 21070 21076 21082 21088) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 1039
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4444
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 1403
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4737
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 77
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 590
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 13
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 483
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564
Number of reverse mapping hits = 3
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 453
mri_label2label: Done

PIDs (21064 21070 21076 21082 21088) completed and logs appended.

 mris_label2annot --s 0051105 --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-6.0.0/0051105/label
cmdline mris_label2annot --s 0051105 --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-967
machine  x86_64
user     ntraut

subject 0051105
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-6.0.0/0051105/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 94361 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051105 --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-6.0.0/0051105/label
cmdline mris_label2annot --s 0051105 --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-967
machine  x86_64
user     ntraut

subject 0051105
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-6.0.0/0051105/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 111447 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 256923
Total vertex volume 252720 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1301    768   2426  2.305 0.576     0.131     0.042       22     1.9  BA1_exvivo
 4705   3136   7467  2.273 0.526     0.111     0.022       39     4.1  BA2_exvivo
 1038    688    894  1.608 0.419     0.137     0.030       10     1.2  BA3a_exvivo
 2447   1587   3295  1.872 0.648     0.114     0.026       26     2.5  BA3b_exvivo
 2110   1156   3874  2.848 0.582     0.111     0.032       22     3.0  BA4a_exvivo
 1321    849   1916  2.337 0.651     0.111     0.027        9     1.6  BA4p_exvivo
 9069   5941  20233  2.876 0.567     0.118     0.029       97    10.1  BA6_exvivo
 2108   1442   5099  2.872 0.545     0.126     0.029       25     2.5  BA44_exvivo
 2992   2052   6162  2.596 0.519     0.124     0.028       38     3.2  BA45_exvivo
 3720   2536   4235  1.708 0.460     0.152     0.047       56     7.3  V1_exvivo
 8285   5484  11624  1.964 0.548     0.159     0.048      144    16.3  V2_exvivo
 2087   1375   4077  2.468 0.537     0.137     0.033       29     2.6  MT_exvivo
  478    306   1494  3.399 0.878     0.097     0.024        4     0.4  perirhinal_exvivo
  542    383   1402  2.983 0.972     0.107     0.023        4     0.5  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051105 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 256923
Total vertex volume 252720 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
  837    471   1538  2.323 0.586     0.143     0.052       16     1.4  BA1_exvivo
 2063   1375   3289  2.194 0.508     0.106     0.020       17     1.7  BA2_exvivo
  864    570    682  1.544 0.373     0.136     0.027        8     0.9  BA3a_exvivo
 1377    948   1485  1.479 0.359     0.095     0.018        9     0.9  BA3b_exvivo
 1994   1111   3391  2.740 0.659     0.107     0.032       19     2.8  BA4a_exvivo
 1038    661   1469  2.325 0.563     0.108     0.027        8     1.1  BA4p_exvivo
 5070   3270  11119  2.846 0.594     0.118     0.030       54     6.2  BA6_exvivo
 1390    951   3367  2.811 0.591     0.134     0.030       20     1.9  BA44_exvivo
 1214    813   2925  2.822 0.451     0.128     0.032       16     1.6  BA45_exvivo
 3936   2695   4544  1.716 0.463     0.152     0.046       59     7.7  V1_exvivo
 4345   2839   5858  1.875 0.533     0.172     0.057       87    10.0  V2_exvivo
  479    344   1045  2.389 0.590     0.137     0.030        7     0.5  MT_exvivo
  244    156    918  3.574 0.895     0.072     0.010        1     0.1  perirhinal_exvivo
  266    184    717  3.115 0.896     0.089     0.024        2     0.2  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 01:51:56 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 21309 of (21309 21315 21321 21326 21333) to complete...
Waiting for PID 21315 of (21309 21315 21321 21326 21333) to complete...
Waiting for PID 21321 of (21309 21315 21321 21326 21333) to complete...
Waiting for PID 21326 of (21309 21315 21321 21326 21333) to complete...
Waiting for PID 21333 of (21309 21315 21321 21326 21333) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 406
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4368
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 561
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7248
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 112
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4092
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 267
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4789
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 457
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6204
mri_label2label: Done

PIDs (21309 21315 21321 21326 21333) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 21388 of (21388 21394 21400 21406) to complete...
Waiting for PID 21394 of (21388 21394 21400 21406) to complete...
Waiting for PID 21400 of (21388 21394 21400 21406) to complete...
Waiting for PID 21406 of (21388 21394 21400 21406) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 266
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4739
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 928
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13184
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 983
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7895
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 1341
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6696
mri_label2label: Done

PIDs (21388 21394 21400 21406) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 21453 of (21453 21459 21465 21470 21476) to complete...
Waiting for PID 21459 of (21453 21459 21465 21470 21476) to complete...
Waiting for PID 21465 of (21453 21459 21465 21470 21476) to complete...
Waiting for PID 21470 of (21453 21459 21465 21470 21476) to complete...
Waiting for PID 21476 of (21453 21459 21465 21470 21476) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 1743
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6470
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 2704
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10720
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 584
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2516
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 78
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1116
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 73
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 825
mri_label2label: Done

PIDs (21453 21459 21465 21470 21476) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 21526 of (21526 21532 21538 21548 21573) to complete...
Waiting for PID 21532 of (21526 21532 21538 21548 21573) to complete...
Waiting for PID 21538 of (21526 21532 21538 21548 21573) to complete...
Waiting for PID 21548 of (21526 21532 21538 21548 21573) to complete...
Waiting for PID 21573 of (21526 21532 21538 21548 21573) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 111
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 987
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 199
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2887
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 28
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1726
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 94
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2277
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 113
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1501
mri_label2label: Done

