ABIDE_fs-6.0.0/0050166/scripts/recon-all.log

Sat Oct  7 18:00:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050166 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/OHSU/0050166/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050166
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-960 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   50970880   15103956    1772000          0   43361988
-/+ buffers/cache:    7608892   58465944
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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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: 2017/10/07-16:00:46-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-960  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-6.0.0/0050166

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/OHSU/0050166/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/OHSU/0050166/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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/OHSU/0050166/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-6.0.0/0050166/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 18:00:49 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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-6.0.0/0050166/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 18:00:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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-960 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 18:00:58 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.25928
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25928/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25928/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.25928/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:01:01 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.25928/nu0.mnc ./tmp.mri_nu_correct.mni.25928/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25928/0/ -iterations 1000 -distance 50
[ntraut@tars-960:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/] [2017-10-07 18:01:02] 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.25928/0/ ./tmp.mri_nu_correct.mni.25928/nu0.mnc ./tmp.mri_nu_correct.mni.25928/nu1.imp

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Number of iterations: 48 
CV of field change: 0.000968647
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.25928/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.25928/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.25928/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 18:02:16 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 18:02:16 CEST 2017
Ended   at Sat Oct  7 18:02:59 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 18:03:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7128, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/transforms/talairach_avi.log 

TalAviQA: 0.97900
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 18:03:01 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-6.0.0/0050166/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-960 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 18:03:01 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.26820
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26820/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.26820/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.26820/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:03:04 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.26820/nu0.mnc ./tmp.mri_nu_correct.mni.26820/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.26820/0/
[ntraut@tars-960:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/] [2017-10-07 18:03:04] 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.26820/0/ ./tmp.mri_nu_correct.mni.26820/nu0.mnc ./tmp.mri_nu_correct.mni.26820/nu1.imp

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Number of iterations: 43 
CV of field change: 0.000955994
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 18:03:54 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.26820/nu1.mnc ./tmp.mri_nu_correct.mni.26820/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.26820/1/
[ntraut@tars-960:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/] [2017-10-07 18:03:54] 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.26820/1/ ./tmp.mri_nu_correct.mni.26820/nu1.mnc ./tmp.mri_nu_correct.mni.26820/nu2.imp

Processing:.................................................................Done
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Number of iterations: 11 
CV of field change: 0.000962764
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.26820/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.26820/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-6.0.0/0050166/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.26820/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.26820/ones.mgz 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.26820/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.26820/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.26820/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.26820/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26820/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.26820/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.26820/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26820/input.mean.dat 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.26820/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.26820/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.26820/ones.mgz --i ./tmp.mri_nu_correct.mni.26820/nu2.mnc --sum ./tmp.mri_nu_correct.mni.26820/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26820/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.26820/ones.mgz --i ./tmp.mri_nu_correct.mni.26820/nu2.mnc --sum ./tmp.mri_nu_correct.mni.26820/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26820/output.mean.dat 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.26820/ones.mgz
Loading ./tmp.mri_nu_correct.mni.26820/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.26820/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.26820/nu2.mnc ./tmp.mri_nu_correct.mni.26820/nu2.mnc mul .89201430720875566907
Saving result to './tmp.mri_nu_correct.mni.26820/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.26820/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.26820/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.26820/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 9 seconds.
mapping (32, 171) to ( 3, 110)
 
 
Sat Oct  7 18:05:09 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 18:05:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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
 1.07771  -0.02292  -0.00083  -3.31859;
-0.00620   1.03256   0.36399  -11.21619;
-0.00249  -0.27986   1.06246  -20.91811;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 67 (67), valley at 24 (24)
csf peak at 34, setting threshold to 56
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 65 (65), valley at 24 (24)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 54 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 18:07:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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=14.0
skull bounding box = (52, 75, 26) --> (199, 218, 207)
using (101, 123, 117) as brain centroid...
mean wm in atlas = 108, using box (83,105,95) --> (119, 140,139) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 5.1
after smoothing, mri peak at 106, scaling input intensities by 1.019
scaling channel 0 by 1.01887
initial log_p = -4.690
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.452959 @ (9.091, -27.273, -9.091)
max log p =    -4.332222 @ (-13.636, 4.545, 4.545)
max log p =    -4.307806 @ (2.273, -2.273, -2.273)
max log p =    -4.281326 @ (1.136, -1.136, 1.136)
max log p =    -4.265487 @ (1.705, 0.568, 1.705)
max log p =    -4.265487 @ (0.000, 0.000, 0.000)
Found translation: (0.6, -25.6, -4.0): log p = -4.265
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.938, old_max_log_p =-4.265 (thresh=-4.3)
 1.06375   0.00000   0.00000  -7.35639;
 0.00000   1.14215   0.47309  -95.28358;
 0.00000  -0.47309   1.14215   49.44299;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.937, old_max_log_p =-3.938 (thresh=-3.9)
 1.06375   0.00000   0.00000  -7.35639;
 0.00000   1.19413   0.31997  -85.22733;
 0.00000  -0.29597   1.10457   25.87064;
 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=-3.844, old_max_log_p =-3.937 (thresh=-3.9)
 1.08270   0.02741   0.04547  -21.37028;
-0.03739   1.22744   0.36887  -87.82784;
-0.03176  -0.33228   1.07139   43.09039;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.844, old_max_log_p =-3.844 (thresh=-3.8)
 1.08270   0.02741   0.04547  -21.37028;
-0.03739   1.22744   0.36887  -87.82784;
-0.03176  -0.33228   1.07139   43.09039;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.815, old_max_log_p =-3.844 (thresh=-3.8)
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.815, old_max_log_p =-3.815 (thresh=-3.8)
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 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
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.815 (old=-4.690)
transform before final EM align:
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 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
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.3  tol 0.000000
final transform:
 1.08143   0.02714   0.04546  -20.26090;
-0.03693   1.22733   0.35897  -87.21373;
-0.03215  -0.32077   1.07069   40.47495;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1122.133409
mri_em_register stimesec    1.066837
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   157574
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    69
mri_em_register ru_nivcsw   1967
registration took 9 minutes and 50 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=127 y=136 z=112 r=63
      first estimation of the main basin volume: 1071680 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        15 found in the rest of the brain 
      global maximum in x=148, y=126, z=83, Imax=255
      CSF=15, 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=7956312902 voxels, voxel volume =1.000 
                     = 7956312902 mmm3 = 7956313.088 cm3
done.
PostAnalyze...Basin Prior
 5 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=126,y=142, z=107, r=9258 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45494
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1037109166
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1047102914
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1076390735
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1065504788
    OTHER      CSF_MIN=0, CSF_intensity=9, CSF_MAX=60 , nb = 1078758032
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    5,      10,        42,   60
  after  analyzing :    5,      31,        42,   38
   RIGHT_CER   
  before analyzing :    4,      6,        40,   64
  after  analyzing :    4,      28,        40,   37
   LEFT_CER    
  before analyzing :    4,      7,        42,   64
  after  analyzing :    4,      30,        42,   38
  RIGHT_BRAIN  
  before analyzing :    5,      9,        41,   61
  after  analyzing :    5,      30,        41,   37
  LEFT_BRAIN   
  before analyzing :    5,      9,        41,   60
  after  analyzing :    5,      30,        41,   37
     OTHER     
  before analyzing :    60,      58,        57,   91
  after  analyzing :    43,      58,        58,   66
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...60 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 69.560, std = 7.329

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.29, sigma = 3.61
      after  rotation: sse = 2.29, sigma = 3.61
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.30, its var is  2.91   
      before Erosion-Dilatation  0.05% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...45 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1564627 voxels, voxel volume = 1.000 mm3
           = 1564627 mmm3 = 1564.627 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    26.124028
mri_watershed stimesec    0.429934
mri_watershed ru_maxrss   817676
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   210867
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2504
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1381
mri_watershed ru_nivcsw   46
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:17:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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=26.0
skull bounding box = (59, 85, 34) --> (194, 215, 191)
using (104, 128, 113) as brain centroid...
mean wm in atlas = 107, using box (87,112,94) --> (120, 143,132) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 5.0
after smoothing, mri peak at 105, scaling input intensities by 1.019
scaling channel 0 by 1.01905
initial log_p = -4.327
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.093583 @ (-9.091, -27.273, -9.091)
max log p =    -3.919883 @ (4.545, 4.545, 4.545)
max log p =    -3.820370 @ (6.818, -2.273, -2.273)
max log p =    -3.807632 @ (-3.409, 3.409, 3.409)
max log p =    -3.807632 @ (0.000, 0.000, 0.000)
max log p =    -3.807632 @ (0.000, 0.000, 0.000)
Found translation: (-1.1, -21.6, -3.4): log p = -3.808
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.555, old_max_log_p =-3.808 (thresh=-3.8)
 1.06375   0.00000   0.00000  -9.28830;
 0.00000   1.11081   0.29764  -69.60193;
 0.00000  -0.27823   1.03837   31.61154;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.534, old_max_log_p =-3.555 (thresh=-3.6)
 1.06375   0.00000   0.00000  -9.28830;
 0.00000   1.05231   0.14759  -45.02591;
 0.00000  -0.13086   1.06834   7.58784;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5)
 1.06375   0.00000   0.00000  -9.28830;
 0.00000   1.05231   0.14759  -45.02591;
 0.00000  -0.13086   1.06834   7.58784;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.458, old_max_log_p =-3.534 (thresh=-3.5)
 1.04348  -0.00737   0.03151  -7.21278;
-0.00481   1.09398   0.26197  -64.60602;
-0.03188  -0.22790   1.02887   31.50586;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.446, old_max_log_p =-3.458 (thresh=-3.5)
 1.06354   0.00009  -0.00221  -7.18671;
-0.00490   1.11449   0.26688  -66.17905;
 0.00228  -0.22801   1.02935   27.16273;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.446, old_max_log_p =-3.446 (thresh=-3.4)
 1.06354   0.00009  -0.00221  -7.18671;
-0.00490   1.11449   0.26688  -66.17905;
 0.00228  -0.22801   1.02935   27.16273;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.432, old_max_log_p =-3.446 (thresh=-3.4)
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01100  -0.23712   1.02708   28.06864;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.425, old_max_log_p =-3.432 (thresh=-3.4)
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.425, old_max_log_p =-3.425 (thresh=-3.4)
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 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
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.425 (old=-4.327)
transform before final EM align:
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 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
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 013: -log(p) =    3.9  tol 0.000000
final transform:
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1424.951374
mri_em_register stimesec    1.471776
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   158991
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    135
mri_em_register ru_nivcsw   2482
registration took 12 minutes and 10 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:29:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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=27.0
skull bounding box = (60, 85, 34) --> (194, 215, 191)
using (105, 128, 113) as brain centroid...
mean wm in atlas = 107, using box (89,112,94) --> (121, 143,132) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 4.8
after smoothing, mri peak at 105, scaling input intensities by 1.019
scaling channel 0 by 1.01905
using 246344 sample points...
INFO: compute sample coordinates transform
 1.06465   0.01098  -0.00843  -8.66767;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.25000;
 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 (125, 83, 35) --> (188, 187, 190)
Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 1643 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 83, 34) --> (128, 182, 191)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 1519 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 165, 61) --> (172, 202, 113)
Left_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0
0 of 9 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 164, 59) --> (125, 200, 113)
Right_Cerebellum_White_Matter: limiting intensities to 110.0 --> 132.0
5 of 6 (83.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 151, 95) --> (143, 214, 123)
Brain_Stem: limiting intensities to 100.0 --> 132.0
0 of 14 (0.0%) samples deleted
using 3191 total control points for intensity normalization...
bias field = 0.956 +- 0.042
16 of 3186 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (125, 83, 35) --> (188, 187, 190)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
0 of 2320 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 83, 34) --> (128, 182, 191)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
0 of 2069 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 165, 61) --> (172, 202, 113)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 75 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 164, 59) --> (125, 200, 113)
Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 132.0
10 of 61 (16.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 151, 95) --> (143, 214, 123)
Brain_Stem: limiting intensities to 88.0 --> 132.0
10 of 106 (9.4%) samples deleted
using 4631 total control points for intensity normalization...
bias field = 1.022 +- 0.051
36 of 4553 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (125, 83, 35) --> (188, 187, 190)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
0 of 2417 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 83, 34) --> (128, 182, 191)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 2192 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 165, 61) --> (172, 202, 113)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
24 of 123 (19.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 164, 59) --> (125, 200, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
30 of 116 (25.9%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 151, 95) --> (143, 214, 123)
Brain_Stem: limiting intensities to 88.0 --> 132.0
100 of 208 (48.1%) samples deleted
using 5056 total control points for intensity normalization...
bias field = 1.029 +- 0.044
11 of 4808 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 41 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:31:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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) = 1.28 (predicted orig area = 6.2)
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=0.773, neg=0, invalid=762
0001: dt=203.450479, rms=0.726 (6.109%), neg=0, invalid=762
0002: dt=155.026393, rms=0.711 (2.154%), neg=0, invalid=762
0003: dt=221.952000, rms=0.702 (1.146%), neg=0, invalid=762
0004: dt=134.518519, rms=0.698 (0.595%), neg=0, invalid=762
0005: dt=443.904000, rms=0.693 (0.758%), neg=0, invalid=762
0006: dt=110.976000, rms=0.690 (0.401%), neg=0, invalid=762
0007: dt=887.808000, rms=0.685 (0.711%), neg=0, invalid=762
0008: dt=92.480000, rms=0.683 (0.306%), neg=0, invalid=762
0009: dt=2071.552000, rms=0.678 (0.793%), neg=0, invalid=762
0010: dt=110.976000, rms=0.674 (0.531%), neg=0, invalid=762
0011: dt=295.936000, rms=0.674 (0.093%), neg=0, invalid=762
0012: dt=295.936000, rms=0.673 (0.126%), neg=0, invalid=762
0013: dt=295.936000, rms=0.671 (0.218%), neg=0, invalid=762
0014: dt=295.936000, rms=0.668 (0.459%), neg=0, invalid=762
0015: dt=295.936000, rms=0.666 (0.369%), neg=0, invalid=762
0016: dt=295.936000, rms=0.664 (0.288%), neg=0, invalid=762
0017: dt=295.936000, rms=0.661 (0.395%), neg=0, invalid=762
0018: dt=295.936000, rms=0.659 (0.289%), neg=0, invalid=762
0019: dt=295.936000, rms=0.658 (0.178%), neg=0, invalid=762
0020: dt=295.936000, rms=0.657 (0.210%), neg=0, invalid=762
0021: dt=295.936000, rms=0.655 (0.236%), neg=0, invalid=762
0022: dt=295.936000, rms=0.654 (0.096%), neg=0, invalid=762
0023: dt=295.936000, rms=0.654 (0.146%), neg=0, invalid=762
0024: dt=295.936000, rms=0.652 (0.182%), neg=0, invalid=762
0025: dt=295.936000, rms=0.652 (0.115%), neg=0, invalid=762
0026: dt=295.936000, rms=0.651 (0.146%), neg=0, invalid=762
0027: dt=295.936000, rms=0.650 (0.118%), neg=0, invalid=762
0028: dt=295.936000, rms=0.649 (0.093%), neg=0, invalid=762
0029: dt=295.936000, rms=0.649 (0.054%), neg=0, invalid=762
0030: dt=295.936000, rms=0.649 (-0.100%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.649, neg=0, invalid=762
0031: dt=129.472000, rms=0.649 (0.130%), neg=0, invalid=762
0032: dt=517.888000, rms=0.648 (0.127%), neg=0, invalid=762
0033: dt=517.888000, rms=0.647 (0.076%), neg=0, invalid=762
0034: dt=517.888000, rms=0.647 (-0.065%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.654, neg=0, invalid=762
0035: dt=246.802395, rms=0.644 (1.418%), neg=0, invalid=762
0036: dt=93.866667, rms=0.637 (1.175%), neg=0, invalid=762
0037: dt=81.406953, rms=0.633 (0.506%), neg=0, invalid=762
0038: dt=124.416000, rms=0.631 (0.454%), neg=0, invalid=762
0039: dt=78.721550, rms=0.628 (0.439%), neg=0, invalid=762
0040: dt=103.680000, rms=0.626 (0.275%), neg=0, invalid=762
0041: dt=92.812749, rms=0.624 (0.387%), neg=0, invalid=762
0042: dt=62.208000, rms=0.622 (0.201%), neg=0, invalid=762
0043: dt=62.208000, rms=0.621 (0.229%), neg=0, invalid=762
0044: dt=62.208000, rms=0.619 (0.326%), neg=0, invalid=762
0045: dt=62.208000, rms=0.616 (0.425%), neg=0, invalid=762
0046: dt=62.208000, rms=0.614 (0.457%), neg=0, invalid=762
0047: dt=62.208000, rms=0.610 (0.505%), neg=0, invalid=762
0048: dt=62.208000, rms=0.607 (0.485%), neg=0, invalid=762
0049: dt=62.208000, rms=0.605 (0.431%), neg=0, invalid=762
0050: dt=62.208000, rms=0.603 (0.378%), neg=0, invalid=762
0051: dt=62.208000, rms=0.601 (0.319%), neg=0, invalid=762
0052: dt=62.208000, rms=0.599 (0.311%), neg=0, invalid=762
0053: dt=62.208000, rms=0.597 (0.276%), neg=0, invalid=762
0054: dt=62.208000, rms=0.596 (0.230%), neg=0, invalid=762
0055: dt=62.208000, rms=0.595 (0.202%), neg=0, invalid=762
0056: dt=62.208000, rms=0.593 (0.183%), neg=0, invalid=762
0057: dt=62.208000, rms=0.592 (0.192%), neg=0, invalid=762
0058: dt=62.208000, rms=0.591 (0.151%), neg=0, invalid=762
0059: dt=62.208000, rms=0.591 (0.130%), neg=0, invalid=762
0060: dt=62.208000, rms=0.590 (0.109%), neg=0, invalid=762
0061: dt=62.208000, rms=0.589 (0.127%), neg=0, invalid=762
0062: dt=62.208000, rms=0.589 (0.122%), neg=0, invalid=762
0063: dt=62.208000, rms=0.588 (0.105%), neg=0, invalid=762
0064: dt=36.288000, rms=0.588 (0.007%), neg=0, invalid=762
0065: dt=36.288000, rms=0.588 (0.008%), neg=0, invalid=762
0066: dt=36.288000, rms=0.588 (0.012%), neg=0, invalid=762
0067: dt=36.288000, rms=0.588 (0.015%), neg=0, invalid=762
0068: dt=36.288000, rms=0.588 (0.018%), neg=0, invalid=762
0069: dt=36.288000, rms=0.587 (0.017%), neg=0, invalid=762
0070: dt=36.288000, rms=0.587 (0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.588, neg=0, invalid=762
0071: dt=103.680000, rms=0.586 (0.295%), neg=0, invalid=762
0072: dt=82.944000, rms=0.586 (0.068%), neg=0, invalid=762
0073: dt=82.944000, rms=0.586 (0.012%), neg=0, invalid=762
0074: dt=82.944000, rms=0.586 (0.025%), neg=0, invalid=762
0075: dt=82.944000, rms=0.585 (0.024%), neg=0, invalid=762
0076: dt=82.944000, rms=0.585 (-0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.609, neg=0, invalid=762
0077: dt=2.800000, rms=0.608 (0.096%), neg=0, invalid=762
0078: dt=0.500000, rms=0.608 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.609, neg=0, invalid=762
0079: dt=0.000000, rms=0.608 (0.084%), neg=0, invalid=762
0080: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.676, neg=0, invalid=762
0081: dt=5.519126, rms=0.654 (3.217%), neg=0, invalid=762
0082: dt=3.169811, rms=0.653 (0.155%), neg=0, invalid=762
0083: dt=3.169811, rms=0.653 (-0.046%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.653, neg=0, invalid=762
0084: dt=0.000000, rms=0.653 (0.062%), neg=0, invalid=762
0085: dt=0.000000, rms=0.653 (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=0.712, neg=0, invalid=762
0086: dt=1.024000, rms=0.709 (0.426%), neg=0, invalid=762
0087: dt=2.062016, rms=0.704 (0.719%), neg=0, invalid=762
0088: dt=1.024000, rms=0.703 (0.095%), neg=0, invalid=762
0089: dt=1.024000, rms=0.702 (0.213%), neg=0, invalid=762
0090: dt=1.024000, rms=0.701 (0.153%), neg=0, invalid=762
0091: dt=1.024000, rms=0.701 (-0.109%), neg=0, invalid=762
0092: dt=0.024000, rms=0.701 (0.000%), neg=0, invalid=762
0093: dt=0.028000, rms=0.701 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.701, neg=0, invalid=762
0094: dt=1.280000, rms=0.700 (0.158%), neg=0, invalid=762
0095: dt=1.024000, rms=0.700 (0.049%), neg=0, invalid=762
0096: dt=1.024000, rms=0.700 (0.020%), neg=0, invalid=762
0097: dt=1.024000, rms=0.700 (-0.015%), 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
0098: dt=0.847939, rms=0.647 (2.751%), neg=0, invalid=762
0099: dt=0.080000, rms=0.646 (0.145%), neg=0, invalid=762
0100: dt=0.080000, rms=0.646 (-0.082%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.647, neg=0, invalid=762
0101: dt=0.028000, rms=0.646 (0.078%), neg=0, invalid=762
0102: dt=0.001750, rms=0.646 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.12189 (12)
Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (960 voxels, overlap=0.359)
Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (960 voxels, peak = 12), gca=12.1
gca peak = 0.15565 (16)
mri peak = 0.10447 (13)
Right_Lateral_Ventricle (43): linear fit = 0.74 x + 0.0 (939 voxels, overlap=0.516)
Right_Lateral_Ventricle (43): linear fit = 0.74 x + 0.0 (939 voxels, peak = 12), gca=11.8
gca peak = 0.26829 (96)
mri peak = 0.10885 (87)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (837 voxels, overlap=0.237)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (837 voxels, peak = 88), gca=87.8
gca peak = 0.20183 (93)
mri peak = 0.07702 (89)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (781 voxels, overlap=0.433)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (781 voxels, peak = 85), gca=85.1
gca peak = 0.21683 (55)
mri peak = 0.10988 (63)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (811 voxels, overlap=0.716)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (811 voxels, peak = 62), gca=62.4
gca peak = 0.30730 (58)
mri peak = 0.08795 (65)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (658 voxels, overlap=0.866)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (658 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.11764 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52620 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52620 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.11298 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (53387 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (53387 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.05257 (63)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24611 voxels, overlap=0.973)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24611 voxels, peak = 60), gca=60.5
gca peak = 0.15082 (58)
mri peak = 0.05178 (61)
Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (25337 voxels, overlap=0.979)
Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (25337 voxels, peak = 61), gca=60.6
gca peak = 0.14161 (67)
mri peak = 0.12844 (71)
Right_Caudate (50): linear fit = 1.05 x + 0.0 (512 voxels, overlap=0.878)
Right_Caudate (50): linear fit = 1.05 x + 0.0 (512 voxels, peak = 71), gca=70.7
gca peak = 0.15243 (71)
mri peak = 0.12740 (71)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (978 voxels, overlap=0.898)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (978 voxels, peak = 69), gca=69.2
gca peak = 0.13336 (57)
mri peak = 0.05431 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21617 voxels, overlap=0.809)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21617 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.05476 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (25349 voxels, overlap=0.758)
Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (25349 voxels, peak = 64), gca=63.6
gca peak = 0.18181 (84)
mri peak = 0.06558 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8036 voxels, overlap=0.730)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8036 voxels, peak = 89), gca=89.5
gca peak = 0.20573 (83)
mri peak = 0.08283 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7473 voxels, overlap=0.680)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7473 voxels, peak = 90), gca=90.1
gca peak = 0.21969 (57)
mri peak = 0.08989 (63)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (445 voxels, overlap=0.774)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (445 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.09110 (64)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (489 voxels, overlap=0.734)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (489 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.06488 (87)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5192 voxels, overlap=0.987)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5192 voxels, peak = 86), gca=86.3
gca peak = 0.11978 (83)
mri peak = 0.06853 (85)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4456 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4456 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.06940 (80)
Left_Putamen (12): linear fit = 0.98 x + 0.0 (2242 voxels, overlap=0.997)
Left_Putamen (12): linear fit = 0.98 x + 0.0 (2242 voxels, peak = 77), gca=77.0
gca peak = 0.14159 (79)
mri peak = 0.07720 (79)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2487 voxels, overlap=0.997)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2487 voxels, peak = 78), gca=77.8
gca peak = 0.10025 (80)
mri peak = 0.08480 (85)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11771 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11771 voxels, peak = 88), gca=88.4
gca peak = 0.13281 (86)
mri peak = 0.07112 (95)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1338 voxels, overlap=0.728)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1338 voxels, peak = 96), gca=95.9
gca peak = 0.12801 (89)
mri peak = 0.07073 (97)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1546 voxels, overlap=0.851)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1546 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
mri peak = 0.06899 (20)
gca peak = 0.15061 (21)
mri peak = 0.10170 (18)
Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (379 voxels, overlap=0.683)
Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (379 voxels, peak = 17), gca=17.3
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 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 1.09 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.72 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=0.658, neg=0, invalid=762
0103: dt=140.715232, rms=0.651 (1.020%), neg=0, invalid=762
0104: dt=129.472000, rms=0.649 (0.322%), neg=0, invalid=762
0105: dt=369.920000, rms=0.646 (0.423%), neg=0, invalid=762
0106: dt=92.480000, rms=0.645 (0.176%), neg=0, invalid=762
0107: dt=517.888000, rms=0.642 (0.443%), neg=0, invalid=762
0108: dt=73.984000, rms=0.642 (0.092%), neg=0, invalid=762
0109: dt=887.808000, rms=0.640 (0.242%), neg=0, invalid=762
0110: dt=129.472000, rms=0.638 (0.237%), neg=0, invalid=762
0111: dt=92.480000, rms=0.638 (0.031%), neg=0, invalid=762
0112: dt=92.480000, rms=0.638 (0.043%), neg=0, invalid=762
0113: dt=92.480000, rms=0.638 (0.069%), neg=0, invalid=762
0114: dt=92.480000, rms=0.637 (0.083%), neg=0, invalid=762
0115: dt=92.480000, rms=0.636 (0.088%), neg=0, invalid=762
0116: dt=92.480000, rms=0.636 (0.092%), neg=0, invalid=762
0117: dt=92.480000, rms=0.635 (0.095%), neg=0, invalid=762
0118: dt=92.480000, rms=0.635 (0.097%), neg=0, invalid=762
0119: dt=92.480000, rms=0.634 (0.095%), neg=0, invalid=762
0120: dt=92.480000, rms=0.634 (0.086%), neg=0, invalid=762
0121: dt=92.480000, rms=0.633 (0.080%), neg=0, invalid=762
0122: dt=92.480000, rms=0.633 (0.075%), neg=0, invalid=762
0123: dt=92.480000, rms=0.632 (0.071%), neg=0, invalid=762
0124: dt=92.480000, rms=0.632 (0.066%), neg=0, invalid=762
0125: dt=92.480000, rms=0.631 (0.055%), neg=0, invalid=762
0126: dt=92.480000, rms=0.631 (0.047%), neg=0, invalid=762
0127: dt=92.480000, rms=0.631 (0.050%), neg=0, invalid=762
0128: dt=92.480000, rms=0.630 (0.051%), neg=0, invalid=762
0129: dt=92.480000, rms=0.630 (0.048%), neg=0, invalid=762
0130: dt=92.480000, rms=0.630 (0.045%), neg=0, invalid=762
0131: dt=92.480000, rms=0.630 (0.046%), neg=0, invalid=762
0132: dt=92.480000, rms=0.629 (0.048%), neg=0, invalid=762
0133: dt=92.480000, rms=0.629 (0.051%), neg=0, invalid=762
0134: dt=92.480000, rms=0.629 (0.047%), neg=0, invalid=762
0135: dt=92.480000, rms=0.628 (0.043%), neg=0, invalid=762
0136: dt=92.480000, rms=0.628 (0.046%), neg=0, invalid=762
0137: dt=92.480000, rms=0.628 (0.047%), neg=0, invalid=762
0138: dt=92.480000, rms=0.627 (0.048%), neg=0, invalid=762
0139: dt=92.480000, rms=0.627 (0.046%), neg=0, invalid=762
0140: dt=92.480000, rms=0.627 (0.044%), neg=0, invalid=762
0141: dt=92.480000, rms=0.627 (0.046%), neg=0, invalid=762
0142: dt=92.480000, rms=0.626 (0.044%), neg=0, invalid=762
0143: dt=92.480000, rms=0.626 (0.045%), neg=0, invalid=762
0144: dt=92.480000, rms=0.626 (0.042%), neg=0, invalid=762
0145: dt=92.480000, rms=0.626 (0.041%), neg=0, invalid=762
0146: dt=92.480000, rms=0.625 (0.040%), neg=0, invalid=762
0147: dt=92.480000, rms=0.625 (0.041%), neg=0, invalid=762
0148: dt=92.480000, rms=0.625 (0.041%), neg=0, invalid=762
0149: dt=92.480000, rms=0.625 (0.040%), neg=0, invalid=762
0150: dt=92.480000, rms=0.624 (0.038%), neg=0, invalid=762
0151: dt=92.480000, rms=0.624 (0.036%), neg=0, invalid=762
0152: dt=92.480000, rms=0.624 (0.034%), neg=0, invalid=762
0153: dt=92.480000, rms=0.624 (0.033%), neg=0, invalid=762
0154: dt=92.480000, rms=0.623 (0.032%), neg=0, invalid=762
0155: dt=92.480000, rms=0.623 (0.031%), neg=0, invalid=762
0156: dt=92.480000, rms=0.623 (0.030%), neg=0, invalid=762
0157: dt=92.480000, rms=0.623 (0.031%), neg=0, invalid=762
0158: dt=92.480000, rms=0.623 (0.028%), neg=0, invalid=762
0159: dt=92.480000, rms=0.623 (0.027%), neg=0, invalid=762
0160: dt=92.480000, rms=0.622 (0.030%), neg=0, invalid=762
0161: dt=92.480000, rms=0.622 (0.030%), neg=0, invalid=762
0162: dt=92.480000, rms=0.622 (0.027%), neg=0, invalid=762
0163: dt=92.480000, rms=0.622 (0.024%), neg=0, invalid=762
0164: dt=92.480000, rms=0.622 (0.021%), neg=0, invalid=762
0165: dt=3551.232000, rms=0.621 (0.050%), neg=0, invalid=762
0166: dt=73.984000, rms=0.621 (0.014%), neg=0, invalid=762
0167: dt=73.984000, rms=0.621 (0.008%), neg=0, invalid=762
0168: dt=73.984000, rms=0.621 (0.006%), neg=0, invalid=762
0169: dt=73.984000, rms=0.621 (0.007%), neg=0, invalid=762
0170: dt=73.984000, rms=0.621 (0.010%), neg=0, invalid=762
0171: dt=73.984000, rms=0.621 (0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.622, neg=0, invalid=762
0172: dt=129.472000, rms=0.621 (0.148%), neg=0, invalid=762
0173: dt=517.888000, rms=0.620 (0.160%), neg=0, invalid=762
0174: dt=32.368000, rms=0.620 (0.003%), neg=0, invalid=762
0175: dt=32.368000, rms=0.620 (0.004%), neg=0, invalid=762
0176: dt=32.368000, rms=0.620 (0.002%), neg=0, invalid=762
0177: dt=32.368000, rms=0.620 (-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=0.621, neg=0, invalid=762
0178: dt=196.215569, rms=0.614 (1.054%), neg=0, invalid=762
0179: dt=117.615894, rms=0.607 (1.247%), neg=0, invalid=762
0180: dt=63.157895, rms=0.605 (0.326%), neg=0, invalid=762
0181: dt=145.152000, rms=0.601 (0.679%), neg=0, invalid=762
0182: dt=36.288000, rms=0.599 (0.208%), neg=0, invalid=762
0183: dt=497.664000, rms=0.594 (0.879%), neg=0, invalid=762
0184: dt=77.419355, rms=0.590 (0.750%), neg=0, invalid=762
0185: dt=36.288000, rms=0.589 (0.170%), neg=0, invalid=762
0186: dt=248.832000, rms=0.587 (0.246%), neg=0, invalid=762
0187: dt=78.353562, rms=0.585 (0.373%), neg=0, invalid=762
0188: dt=36.288000, rms=0.585 (0.059%), neg=0, invalid=762
0189: dt=580.608000, rms=0.582 (0.467%), neg=0, invalid=762
0190: dt=36.288000, rms=0.580 (0.387%), neg=0, invalid=762
0191: dt=145.152000, rms=0.578 (0.223%), neg=0, invalid=762
0192: dt=36.288000, rms=0.578 (0.050%), neg=0, invalid=762
0193: dt=36.288000, rms=0.578 (0.032%), neg=0, invalid=762
0194: dt=36.288000, rms=0.578 (0.064%), neg=0, invalid=762
0195: dt=36.288000, rms=0.577 (0.102%), neg=0, invalid=762
0196: dt=36.288000, rms=0.576 (0.142%), neg=0, invalid=762
0197: dt=36.288000, rms=0.575 (0.165%), neg=0, invalid=762
0198: dt=36.288000, rms=0.575 (0.032%), neg=0, invalid=762
0199: dt=18.144000, rms=0.575 (0.017%), neg=0, invalid=762
0200: dt=9.072000, rms=0.575 (0.009%), neg=0, invalid=762
0201: dt=2.268000, rms=0.575 (0.002%), neg=0, invalid=762
0202: dt=2.268000, rms=0.575 (0.002%), neg=0, invalid=762
0203: dt=0.567000, rms=0.575 (0.001%), neg=0, invalid=762
0204: dt=0.283500, rms=0.575 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.575, neg=0, invalid=762
0205: dt=145.152000, rms=0.572 (0.629%), neg=0, invalid=762
0206: dt=82.944000, rms=0.571 (0.152%), neg=0, invalid=762
0207: dt=145.152000, rms=0.570 (0.198%), neg=0, invalid=762
0208: dt=36.288000, rms=0.569 (0.086%), neg=0, invalid=762
0209: dt=331.776000, rms=0.568 (0.232%), neg=0, invalid=762
0210: dt=36.288000, rms=0.567 (0.159%), neg=0, invalid=762
0211: dt=145.152000, rms=0.566 (0.115%), neg=0, invalid=762
0212: dt=62.208000, rms=0.566 (0.072%), neg=0, invalid=762
0213: dt=331.776000, rms=0.565 (0.158%), neg=0, invalid=762
0214: dt=36.288000, rms=0.564 (0.115%), neg=0, invalid=762
0215: dt=145.152000, rms=0.564 (0.081%), neg=0, invalid=762
0216: dt=82.944000, rms=0.564 (0.067%), neg=0, invalid=762
0217: dt=103.680000, rms=0.563 (0.056%), neg=0, invalid=762
0218: dt=82.944000, rms=0.563 (0.059%), neg=0, invalid=762
0219: dt=103.680000, rms=0.563 (0.055%), neg=0, invalid=762
0220: dt=82.944000, rms=0.562 (0.052%), neg=0, invalid=762
0221: dt=82.944000, rms=0.562 (0.051%), neg=0, invalid=762
0222: dt=82.944000, rms=0.562 (0.040%), neg=0, invalid=762
0223: dt=82.944000, rms=0.562 (0.052%), neg=0, invalid=762
0224: dt=82.944000, rms=0.561 (0.090%), neg=0, invalid=762
0225: dt=82.944000, rms=0.560 (0.107%), neg=0, invalid=762
0226: dt=82.944000, rms=0.560 (0.167%), neg=0, invalid=762
0227: dt=82.944000, rms=0.559 (0.156%), neg=0, invalid=762
0228: dt=82.944000, rms=0.558 (0.177%), neg=0, invalid=762
0229: dt=82.944000, rms=0.557 (0.200%), neg=0, invalid=762
0230: dt=82.944000, rms=0.555 (0.209%), neg=0, invalid=762
0231: dt=82.944000, rms=0.554 (0.201%), neg=0, invalid=762
0232: dt=82.944000, rms=0.553 (0.189%), neg=0, invalid=762
0233: dt=82.944000, rms=0.552 (0.201%), neg=0, invalid=762
0234: dt=82.944000, rms=0.551 (0.179%), neg=0, invalid=762
0235: dt=82.944000, rms=0.550 (0.174%), neg=0, invalid=762
0236: dt=82.944000, rms=0.549 (0.164%), neg=0, invalid=762
0237: dt=82.944000, rms=0.548 (0.171%), neg=0, invalid=762
0238: dt=82.944000, rms=0.547 (0.153%), neg=0, invalid=762
0239: dt=82.944000, rms=0.547 (0.150%), neg=0, invalid=762
0240: dt=82.944000, rms=0.546 (0.145%), neg=0, invalid=762
0241: dt=82.944000, rms=0.545 (0.146%), neg=0, invalid=762
0242: dt=82.944000, rms=0.544 (0.135%), neg=0, invalid=762
0243: dt=82.944000, rms=0.544 (0.121%), neg=0, invalid=762
0244: dt=82.944000, rms=0.543 (0.124%), neg=0, invalid=762
0245: dt=82.944000, rms=0.542 (0.114%), neg=0, invalid=762
0246: dt=82.944000, rms=0.542 (0.108%), neg=0, invalid=762
0247: dt=82.944000, rms=0.541 (0.110%), neg=0, invalid=762
0248: dt=82.944000, rms=0.541 (0.099%), neg=0, invalid=762
0249: dt=82.944000, rms=0.540 (0.090%), neg=0, invalid=762
0250: dt=82.944000, rms=0.540 (0.085%), neg=0, invalid=762
0251: dt=82.944000, rms=0.539 (0.085%), neg=0, invalid=762
0252: dt=82.944000, rms=0.539 (0.075%), neg=0, invalid=762
0253: dt=82.944000, rms=0.538 (0.075%), neg=0, invalid=762
0254: dt=82.944000, rms=0.538 (0.071%), neg=0, invalid=762
0255: dt=82.944000, rms=0.538 (0.064%), neg=0, invalid=762
0256: dt=82.944000, rms=0.538 (0.007%), neg=0, invalid=762
0257: dt=82.944000, rms=0.538 (0.014%), neg=0, invalid=762
0258: dt=82.944000, rms=0.538 (0.014%), neg=0, invalid=762
0259: dt=36.288000, rms=0.538 (0.003%), neg=0, invalid=762
0260: dt=36.288000, rms=0.538 (0.004%), neg=0, invalid=762
0261: dt=36.288000, rms=0.537 (0.005%), neg=0, invalid=762
0262: dt=36.288000, rms=0.537 (0.006%), neg=0, invalid=762
0263: dt=36.288000, rms=0.537 (0.008%), neg=0, invalid=762
0264: dt=36.288000, rms=0.537 (0.010%), neg=0, invalid=762
0265: dt=36.288000, rms=0.537 (0.011%), neg=0, invalid=762
0266: dt=36.288000, rms=0.537 (0.013%), neg=0, invalid=762
0267: dt=36.288000, rms=0.537 (0.015%), neg=0, invalid=762
0268: dt=36.288000, rms=0.537 (0.015%), neg=0, invalid=762
0269: dt=36.288000, rms=0.537 (0.015%), neg=0, invalid=762
0270: dt=36.288000, rms=0.537 (0.016%), neg=0, invalid=762
0271: dt=36.288000, rms=0.537 (0.017%), neg=0, invalid=762
0272: dt=36.288000, rms=0.537 (0.018%), neg=0, invalid=762
0273: dt=36.288000, rms=0.537 (0.017%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.545, neg=0, invalid=762
0274: dt=2.800000, rms=0.544 (0.168%), neg=0, invalid=762
0275: dt=2.800000, rms=0.544 (0.062%), neg=0, invalid=762
0276: dt=2.800000, rms=0.543 (0.060%), neg=0, invalid=762
0277: dt=0.043750, rms=0.543 (0.001%), neg=0, invalid=762
0278: dt=0.043750, rms=0.543 (0.001%), neg=0, invalid=762
0279: dt=0.010937, rms=0.543 (0.001%), neg=0, invalid=762
0280: dt=0.005469, rms=0.543 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.544, neg=0, invalid=762
0281: dt=93.866667, rms=0.540 (0.799%), neg=0, invalid=762
0282: dt=38.400000, rms=0.536 (0.760%), neg=0, invalid=762