PIDs (21526 21532 21538 21548 21573) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 21640 of (21640 21646 21652 21658) to complete...
Waiting for PID 21646 of (21640 21646 21652 21658) to complete...
Waiting for PID 21652 of (21640 21646 21652 21658) to complete...
Waiting for PID 21658 of (21640 21646 21652 21658) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1594
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 448
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7407
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 149
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1161
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 210
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1388
mri_label2label: Done

PIDs (21640 21646 21652 21658) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 21720 of (21720 21726 21732 21738 21744) to complete...
Waiting for PID 21726 of (21720 21726 21732 21738 21744) to complete...
Waiting for PID 21732 of (21720 21726 21732 21738 21744) to complete...
Waiting for PID 21738 of (21720 21726 21732 21738 21744) to complete...
Waiting for PID 21744 of (21720 21726 21732 21738 21744) 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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 1171
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4403
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 1423
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4860
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 67
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 335
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 47
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 741
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 0051105 --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 = 0051105
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-6.0.0/0051105/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698
Number of reverse mapping hits = 26
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 317
mri_label2label: Done

PIDs (21720 21726 21732 21738 21744) completed and logs appended.

 mris_label2annot --s 0051105 --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-6.0.0/0051105/label
cmdline mris_label2annot --s 0051105 --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-967
machine  x86_64
user     ntraut

subject 0051105
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-6.0.0/0051105/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 93499 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051105 --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-6.0.0/0051105/label
cmdline mris_label2annot --s 0051105 --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-967
machine  x86_64
user     ntraut

subject 0051105
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-6.0.0/0051105/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 112163 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 253688
Total vertex volume 250027 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
 1111    624   1976  2.304 0.554     0.148     0.045       20     1.8  BA1_exvivo
 3662   2372   5411  2.229 0.496     0.106     0.025       30     3.5  BA2_exvivo
 1026    670    893  1.755 0.361     0.145     0.035       12     1.3  BA3a_exvivo
 1944   1325   2368  1.591 0.491     0.106     0.024       15     1.9  BA3b_exvivo
 1653    951   3227  2.823 0.556     0.108     0.036       17     2.4  BA4a_exvivo
 1223    786   1823  2.441 0.544     0.108     0.032        8     1.7  BA4p_exvivo
 7809   5041  17613  2.913 0.583     0.114     0.031       78     9.6  BA6_exvivo
 3647   2517   8037  2.834 0.593     0.114     0.024       35     3.6  BA44_exvivo
 4762   3336  10471  2.655 0.586     0.139     0.037       74     6.7  BA45_exvivo
 4079   2829   5404  1.817 0.517     0.163     0.052       69     8.6  V1_exvivo
 8072   5329  12214  2.058 0.569     0.158     0.048      133    15.2  V2_exvivo
 2315   1536   3542  2.210 0.463     0.137     0.033       33     3.1  MT_exvivo
  539    401   1938  3.322 0.774     0.128     0.040        5     0.9  perirhinal_exvivo
  357    252   1022  3.005 0.835     0.108     0.023        3     0.3  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 0051105 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 253688
Total vertex volume 250027 (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) = 1405286 mm^3    (det: 1.386270 )
lhCtxGM: 252281.745 251684.000  diff=  597.7  pctdiff= 0.237
rhCtxGM: 249143.146 248405.000  diff=  738.1  pctdiff= 0.296
lhCtxWM: 211113.416 211527.000  diff= -413.6  pctdiff=-0.196
rhCtxWM: 211287.381 211771.000  diff= -483.6  pctdiff=-0.229
SubCortGMVol  57913.000
SupraTentVol  992874.688 (990095.000) diff=2779.688 pctdiff=0.280
SupraTentVolNotVent  984157.688 (981378.000) diff=2779.688 pctdiff=0.282
BrainSegVol  1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136
BrainSegVolNotVent  1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026
BrainSegVolNotVent  1106260.000
CerebellumVol 124736.000
VentChorVol    8717.000
3rd4th5thCSF   2110.000
CSFVol   588.000, OptChiasmVol   146.000
MaskVol 1488370.000
  716    405   1125  2.056 0.559     0.151     0.049       15     1.4  BA1_exvivo
 2052   1310   3106  2.201 0.485     0.100     0.024       15     1.9  BA2_exvivo
  887    586    724  1.732 0.336     0.142     0.034        9     1.2  BA3a_exvivo
 1496   1038   1561  1.431 0.323     0.096     0.020        9     1.2  BA3b_exvivo
  968    565   1901  2.740 0.595     0.119     0.039       11     1.5  BA4a_exvivo
 1089    681   1565  2.448 0.526     0.105     0.036        7     1.8  BA4p_exvivo
 4990   3198  11339  2.944 0.603     0.114     0.032       51     6.4  BA6_exvivo
  944    666   2350  2.909 0.541     0.119     0.026       11     1.2  BA44_exvivo
 1118    804   2683  2.634 0.634     0.143     0.040       20     1.6  BA45_exvivo
 3937   2699   4912  1.786 0.494     0.160     0.051       67     8.1  V1_exvivo
 4474   2939   7076  2.070 0.592     0.170     0.056       85     9.8  V2_exvivo
  303    205    635  2.338 0.462     0.154     0.037        6     0.5  MT_exvivo
  311    223   1158  3.407 0.679     0.111     0.032        2     0.5  perirhinal_exvivo
  250    185    512  2.683 0.527     0.124     0.030        2     0.2  entorhinal_exvivo

Started at Sat Oct 7 17:43:51 CEST 2017 
Ended   at Sun Oct 8 01:54:58 CEST 2017
#@#%# recon-all-run-time-hours 8.185
recon-all -s 0051105 finished without error at Sun Oct  8 01:54:58 CEST 2017