0283: dt=23.915194, rms=0.533 (0.436%), neg=0, invalid=762
0284: dt=32.000000, rms=0.532 (0.276%), neg=0, invalid=762
0285: dt=24.218362, rms=0.530 (0.315%), neg=0, invalid=762
0286: dt=25.600000, rms=0.529 (0.221%), neg=0, invalid=762
0287: dt=25.600000, rms=0.528 (0.245%), neg=0, invalid=762
0288: dt=25.600000, rms=0.527 (0.183%), neg=0, invalid=762
0289: dt=25.600000, rms=0.526 (0.209%), neg=0, invalid=762
0290: dt=11.200000, rms=0.525 (0.111%), neg=0, invalid=762
0291: dt=11.200000, rms=0.525 (0.076%), neg=0, invalid=762
0292: dt=8.000000, rms=0.524 (0.056%), neg=0, invalid=762
0293: dt=0.175000, rms=0.524 (0.001%), neg=0, invalid=762
0294: dt=0.175000, rms=0.524 (0.001%), neg=0, invalid=762
0295: dt=0.021875, rms=0.524 (0.000%), neg=0, invalid=762
0296: dt=0.010937, rms=0.524 (0.000%), neg=0, invalid=762
0297: dt=0.000000, rms=0.524 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.542, neg=0, invalid=762
0298: dt=7.537778, rms=0.539 (0.439%), neg=0, invalid=762
0299: dt=4.032000, rms=0.539 (0.130%), neg=0, invalid=762
0300: dt=11.520000, rms=0.537 (0.248%), neg=0, invalid=762
0301: dt=1.008000, rms=0.537 (0.027%), neg=0, invalid=762
0302: dt=1.008000, rms=0.537 (0.024%), neg=0, invalid=762
0303: dt=1.008000, rms=0.537 (0.023%), neg=0, invalid=762
0304: dt=0.015750, rms=0.537 (0.001%), neg=0, invalid=762
0305: dt=0.011250, rms=0.537 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.538, neg=0, invalid=762
0306: dt=10.832298, rms=0.536 (0.273%), neg=0, invalid=762
0307: dt=21.866667, rms=0.535 (0.158%), neg=0, invalid=762
0308: dt=13.824000, rms=0.534 (0.157%), neg=0, invalid=762
0309: dt=18.526316, rms=0.534 (0.131%), neg=0, invalid=762
0310: dt=0.063000, rms=0.534 (-0.005%), neg=0, invalid=762
0311: dt=0.063000, rms=0.534 (0.001%), neg=0, invalid=762
0312: dt=0.063000, rms=0.534 (0.003%), neg=0, invalid=762
0313: dt=0.063000, rms=0.534 (0.003%), neg=0, invalid=762
0314: dt=0.063000, rms=0.534 (0.002%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.552, neg=0, invalid=762
0315: dt=0.000000, rms=0.552 (0.102%), neg=0, invalid=762
0316: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=762
0317: dt=0.100000, rms=0.552 (-0.096%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.552, neg=0, invalid=762
0318: dt=0.000000, rms=0.552 (0.102%), neg=0, invalid=762
0319: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=762
0320: dt=0.100000, rms=0.552 (-0.078%), 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=0.522, neg=0, invalid=762
0321: dt=0.448000, rms=0.508 (2.722%), neg=0, invalid=762
0322: dt=0.448000, rms=0.504 (0.663%), neg=0, invalid=762
0323: dt=0.448000, rms=0.502 (0.402%), neg=0, invalid=762
0324: dt=0.448000, rms=0.501 (0.264%), neg=0, invalid=762
0325: dt=0.448000, rms=0.500 (0.195%), neg=0, invalid=762
0326: dt=0.448000, rms=0.499 (0.148%), neg=0, invalid=762
0327: dt=0.448000, rms=0.499 (0.121%), neg=0, invalid=762
0328: dt=0.448000, rms=0.498 (0.097%), neg=0, invalid=762
0329: dt=0.448000, rms=0.498 (0.083%), neg=0, invalid=762
0330: dt=0.448000, rms=0.498 (0.068%), neg=0, invalid=762
0331: dt=0.448000, rms=0.497 (0.063%), neg=0, invalid=762
0332: dt=0.448000, rms=0.497 (0.051%), neg=0, invalid=762
0333: dt=0.448000, rms=0.497 (0.048%), neg=0, invalid=762
0334: dt=0.448000, rms=0.497 (0.039%), neg=0, invalid=762
0335: dt=0.448000, rms=0.496 (0.073%), neg=0, invalid=762
0336: dt=0.448000, rms=0.496 (0.093%), neg=0, invalid=762
0337: dt=0.448000, rms=0.495 (0.100%), neg=0, invalid=762
0338: dt=0.448000, rms=0.495 (0.011%), neg=0, invalid=762
0339: dt=0.448000, rms=0.495 (0.011%), neg=0, invalid=762
0340: dt=0.448000, rms=0.495 (0.018%), neg=0, invalid=762
0341: dt=0.448000, rms=0.495 (0.011%), neg=0, invalid=762
0342: dt=0.384000, rms=0.495 (0.009%), neg=0, invalid=762
0343: dt=0.384000, rms=0.495 (0.009%), neg=0, invalid=762
0344: dt=0.384000, rms=0.495 (0.014%), neg=0, invalid=762
0345: dt=0.384000, rms=0.495 (0.008%), neg=0, invalid=762
0346: dt=0.384000, rms=0.495 (0.008%), neg=0, invalid=762
0347: dt=0.384000, rms=0.495 (0.009%), neg=0, invalid=762
0348: dt=0.384000, rms=0.495 (0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.495, neg=0, invalid=762
0349: dt=0.448000, rms=0.490 (0.974%), neg=0, invalid=762
0350: dt=0.448000, rms=0.490 (0.095%), neg=0, invalid=762
0351: dt=0.448000, rms=0.490 (0.023%), neg=0, invalid=762
0352: dt=0.448000, rms=0.490 (-0.003%), 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=0.488, neg=0, invalid=762
0353: dt=8.092000, rms=0.487 (0.121%), neg=0, invalid=762
0354: dt=0.505750, rms=0.487 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.488, neg=0, invalid=762
0355: dt=221.952000, rms=0.487 (0.188%), neg=0, invalid=762
0356: dt=92.480000, rms=0.487 (0.024%), neg=0, invalid=762
0357: dt=92.480000, rms=0.487 (0.018%), neg=0, invalid=762
0358: dt=92.480000, rms=0.486 (0.023%), neg=0, invalid=762
0359: dt=92.480000, rms=0.486 (0.026%), neg=0, invalid=762
0360: dt=92.480000, rms=0.486 (0.023%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0361: dt=92.480000, rms=0.486 (0.028%), neg=0, invalid=762
0362: dt=92.480000, rms=0.486 (0.023%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.487, neg=0, invalid=762
0363: dt=31.104000, rms=0.486 (0.195%), neg=0, invalid=762
0364: dt=36.288000, rms=0.485 (0.042%), neg=0, invalid=762
0365: dt=36.288000, rms=0.485 (0.042%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 11 iterations, nbhd size=1, neg = 0
0366: dt=36.288000, rms=0.485 (0.013%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0367: dt=36.288000, rms=0.485 (-0.054%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.486, neg=0, invalid=762
0368: dt=98.657040, rms=0.483 (0.656%), neg=0, invalid=762
0369: dt=36.288000, rms=0.482 (0.144%), neg=0, invalid=762
0370: dt=36.288000, rms=0.482 (0.063%), neg=0, invalid=762
0371: dt=36.288000, rms=0.481 (0.101%), neg=0, invalid=762
0372: dt=36.288000, rms=0.480 (0.127%), neg=0, invalid=762
0373: dt=36.288000, rms=0.480 (0.145%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0374: dt=36.288000, rms=0.479 (0.142%), neg=0, invalid=762
0375: dt=36.288000, rms=0.478 (0.135%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0376: dt=36.288000, rms=0.478 (0.121%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0377: dt=36.288000, rms=0.477 (0.106%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0378: dt=248.832000, rms=0.477 (0.055%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0379: dt=248.832000, rms=0.477 (-0.432%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.478, neg=0, invalid=762
iter 0, gcam->neg = 26
after 2 iterations, nbhd size=0, neg = 0
0380: dt=38.400000, rms=0.475 (0.679%), neg=0, invalid=762
iter 0, gcam->neg = 25
after 12 iterations, nbhd size=1, neg = 0
0381: dt=54.289655, rms=0.472 (0.578%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 0 iterations, nbhd size=0, neg = 0
0382: dt=21.524664, rms=0.471 (0.305%), neg=0, invalid=762
iter 0, gcam->neg = 44
after 12 iterations, nbhd size=1, neg = 0
0383: dt=125.057471, rms=0.468 (0.562%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0384: dt=20.616915, rms=0.467 (0.257%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 3 iterations, nbhd size=0, neg = 0
0385: dt=44.800000, rms=0.466 (0.265%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0386: dt=25.600000, rms=0.465 (0.059%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0387: dt=25.600000, rms=0.465 (0.090%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 4 iterations, nbhd size=0, neg = 0
0388: dt=25.600000, rms=0.464 (0.161%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 2 iterations, nbhd size=0, neg = 0
0389: dt=25.600000, rms=0.463 (0.178%), neg=0, invalid=762
iter 0, gcam->neg = 17
after 12 iterations, nbhd size=1, neg = 0
0390: dt=25.600000, rms=0.463 (0.187%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 9 iterations, nbhd size=1, neg = 0
0391: dt=25.600000, rms=0.462 (0.193%), neg=0, invalid=762
iter 0, gcam->neg = 27
after 12 iterations, nbhd size=1, neg = 0
0392: dt=25.600000, rms=0.461 (0.188%), neg=0, invalid=762
iter 0, gcam->neg = 20
after 10 iterations, nbhd size=1, neg = 0
0393: dt=25.600000, rms=0.460 (0.171%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 10 iterations, nbhd size=1, neg = 0
0394: dt=25.600000, rms=0.459 (0.159%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 4 iterations, nbhd size=0, neg = 0
0395: dt=25.600000, rms=0.459 (0.148%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 13 iterations, nbhd size=1, neg = 0
0396: dt=25.600000, rms=0.458 (0.140%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 2 iterations, nbhd size=0, neg = 0
0397: dt=25.600000, rms=0.457 (0.132%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 10 iterations, nbhd size=1, neg = 0
0398: dt=25.600000, rms=0.457 (0.090%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 2 iterations, nbhd size=0, neg = 0
0399: dt=25.600000, rms=0.456 (0.116%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 2 iterations, nbhd size=0, neg = 0
0400: dt=25.600000, rms=0.456 (0.086%), neg=0, invalid=762
0401: dt=11.200000, rms=0.456 (0.026%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0402: dt=11.200000, rms=0.456 (0.019%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0403: dt=11.200000, rms=0.456 (0.010%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0404: dt=11.200000, rms=0.456 (0.015%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0405: dt=11.200000, rms=0.456 (0.015%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0406: dt=11.200000, rms=0.456 (0.008%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.456, neg=0, invalid=762
0407: dt=44.800000, rms=0.453 (0.774%), neg=0, invalid=762
0408: dt=25.600000, rms=0.452 (0.165%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0409: dt=25.600000, rms=0.451 (0.109%), neg=0, invalid=762
0410: dt=25.600000, rms=0.451 (0.148%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0411: dt=25.600000, rms=0.450 (0.110%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 10 iterations, nbhd size=1, neg = 0
0412: dt=25.600000, rms=0.450 (0.079%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 8 iterations, nbhd size=1, neg = 0
0413: dt=38.400000, rms=0.450 (0.088%), neg=0, invalid=762
0414: dt=11.200000, rms=0.449 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0415: dt=11.200000, rms=0.449 (0.014%), neg=0, invalid=762
0416: dt=11.200000, rms=0.449 (0.022%), neg=0, invalid=762
0417: dt=11.200000, rms=0.449 (0.027%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0418: dt=11.200000, rms=0.449 (0.031%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0419: dt=11.200000, rms=0.449 (0.034%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0420: dt=11.200000, rms=0.449 (0.030%), neg=0, invalid=762
0421: dt=11.200000, rms=0.449 (0.025%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0422: dt=0.000000, rms=0.457 (0.133%), neg=0, invalid=762
0423: dt=0.000000, rms=0.457 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0424: dt=2.304000, rms=0.457 (0.153%), neg=0, invalid=762
0425: dt=1.008000, rms=0.457 (0.004%), neg=0, invalid=762
0426: dt=1.008000, rms=0.457 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
0427: dt=1.280000, rms=0.470 (0.426%), neg=0, invalid=762
0428: dt=0.448000, rms=0.469 (0.029%), neg=0, invalid=762
0429: dt=0.448000, rms=0.469 (0.003%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0430: dt=0.448000, rms=0.469 (-0.058%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.470, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0431: dt=1.792000, rms=0.468 (0.371%), neg=0, invalid=762
0432: dt=1.024000, rms=0.468 (0.034%), neg=0, invalid=762
0433: dt=1.024000, rms=0.468 (0.003%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0434: dt=1.024000, rms=0.468 (-0.073%), 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=0.460, neg=0, invalid=762
iter 0, gcam->neg = 939
after 14 iterations, nbhd size=1, neg = 0
0435: dt=2.239053, rms=0.429 (6.617%), neg=0, invalid=762
0436: dt=0.080000, rms=0.429 (0.055%), neg=0, invalid=762
0437: dt=0.080000, rms=0.429 (-0.048%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.430, neg=0, invalid=762
0438: dt=0.080000, rms=0.429 (0.205%), neg=0, invalid=762
0439: dt=0.000000, rms=0.429 (-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=0.414, neg=0, invalid=762
0440: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.414, neg=0, invalid=762
0441: dt=129.472000, rms=0.414 (0.014%), neg=0, invalid=762
0442: dt=129.472000, rms=0.414 (0.006%), neg=0, invalid=762
0443: dt=129.472000, rms=0.414 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0444: dt=0.486000, rms=0.415 (0.000%), neg=0, invalid=762
0445: dt=0.035437, rms=0.415 (0.000%), neg=0, invalid=762
0446: dt=0.035437, rms=0.415 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0447: dt=124.416000, rms=0.414 (0.096%), neg=0, invalid=762
0448: dt=145.152000, rms=0.414 (0.107%), neg=0, invalid=762
0449: dt=31.104000, rms=0.414 (0.024%), neg=0, invalid=762
0450: dt=31.104000, rms=0.414 (0.009%), neg=0, invalid=762
0451: dt=31.104000, rms=0.413 (0.015%), neg=0, invalid=762
0452: dt=31.104000, rms=0.413 (0.023%), neg=0, invalid=762
0453: dt=31.104000, rms=0.413 (0.033%), neg=0, invalid=762
0454: dt=31.104000, rms=0.413 (0.037%), neg=0, invalid=762
0455: dt=31.104000, rms=0.413 (0.033%), neg=0, invalid=762
0456: dt=31.104000, rms=0.413 (0.027%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.414, neg=0, invalid=762
0457: dt=11.200000, rms=0.413 (0.108%), neg=0, invalid=762
0458: dt=11.200000, rms=0.413 (0.048%), neg=0, invalid=762
0459: dt=11.200000, rms=0.413 (0.031%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 8 iterations, nbhd size=1, neg = 0
0460: dt=11.200000, rms=0.413 (-0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0461: dt=44.800000, rms=0.410 (0.653%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0462: dt=25.600000, rms=0.409 (0.240%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0463: dt=25.600000, rms=0.408 (0.168%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0464: dt=25.600000, rms=0.407 (0.227%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 10 iterations, nbhd size=1, neg = 0
0465: dt=25.600000, rms=0.406 (0.247%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 9 iterations, nbhd size=1, neg = 0
0466: dt=25.600000, rms=0.406 (0.214%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 0 iterations, nbhd size=0, neg = 0
0467: dt=25.600000, rms=0.405 (0.244%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 10 iterations, nbhd size=1, neg = 0
0468: dt=25.600000, rms=0.404 (0.191%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 13 iterations, nbhd size=1, neg = 0
0469: dt=25.600000, rms=0.403 (0.157%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 10 iterations, nbhd size=1, neg = 0
0470: dt=25.600000, rms=0.403 (0.077%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 19 iterations, nbhd size=1, neg = 0
0471: dt=25.600000, rms=0.403 (0.073%), neg=0, invalid=762
0472: dt=38.400000, rms=0.402 (0.045%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0473: dt=38.400000, rms=0.402 (0.003%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0474: dt=38.400000, rms=0.402 (0.050%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0475: dt=38.400000, rms=0.402 (0.007%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0476: dt=38.400000, rms=0.402 (0.023%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 3 iterations, nbhd size=0, neg = 0
0477: dt=38.400000, rms=0.402 (-0.008%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.407, neg=0, invalid=762
0478: dt=0.000450, rms=0.407 (0.000%), neg=0, invalid=762
0479: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.407, neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0480: dt=2.304000, rms=0.407 (0.011%), neg=0, invalid=762
0481: dt=1.008000, rms=0.407 (0.003%), neg=0, invalid=762
0482: dt=1.008000, rms=0.407 (0.001%), neg=0, invalid=762
0483: dt=1.008000, rms=0.407 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0484: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0485: dt=0.000000, rms=0.415 (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=0.401, neg=0, invalid=762
iter 0, gcam->neg = 549
after 14 iterations, nbhd size=1, neg = 0
0486: dt=1.121372, rms=0.392 (2.165%), neg=0, invalid=762
0487: dt=0.000027, rms=0.392 (0.000%), neg=0, invalid=762
0488: dt=0.000027, rms=0.392 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.392, neg=0, invalid=762
0489: dt=0.112000, rms=0.392 (0.065%), neg=0, invalid=762
0490: dt=0.112000, rms=0.392 (0.028%), neg=0, invalid=762
0491: dt=0.112000, rms=0.392 (0.024%), neg=0, invalid=762
0492: dt=0.112000, rms=0.392 (-0.005%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 43 minutes and 36 seconds.
mri_ca_register utimesec    10789.353768
mri_ca_register stimesec    9.617537
mri_ca_register ru_maxrss   1336680
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4914616
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  62912
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3733
mri_ca_register ru_nivcsw   14109
FSRUNTIME@ mri_ca_register  2.7267 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 21:14:49 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-960
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-6.0.0/0050166/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 6.23
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 = 0.14074 (13)
Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (972 voxels, overlap=0.233)
Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (972 voxels, peak = 12), gca=11.9
gca peak = 0.17677 (13)
mri peak = 0.14153 (13)
Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (1021 voxels, overlap=0.627)
Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (1021 voxels, peak = 10), gca=10.1
gca peak = 0.28129 (95)
mri peak = 0.11348 (87)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (705 voxels, overlap=0.295)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (705 voxels, peak = 87), gca=86.9
gca peak = 0.16930 (96)
mri peak = 0.10014 (87)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (726 voxels, overlap=0.530)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (726 voxels, peak = 90), gca=89.8
gca peak = 0.24553 (55)
mri peak = 0.11411 (63)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1000 voxels, overlap=0.715)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1000 voxels, peak = 62), gca=62.4
gca peak = 0.30264 (59)
mri peak = 0.10224 (63)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (940 voxels, overlap=0.714)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (940 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.12553 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (30454 voxels, overlap=0.643)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (30454 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.11656 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30772 voxels, overlap=0.659)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30772 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.05672 (61)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (35386 voxels, overlap=0.964)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (35386 voxels, peak = 59), gca=59.4
gca peak = 0.11620 (58)
mri peak = 0.05385 (63)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (33819 voxels, overlap=0.917)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (33819 voxels, peak = 59), gca=59.4
gca peak = 0.30970 (66)
mri peak = 0.12304 (74)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (1146 voxels, overlap=0.909)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (1146 voxels, peak = 72), gca=72.3
gca peak = 0.15280 (69)
mri peak = 0.14489 (72)
Left_Caudate (11): linear fit = 0.96 x + 0.0 (1194 voxels, overlap=0.934)
Left_Caudate (11): linear fit = 0.96 x + 0.0 (1194 voxels, peak = 67), gca=66.6
gca peak = 0.13902 (56)
mri peak = 0.05905 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (24998 voxels, overlap=0.797)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (24998 voxels, peak = 64), gca=63.6
gca peak = 0.14777 (55)
mri peak = 0.06106 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (26643 voxels, overlap=0.721)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (26643 voxels, peak = 64), gca=63.5
gca peak = 0.16765 (84)
mri peak = 0.09782 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4953 voxels, overlap=0.810)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4953 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.11036 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4771 voxels, overlap=0.743)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4771 voxels, peak = 89), gca=89.5
gca peak = 0.29869 (57)
mri peak = 0.09282 (63)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (571 voxels, overlap=1.017)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (571 voxels, peak = 62), gca=62.4
gca peak = 0.33601 (57)
mri peak = 0.08778 (63)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (585 voxels, overlap=0.919)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (585 voxels, peak = 64), gca=63.6
gca peak = 0.11131 (90)
mri peak = 0.07493 (87)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4729 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4729 voxels, peak = 88), gca=87.8
gca peak = 0.11793 (83)
mri peak = 0.07237 (85)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4779 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4779 voxels, peak = 84), gca=84.2
gca peak = 0.08324 (81)
mri peak = 0.08619 (76)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (1936 voxels, overlap=0.915)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (1936 voxels, peak = 78), gca=78.2
gca peak = 0.10360 (77)
mri peak = 0.07897 (76)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2140 voxels, overlap=0.988)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2140 voxels, peak = 76), gca=75.8
gca peak = 0.08424 (78)
mri peak = 0.08174 (85)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11341 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11341 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.06877 (95)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1331 voxels, overlap=0.829)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1331 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.07172 (94)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1377 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1377 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.19055 (20)
gca peak = 0.19357 (14)
mri peak = 0.13334 (16)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (308 voxels, overlap=0.795)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (308 voxels, peak = 14), gca=14.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.07 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 0.80 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.26699 (12)
mri peak = 0.14074 (13)
Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (972 voxels, overlap=0.975)
Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (972 voxels, peak = 12), gca=12.4
gca peak = 0.23368 (10)
mri peak = 0.14153 (13)
Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (1021 voxels, overlap=0.823)
Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (1021 voxels, peak = 10), gca=10.4
gca peak = 0.28453 (87)
mri peak = 0.11348 (87)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (705 voxels, overlap=1.001)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (705 voxels, peak = 87), gca=86.6
gca peak = 0.16434 (88)
mri peak = 0.10014 (87)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (726 voxels, overlap=1.006)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (726 voxels, peak = 88), gca=87.6
gca peak = 0.26479 (63)
mri peak = 0.11411 (63)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1000 voxels, overlap=0.948)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1000 voxels, peak = 62), gca=62.1
gca peak = 0.29363 (59)
mri peak = 0.10224 (63)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (940 voxels, overlap=1.009)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (940 voxels, peak = 60), gca=60.5
gca peak = 0.07767 (104)
mri peak = 0.12553 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (30454 voxels, overlap=0.706)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (30454 voxels, peak = 104), gca=104.0
gca peak = 0.07714 (104)
mri peak = 0.11656 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30772 voxels, overlap=0.659)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30772 voxels, peak = 104), gca=104.0
gca peak = 0.09479 (59)
mri peak = 0.05672 (61)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (35386 voxels, overlap=0.968)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (35386 voxels, peak = 59), gca=59.0
gca peak = 0.11303 (59)
mri peak = 0.05385 (63)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (33819 voxels, overlap=0.950)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (33819 voxels, peak = 60), gca=60.5
gca peak = 0.25725 (73)
mri peak = 0.12304 (74)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1146 voxels, overlap=1.003)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1146 voxels, peak = 72), gca=71.9
gca peak = 0.14387 (75)
mri peak = 0.14489 (72)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1194 voxels, overlap=0.983)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1194 voxels, peak = 76), gca=76.1
gca peak = 0.12556 (63)
mri peak = 0.05905 (62)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (24998 voxels, overlap=0.997)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (24998 voxels, peak = 62), gca=62.1
gca peak = 0.12906 (63)
mri peak = 0.06106 (64)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (26643 voxels, overlap=0.990)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (26643 voxels, peak = 62), gca=62.1
gca peak = 0.15888 (90)
mri peak = 0.09782 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4953 voxels, overlap=0.975)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4953 voxels, peak = 90), gca=89.6
gca peak = 0.15222 (90)
mri peak = 0.11036 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4771 voxels, overlap=0.967)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4771 voxels, peak = 91), gca=91.3
gca peak = 0.26686 (62)
mri peak = 0.09282 (63)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (571 voxels, overlap=1.024)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (571 voxels, peak = 62), gca=62.0
gca peak = 0.30423 (64)
mri peak = 0.08778 (63)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (585 voxels, overlap=1.011)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (585 voxels, peak = 64), gca=64.0
gca peak = 0.11017 (86)
mri peak = 0.07493 (87)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4729 voxels, overlap=0.996)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4729 voxels, peak = 86), gca=85.6
gca peak = 0.10950 (82)
mri peak = 0.07237 (85)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4779 voxels, overlap=0.986)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4779 voxels, peak = 82), gca=81.6
gca peak = 0.08891 (78)
mri peak = 0.08619 (76)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (1936 voxels, overlap=0.905)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (1936 voxels, peak = 79), gca=79.2
gca peak = 0.09873 (76)
mri peak = 0.07897 (76)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2140 voxels, overlap=0.987)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2140 voxels, peak = 77), gca=77.1
gca peak = 0.07357 (86)
mri peak = 0.08174 (85)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11341 voxels, overlap=0.805)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11341 voxels, peak = 86), gca=85.6
gca peak = 0.11321 (96)
mri peak = 0.06877 (95)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1331 voxels, overlap=0.887)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1331 voxels, peak = 96), gca=95.5
gca peak = 0.15997 (91)
mri peak = 0.07172 (94)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1377 voxels, overlap=0.975)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1377 voxels, peak = 92), gca=92.4
gca peak = 0.20285 (21)
mri peak = 0.19055 (20)
gca peak = 0.18343 (17)
mri peak = 0.13334 (16)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (308 voxels, overlap=0.780)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (308 voxels, peak = 17), gca=17.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16503 (28)
gca peak Left_Thalamus = 0.63354 (101)
gca peak Third_Ventricle = 0.20285 (21)
gca peak CSF = 0.32583 (29)
gca peak Left_Accumbens_area = 0.78727 (60)
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 = 0.21976 (26)
gca peak Right_Accumbens_area = 0.29943 (71)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.54107 (26)
gca peak WM_hypointensities = 0.07482 (77)
gca peak non_WM_hypointensities = 0.09318 (44)
gca peak Optic_Chiasm = 0.70879 (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 1.03 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
51478 voxels changed in iteration 0 of unlikely voxel relabeling
217 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
31831 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
415 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 58513 changed. image ll: -2.088, PF=0.500
pass 2: 15486 changed. image ll: -2.088, PF=0.500
pass 3: 4469 changed.
31418 voxels changed in iteration 0 of unlikely voxel relabeling
197 voxels changed in iteration 1 of unlikely voxel relabeling
10 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5483 voxels changed in iteration 0 of unlikely voxel relabeling
144 voxels changed in iteration 1 of unlikely voxel relabeling
8 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5325 voxels changed in iteration 0 of unlikely voxel relabeling
65 voxels changed in iteration 1 of unlikely voxel relabeling
5 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4439 voxels changed in iteration 0 of unlikely voxel relabeling
30 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3345.533401
mri_ca_label stimesec    1.415784
mri_ca_label ru_maxrss   2098112
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   651874
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  62904
mri_ca_label ru_oublock  464
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    280
mri_ca_label ru_nivcsw   4797
auto-labeling took 55 minutes and 2 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/transforms/cc_up.lta 0050166 

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-6.0.0/0050166/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/norm.mgz
19608 voxels in left wm, 22820 in right wm, xrange [124, 129]
searching rotation angles z=[-6  8], y=[-6  8]

searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.0  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.5  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 6.0  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.5  
searching scale 1 Z rot 6.7  
searching scale 1 Z rot 7.0  
searching scale 1 Z rot 7.2  
searching scale 1 Z rot 7.5  global minimum found at slice 126.3, rotations (1.16, 0.73)
final transformation (x=126.3, yr=1.158, zr=0.730):
 0.99971  -0.01274   0.02022   1.21092;
 0.01273   0.99992   0.00026   1.37498;
-0.02022   0.00000   0.99980   24.57457;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 125 106
eigenvectors:
-0.00005   0.00078   1.00000;
-0.08204  -0.99663   0.00077;
 0.99663  -0.08204   0.00011;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.5 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 22:10:21 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 22:10:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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...
726 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 67 (67), valley at 22 (22)
csf peak at 34, setting threshold to 56
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 66 (66), valley at 20 (20)
csf peak at 33, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 1 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 22:13:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1515250 voxels in mask (pct=  9.03)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 22:13:26 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 (105.0): 105.7 +- 5.7 [79.0 --> 125.0]
GM (71.0) : 69.8 +- 8.9 [30.0 --> 95.0]
setting bottom of white matter range to 78.6
setting top of gray matter range to 87.5
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...
6709 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5085 filled
331 bright non-wm voxels segmented.
3732 diagonally connected voxels added...
white matter segmentation took 1.6 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 0.56 minutes
reading wm segmentation from wm.seg.mgz...
75 voxels added to wm to prevent paths from MTL structures to cortex
2347 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 40785 voxels turned on, 51125 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  14 found -  14 modified     |    TOTAL:  14
pass   2 (xy+):   0 found -  14 modified     |    TOTAL:  14
pass   1 (xy-):  13 found -  13 modified     |    TOTAL:  27
pass   2 (xy-):   0 found -  13 modified     |    TOTAL:  27
pass   1 (yz+):  13 found -  13 modified     |    TOTAL:  40
pass   2 (yz+):   0 found -  13 modified     |    TOTAL:  40
pass   1 (yz-):  16 found -  16 modified     |    TOTAL:  56
pass   2 (yz-):   0 found -  16 modified     |    TOTAL:  56
pass   1 (xz+):  12 found -  12 modified     |    TOTAL:  68
pass   2 (xz+):   0 found -  12 modified     |    TOTAL:  68
pass   1 (xz-):  15 found -  15 modified     |    TOTAL:  83
pass   2 (xz-):   0 found -  15 modified     |    TOTAL:  83
Iteration Number : 1
pass   1 (+++):  14 found -  14 modified     |    TOTAL:  14
pass   2 (+++):   0 found -  14 modified     |    TOTAL:  14
pass   1 (+++):  27 found -  27 modified     |    TOTAL:  41
pass   2 (+++):   0 found -  27 modified     |    TOTAL:  41
pass   1 (+++):  13 found -  13 modified     |    TOTAL:  54
pass   2 (+++):   0 found -  13 modified     |    TOTAL:  54
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  60
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  60
Iteration Number : 1
pass   1 (++): 150 found - 150 modified     |    TOTAL: 150
pass   2 (++):   0 found - 150 modified     |    TOTAL: 150
pass   1 (+-): 171 found - 171 modified     |    TOTAL: 321
pass   2 (+-):   0 found - 171 modified     |    TOTAL: 321
pass   1 (--): 161 found - 161 modified     |    TOTAL: 482
pass   2 (--):   0 found - 161 modified     |    TOTAL: 482
pass   1 (-+): 170 found - 170 modified     |    TOTAL: 652
pass   2 (-+):   0 found - 170 modified     |    TOTAL: 652
Iteration Number : 2
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   5
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   7
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  11
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  11
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  14
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  14
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:  14
Iteration Number : 2
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 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   1 found -   1 modified     |    TOTAL:   3
pass   2 (--):   0 found -   1 modified     |    TOTAL:   3
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   4
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 818 (out of 486074: 0.168287)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 22:15:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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
 1.06465   0.01098  -0.00843  -8.66768;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.24999;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.06465   0.01098  -0.00843  -8.66768;
-0.01348   1.11384   0.27569  -65.94122;
 0.01098  -0.23656   1.02467   28.24999;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1259 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75)
no need to search
using seed (126, 122, 149), TAL = (2.0, 21.0, 6.0)
talairach voxel to voxel transform
 0.93908  -0.00720   0.00966   7.39162;
 0.01310   0.84917  -0.22836   62.56007;
-0.00703   0.19612   0.92310  -13.20609;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  122,  149) --> (2.0, 21.0, 6.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (2.00, 21.00, 6.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 21.00, 6.00) SRC: (109.37, 133.55, 147.50)
search lh wm seed point around talairach space (-16.00, 21.00, 6.00), SRC: (143.18, 134.02, 147.25)
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 22:16:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   6
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 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 = 7 (out of 231042: 0.003030)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 496 vertices, 575 faces
slice 50: 6742 vertices, 7036 faces
slice 60: 17134 vertices, 17539 faces
slice 70: 29264 vertices, 29682 faces
slice 80: 41647 vertices, 42096 faces
slice 90: 54088 vertices, 54513 faces
slice 100: 65772 vertices, 66227 faces
slice 110: 77853 vertices, 78282 faces
slice 120: 89652 vertices, 90067 faces
slice 130: 100520 vertices, 100927 faces
slice 140: 110974 vertices, 111314 faces
slice 150: 120082 vertices, 120434 faces
slice 160: 128367 vertices, 128614 faces
slice 170: 134746 vertices, 134988 faces
slice 180: 139350 vertices, 139515 faces
slice 190: 141752 vertices, 141810 faces
slice 200: 141796 vertices, 141834 faces
slice 210: 141796 vertices, 141834 faces
slice 220: 141796 vertices, 141834 faces
slice 230: 141796 vertices, 141834 faces
slice 240: 141796 vertices, 141834 faces
slice 250: 141796 vertices, 141834 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...
   141796 voxel in cpt #1: X=-38 [v=141796,e=425502,f=283668] located at (-25.997482, -22.764437, -8.682579)
For the whole surface: X=-38 [v=141796,e=425502,f=283668]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 22:16:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   4
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 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 = 5 (out of 235445: 0.002124)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 491 vertices, 562 faces
slice 50: 6190 vertices, 6448 faces
slice 60: 15808 vertices, 16239 faces
slice 70: 27384 vertices, 27795 faces
slice 80: 39410 vertices, 39849 faces
slice 90: 52125 vertices, 52535 faces
slice 100: 65031 vertices, 65453 faces
slice 110: 76733 vertices, 77164 faces
slice 120: 88583 vertices, 89005 faces
slice 130: 99576 vertices, 99990 faces
slice 140: 110382 vertices, 110745 faces
slice 150: 120536 vertices, 120904 faces
slice 160: 129204 vertices, 129490 faces
slice 170: 135828 vertices, 136085 faces
slice 180: 140962 vertices, 141193 faces
slice 190: 143910 vertices, 144008 faces
slice 200: 144170 vertices, 144224 faces
slice 210: 144170 vertices, 144224 faces
slice 220: 144170 vertices, 144224 faces
slice 230: 144170 vertices, 144224 faces
slice 240: 144170 vertices, 144224 faces
slice 250: 144170 vertices, 144224 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...
   144170 voxel in cpt #1: X=-54 [v=144170,e=432672,f=288448] located at (29.211992, -20.854221, -7.757765)
For the whole surface: X=-54 [v=144170,e=432672,f=288448]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 22:16:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 22:16:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

Waiting for PID 8906 of (8906 8909) to complete...
Waiting for PID 8909 of (8906 8909) 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 (8906 8909) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 22:16:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 22:16:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

Waiting for PID 8951 of (8951 8954) to complete...
Waiting for PID 8954 of (8951 8954) 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 = 45.5 mm, total surface area = 74551 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.155 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.057 (target=0.015)   
step 030: RMS=0.051 (target=0.015)   
step 035: RMS=0.047 (target=0.015)   
step 040: RMS=0.043 (target=0.015)   
step 045: RMS=0.040 (target=0.015)   
step 050: RMS=0.038 (target=0.015)   
step 055: RMS=0.037 (target=0.015)   
step 060: RMS=0.036 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    46.975858
mris_inflate stimesec    0.130980
mris_inflate ru_maxrss   207480
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29833
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  9976
mris_inflate ru_oublock  9992
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5621
mris_inflate ru_nivcsw   3408

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 45.6 mm, total surface area = 76329 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.156 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.089 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.060 (target=0.015)   
step 030: RMS=0.055 (target=0.015)   
step 035: RMS=0.050 (target=0.015)   
step 040: RMS=0.047 (target=0.015)   
step 045: RMS=0.045 (target=0.015)   
step 050: RMS=0.044 (target=0.015)   
step 055: RMS=0.043 (target=0.015)   
step 060: RMS=0.043 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    48.291658
mris_inflate stimesec    0.124981
mris_inflate ru_maxrss   210608
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30614
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10144
mris_inflate ru_oublock  10160
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2267
mris_inflate ru_nivcsw   5288
PIDs (8951 8954) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 22:17:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 22:17:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

Waiting for PID 9023 of (9023 9026) to complete...
Waiting for PID 9026 of (9023 9026) 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 0.97 +- 0.57 (0.00-->7.17) (max @ vno 52462 --> 53690)
face area 0.03 +- 0.03 (-0.05-->0.80)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.319...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.833, avgs=0
005/300: dt: 0.9000, rms radial error=175.573, avgs=0
010/300: dt: 0.9000, rms radial error=175.017, avgs=0
015/300: dt: 0.9000, rms radial error=174.286, avgs=0
020/300: dt: 0.9000, rms radial error=173.454, avgs=0
025/300: dt: 0.9000, rms radial error=172.568, avgs=0
030/300: dt: 0.9000, rms radial error=171.650, avgs=0
035/300: dt: 0.9000, rms radial error=170.715, avgs=0
040/300: dt: 0.9000, rms radial error=169.773, avgs=0
045/300: dt: 0.9000, rms radial error=168.828, avgs=0
050/300: dt: 0.9000, rms radial error=167.883, avgs=0
055/300: dt: 0.9000, rms radial error=166.942, avgs=0
060/300: dt: 0.9000, rms radial error=166.004, avgs=0
065/300: dt: 0.9000, rms radial error=165.071, avgs=0
070/300: dt: 0.9000, rms radial error=164.142, avgs=0
075/300: dt: 0.9000, rms radial error=163.221, avgs=0
080/300: dt: 0.9000, rms radial error=162.305, avgs=0
085/300: dt: 0.9000, rms radial error=161.394, avgs=0
090/300: dt: 0.9000, rms radial error=160.488, avgs=0
095/300: dt: 0.9000, rms radial error=159.587, avgs=0
100/300: dt: 0.9000, rms radial error=158.691, avgs=0
105/300: dt: 0.9000, rms radial error=157.800, avgs=0
110/300: dt: 0.9000, rms radial error=156.915, avgs=0
115/300: dt: 0.9000, rms radial error=156.034, avgs=0
120/300: dt: 0.9000, rms radial error=155.157, avgs=0
125/300: dt: 0.9000, rms radial error=154.286, avgs=0
130/300: dt: 0.9000, rms radial error=153.419, avgs=0
135/300: dt: 0.9000, rms radial error=152.556, avgs=0
140/300: dt: 0.9000, rms radial error=151.699, avgs=0
145/300: dt: 0.9000, rms radial error=150.845, avgs=0
150/300: dt: 0.9000, rms radial error=149.997, avgs=0
155/300: dt: 0.9000, rms radial error=149.153, avgs=0
160/300: dt: 0.9000, rms radial error=148.314, avgs=0
165/300: dt: 0.9000, rms radial error=147.480, avgs=0
170/300: dt: 0.9000, rms radial error=146.650, avgs=0
175/300: dt: 0.9000, rms radial error=145.825, avgs=0
180/300: dt: 0.9000, rms radial error=145.005, avgs=0
185/300: dt: 0.9000, rms radial error=144.189, avgs=0
190/300: dt: 0.9000, rms radial error=143.377, avgs=0
195/300: dt: 0.9000, rms radial error=142.570, avgs=0
200/300: dt: 0.9000, rms radial error=141.767, avgs=0
205/300: dt: 0.9000, rms radial error=140.969, avgs=0
210/300: dt: 0.9000, rms radial error=140.175, avgs=0
215/300: dt: 0.9000, rms radial error=139.385, avgs=0
220/300: dt: 0.9000, rms radial error=138.600, avgs=0
225/300: dt: 0.9000, rms radial error=137.820, avgs=0
230/300: dt: 0.9000, rms radial error=137.043, avgs=0
235/300: dt: 0.9000, rms radial error=136.271, avgs=0
240/300: dt: 0.9000, rms radial error=135.503, avgs=0
245/300: dt: 0.9000, rms radial error=134.739, avgs=0
250/300: dt: 0.9000, rms radial error=133.980, avgs=0
255/300: dt: 0.9000, rms radial error=133.225, avgs=0
260/300: dt: 0.9000, rms radial error=132.474, avgs=0
265/300: dt: 0.9000, rms radial error=131.727, avgs=0
270/300: dt: 0.9000, rms radial error=130.984, avgs=0
275/300: dt: 0.9000, rms radial error=130.246, avgs=0
280/300: dt: 0.9000, rms radial error=129.511, avgs=0
285/300: dt: 0.9000, rms radial error=128.781, avgs=0
290/300: dt: 0.9000, rms radial error=128.055, avgs=0
295/300: dt: 0.9000, rms radial error=127.333, avgs=0
300/300: dt: 0.9000, rms radial error=126.615, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16473.72
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 2 (K=40.0), pass 1, starting sse = 2732.68
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00024
epoch 3 (K=160.0), pass 1, starting sse = 272.12
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00711
epoch 4 (K=640.0), pass 1, starting sse = 18.04
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.13/15 = 0.00838
final distance error %25.23
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    289.231030
mris_sphere stimesec    0.209968
mris_sphere ru_maxrss   207676
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   30391
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10016
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    9257
mris_sphere ru_nivcsw   20792
FSRUNTIME@ mris_sphere  0.0797 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 0.96 +- 0.56 (0.00-->6.82) (max @ vno 110089 --> 110090)
face area 0.03 +- 0.03 (-0.11-->0.84)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.311...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.166, avgs=0
005/300: dt: 0.9000, rms radial error=175.907, avgs=0
010/300: dt: 0.9000, rms radial error=175.351, avgs=0
015/300: dt: 0.9000, rms radial error=174.621, avgs=0
020/300: dt: 0.9000, rms radial error=173.790, avgs=0
025/300: dt: 0.9000, rms radial error=172.900, avgs=0
030/300: dt: 0.9000, rms radial error=171.979, avgs=0
035/300: dt: 0.9000, rms radial error=171.045, avgs=0
040/300: dt: 0.9000, rms radial error=170.103, avgs=0
045/300: dt: 0.9000, rms radial error=169.160, avgs=0
050/300: dt: 0.9000, rms radial error=168.217, avgs=0
055/300: dt: 0.9000, rms radial error=167.277, avgs=0
060/300: dt: 0.9000, rms radial error=166.340, avgs=0
065/300: dt: 0.9000, rms radial error=165.408, avgs=0
070/300: dt: 0.9000, rms radial error=164.481, avgs=0
075/300: dt: 0.9000, rms radial error=163.558, avgs=0
080/300: dt: 0.9000, rms radial error=162.641, avgs=0
085/300: dt: 0.9000, rms radial error=161.728, avgs=0
090/300: dt: 0.9000, rms radial error=160.821, avgs=0
095/300: dt: 0.9000, rms radial error=159.918, avgs=0
100/300: dt: 0.9000, rms radial error=159.021, avgs=0
105/300: dt: 0.9000, rms radial error=158.128, avgs=0
110/300: dt: 0.9000, rms radial error=157.239, avgs=0
115/300: dt: 0.9000, rms radial error=156.356, avgs=0
120/300: dt: 0.9000, rms radial error=155.477, avgs=0
125/300: dt: 0.9000, rms radial error=154.603, avgs=0
130/300: dt: 0.9000, rms radial error=153.734, avgs=0
135/300: dt: 0.9000, rms radial error=152.870, avgs=0
140/300: dt: 0.9000, rms radial error=152.010, avgs=0
145/300: dt: 0.9000, rms radial error=151.155, avgs=0
150/300: dt: 0.9000, rms radial error=150.305, avgs=0
155/300: dt: 0.9000, rms radial error=149.459, avgs=0
160/300: dt: 0.9000, rms radial error=148.618, avgs=0
165/300: dt: 0.9000, rms radial error=147.782, avgs=0
170/300: dt: 0.9000, rms radial error=146.950, avgs=0
175/300: dt: 0.9000, rms radial error=146.123, avgs=0
180/300: dt: 0.9000, rms radial error=145.300, avgs=0
185/300: dt: 0.9000, rms radial error=144.482, avgs=0
190/300: dt: 0.9000, rms radial error=143.669, avgs=0
195/300: dt: 0.9000, rms radial error=142.860, avgs=0
200/300: dt: 0.9000, rms radial error=142.055, avgs=0
205/300: dt: 0.9000, rms radial error=141.255, avgs=0
210/300: dt: 0.9000, rms radial error=140.460, avgs=0
215/300: dt: 0.9000, rms radial error=139.669, avgs=0
220/300: dt: 0.9000, rms radial error=138.882, avgs=0
225/300: dt: 0.9000, rms radial error=138.099, avgs=0
230/300: dt: 0.9000, rms radial error=137.321, avgs=0
235/300: dt: 0.9000, rms radial error=136.548, avgs=0
240/300: dt: 0.9000, rms radial error=135.778, avgs=0
245/300: dt: 0.9000, rms radial error=135.013, avgs=0
250/300: dt: 0.9000, rms radial error=134.253, avgs=0
255/300: dt: 0.9000, rms radial error=133.497, avgs=0
260/300: dt: 0.9000, rms radial error=132.745, avgs=0
265/300: dt: 0.9000, rms radial error=131.998, avgs=0
270/300: dt: 0.9000, rms radial error=131.254, avgs=0
275/300: dt: 0.9000, rms radial error=130.515, avgs=0
280/300: dt: 0.9000, rms radial error=129.780, avgs=0
285/300: dt: 0.9000, rms radial error=129.049, avgs=0
290/300: dt: 0.9000, rms radial error=128.322, avgs=0
295/300: dt: 0.9000, rms radial error=127.599, avgs=0
300/300: dt: 0.9000, rms radial error=126.880, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16853.14
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 2809.52
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 3 (K=160.0), pass 1, starting sse = 289.54
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/11 = 0.00823
epoch 4 (K=640.0), pass 1, starting sse = 18.66
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/12 = 0.00880
final distance error %25.98
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    282.186101
mris_sphere stimesec    0.204968
mris_sphere ru_maxrss   210812
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   30663
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10184
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8897
mris_sphere ru_nivcsw   20544
FSRUNTIME@ mris_sphere  0.0785 hours 1 threads
PIDs (9023 9026) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 22:22:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 22:22:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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


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

#@# Fix Topology lh Sat Oct  7 22:22:21 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050166 lh 

#@# Fix Topology rh Sat Oct  7 22:22:21 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050166 rh 

Waiting for PID 9248 of (9248 9251) to complete...
Waiting for PID 9251 of (9248 9251) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050166 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=-38 (nv=141796, nf=283668, ne=425502, g=20)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
4971 ambiguous faces found in tessellation
segmenting defects...
33 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 9 into 8
32 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4766  (-4.7383)
      -vertex     loglikelihood: -6.3516  (-3.1758)
      -normal dot loglikelihood: -3.6796  (-3.6796)
      -quad curv  loglikelihood: -6.4982  (-3.2491)
      Total Loglikelihood : -26.0059

CORRECTING DEFECT 0 (vertices=49, convex hull=88, v0=2582)
After retessellation of defect 0 (v0=2582), euler #=-28 (138879,415694,276787) : difference with theory (-29) = -1 

CORRECTING DEFECT 1 (vertices=1125, convex hull=373, v0=7986)
L defect detected...
After retessellation of defect 1 (v0=7986), euler #=-28 (139123,416625,277474) : difference with theory (-28) = 0 

CORRECTING DEFECT 2 (vertices=12, convex hull=34, v0=9313)
After retessellation of defect 2 (v0=9313), euler #=-27 (139126,416648,277495) : difference with theory (-27) = 0 

CORRECTING DEFECT 3 (vertices=23, convex hull=52, v0=10905)
After retessellation of defect 3 (v0=10905), euler #=-26 (139136,416699,277537) : difference with theory (-26) = 0 

CORRECTING DEFECT 4 (vertices=57, convex hull=52, v0=14608)
After retessellation of defect 4 (v0=14608), euler #=-25 (139149,416759,277585) : difference with theory (-25) = 0 

CORRECTING DEFECT 5 (vertices=41, convex hull=77, v0=32943)
After retessellation of defect 5 (v0=32943), euler #=-24 (139158,416823,277641) : difference with theory (-24) = 0 

CORRECTING DEFECT 6 (vertices=31, convex hull=39, v0=51623)
After retessellation of defect 6 (v0=51623), euler #=-23 (139162,416850,277665) : difference with theory (-23) = 0 

CORRECTING DEFECT 7 (vertices=8, convex hull=24, v0=58245)
After retessellation of defect 7 (v0=58245), euler #=-22 (139164,416863,277677) : difference with theory (-22) = 0 

CORRECTING DEFECT 8 (vertices=957, convex hull=452, v0=61647)
L defect detected...
After retessellation of defect 8 (v0=61647), euler #=-21 (139376,417741,278344) : difference with theory (-21) = 0 

CORRECTING DEFECT 9 (vertices=27, convex hull=67, v0=70206)
After retessellation of defect 9 (v0=70206), euler #=-20 (139385,417790,278385) : difference with theory (-20) = 0 

CORRECTING DEFECT 10 (vertices=33, convex hull=67, v0=81552)
After retessellation of defect 10 (v0=81552), euler #=-19 (139406,417883,278458) : difference with theory (-19) = 0 

CORRECTING DEFECT 11 (vertices=36, convex hull=29, v0=82787)
After retessellation of defect 11 (v0=82787), euler #=-18 (139411,417907,278478) : difference with theory (-18) = 0 

CORRECTING DEFECT 12 (vertices=18, convex hull=30, v0=89158)
After retessellation of defect 12 (v0=89158), euler #=-17 (139415,417929,278497) : difference with theory (-17) = 0 

CORRECTING DEFECT 13 (vertices=9, convex hull=17, v0=91658)
After retessellation of defect 13 (v0=91658), euler #=-16 (139416,417937,278505) : difference with theory (-16) = 0 

CORRECTING DEFECT 14 (vertices=30, convex hull=32, v0=98921)
After retessellation of defect 14 (v0=98921), euler #=-15 (139421,417962,278526) : difference with theory (-15) = 0 

CORRECTING DEFECT 15 (vertices=13, convex hull=18, v0=101269)
After retessellation of defect 15 (v0=101269), euler #=-14 (139423,417972,278535) : difference with theory (-14) = 0 

CORRECTING DEFECT 16 (vertices=55, convex hull=60, v0=105406)
After retessellation of defect 16 (v0=105406), euler #=-13 (139444,418060,278603) : difference with theory (-13) = 0 

CORRECTING DEFECT 17 (vertices=19, convex hull=44, v0=105421)
After retessellation of defect 17 (v0=105421), euler #=-12 (139453,418102,278637) : difference with theory (-12) = 0 

CORRECTING DEFECT 18 (vertices=20, convex hull=27, v0=106571)
After retessellation of defect 18 (v0=106571), euler #=-11 (139455,418120,278654) : difference with theory (-11) = 0 

CORRECTING DEFECT 19 (vertices=14, convex hull=24, v0=108784)
After retessellation of defect 19 (v0=108784), euler #=-10 (139460,418142,278672) : difference with theory (-10) = 0 

CORRECTING DEFECT 20 (vertices=24, convex hull=36, v0=113609)
After retessellation of defect 20 (v0=113609), euler #=-9 (139465,418169,278695) : difference with theory (-9) = 0 

CORRECTING DEFECT 21 (vertices=25, convex hull=30, v0=113752)
After retessellation of defect 21 (v0=113752), euler #=-8 (139469,418191,278714) : difference with theory (-8) = 0 

CORRECTING DEFECT 22 (vertices=44, convex hull=68, v0=125821)
After retessellation of defect 22 (v0=125821), euler #=-7 (139492,418288,278789) : difference with theory (-7) = 0 

CORRECTING DEFECT 23 (vertices=6, convex hull=19, v0=126326)
After retessellation of defect 23 (v0=126326), euler #=-6 (139493,418297,278798) : difference with theory (-6) = 0 

CORRECTING DEFECT 24 (vertices=40, convex hull=80, v0=128328)
After retessellation of defect 24 (v0=128328), euler #=-5 (139506,418369,278858) : difference with theory (-5) = 0 

CORRECTING DEFECT 25 (vertices=66, convex hull=92, v0=129789)
After retessellation of defect 25 (v0=129789), euler #=-4 (139527,418471,278940) : difference with theory (-4) = 0 

CORRECTING DEFECT 26 (vertices=24, convex hull=55, v0=133353)
After retessellation of defect 26 (v0=133353), euler #=-3 (139545,418546,278998) : difference with theory (-3) = 0 

CORRECTING DEFECT 27 (vertices=6, convex hull=23, v0=134735)
After retessellation of defect 27 (v0=134735), euler #=-2 (139546,418555,279007) : difference with theory (-2) = 0 

CORRECTING DEFECT 28 (vertices=20, convex hull=48, v0=135823)
After retessellation of defect 28 (v0=135823), euler #=-1 (139555,418601,279045) : difference with theory (-1) = 0 

CORRECTING DEFECT 29 (vertices=64, convex hull=45, v0=136377)
After retessellation of defect 29 (v0=136377), euler #=0 (139564,418645,279081) : difference with theory (0) = 0 

CORRECTING DEFECT 30 (vertices=29, convex hull=81, v0=140140)
After retessellation of defect 30 (v0=140140), euler #=1 (139580,418727,279148) : difference with theory (1) = 0 

CORRECTING DEFECT 31 (vertices=13, convex hull=22, v0=140459)
After retessellation of defect 31 (v0=140459), euler #=2 (139581,418737,279158) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.06-->7.77) (max @ vno 13998 --> 19617)
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 (0.06-->7.77) (max @ vno 13998 --> 19617)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
134 mutations (40.6%), 196 crossovers (59.4%), 126 vertices were eliminated
building final representation...
2215 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=139581, nf=279158, ne=418737, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 24.6 minutes
0 defective edges
removing intersecting faces
000: 307 intersecting
001: 9 intersecting
mris_fix_topology utimesec    1473.955924
mris_fix_topology stimesec    0.335948
mris_fix_topology ru_maxrss   460248
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   65698
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  19952
mris_fix_topology ru_oublock  13320
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    633
mris_fix_topology ru_nivcsw   4545
FSRUNTIME@ mris_fix_topology lh  0.4094 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050166 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=-54 (nv=144170, nf=288448, ne=432672, g=28)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
5121 ambiguous faces found in tessellation
segmenting defects...
43 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 33 into 31
42 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4061  (-4.7030)
      -vertex     loglikelihood: -6.2413  (-3.1206)
      -normal dot loglikelihood: -3.6013  (-3.6013)
      -quad curv  loglikelihood: -6.4243  (-3.2122)
      Total Loglikelihood : -25.6730

CORRECTING DEFECT 0 (vertices=5, convex hull=19, v0=2533)
After retessellation of defect 0 (v0=2533), euler #=-39 (141096,422226,281091) : difference with theory (-39) = 0 

CORRECTING DEFECT 1 (vertices=26, convex hull=71, v0=28167)
After retessellation of defect 1 (v0=28167), euler #=-38 (141106,422289,281145) : difference with theory (-38) = 0 

CORRECTING DEFECT 2 (vertices=33, convex hull=68, v0=30265)
After retessellation of defect 2 (v0=30265), euler #=-37 (141123,422367,281207) : difference with theory (-37) = 0 

CORRECTING DEFECT 3 (vertices=126, convex hull=77, v0=30447)
After retessellation of defect 3 (v0=30447), euler #=-36 (141148,422472,281288) : difference with theory (-36) = 0 

CORRECTING DEFECT 4 (vertices=87, convex hull=114, v0=49597)
After retessellation of defect 4 (v0=49597), euler #=-35 (141187,422634,281412) : difference with theory (-35) = 0 

CORRECTING DEFECT 5 (vertices=250, convex hull=217, v0=52971)
After retessellation of defect 5 (v0=52971), euler #=-34 (141224,422844,281586) : difference with theory (-34) = 0 

CORRECTING DEFECT 6 (vertices=50, convex hull=86, v0=55801)
After retessellation of defect 6 (v0=55801), euler #=-33 (141249,422949,281667) : difference with theory (-33) = 0 

CORRECTING DEFECT 7 (vertices=20, convex hull=26, v0=55949)
After retessellation of defect 7 (v0=55949), euler #=-32 (141251,422962,281679) : difference with theory (-32) = 0 

CORRECTING DEFECT 8 (vertices=28, convex hull=65, v0=60848)
After retessellation of defect 8 (v0=60848), euler #=-31 (141264,423022,281727) : difference with theory (-31) = 0 

CORRECTING DEFECT 9 (vertices=11, convex hull=29, v0=67336)
After retessellation of defect 9 (v0=67336), euler #=-30 (141265,423035,281740) : difference with theory (-30) = 0 

CORRECTING DEFECT 10 (vertices=241, convex hull=115, v0=71583)
After retessellation of defect 10 (v0=71583), euler #=-29 (141320,423259,281910) : difference with theory (-29) = 0 

CORRECTING DEFECT 11 (vertices=70, convex hull=75, v0=75458)
After retessellation of defect 11 (v0=75458), euler #=-28 (141350,423379,282001) : difference with theory (-28) = 0 

CORRECTING DEFECT 12 (vertices=6, convex hull=15, v0=76721)
After retessellation of defect 12 (v0=76721), euler #=-27 (141351,423388,282010) : difference with theory (-27) = 0 

CORRECTING DEFECT 13 (vertices=15, convex hull=21, v0=77409)
After retessellation of defect 13 (v0=77409), euler #=-26 (141354,423404,282024) : difference with theory (-26) = 0 

CORRECTING DEFECT 14 (vertices=20, convex hull=28, v0=85881)
After retessellation of defect 14 (v0=85881), euler #=-25 (141356,423419,282038) : difference with theory (-25) = 0 

CORRECTING DEFECT 15 (vertices=13, convex hull=23, v0=90489)
After retessellation of defect 15 (v0=90489), euler #=-24 (141358,423431,282049) : difference with theory (-24) = 0 

CORRECTING DEFECT 16 (vertices=16, convex hull=21, v0=90825)
After retessellation of defect 16 (v0=90825), euler #=-23 (141359,423440,282058) : difference with theory (-23) = 0 

CORRECTING DEFECT 17 (vertices=69, convex hull=32, v0=95332)
After retessellation of defect 17 (v0=95332), euler #=-22 (141366,423469,282081) : difference with theory (-22) = 0 

CORRECTING DEFECT 18 (vertices=78, convex hull=52, v0=97233)
After retessellation of defect 18 (v0=97233), euler #=-21 (141375,423517,282121) : difference with theory (-21) = 0 

CORRECTING DEFECT 19 (vertices=6, convex hull=10, v0=99167)
After retessellation of defect 19 (v0=99167), euler #=-20 (141376,423522,282126) : difference with theory (-20) = 0 

CORRECTING DEFECT 20 (vertices=23, convex hull=41, v0=99567)
After retessellation of defect 20 (v0=99567), euler #=-19 (141387,423569,282163) : difference with theory (-19) = 0 

CORRECTING DEFECT 21 (vertices=23, convex hull=53, v0=101229)
After retessellation of defect 21 (v0=101229), euler #=-18 (141398,423622,282206) : difference with theory (-18) = 0 

CORRECTING DEFECT 22 (vertices=15, convex hull=28, v0=101387)
After retessellation of defect 22 (v0=101387), euler #=-17 (141403,423647,282227) : difference with theory (-17) = 0 

CORRECTING DEFECT 23 (vertices=28, convex hull=29, v0=101440)
After retessellation of defect 23 (v0=101440), euler #=-16 (141407,423672,282249) : difference with theory (-16) = 0 

CORRECTING DEFECT 24 (vertices=40, convex hull=59, v0=103759)
After retessellation of defect 24 (v0=103759), euler #=-15 (141427,423755,282313) : difference with theory (-15) = 0 

CORRECTING DEFECT 25 (vertices=251, convex hull=62, v0=103941)
After retessellation of defect 25 (v0=103941), euler #=-14 (141436,423812,282362) : difference with theory (-14) = 0 

CORRECTING DEFECT 26 (vertices=76, convex hull=92, v0=104991)
After retessellation of defect 26 (v0=104991), euler #=-13 (141459,423920,282448) : difference with theory (-13) = 0 

CORRECTING DEFECT 27 (vertices=8, convex hull=25, v0=106578)
After retessellation of defect 27 (v0=106578), euler #=-12 (141460,423931,282459) : difference with theory (-12) = 0 

CORRECTING DEFECT 28 (vertices=11, convex hull=32, v0=107433)
After retessellation of defect 28 (v0=107433), euler #=-11 (141464,423955,282480) : difference with theory (-11) = 0 

CORRECTING DEFECT 29 (vertices=7, convex hull=22, v0=110390)
After retessellation of defect 29 (v0=110390), euler #=-10 (141465,423965,282490) : difference with theory (-10) = 0 

CORRECTING DEFECT 30 (vertices=293, convex hull=95, v0=111269)
After retessellation of defect 30 (v0=111269), euler #=-10 (141492,424102,282600) : difference with theory (-9) = 1 

CORRECTING DEFECT 31 (vertices=195, convex hull=58, v0=111306)
After retessellation of defect 31 (v0=111306), euler #=-8 (141506,424168,282654) : difference with theory (-8) = 0 

CORRECTING DEFECT 32 (vertices=30, convex hull=57, v0=114234)
After retessellation of defect 32 (v0=114234), euler #=-7 (141524,424242,282711) : difference with theory (-7) = 0 

CORRECTING DEFECT 33 (vertices=62, convex hull=82, v0=120262)
After retessellation of defect 33 (v0=120262), euler #=-6 (141552,424363,282805) : difference with theory (-6) = 0 

CORRECTING DEFECT 34 (vertices=23, convex hull=48, v0=121478)
After retessellation of defect 34 (v0=121478), euler #=-5 (141563,424415,282847) : difference with theory (-5) = 0 

CORRECTING DEFECT 35 (vertices=20, convex hull=32, v0=123295)
After retessellation of defect 35 (v0=123295), euler #=-4 (141566,424432,282862) : difference with theory (-4) = 0 

CORRECTING DEFECT 36 (vertices=248, convex hull=130, v0=124156)
After retessellation of defect 36 (v0=124156), euler #=-3 (141620,424663,283040) : difference with theory (-3) = 0 

CORRECTING DEFECT 37 (vertices=60, convex hull=27, v0=129883)
After retessellation of defect 37 (v0=129883), euler #=-2 (141624,424683,283057) : difference with theory (-2) = 0 

CORRECTING DEFECT 38 (vertices=56, convex hull=90, v0=133541)
After retessellation of defect 38 (v0=133541), euler #=-1 (141634,424746,283111) : difference with theory (-1) = 0 

CORRECTING DEFECT 39 (vertices=331, convex hull=143, v0=134661)
After retessellation of defect 39 (v0=134661), euler #=0 (141704,425025,283321) : difference with theory (0) = 0 

CORRECTING DEFECT 40 (vertices=57, convex hull=99, v0=139127)
After retessellation of defect 40 (v0=139127), euler #=1 (141716,425105,283390) : difference with theory (1) = 0 

CORRECTING DEFECT 41 (vertices=46, convex hull=99, v0=139794)
After retessellation of defect 41 (v0=139794), euler #=2 (141740,425214,283476) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.04-->9.34) (max @ vno 123841 --> 130904)
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 (0.04-->9.34) (max @ vno 123841 --> 130904)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
131 mutations (35.0%), 243 crossovers (65.0%), 146 vertices were eliminated
building final representation...
2430 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=141740, nf=283476, ne=425214, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 22.5 minutes
0 defective edges
removing intersecting faces
000: 234 intersecting
001: 13 intersecting
mris_fix_topology utimesec    1351.878483
mris_fix_topology stimesec    0.224965
mris_fix_topology ru_maxrss   444196
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   55789
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  13592
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    548
mris_fix_topology ru_nivcsw   2285
FSRUNTIME@ mris_fix_topology rh  0.3755 hours 1 threads
PIDs (9248 9251) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 139581 - 418737 + 279158 = 2 --> 0 holes
      F =2V-4:          279158 = 279162-4 (0)
      2E=3F:            837474 = 837474 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 141740 - 425214 + 283476 = 2 --> 0 holes
      F =2V-4:          283476 = 283480-4 (0)
      2E=3F:            850428 = 850428 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 67 intersecting
001: 2 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 6 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 22:47:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050166 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 22:47:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050166 rh 

Waiting for PID 10435 of (10435 10438) to complete...
Waiting for PID 10438 of (10435 10438) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050166 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-6.0.0/0050166/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
25576 bright wm thresholded.
364 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.orig...
computing class statistics...
border white:    247893 voxels (1.48%)
border gray      298590 voxels (1.78%)
WM (98.0): 98.1 +- 9.0 [70.0 --> 110.0]
GM (70.0) : 70.6 +- 9.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 56.8 (was 70)
setting MAX_BORDER_WHITE to 113.0 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 47.6 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 56.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->5.38) (max @ vno 24216 --> 139039)
face area 0.28 +- 0.13 (0.00-->7.63)
mean absolute distance = 0.63 +- 0.73
4360 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=104+-7.8,    GM=66+-6.1
mean inside = 93.3, mean outside = 73.6
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=77.7, 87 (87) missing vertices, mean dist 0.3 [0.5 (%33.1)->0.7 (%66.9))]
%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 +- 0.25 (0.10-->5.40) (max @ vno 24216 --> 139039)
face area 0.28 +- 0.13 (0.00-->6.80)
mean absolute distance = 0.32 +- 0.43
3081 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3422484.2, rms=10.279
001: dt: 0.5000, sse=1927219.8, rms=7.153 (30.408%)
002: dt: 0.5000, sse=1338907.9, rms=5.433 (24.048%)
003: dt: 0.5000, sse=1076133.8, rms=4.445 (18.191%)
004: dt: 0.5000, sse=954683.8, rms=3.902 (12.210%)
005: dt: 0.5000, sse=907177.7, rms=3.663 (6.139%)
006: dt: 0.5000, sse=883027.7, rms=3.531 (3.584%)
rms = 3.49, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=875538.8, rms=3.489 (1.202%)
008: dt: 0.2500, sse=692111.8, rms=2.198 (37.003%)
009: dt: 0.2500, sse=656329.7, rms=1.860 (15.381%)
010: dt: 0.2500, sse=646855.9, rms=1.766 (5.029%)
011: dt: 0.2500, sse=642153.3, rms=1.708 (3.290%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=639886.9, rms=1.680 (1.649%)
013: dt: 0.1250, sse=634286.0, rms=1.612 (4.023%)
rms = 1.60, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=633469.1, rms=1.602 (0.639%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.8, 76 (26) missing vertices, mean dist -0.2 [0.3 (%81.2)->0.3 (%18.8))]
%86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.11-->5.32) (max @ vno 24216 --> 139039)
face area 0.35 +- 0.16 (0.00-->8.86)
mean absolute distance = 0.20 +- 0.30
2967 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1461638.6, rms=5.323
015: dt: 0.5000, sse=993979.2, rms=3.299 (38.018%)
rms = 3.39, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=864824.4, rms=2.458 (25.511%)
017: dt: 0.2500, sse=793809.0, rms=1.832 (25.461%)
018: dt: 0.2500, sse=768239.6, rms=1.546 (15.598%)
019: dt: 0.2500, sse=761468.9, rms=1.458 (5.683%)
020: dt: 0.2500, sse=758238.3, rms=1.407 (3.540%)
rms = 1.39, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=755923.3, rms=1.390 (1.209%)
022: dt: 0.1250, sse=752769.1, rms=1.337 (3.817%)
rms = 1.33, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=753326.0, rms=1.331 (0.409%)
positioning took 1.0 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
mean border=84.1, 88 (12) missing vertices, mean dist -0.1 [0.2 (%72.9)->0.2 (%27.1))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.24 (0.11-->5.41) (max @ vno 24216 --> 139039)
face area 0.34 +- 0.16 (0.00-->8.80)
mean absolute distance = 0.17 +- 0.26
2650 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=942630.1, rms=3.086
024: dt: 0.5000, sse=916334.0, rms=2.888 (6.413%)
rms = 3.24, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=781382.9, rms=1.843 (36.183%)
026: dt: 0.2500, sse=742257.0, rms=1.418 (23.077%)
027: dt: 0.2500, sse=731165.6, rms=1.273 (10.235%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=732133.6, rms=1.258 (1.153%)
029: dt: 0.1250, sse=724178.8, rms=1.178 (6.372%)
rms = 1.17, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=723918.2, rms=1.172 (0.476%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=84.8, 108 (11) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))]
%92 local maxima, % 3 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-6.0.0/0050166/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=733681.6, rms=1.419
rms = 1.74, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=706764.0, rms=1.006 (29.117%)
032: dt: 0.2500, sse=700348.4, rms=0.874 (13.090%)
rms = 0.89, time step reduction 2 of 3 to 0.125...
rms = 0.87, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=699445.5, rms=0.872 (0.321%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 6796 vertices
erasing segment 1 (vno[0] = 55869)
erasing segment 2 (vno[0] = 75943)
erasing segment 3 (vno[0] = 80782)
erasing segment 4 (vno[0] = 99939)
erasing segment 5 (vno[0] = 100806)
erasing segment 6 (vno[0] = 100816)
erasing segment 7 (vno[0] = 100841)
erasing segment 8 (vno[0] = 103920)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.03-->5.42) (max @ vno 24216 --> 139039)
face area 0.34 +- 0.16 (0.00-->8.78)
refinement took 5.5 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050166 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-6.0.0/0050166/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
25576 bright wm thresholded.
364 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.orig...
computing class statistics...
border white:    247893 voxels (1.48%)
border gray      298590 voxels (1.78%)
WM (98.0): 98.1 +- 9.0 [70.0 --> 110.0]
GM (70.0) : 70.6 +- 9.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 58.8 (was 70)
setting MAX_BORDER_WHITE to 113.0 (was 105)
setting MIN_BORDER_WHITE to 68.0 (was 85)
setting MAX_CSF to 49.6 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 58.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 40.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.04-->4.92) (max @ vno 55239 --> 55369)
face area 0.28 +- 0.12 (0.00-->5.74)
mean absolute distance = 0.63 +- 0.76
4868 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=104+-7.0,    GM=68+-6.1
mean inside = 93.4, mean outside = 74.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=79.1, 162 (162) missing vertices, mean dist 0.3 [0.5 (%35.0)->0.7 (%65.0))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.02-->4.82) (max @ vno 141199 --> 57859)
face area 0.28 +- 0.13 (0.00-->3.96)
mean absolute distance = 0.33 +- 0.46
3763 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3093634.5, rms=9.580
001: dt: 0.5000, sse=1758118.2, rms=6.613 (30.969%)
002: dt: 0.5000, sse=1249104.2, rms=5.023 (24.047%)
003: dt: 0.5000, sse=1023895.7, rms=4.129 (17.796%)
004: dt: 0.5000, sse=919399.6, rms=3.634 (11.987%)
005: dt: 0.5000, sse=879559.2, rms=3.421 (5.857%)
006: dt: 0.5000, sse=857225.3, rms=3.294 (3.718%)
rms = 3.26, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=852095.8, rms=3.263 (0.932%)
008: dt: 0.2500, sse=688234.1, rms=2.016 (38.222%)
009: dt: 0.2500, sse=654521.8, rms=1.705 (15.413%)
010: dt: 0.2500, sse=648044.9, rms=1.623 (4.849%)
011: dt: 0.2500, sse=644095.8, rms=1.572 (3.142%)
rms = 1.55, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=642262.1, rms=1.546 (1.648%)
013: dt: 0.1250, sse=637857.1, rms=1.494 (3.318%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=637167.3, rms=1.486 (0.576%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=83.1, 115 (40) missing vertices, mean dist -0.2 [0.3 (%81.0)->0.3 (%19.0))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.08-->5.90) (max @ vno 141199 --> 57859)
face area 0.35 +- 0.16 (0.00-->4.43)
mean absolute distance = 0.21 +- 0.31
3289 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1463152.6, rms=5.254
015: dt: 0.5000, sse=988978.0, rms=3.185 (39.382%)
rms = 3.16, time step reduction 1 of 3 to 0.250...
016: dt: 0.5000, sse=980475.4, rms=3.161 (0.770%)
017: dt: 0.2500, sse=797938.7, rms=1.760 (44.307%)
018: dt: 0.2500, sse=772098.5, rms=1.471 (16.402%)
019: dt: 0.2500, sse=764406.6, rms=1.370 (6.891%)
020: dt: 0.2500, sse=761050.4, rms=1.317 (3.907%)
rms = 1.30, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=760466.9, rms=1.303 (1.034%)
022: dt: 0.1250, sse=755631.1, rms=1.247 (4.283%)
rms = 1.24, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=756791.4, rms=1.244 (0.286%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=85.3, 122 (21) missing vertices, mean dist -0.1 [0.2 (%72.6)->0.2 (%27.4))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.07-->6.35) (max @ vno 141199 --> 57859)
face area 0.34 +- 0.16 (0.00-->4.12)
mean absolute distance = 0.18 +- 0.27
3018 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=931702.1, rms=2.951
024: dt: 0.5000, sse=889984.4, rms=2.631 (10.845%)
rms = 2.98, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=775330.5, rms=1.698 (35.456%)
026: dt: 0.2500, sse=752483.5, rms=1.297 (23.641%)
027: dt: 0.2500, sse=733349.9, rms=1.173 (9.523%)
rms = 1.17, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=733982.5, rms=1.167 (0.504%)
029: dt: 0.1250, sse=727520.8, rms=1.104 (5.439%)
rms = 1.10, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=727389.7, rms=1.103 (0.057%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=86.0, 110 (14) missing vertices, mean dist -0.0 [0.2 (%56.2)->0.2 (%43.8))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=736294.9, rms=1.356
rms = 1.57, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=711714.4, rms=0.967 (28.707%)
032: dt: 0.2500, sse=706761.1, rms=0.814 (15.762%)
rms = 0.85, time step reduction 2 of 3 to 0.125...
rms = 0.81, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=704398.4, rms=0.813 (0.225%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7013 vertices
erasing segment 1 (vno[0] = 101267)
erasing segment 2 (vno[0] = 102419)
erasing segment 3 (vno[0] = 103708)
erasing segment 4 (vno[0] = 103771)
erasing segment 5 (vno[0] = 103787)
erasing segment 6 (vno[0] = 105901)
erasing segment 7 (vno[0] = 109520)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.04-->6.42) (max @ vno 57859 --> 141199)
face area 0.33 +- 0.15 (0.00-->4.03)
refinement took 5.5 minutes
PIDs (10435 10438) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 22:52:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 22:52:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

Waiting for PID 10666 of (10666 10669) to complete...
Waiting for PID 10669 of (10666 10669) 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 (10666 10669) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 22:52:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 22:52:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 10710 of (10710 10713) to complete...
Waiting for PID 10713 of (10710 10713) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 45.7 mm, total surface area = 85211 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.126 (target=0.015)   
step 010: RMS=0.095 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.066 (target=0.015)   
step 025: RMS=0.056 (target=0.015)   
step 030: RMS=0.048 (target=0.015)   
step 035: RMS=0.040 (target=0.015)   
step 040: RMS=0.034 (target=0.015)   
step 045: RMS=0.030 (target=0.015)   
step 050: RMS=0.028 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    45.629063
mris_inflate stimesec    0.100984
mris_inflate ru_maxrss   204392
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30211
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10936
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2046
mris_inflate ru_nivcsw   3352

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 45.7 mm, total surface area = 86427 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.175 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.054 (target=0.015)   
step 030: RMS=0.047 (target=0.015)   
step 035: RMS=0.039 (target=0.015)   
step 040: RMS=0.035 (target=0.015)   
step 045: RMS=0.030 (target=0.015)   
step 050: RMS=0.028 (target=0.015)   
step 055: RMS=0.026 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    46.596916
mris_inflate stimesec    0.113982
mris_inflate ru_maxrss   207276
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29909
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  9976
mris_inflate ru_oublock  11104
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2325
mris_inflate ru_nivcsw   3448
PIDs (10710 10713) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 22:53:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 22:53:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 10825 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10828 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10831 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10834 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10837 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10840 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10843 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10846 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10849 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10853 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10856 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...
Waiting for PID 10859 of (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 2.756*4pi (34.639) --> -2 handles
ICI = 155.0, FI = 1872.9, variation=28603.454
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
164 vertices thresholded to be in k1 ~ [-0.30 0.34], k2 ~ [-0.12 0.07]
total integrated curvature = 0.475*4pi (5.964) --> 1 handles
ICI = 1.5, FI = 9.7, variation=165.031
129 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
135 vertices thresholded to be in [-0.16 0.13]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 2.036*4pi (25.588) --> -1 handles
ICI = 156.5, FI = 1844.8, variation=28324.389
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
157 vertices thresholded to be in k1 ~ [-0.37 0.29], k2 ~ [-0.12 0.10]
total integrated curvature = 0.480*4pi (6.031) --> 1 handles
ICI = 1.5, FI = 10.3, variation=174.781
135 vertices thresholded to be in [-0.02 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
128 vertices thresholded to be in [-0.15 0.13]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023
done.
PIDs (10825 10828 10831 10834 10837 10840 10843 10846 10849 10853 10856 10859) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 22:54:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050166 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      [ 0050166/lh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 245 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.346507
WARN:    S explicit min:                          0.000000	vertex = 221

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 22:55:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050166 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      [ 0050166/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                      [ 278 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.031167
WARN:    S explicit min:                          0.000000	vertex = 489
#--------------------------------------------
#@# Sphere lh Sat Oct  7 22:55:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 22:55:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 11030 of (11030 11033) to complete...
Waiting for PID 11033 of (11030 11033) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0.296...
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 %20.40
pass 1: epoch 2 of 3 starting distance error %20.38
unfolding complete - removing small folds...
starting distance error %20.29
removing remaining folds...
final distance error %20.32
MRISunfold() return, current seed 1234
-01: dt=0.0000, 140 negative triangles
189: dt=0.9900, 140 negative triangles
190: dt=0.9900, 69 negative triangles
191: dt=0.9900, 50 negative triangles
192: dt=0.9900, 35 negative triangles
193: dt=0.9900, 23 negative triangles
194: dt=0.9900, 18 negative triangles
195: dt=0.9900, 22 negative triangles
196: dt=0.9900, 15 negative triangles
197: dt=0.9900, 13 negative triangles
198: dt=0.9900, 16 negative triangles
199: dt=0.9900, 13 negative triangles
200: dt=0.9900, 7 negative triangles
201: dt=0.9900, 4 negative triangles
202: dt=0.9900, 6 negative triangles
203: dt=0.9900, 3 negative triangles
204: dt=0.9900, 3 negative triangles
205: dt=0.9900, 6 negative triangles
206: dt=0.9900, 4 negative triangles
207: dt=0.9900, 1 negative triangles
208: dt=0.9900, 3 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.05 hours
mris_sphere utimesec    3817.723617
mris_sphere stimesec    2.254657
mris_sphere ru_maxrss   287648
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   50656
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9848
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    149199
mris_sphere ru_nivcsw   295950
FSRUNTIME@ mris_sphere  1.0523 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0.290...
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 %20.33
pass 1: epoch 2 of 3 starting distance error %20.25
unfolding complete - removing small folds...
starting distance error %20.19
removing remaining folds...
final distance error %20.22
MRISunfold() return, current seed 1234
-01: dt=0.0000, 122 negative triangles
183: dt=0.9900, 122 negative triangles
184: dt=0.9900, 52 negative triangles
185: dt=0.9900, 44 negative triangles
186: dt=0.9900, 44 negative triangles
187: dt=0.9900, 39 negative triangles
188: dt=0.9900, 47 negative triangles
189: dt=0.9900, 32 negative triangles
190: dt=0.9900, 34 negative triangles
191: dt=0.9900, 34 negative triangles
192: dt=0.9900, 23 negative triangles
193: dt=0.9900, 26 negative triangles
194: dt=0.9900, 23 negative triangles
195: dt=0.9900, 16 negative triangles
196: dt=0.9900, 18 negative triangles
197: dt=0.9900, 12 negative triangles
198: dt=0.9900, 16 negative triangles
199: dt=0.9900, 15 negative triangles
200: dt=0.9900, 9 negative triangles
201: dt=0.9900, 8 negative triangles
202: dt=0.9900, 6 negative triangles
203: dt=0.9900, 5 negative triangles
204: dt=0.9900, 7 negative triangles
205: dt=0.9900, 5 negative triangles
206: dt=0.9900, 3 negative triangles
207: dt=0.9900, 1 negative triangles
208: dt=0.9900, 4 negative triangles
209: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.04 hours
mris_sphere utimesec    3751.546678
mris_sphere stimesec    1.965701
mris_sphere ru_maxrss   291860
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   51209
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10016
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    126185
mris_sphere ru_nivcsw   306900
FSRUNTIME@ mris_sphere  1.0422 hours 1 threads
PIDs (11030 11033) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sat Oct  7 23:58:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 23:58:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 13597 of (13597 13600) to complete...
Waiting for PID 13600 of (13597 13600) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 5.670
curvature mean = 0.035, std = 0.820
curvature mean = 0.021, std = 0.860
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 309998.8, tmin=1.1725
  d=32.00 min @ (0.00, 8.00, -8.00) sse = 254786.1, tmin=2.3613
  d=16.00 min @ (0.00, -4.00, 4.00) sse = 217039.2, tmin=3.5602
  d=8.00 min @ (0.00, 0.00, -2.00) sse = 210428.9, tmin=4.7879
  d=4.00 min @ (0.00, 1.00, 1.00) sse = 208935.5, tmin=6.0221
  d=2.00 min @ (0.00, -0.50, -0.50) sse = 208101.4, tmin=7.2306
  d=1.00 min @ (0.25, 0.25, 0.00) sse = 207934.6, tmin=8.4582
  d=0.50 min @ (-0.12, 0.00, 0.00) sse = 207916.7, tmin=9.6838
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   9.68 min
curvature mean = 0.002, std = 0.835
curvature mean = 0.007, std = 0.947
curvature mean = 0.001, std = 0.846
curvature mean = 0.003, std = 0.979
curvature mean = 0.000, std = 0.849
curvature mean = 0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.032, std = 0.315
curvature mean = 0.042, std = 0.250
curvature mean = 0.070, std = 0.327
curvature mean = 0.034, std = 0.309
curvature mean = 0.042, std = 0.504
curvature mean = 0.033, std = 0.337
curvature mean = 0.023, std = 0.641
curvature mean = 0.033, std = 0.348
curvature mean = 0.008, std = 0.754
MRISregister() return, current seed 0
-01: dt=0.0000, 60 negative triangles
115: dt=0.9900, 60 negative triangles
expanding nbhd size to 1
116: dt=0.9900, 78 negative triangles
117: dt=0.9900, 64 negative triangles
118: dt=0.9900, 58 negative triangles
119: dt=0.9900, 61 negative triangles
120: dt=0.9900, 61 negative triangles
121: dt=0.9900, 56 negative triangles
122: dt=0.9900, 55 negative triangles
123: dt=0.9900, 50 negative triangles
124: dt=0.9900, 46 negative triangles
125: dt=0.9900, 48 negative triangles
126: dt=0.9900, 43 negative triangles
127: dt=0.9900, 44 negative triangles
128: dt=0.9900, 43 negative triangles
129: dt=0.9900, 43 negative triangles
130: dt=0.9900, 43 negative triangles
131: dt=0.9900, 36 negative triangles
132: dt=0.9900, 29 negative triangles
133: dt=0.9900, 25 negative triangles
134: dt=0.9900, 25 negative triangles
135: dt=0.9900, 24 negative triangles
136: dt=0.9900, 24 negative triangles
137: dt=0.9900, 22 negative triangles
138: dt=0.9900, 21 negative triangles
139: dt=0.9900, 20 negative triangles
140: dt=0.9900, 17 negative triangles
141: dt=0.9900, 15 negative triangles
142: dt=0.9900, 14 negative triangles
143: dt=0.9900, 14 negative triangles
144: dt=0.9900, 15 negative triangles
145: dt=0.9900, 16 negative triangles
146: dt=0.9900, 15 negative triangles
147: dt=0.9900, 14 negative triangles
148: dt=0.9900, 13 negative triangles
149: dt=0.9900, 13 negative triangles
150: dt=0.9900, 12 negative triangles
151: dt=0.9900, 12 negative triangles
152: dt=0.9900, 9 negative triangles
153: dt=0.9900, 11 negative triangles
154: dt=0.9900, 8 negative triangles
155: dt=0.9900, 9 negative triangles
156: dt=0.9900, 7 negative triangles
157: dt=0.9900, 8 negative triangles
158: dt=0.9900, 9 negative triangles
159: dt=0.9900, 6 negative triangles
160: dt=0.9900, 5 negative triangles
161: dt=0.9900, 7 negative triangles
162: dt=0.9900, 3 negative triangles
163: dt=0.9900, 4 negative triangles
164: dt=0.9900, 3 negative triangles
165: dt=0.9900, 2 negative triangles
166: dt=0.9900, 1 negative triangles
167: dt=0.9900, 1 negative triangles
168: dt=0.9900, 2 negative triangles
169: dt=0.9900, 1 negative triangles
170: dt=0.9900, 1 negative triangles
171: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.42 hours
mris_register utimesec    5111.394949
mris_register stimesec    5.043233
mris_register ru_maxrss   259412
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   37410
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  9928
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    312655
mris_register ru_nivcsw   240307
FSRUNTIME@ mris_register  1.4212 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 5.790
curvature mean = 0.010, std = 0.811
curvature mean = 0.023, std = 0.862
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 313854.2, tmin=1.1862
  d=32.00 min @ (-8.00, 0.00, 0.00) sse = 246927.0, tmin=2.3896
  d=16.00 min @ (0.00, -4.00, 0.00) sse = 221030.7, tmin=3.5957
  d=8.00 min @ (-2.00, 0.00, 2.00) sse = 219063.4, tmin=4.8241
  d=4.00 min @ (1.00, 1.00, -1.00) sse = 213732.6, tmin=6.0621
  d=2.00 min @ (0.00, -0.50, 0.00) sse = 213631.0, tmin=7.2763
  d=1.00 min @ (0.00, 0.25, 0.00) sse = 213461.2, tmin=8.5087
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   9.74 min
curvature mean = -0.006, std = 0.826
curvature mean = 0.009, std = 0.948
curvature mean = -0.008, std = 0.835
curvature mean = 0.003, std = 0.979
curvature mean = -0.008, std = 0.837
curvature mean = 0.001, std = 0.992
2 Reading smoothwm
curvature mean = -0.033, std = 0.319
curvature mean = 0.034, std = 0.240
curvature mean = 0.073, std = 0.322
curvature mean = 0.028, std = 0.301
curvature mean = 0.042, std = 0.493
curvature mean = 0.027, std = 0.328
curvature mean = 0.024, std = 0.625
curvature mean = 0.027, std = 0.339
curvature mean = 0.009, std = 0.734
MRISregister() return, current seed 0
-01: dt=0.0000, 56 negative triangles
109: dt=0.9900, 56 negative triangles
110: dt=0.9405, 73 negative triangles
expanding nbhd size to 1
111: dt=0.9900, 65 negative triangles
112: dt=0.9900, 51 negative triangles
113: dt=0.9900, 51 negative triangles
114: dt=0.9900, 53 negative triangles
115: dt=0.9900, 51 negative triangles
116: dt=0.9900, 52 negative triangles
117: dt=0.9900, 46 negative triangles
118: dt=0.9900, 46 negative triangles
119: dt=0.9900, 45 negative triangles
120: dt=0.9900, 44 negative triangles
121: dt=0.9900, 36 negative triangles
122: dt=0.9900, 35 negative triangles
123: dt=0.9900, 31 negative triangles
124: dt=0.9900, 32 negative triangles
125: dt=0.9900, 29 negative triangles
126: dt=0.9900, 28 negative triangles
127: dt=0.9900, 25 negative triangles
128: dt=0.9900, 20 negative triangles
129: dt=0.9900, 25 negative triangles
130: dt=0.9900, 26 negative triangles
131: dt=0.9900, 22 negative triangles
132: dt=0.9900, 21 negative triangles
133: dt=0.9900, 20 negative triangles
134: dt=0.9900, 21 negative triangles
135: dt=0.9900, 21 negative triangles
136: dt=0.9900, 18 negative triangles
137: dt=0.9900, 18 negative triangles
138: dt=0.9900, 19 negative triangles
139: dt=0.9900, 19 negative triangles
140: dt=0.9900, 19 negative triangles
141: dt=0.9900, 18 negative triangles
142: dt=0.9900, 17 negative triangles
143: dt=0.9900, 17 negative triangles
144: dt=0.9900, 17 negative triangles
145: dt=0.9900, 17 negative triangles
146: dt=0.9900, 17 negative triangles
147: dt=0.9900, 17 negative triangles
148: dt=0.9900, 17 negative triangles
149: dt=0.9900, 17 negative triangles
150: dt=0.9900, 19 negative triangles
151: dt=0.9900, 18 negative triangles
152: dt=0.9405, 18 negative triangles
153: dt=0.9405, 17 negative triangles
154: dt=0.9405, 16 negative triangles
155: dt=0.9405, 16 negative triangles
156: dt=0.9405, 16 negative triangles
157: dt=0.9405, 16 negative triangles
158: dt=0.9405, 16 negative triangles
159: dt=0.9405, 16 negative triangles
160: dt=0.9405, 17 negative triangles
161: dt=0.9405, 16 negative triangles
162: dt=0.9405, 16 negative triangles
163: dt=0.9405, 16 negative triangles
164: dt=0.8935, 18 negative triangles
165: dt=0.8935, 16 negative triangles
166: dt=0.8935, 13 negative triangles
167: dt=0.8935, 12 negative triangles
168: dt=0.8935, 9 negative triangles
169: dt=0.8935, 9 negative triangles
170: dt=0.8935, 9 negative triangles
171: dt=0.8935, 9 negative triangles
172: dt=0.8935, 9 negative triangles
173: dt=0.8935, 9 negative triangles
174: dt=0.8935, 10 negative triangles
175: dt=0.8935, 10 negative triangles
176: dt=0.8935, 11 negative triangles
177: dt=0.8935, 9 negative triangles
178: dt=0.8488, 9 negative triangles
179: dt=0.8488, 8 negative triangles
180: dt=0.8488, 8 negative triangles
181: dt=0.8488, 8 negative triangles
182: dt=0.8488, 8 negative triangles
183: dt=0.8488, 7 negative triangles
184: dt=0.8488, 7 negative triangles
185: dt=0.8488, 7 negative triangles
186: dt=0.8488, 7 negative triangles
187: dt=0.8488, 7 negative triangles
188: dt=0.8488, 5 negative triangles
189: dt=0.8488, 5 negative triangles
190: dt=0.8488, 7 negative triangles
191: dt=0.8488, 5 negative triangles
192: dt=0.8488, 4 negative triangles
193: dt=0.8488, 4 negative triangles
194: dt=0.8488, 4 negative triangles
195: dt=0.8488, 3 negative triangles
196: dt=0.8488, 2 negative triangles
197: dt=0.8488, 2 negative triangles
198: dt=0.8488, 2 negative triangles
199: dt=0.8488, 2 negative triangles
200: dt=0.8488, 2 negative triangles
201: dt=0.8488, 1 negative triangles
202: dt=0.8488, 1 negative triangles
203: dt=0.8488, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.52 hours
mris_register utimesec    5680.268467
mris_register stimesec    5.066229
mris_register ru_maxrss   261492
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   37611
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10072
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    339549
mris_register ru_nivcsw   235460
FSRUNTIME@ mris_register  1.5174 hours 1 threads
PIDs (13597 13600) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 01:29:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 01:29:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

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

Waiting for PID 18587 of (18587 18592) to complete...
Waiting for PID 18592 of (18587 18592) 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 (18587 18592) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 01:29:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 01:29:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 18664 of (18664 18667) to complete...
Waiting for PID 18667 of (18664 18667) 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 (18664 18667) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 01:29:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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 01:29:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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 18742 of (18742 18745) to complete...
Waiting for PID 18745 of (18742 18745) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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...
1340 labels changed using aseg
relabeling using gibbs priors...
000:   3095 changed, 139581 examined...
001:    675 changed, 13041 examined...
002:    171 changed, 3781 examined...
003:     65 changed, 1012 examined...
004:     25 changed, 386 examined...
005:     14 changed, 156 examined...
006:      6 changed, 97 examined...
007:      1 changed, 37 examined...
008:      1 changed, 6 examined...
009:      0 changed, 7 examined...
261 labels changed using aseg
000: 127 total segments, 83 labels (382 vertices) changed
001: 43 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2061 vertices marked for relabeling...
2061 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 0050166 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...
1110 labels changed using aseg
relabeling using gibbs priors...
000:   2887 changed, 141740 examined...
001:    670 changed, 12404 examined...
002:    158 changed, 3823 examined...
003:     55 changed, 964 examined...
004:     15 changed, 328 examined...
005:      3 changed, 102 examined...
006:      2 changed, 21 examined...
007:      0 changed, 17 examined...
158 labels changed using aseg
000: 106 total segments, 68 labels (240 vertices) changed
001: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1785 vertices marked for relabeling...
1785 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 15 seconds.
PIDs (18742 18745) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 01:29:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050166 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 01:29:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050166 rh 

Waiting for PID 19008 of (19008 19011) to complete...
Waiting for PID 19011 of (19008 19011) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050166 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-6.0.0/0050166/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
25576 bright wm thresholded.
364 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.orig...
computing class statistics...
border white:    247893 voxels (1.48%)
border gray      298590 voxels (1.78%)
WM (98.0): 98.1 +- 9.0 [70.0 --> 110.0]
GM (70.0) : 70.6 +- 9.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 56.8 (was 70)
setting MAX_BORDER_WHITE to 113.0 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 47.6 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 56.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104+-7.8,    GM=66+-6.1
mean inside = 93.3, mean outside = 73.6
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.03-->5.42) (max @ vno 24216 --> 139039)
face area 0.33 +- 0.16 (0.00-->8.75)
mean absolute distance = 0.57 +- 0.72
3234 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 3 with 328 points - only 0.00% unknown
deleting segment 4 with 11 points - only 0.00% unknown
deleting segment 5 with 33 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
deleting segment 7 with 28 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
mean border=77.2, 140 (140) missing vertices, mean dist 0.4 [0.8 (%9.1)->0.5 (%90.9))]
%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 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.11-->5.26) (max @ vno 24216 --> 139039)
face area 0.33 +- 0.16 (0.00-->7.36)
mean absolute distance = 0.33 +- 0.44
2968 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2840680.0, rms=8.984
001: dt: 0.5000, sse=1351832.0, rms=5.022 (44.102%)
002: dt: 0.5000, sse=1023126.2, rms=3.622 (27.883%)
003: dt: 0.5000, sse=978771.2, rms=3.402 (6.072%)
004: dt: 0.5000, sse=943980.6, rms=3.208 (5.700%)
rms = 3.34, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=811116.9, rms=2.258 (29.621%)
006: dt: 0.2500, sse=767530.3, rms=1.835 (18.730%)
007: dt: 0.2500, sse=754045.4, rms=1.679 (8.480%)
rms = 1.65, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=751617.0, rms=1.650 (1.760%)
009: dt: 0.1250, sse=746936.6, rms=1.588 (3.763%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=745712.7, rms=1.575 (0.794%)
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
removing 1 vertex label from ripped group
deleting segment 2 with 16 points - only 0.00% unknown
deleting segment 3 with 144 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 33 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 50 points - only 10.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
mean border=81.6, 102 (31) missing vertices, mean dist -0.2 [0.3 (%83.5)->0.3 (%16.5))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.06-->5.22) (max @ vno 24216 --> 139039)
face area 0.36 +- 0.17 (0.00-->8.00)
mean absolute distance = 0.21 +- 0.31
3003 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1500416.0, rms=5.388
011: dt: 0.5000, sse=1005913.8, rms=3.234 (39.991%)
rms = 3.29, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=875908.8, rms=2.382 (26.328%)
013: dt: 0.2500, sse=805250.0, rms=1.719 (27.842%)
014: dt: 0.2500, sse=778942.8, rms=1.428 (16.942%)
015: dt: 0.2500, sse=773969.6, rms=1.360 (4.743%)
rms = 1.33, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=771984.0, rms=1.328 (2.343%)
rms = 1.28, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=768183.5, rms=1.280 (3.637%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 23 points - only 0.00% unknown
deleting segment 2 with 163 points - only 0.00% unknown
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 33 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 7 with 18 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
mean border=83.9, 119 (17) missing vertices, mean dist -0.1 [0.2 (%73.6)->0.2 (%26.4))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.09-->5.26) (max @ vno 24216 --> 139039)
face area 0.34 +- 0.17 (0.00-->7.95)
mean absolute distance = 0.17 +- 0.27
2725 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=956204.9, rms=3.105
018: dt: 0.5000, sse=922331.7, rms=2.861 (7.866%)
rms = 3.21, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=789518.8, rms=1.823 (36.268%)
020: dt: 0.2500, sse=752105.3, rms=1.393 (23.608%)
021: dt: 0.2500, sse=741319.0, rms=1.251 (10.211%)
rms = 1.25, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=741399.9, rms=1.247 (0.262%)
023: dt: 0.1250, sse=736495.3, rms=1.162 (6.832%)
rms = 1.16, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=734279.7, rms=1.157 (0.465%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
deleting segment 1 with 215 points - only 0.00% unknown
deleting segment 2 with 8 points - only 0.00% unknown
deleting segment 3 with 33 points - only 0.00% unknown
deleting segment 4 with 11 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
deleting segment 6 with 26 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
mean border=84.7, 135 (9) missing vertices, mean dist -0.0 [0.2 (%57.1)->0.2 (%42.9))]
%92 local maxima, % 3 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-6.0.0/0050166/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=742762.9, rms=1.420
rms = 1.74, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=715544.1, rms=0.990 (30.322%)
026: dt: 0.2500, sse=708786.6, rms=0.843 (14.761%)
rms = 0.87, time step reduction 2 of 3 to 0.125...
rms = 0.84, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=707378.8, rms=0.840 (0.389%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 6795 vertices
erasing segment 0 (vno[0] = 38679)
erasing segment 2 (vno[0] = 56936)
erasing segment 3 (vno[0] = 75943)
erasing segment 4 (vno[0] = 80782)
erasing segment 5 (vno[0] = 100816)
erasing segment 6 (vno[0] = 100841)
erasing segment 7 (vno[0] = 102906)
erasing segment 8 (vno[0] = 103920)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.area
vertex spacing 0.90 +- 0.26 (0.03-->5.29) (max @ vno 24216 --> 139039)
face area 0.34 +- 0.16 (0.00-->8.01)
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
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=55.1, 149 (149) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.9 (%100.0))]
%13 local maxima, %46 large gradients and %38 min vals, 287 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=25247300.0, rms=30.258
001: dt: 0.0500, sse=21931674.0, rms=28.142 (6.992%)
002: dt: 0.0500, sse=19582836.0, rms=26.541 (5.689%)
003: dt: 0.0500, sse=17812320.0, rms=25.267 (4.799%)
004: dt: 0.0500, sse=16402589.0, rms=24.205 (4.204%)
005: dt: 0.0500, sse=15236259.0, rms=23.290 (3.782%)
006: dt: 0.0500, sse=14243920.0, rms=22.481 (3.471%)
007: dt: 0.0500, sse=13381796.0, rms=21.755 (3.232%)
008: dt: 0.0500, sse=12620334.0, rms=21.092 (3.046%)
009: dt: 0.0500, sse=11939336.0, rms=20.481 (2.896%)
010: dt: 0.0500, sse=11324348.0, rms=19.913 (2.773%)
positioning took 1.0 minutes
mean border=54.9, 119 (83) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.4 (%100.0))]
%14 local maxima, %45 large gradients and %37 min vals, 256 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=11921205.0, rms=20.465
011: dt: 0.0500, sse=11360246.0, rms=19.947 (2.529%)
012: dt: 0.0500, sse=10847970.0, rms=19.463 (2.430%)
013: dt: 0.0500, sse=10377797.0, rms=19.007 (2.342%)
014: dt: 0.0500, sse=9945010.0, rms=18.577 (2.260%)
015: dt: 0.0500, sse=9546091.0, rms=18.172 (2.180%)
016: dt: 0.0500, sse=9178096.0, rms=17.790 (2.101%)
017: dt: 0.0500, sse=8837773.0, rms=17.430 (2.027%)
018: dt: 0.0500, sse=8522612.0, rms=17.089 (1.956%)
019: dt: 0.0500, sse=8230671.5, rms=16.767 (1.885%)
020: dt: 0.0500, sse=7959690.0, rms=16.462 (1.817%)
positioning took 1.0 minutes
mean border=54.8, 139 (67) missing vertices, mean dist 1.3 [0.1 (%0.6)->2.1 (%99.4))]
%14 local maxima, %45 large gradients and %37 min vals, 261 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=8077811.5, rms=16.602
021: dt: 0.0500, sse=7821763.0, rms=16.312 (1.751%)
022: dt: 0.0500, sse=7583604.5, rms=16.036 (1.687%)
023: dt: 0.0500, sse=7360749.5, rms=15.774 (1.634%)
024: dt: 0.0500, sse=7152809.5, rms=15.526 (1.576%)
025: dt: 0.0500, sse=6958228.5, rms=15.289 (1.522%)
026: dt: 0.0500, sse=6775646.0, rms=15.064 (1.473%)
027: dt: 0.0500, sse=6603473.5, rms=14.848 (1.432%)
028: dt: 0.0500, sse=6439935.0, rms=14.641 (1.400%)
029: dt: 0.0500, sse=6284103.0, rms=14.440 (1.373%)
030: dt: 0.0500, sse=6135497.0, rms=14.245 (1.346%)
positioning took 1.0 minutes
mean border=54.7, 168 (55) missing vertices, mean dist 1.1 [0.1 (%4.7)->1.9 (%95.3))]
%15 local maxima, %45 large gradients and %36 min vals, 223 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=6202281.0, rms=14.335
031: dt: 0.5000, sse=5140268.5, rms=12.870 (10.222%)
032: dt: 0.5000, sse=4376175.0, rms=11.695 (9.126%)
033: dt: 0.5000, sse=3783101.8, rms=10.695 (8.551%)
034: dt: 0.5000, sse=3306757.8, rms=9.812 (8.260%)
035: dt: 0.5000, sse=2905157.8, rms=9.000 (8.273%)
036: dt: 0.5000, sse=2550675.5, rms=8.214 (8.728%)
037: dt: 0.5000, sse=2234964.5, rms=7.451 (9.299%)
038: dt: 0.5000, sse=1966139.5, rms=6.730 (9.676%)
039: dt: 0.5000, sse=1752102.2, rms=6.099 (9.365%)
040: dt: 0.5000, sse=1590648.6, rms=5.575 (8.602%)
041: dt: 0.5000, sse=1478032.9, rms=5.181 (7.060%)
042: dt: 0.5000, sse=1405771.5, rms=4.908 (5.264%)
043: dt: 0.5000, sse=1355718.9, rms=4.715 (3.937%)
044: dt: 0.5000, sse=1325831.4, rms=4.592 (2.614%)
045: dt: 0.5000, sse=1302609.0, rms=4.499 (2.024%)
rms = 4.46, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1294114.2, rms=4.461 (0.839%)
047: dt: 0.2500, sse=1204094.6, rms=4.014 (10.035%)
048: dt: 0.2500, sse=1180616.4, rms=3.900 (2.819%)
rms = 3.89, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1179870.6, rms=3.895 (0.146%)
050: dt: 0.1250, sse=1164576.1, rms=3.815 (2.051%)
rms = 3.80, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1162140.6, rms=3.803 (0.325%)
positioning took 2.7 minutes
mean border=53.7, 1943 (12) missing vertices, mean dist 0.1 [0.2 (%46.3)->0.5 (%53.7))]
%28 local maxima, %34 large gradients and %33 min vals, 143 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=1485191.6, rms=4.216
052: dt: 0.5000, sse=1427874.0, rms=3.964 (5.986%)
053: dt: 0.5000, sse=1386138.5, rms=3.800 (4.135%)
rms = 3.92, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1298187.4, rms=3.284 (13.583%)
055: dt: 0.2500, sse=1273204.9, rms=3.117 (5.069%)
rms = 3.10, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1270324.8, rms=3.100 (0.542%)
057: dt: 0.1250, sse=1249999.0, rms=2.964 (4.383%)
rms = 2.94, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1245961.5, rms=2.940 (0.812%)
positioning took 1.2 minutes
mean border=52.8, 2084 (9) missing vertices, mean dist 0.1 [0.2 (%42.3)->0.4 (%57.7))]
%43 local maxima, %20 large gradients and %32 min vals, 147 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=1303455.5, rms=3.247
rms = 3.52, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1273066.4, rms=3.057 (5.856%)
060: dt: 0.2500, sse=1259920.0, rms=2.978 (2.598%)
rms = 2.97, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1258171.4, rms=2.975 (0.094%)
062: dt: 0.1250, sse=1245831.5, rms=2.891 (2.832%)
rms = 2.87, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1242530.4, rms=2.873 (0.624%)
positioning took 1.0 minutes
mean border=52.3, 4528 (8) missing vertices, mean dist 0.0 [0.2 (%44.8)->0.3 (%55.2))]
%46 local maxima, %15 large gradients and %31 min vals, 151 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-6.0.0/0050166/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1253750.5, rms=2.937
rms = 3.21, time step reduction 1 of 3 to 0.250...
064: dt: 0.2500, sse=1241414.0, rms=2.854 (2.830%)
rms = 2.82, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1233668.0, rms=2.820 (1.207%)
rms = 2.78, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1228190.6, rms=2.779 (1.451%)
positioning took 0.6 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.area.pial
vertex spacing 1.05 +- 0.47 (0.07-->6.73) (max @ vno 97940 --> 97945)
face area 0.43 +- 0.35 (0.00-->9.16)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 139581 vertices processed
25000 of 139581 vertices processed
50000 of 139581 vertices processed
75000 of 139581 vertices processed
100000 of 139581 vertices processed
125000 of 139581 vertices processed
0 of 139581 vertices processed
25000 of 139581 vertices processed
50000 of 139581 vertices processed
75000 of 139581 vertices processed
100000 of 139581 vertices processed
125000 of 139581 vertices processed
thickness calculation complete, 398:1334 truncations.
30474 vertices at 0 distance
92868 vertices at 1 distance
86930 vertices at 2 distance
39308 vertices at 3 distance
12819 vertices at 4 distance
3794 vertices at 5 distance
1305 vertices at 6 distance
455 vertices at 7 distance
182 vertices at 8 distance
99 vertices at 9 distance
73 vertices at 10 distance
53 vertices at 11 distance
47 vertices at 12 distance
49 vertices at 13 distance
41 vertices at 14 distance
35 vertices at 15 distance
28 vertices at 16 distance
21 vertices at 17 distance
24 vertices at 18 distance
16 vertices at 19 distance
11 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.thickness
positioning took 15.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050166 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-6.0.0/0050166/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
25576 bright wm thresholded.
364 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.orig...
computing class statistics...
border white:    247893 voxels (1.48%)
border gray      298590 voxels (1.78%)
WM (98.0): 98.1 +- 9.0 [70.0 --> 110.0]
GM (70.0) : 70.6 +- 9.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 58.8 (was 70)
setting MAX_BORDER_WHITE to 113.0 (was 105)
setting MIN_BORDER_WHITE to 68.0 (was 85)
setting MAX_CSF to 49.6 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 58.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 40.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104+-7.0,    GM=68+-6.1
mean inside = 93.4, mean outside = 74.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.04-->6.42) (max @ vno 57859 --> 141199)
face area 0.33 +- 0.15 (0.00-->4.02)
mean absolute distance = 0.60 +- 0.74
3282 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 3 with 139 points - only 0.00% unknown
deleting segment 4 with 13 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 39 points - only 0.00% unknown
deleting segment 7 with 81 points - only 0.00% unknown
removing 1 vertex label from ripped group
mean border=78.7, 235 (235) missing vertices, mean dist 0.4 [0.8 (%9.3)->0.6 (%90.7))]
%71 local maxima, %25 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 (0.07-->6.49) (max @ vno 141199 --> 57859)
face area 0.33 +- 0.16 (0.00-->3.90)
mean absolute distance = 0.34 +- 0.46
2760 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2707069.0, rms=8.620
001: dt: 0.5000, sse=1316243.9, rms=4.824 (44.033%)
002: dt: 0.5000, sse=996590.8, rms=3.424 (29.033%)
003: dt: 0.5000, sse=950405.5, rms=3.178 (7.165%)
004: dt: 0.5000, sse=914748.1, rms=2.976 (6.376%)
rms = 3.10, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=800680.9, rms=2.100 (29.424%)
006: dt: 0.2500, sse=760910.2, rms=1.687 (19.651%)
007: dt: 0.2500, sse=748468.7, rms=1.547 (8.316%)
rms = 1.51, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=746487.6, rms=1.514 (2.169%)
009: dt: 0.1250, sse=743056.8, rms=1.461 (3.480%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=741268.6, rms=1.450 (0.735%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 81 points - only 0.00% unknown
deleting segment 4 with 10 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 9 points - only 0.00% unknown
deleting segment 7 with 36 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 15 points - only 0.00% unknown
mean border=83.0, 89 (47) missing vertices, mean dist -0.3 [0.4 (%83.0)->0.3 (%17.0))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.09-->6.66) (max @ vno 141199 --> 57859)
face area 0.35 +- 0.17 (0.00-->4.50)
mean absolute distance = 0.21 +- 0.31
3257 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1490830.5, rms=5.298
011: dt: 0.5000, sse=992725.6, rms=3.114 (41.225%)
012: dt: 0.5000, sse=986468.1, rms=3.054 (1.919%)
rms = 3.07, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=843717.6, rms=2.062 (32.476%)
014: dt: 0.2500, sse=787182.6, rms=1.435 (30.400%)
015: dt: 0.2500, sse=774448.2, rms=1.296 (9.697%)
016: dt: 0.2500, sse=771438.2, rms=1.242 (4.170%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=770399.9, rms=1.230 (0.994%)
rms = 1.18, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=766608.8, rms=1.182 (3.887%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 1 with 123 points - only 0.00% unknown
deleting segment 2 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 22 points - only 0.00% unknown
deleting segment 5 with 58 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 15 points - only 0.00% unknown
mean border=85.2, 83 (22) missing vertices, mean dist -0.1 [0.2 (%73.2)->0.2 (%26.8))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.09-->6.66) (max @ vno 141199 --> 57859)
face area 0.34 +- 0.16 (0.00-->4.45)
mean absolute distance = 0.18 +- 0.27
3090 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=941013.6, rms=2.964
019: dt: 0.5000, sse=897405.6, rms=2.620 (11.604%)
rms = 2.97, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=782245.9, rms=1.677 (35.988%)
021: dt: 0.2500, sse=749518.4, rms=1.271 (24.213%)
022: dt: 0.2500, sse=740237.9, rms=1.145 (9.878%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=739492.2, rms=1.141 (0.358%)
024: dt: 0.1250, sse=734912.1, rms=1.075 (5.791%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=734345.4, rms=1.074 (0.111%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 2 with 139 points - only 0.00% unknown
deleting segment 3 with 13 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 34 points - only 0.00% unknown
deleting segment 6 with 76 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 15 points - only 0.00% unknown
mean border=85.9, 89 (15) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=743471.2, rms=1.351
rms = 1.57, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=720314.9, rms=0.956 (29.212%)
027: dt: 0.2500, sse=712310.7, rms=0.814 (14.884%)
rms = 0.84, time step reduction 2 of 3 to 0.125...
rms = 0.81, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=711369.2, rms=0.811 (0.403%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 6995 vertices
erasing segment 1 (vno[0] = 99233)
erasing segment 2 (vno[0] = 100174)
erasing segment 3 (vno[0] = 103708)
erasing segment 4 (vno[0] = 103771)
erasing segment 5 (vno[0] = 103787)
erasing segment 6 (vno[0] = 105901)
erasing segment 7 (vno[0] = 109520)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.area
vertex spacing 0.89 +- 0.26 (0.06-->6.66) (max @ vno 57859 --> 141199)
face area 0.34 +- 0.16 (0.00-->4.44)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=57.1, 211 (211) missing vertices, mean dist 1.7 [0.9 (%0.0)->2.9 (%100.0))]
%13 local maxima, %45 large gradients and %38 min vals, 300 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=24343620.0, rms=29.488
001: dt: 0.0500, sse=21189352.0, rms=27.453 (6.904%)
002: dt: 0.0500, sse=18971972.0, rms=25.926 (5.562%)
003: dt: 0.0500, sse=17300800.0, rms=24.713 (4.679%)
004: dt: 0.0500, sse=15973378.0, rms=23.705 (4.078%)
005: dt: 0.0500, sse=14877781.0, rms=22.839 (3.651%)
006: dt: 0.0500, sse=13946210.0, rms=22.077 (3.339%)
007: dt: 0.0500, sse=13136523.0, rms=21.392 (3.103%)
008: dt: 0.0500, sse=12422055.0, rms=20.769 (2.913%)
009: dt: 0.0500, sse=11782654.0, rms=20.195 (2.764%)
010: dt: 0.0500, sse=11204872.0, rms=19.661 (2.640%)
positioning took 1.0 minutes
mean border=56.9, 168 (118) missing vertices, mean dist 1.5 [0.2 (%0.1)->2.4 (%99.9))]
%14 local maxima, %44 large gradients and %38 min vals, 293 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=11850777.0, rms=20.253
011: dt: 0.0500, sse=11323039.0, rms=19.769 (2.393%)
012: dt: 0.0500, sse=10840263.0, rms=19.314 (2.297%)
013: dt: 0.0500, sse=10397139.0, rms=18.888 (2.208%)
014: dt: 0.0500, sse=9989005.0, rms=18.486 (2.126%)
015: dt: 0.0500, sse=9612215.0, rms=18.107 (2.049%)
016: dt: 0.0500, sse=9263730.0, rms=17.750 (1.975%)
017: dt: 0.0500, sse=8940462.0, rms=17.411 (1.906%)
018: dt: 0.0500, sse=8640683.0, rms=17.092 (1.837%)
019: dt: 0.0500, sse=8362315.0, rms=16.789 (1.770%)
020: dt: 0.0500, sse=8103490.0, rms=16.503 (1.706%)
positioning took 1.0 minutes
mean border=56.8, 152 (86) missing vertices, mean dist 1.3 [0.1 (%0.7)->2.1 (%99.3))]
%15 local maxima, %44 large gradients and %37 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=8223781.5, rms=16.641
021: dt: 0.0500, sse=7978489.5, rms=16.368 (1.645%)
022: dt: 0.0500, sse=7750032.0, rms=16.108 (1.584%)
023: dt: 0.0500, sse=7535661.0, rms=15.861 (1.535%)
024: dt: 0.0500, sse=7335045.0, rms=15.626 (1.481%)
025: dt: 0.0500, sse=7146397.0, rms=15.402 (1.436%)
026: dt: 0.0500, sse=6968344.5, rms=15.187 (1.395%)
027: dt: 0.0500, sse=6799416.5, rms=14.980 (1.362%)
028: dt: 0.0500, sse=6638234.0, rms=14.780 (1.336%)
029: dt: 0.0500, sse=6483764.0, rms=14.586 (1.316%)
030: dt: 0.0500, sse=6335228.5, rms=14.396 (1.300%)
positioning took 1.0 minutes
mean border=56.7, 149 (65) missing vertices, mean dist 1.1 [0.1 (%4.8)->1.8 (%95.2))]
%15 local maxima, %44 large gradients and %37 min vals, 250 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=6413154.0, rms=14.497
031: dt: 0.5000, sse=5337369.0, rms=13.052 (9.964%)
032: dt: 0.5000, sse=4541524.0, rms=11.865 (9.100%)
033: dt: 0.5000, sse=3914203.5, rms=10.837 (8.664%)
034: dt: 0.5000, sse=3395822.0, rms=9.902 (8.629%)
035: dt: 0.5000, sse=2962054.0, rms=9.046 (8.646%)
036: dt: 0.5000, sse=2573913.0, rms=8.201 (9.336%)
037: dt: 0.5000, sse=2228766.8, rms=7.374 (10.083%)
038: dt: 0.5000, sse=1935579.8, rms=6.588 (10.654%)
039: dt: 0.5000, sse=1715707.6, rms=5.935 (9.916%)
040: dt: 0.5000, sse=1560702.9, rms=5.425 (8.595%)
041: dt: 0.5000, sse=1462564.2, rms=5.078 (6.391%)
042: dt: 0.5000, sse=1398038.4, rms=4.833 (4.823%)
043: dt: 0.5000, sse=1362187.9, rms=4.693 (2.911%)
044: dt: 0.5000, sse=1336084.2, rms=4.587 (2.261%)
045: dt: 0.5000, sse=1322209.1, rms=4.531 (1.210%)
046: dt: 0.5000, sse=1308702.6, rms=4.474 (1.266%)
rms = 4.45, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1303911.8, rms=4.453 (0.470%)
048: dt: 0.2500, sse=1205315.8, rms=3.967 (10.913%)
049: dt: 0.2500, sse=1175994.4, rms=3.828 (3.507%)
rms = 3.84, time step reduction 2 of 3 to 0.125...
rms = 3.78, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1167554.9, rms=3.783 (1.154%)
positioning took 2.7 minutes
mean border=55.5, 1818 (23) missing vertices, mean dist 0.1 [0.2 (%44.8)->0.5 (%55.2))]
%29 local maxima, %33 large gradients and %33 min vals, 135 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=1508937.6, rms=4.321
051: dt: 0.5000, sse=1448697.6, rms=4.063 (5.957%)
052: dt: 0.5000, sse=1389198.5, rms=3.814 (6.149%)
rms = 4.00, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1293838.4, rms=3.264 (14.411%)
054: dt: 0.2500, sse=1267536.2, rms=3.090 (5.333%)
rms = 3.09, time step reduction 2 of 3 to 0.125...
055: dt: 0.1250, sse=1257938.2, rms=3.026 (2.057%)
056: dt: 0.1250, sse=1245115.0, rms=2.939 (2.887%)
rms = 2.91, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1241112.0, rms=2.912 (0.907%)
positioning took 1.3 minutes
mean border=54.7, 2133 (17) missing vertices, mean dist 0.1 [0.2 (%40.5)->0.4 (%59.5))]
%43 local maxima, %19 large gradients and %32 min vals, 149 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=1309677.8, rms=3.298
rms = 3.53, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1275021.1, rms=3.087 (6.404%)
059: dt: 0.2500, sse=1257314.2, rms=2.977 (3.557%)
rms = 2.97, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1255568.0, rms=2.974 (0.114%)
061: dt: 0.1250, sse=1240333.0, rms=2.871 (3.463%)
rms = 2.84, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1235482.1, rms=2.842 (0.995%)
positioning took 1.0 minutes
mean border=54.2, 4327 (15) missing vertices, mean dist 0.1 [0.2 (%43.5)->0.3 (%56.5))]
%46 local maxima, %15 large gradients and %32 min vals, 144 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-6.0.0/0050166/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1250061.1, rms=2.924
rms = 3.22, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1236521.8, rms=2.832 (3.123%)
rms = 2.79, time step reduction 2 of 3 to 0.125...
064: dt: 0.2500, sse=1228429.4, rms=2.795 (1.331%)
rms = 2.75, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1222480.0, rms=2.750 (1.588%)
positioning took 0.7 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.area.pial
vertex spacing 1.04 +- 0.46 (0.05-->6.92) (max @ vno 94032 --> 92928)
face area 0.42 +- 0.34 (0.00-->5.78)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 141740 vertices processed
25000 of 141740 vertices processed
50000 of 141740 vertices processed
75000 of 141740 vertices processed
100000 of 141740 vertices processed
125000 of 141740 vertices processed
0 of 141740 vertices processed
25000 of 141740 vertices processed
50000 of 141740 vertices processed
75000 of 141740 vertices processed
100000 of 141740 vertices processed
125000 of 141740 vertices processed
thickness calculation complete, 472:1610 truncations.
31464 vertices at 0 distance
95774 vertices at 1 distance
86262 vertices at 2 distance
39628 vertices at 3 distance
12813 vertices at 4 distance
3961 vertices at 5 distance
1374 vertices at 6 distance
581 vertices at 7 distance
206 vertices at 8 distance
93 vertices at 9 distance
79 vertices at 10 distance
36 vertices at 11 distance
45 vertices at 12 distance
34 vertices at 13 distance
24 vertices at 14 distance
26 vertices at 15 distance
23 vertices at 16 distance
15 vertices at 17 distance
11 vertices at 18 distance
19 vertices at 19 distance
10 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.thickness
positioning took 16.1 minutes
PIDs (19008 19011) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 01:45:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label
Total face volume 288391
Total vertex volume 284396 (mask=0)
#@# 0050166 lh 284396
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 01:45:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label
Total face volume 290970
Total vertex volume 286777 (mask=0)
#@# 0050166 rh 286777
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 01:45:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 

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 = 240
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/ribbon.mgz
mris_volmask took 15.98 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 02:01:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 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 0050166 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 02:01:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 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 0050166 rh pial 

Waiting for PID 22460 of (22460 22463 22466 22469) to complete...
Waiting for PID 22463 of (22460 22463 22466 22469) to complete...
Waiting for PID 22466 of (22460 22463 22466 22469) to complete...
Waiting for PID 22469 of (22460 22463 22466 22469) 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 0050166 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 288391
Total vertex volume 284396 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1149    790   2190  2.760 0.462     0.100     0.015        8     0.7  bankssts
  892    610   2013  2.782 0.808     0.123     0.014       13     0.5  caudalanteriorcingulate
 3557   2403   7648  2.827 0.549     0.105     0.019       30     2.7  caudalmiddlefrontal
 2362   1545   4044  2.313 0.582     0.143     0.031       36     2.9  cuneus
  820    541   2130  3.238 0.715     0.113     0.031        8     1.1  entorhinal
 4777   3164  11041  3.040 0.593     0.130     0.028       64     5.0  fusiform
 5805   3944  13179  2.837 0.560     0.125     0.024       89     5.6  inferiorparietal
 5844   3993  14070  2.912 0.755     0.128     0.031       87     7.8  inferiortemporal
 1565   1004   2797  2.517 0.967     0.124     0.026       22     1.6  isthmuscingulate
 7642   4956  13271  2.398 0.535     0.135     0.029      109     8.7  lateraloccipital
 4169   2833   9726  2.988 0.690     0.133     0.041       69     6.7  lateralorbitofrontal
 4125   2958   6646  2.216 0.666     0.138     0.032       57     5.6  lingual
 3019   1987   6162  2.619 0.816     0.127     0.046       63     5.9  medialorbitofrontal
 4763   3240  12880  3.088 0.675     0.126     0.028       75     5.1  middletemporal
 1333    851   2773  2.823 0.696     0.089     0.017        8     1.0  parahippocampal
 1942   1297   3939  2.749 0.546     0.102     0.019       15     1.4  paracentral
 3015   2062   6805  2.812 0.491     0.129     0.029       50     3.3  parsopercularis
 1073    764   3234  2.979 0.690     0.144     0.032       22     1.4  parsorbitalis
 2289   1573   4962  2.647 0.554     0.121     0.027       31     2.4  parstriangularis
 1798   1390   2568  1.944 0.515     0.127     0.030       19     2.1  pericalcarine
 7001   4497  11006  2.148 0.646     0.103     0.022       74     6.0  postcentral
 1986   1361   4253  2.663 0.890     0.128     0.024       31     1.9  posteriorcingulate
 7818   5052  15301  2.722 0.531     0.109     0.023       88     7.2  precentral
 6363   4236  13478  2.853 0.550     0.117     0.023       74     5.7  precuneus
 1526   1017   3838  3.172 0.749     0.139     0.036       30     2.2  rostralanteriorcingulate
 9413   6558  21234  2.565 0.655     0.136     0.034      162    12.9  rostralmiddlefrontal
10771   7505  26774  3.055 0.567     0.123     0.027      122    11.2  superiorfrontal
 9192   6031  17612  2.533 0.530     0.120     0.022      116     8.0  superiorparietal
 5633   3711  13542  3.002 0.702     0.099     0.021       56     5.1  superiortemporal
 5520   3770  12380  2.801 0.611     0.132     0.028       82     6.0  supramarginal
  378    252   1292  3.275 0.643     0.155     0.043        9     0.6  frontalpole
  694    483   2878  3.904 0.524     0.129     0.037       12     0.9  temporalpole
  708    450   1177  2.482 0.489     0.135     0.029       11     0.7  transversetemporal
 3465   2330   7515  3.098 1.003     0.116     0.030       39     4.0  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 0050166 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 288391
Total vertex volume 284396 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1149    788   2190  2.760 0.462     0.129     0.030       15     1.6  bankssts
  892    785   2013  2.782 0.808     0.146     0.032       20     1.1  caudalanteriorcingulate
 3557   2830   7648  2.827 0.549     0.123     0.026       37     4.0  caudalmiddlefrontal
 2362   1993   4044  2.313 0.582     0.147     0.034       35     3.5  cuneus
  820    777   2130  3.238 0.715     0.161     0.037       12     1.5  entorhinal
 4777   4003  11041  3.040 0.593     0.153     0.040       79     8.7  fusiform
 5805   5250  13179  2.837 0.560     0.155     0.033       83     8.7  inferiorparietal
 5844   5391  14070  2.912 0.755     0.159     0.036       73    10.0  inferiortemporal
 1565   1222   2797  2.517 0.967     0.147     0.041       36     2.7  isthmuscingulate
 7642   6275  13271  2.398 0.535     0.140     0.030      107    11.0  lateraloccipital
 4169   3543   9726  2.988 0.690     0.151     0.036       68     6.9  lateralorbitofrontal
 4125   3343   6646  2.216 0.666     0.142     0.037      128     6.8  lingual
 3019   2702   6162  2.619 0.816     0.165     0.044       54     5.7  medialorbitofrontal
 4763   4813  12880  3.088 0.675     0.165     0.035       63     7.9  middletemporal
 1333   1169   2773  2.823 0.696     0.141     0.033       13     2.1  parahippocampal
 1942   1534   3939  2.749 0.546     0.123     0.026       18     2.2  paracentral
 3015   2738   6805  2.812 0.491     0.157     0.034       36     4.5  parsopercularis
 1073   1294   3234  2.979 0.690     0.204     0.037       17     2.1  parsorbitalis
 2289   2067   4962  2.647 0.554     0.161     0.033       30     3.4  parstriangularis
 1798   1258   2568  1.944 0.515     0.128     0.039       31     3.3  pericalcarine
 7001   5703  11006  2.148 0.646     0.131     0.024       74     7.8  postcentral
 1986   1746   4253  2.663 0.890     0.150     0.035       32     3.0  posteriorcingulate
 7818   5893  15301  2.722 0.531     0.120     0.027       95     9.5  precentral
 6363   5130  13478  2.853 0.550     0.140     0.033       81     9.0  precuneus
 1526   1358   3838  3.172 0.749     0.178     0.053       57     3.5  rostralanteriorcingulate
 9413   9406  21234  2.565 0.655     0.183     0.039      132    19.0  rostralmiddlefrontal
10771   9428  26774  3.055 0.567     0.146     0.034      155    16.1  superiorfrontal
 9192   7723  17612  2.533 0.530     0.145     0.030      122    12.3  superiorparietal
 5633   4994  13542  3.002 0.702     0.146     0.033       71     8.9  superiortemporal
 5520   4968  12380  2.801 0.611     0.160     0.035       80     8.5  supramarginal
  378    505   1292  3.275 0.643     0.220     0.045        5     0.8  frontalpole
  694    954   2878  3.904 0.524     0.184     0.029        8     0.9  temporalpole
  708    514   1177  2.482 0.489     0.127     0.030       10     0.8  transversetemporal
 3465   2210   7515  3.098 1.003     0.131     0.037       70     5.1  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 0050166 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 290970
Total vertex volume 286777 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1402    960   2659  2.942 0.418     0.095     0.014       10     0.8  bankssts
 1129    752   2572  2.739 0.849     0.134     0.024       17     1.0  caudalanteriorcingulate
 4061   2683   8784  2.836 0.577     0.111     0.022       44     3.6  caudalmiddlefrontal
 2591   1719   4576  2.291 0.622     0.143     0.032       41     3.2  cuneus
  625    442   2365  3.649 0.761     0.130     0.030        8     0.7  entorhinal
 4343   2933  10103  3.074 0.536     0.124     0.025       61     4.1  fusiform
 8238   5631  19479  2.909 0.580     0.121     0.024      109     8.2  inferiorparietal
 4877   3258  12334  3.080 0.728     0.124     0.031       73     6.5  inferiortemporal
 1306    827   2597  2.666 0.923     0.144     0.033       28     1.5  isthmuscingulate
 8239   5159  14626  2.492 0.578     0.131     0.032      109    10.0  lateraloccipital
 4428   2966   8942  2.730 0.904     0.131     0.040       73     6.8  lateralorbitofrontal
 4796   3281   7816  2.212 0.612     0.138     0.032       74     6.0  lingual
 2760   1913   5717  2.590 0.697     0.122     0.037       48     4.3  medialorbitofrontal
 4890   3364  13407  3.310 0.590     0.116     0.025       60     4.7  middletemporal
 1111    710   2397  2.938 0.699     0.092     0.020        9     0.8  parahippocampal
 2416   1623   5091  2.757 0.530     0.112     0.019       22     1.8  paracentral
 2372   1638   5305  2.765 0.476     0.117     0.026       30     2.3  parsopercularis
 1227    841   3224  2.898 0.718     0.130     0.029       18     1.4  parsorbitalis
 2439   1714   5524  2.700 0.545     0.132     0.031       45     2.9  parstriangularis
 2226   1520   2622  1.921 0.586     0.121     0.024       22     2.2  pericalcarine
 7122   4439  11029  2.206 0.631     0.100     0.022       72     6.1  postcentral
 2044   1348   4233  2.576 0.860     0.127     0.028       30     2.4  posteriorcingulate
 8052   5077  15803  2.797 0.532     0.103     0.024       74     7.7  precentral
 5632   3871  12058  2.779 0.542     0.121     0.024       70     5.3  precuneus
  995    695   3064  3.335 0.853     0.137     0.040       18     1.8  rostralanteriorcingulate
 9538   6699  20906  2.590 0.586     0.131     0.031      148    11.8  rostralmiddlefrontal
10653   7209  25466  2.952 0.664     0.121     0.028      136    12.5  superiorfrontal
 9521   6197  18169  2.635 0.544     0.114     0.023      108     9.0  superiorparietal
 5301   3542  12351  3.094 0.586     0.098     0.019       49     3.8  superiortemporal
 5201   3541  11206  2.837 0.518     0.118     0.023       61     4.9  supramarginal
  544    361   1359  2.619 0.605     0.166     0.042       13     1.1  frontalpole
  627    454   2401  3.629 0.985     0.141     0.036       11     0.9  temporalpole
  573    351    943  2.422 0.536     0.143     0.035       12     0.5  transversetemporal
 3215   2196   7601  3.291 0.677     0.115     0.028       37     3.3  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 0050166 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 290970
Total vertex volume 286777 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1402    870   2659  2.942 0.418     0.113     0.027       14     1.7  bankssts
 1129    976   2572  2.739 0.849     0.160     0.039       28     1.9  caudalanteriorcingulate
 4061   3404   8784  2.836 0.577     0.129     0.028       40     4.8  caudalmiddlefrontal
 2591   2309   4576  2.291 0.622     0.152     0.035       37     4.1  cuneus
  625    739   2365  3.649 0.761     0.177     0.043       13     1.3  entorhinal
 4343   3580  10103  3.074 0.536     0.142     0.035       70     6.9  fusiform
 8238   7516  19479  2.909 0.580     0.147     0.029       97    11.3  inferiorparietal
 4877   4559  12334  3.080 0.728     0.162     0.038       80     9.3  inferiortemporal
 1306   1055   2597  2.666 0.923     0.145     0.035       20     1.9  isthmuscingulate
 8239   6571  14626  2.492 0.578     0.137     0.033      114    12.5  lateraloccipital
 4428   3610   8942  2.730 0.904     0.168     0.050      107    10.7  lateralorbitofrontal
 4796   3889   7816  2.212 0.612     0.146     0.033       78     7.5  lingual
 2760   2535   5717  2.590 0.697     0.164     0.039       43     5.0  medialorbitofrontal
 4890   4681  13407  3.310 0.590     0.150     0.032       63     7.1  middletemporal
 1111    919   2397  2.938 0.699     0.127     0.028       10     1.4  parahippocampal
 2416   1956   5091  2.757 0.530     0.132     0.026       26     2.8  paracentral
 2372   2130   5305  2.765 0.476     0.150     0.032       24     3.2  parsopercularis
 1227   1315   3224  2.898 0.718     0.197     0.042       21     2.3  parsorbitalis
 2439   2326   5524  2.700 0.545     0.164     0.030       30     3.1  parstriangularis
 2226   1333   2622  1.921 0.586     0.113     0.029       35     3.0  pericalcarine
 7122   5571  11029  2.206 0.631     0.123     0.024       61     7.8  postcentral
 2044   1783   4233  2.576 0.860     0.160     0.037       28     3.5  posteriorcingulate
 8052   5919  15803  2.797 0.532     0.114     0.025      115     9.2  precentral
 5632   4702  12058  2.779 0.542     0.150     0.033       83     8.2  precuneus
  995   1077   3064  3.335 0.853     0.275     0.757     6662    54.6  rostralanteriorcingulate
 9538   8999  20906  2.590 0.586     0.172     0.036      137    16.5  rostralmiddlefrontal
10653   9363  25466  2.952 0.664     0.148     0.034      148    16.3  superiorfrontal
 9521   7432  18169  2.635 0.544     0.130     0.030      112    12.9  superiorparietal
 5301   4467  12351  3.094 0.586     0.129     0.026       51     6.2  superiortemporal
 5201   4277  11206  2.837 0.518     0.142     0.031       62     7.3  supramarginal
  544    670   1359  2.619 0.605     0.204     0.037        6     1.1  frontalpole
  627    862   2401  3.629 0.985     0.189     0.032        7     1.0  temporalpole
  573    426    943  2.422 0.536     0.139     0.033       12     0.9  transversetemporal
 3215   2185   7601  3.291 0.677     0.137     0.035       64     4.8  insula
PIDs (22460 22463 22466 22469) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 02:03:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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 02:03:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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 22682 of (22682 22685) to complete...
Waiting for PID 22685 of (22682 22685) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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...
17 labels changed using aseg
relabeling using gibbs priors...
000:   9166 changed, 139581 examined...
001:   2168 changed, 35744 examined...
002:    657 changed, 11284 examined...
003:    269 changed, 3695 examined...
004:    131 changed, 1525 examined...
005:     64 changed, 741 examined...
006:     38 changed, 341 examined...
007:     15 changed, 204 examined...
008:      7 changed, 98 examined...
009:      5 changed, 49 examined...
010:      3 changed, 20 examined...
011:      3 changed, 22 examined...
012:      0 changed, 21 examined...
1 labels changed using aseg
000: 270 total segments, 185 labels (2197 vertices) changed
001: 89 total segments, 8 labels (347 vertices) changed
002: 81 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 29 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1447 vertices marked for relabeling...
1447 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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...
1 labels changed using aseg
relabeling using gibbs priors...
000:   9085 changed, 141740 examined...
001:   2087 changed, 35340 examined...
002:    610 changed, 10902 examined...
003:    249 changed, 3446 examined...
004:    121 changed, 1408 examined...
005:     54 changed, 651 examined...
006:     20 changed, 305 examined...
007:     10 changed, 119 examined...
008:      3 changed, 61 examined...
009:      2 changed, 24 examined...
010:      1 changed, 12 examined...
011:      3 changed, 8 examined...
012:      0 changed, 12 examined...
0 labels changed using aseg
000: 263 total segments, 177 labels (1627 vertices) changed
001: 89 total segments, 3 labels (14 vertices) changed
002: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 28 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1365 vertices marked for relabeling...
1365 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.
PIDs (22682 22685) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 02:03:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 02:03:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 rh white 

Waiting for PID 22744 of (22744 22747) to complete...
Waiting for PID 22747 of (22744 22747) 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 0050166 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 288391
Total vertex volume 284396 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1564   1083   3367  2.592 0.688     0.138     0.033       30     2.0  G&S_frontomargin
 1494   1008   3023  2.529 0.560     0.135     0.024       21     1.4  G&S_occipital_inf
 1876   1168   3933  2.666 0.602     0.109     0.023       20     1.6  G&S_paracentral
 1594   1085   3729  2.830 0.541     0.138     0.029       24     2.2  G&S_subcentral
  818    582   2838  3.095 0.713     0.175     0.051       20     1.8  G&S_transv_frontopol
 2393   1693   5952  3.115 0.571     0.136     0.029       38     3.1  G&S_cingul-Ant
 1197    866   2816  3.118 0.495     0.105     0.016       11     0.7  G&S_cingul-Mid-Ant
 1336    927   2776  2.823 0.573     0.124     0.026       15     1.3  G&S_cingul-Mid-Post
  612    405   1893  3.276 0.704     0.148     0.035       12     0.9  G_cingul-Post-dorsal
  381    234    887  3.007 0.811     0.155     0.041        8     0.7  G_cingul-Post-ventral
 2200   1440   4148  2.330 0.667     0.148     0.036       37     3.1  G_cuneus
 1879   1275   4813  2.908 0.472     0.140     0.036       39     2.5  G_front_inf-Opercular
  546    357   1878  3.300 0.476     0.158     0.037       12     0.9  G_front_inf-Orbital
 1297    887   3490  2.802 0.531     0.145     0.036       32     1.9  G_front_inf-Triangul
 4667   3171  13452  2.945 0.589     0.143     0.038       96     7.1  G_front_middle
 6951   4787  19920  3.196 0.568     0.134     0.031      109     8.6  G_front_sup
  594    414   1456  3.151 0.834     0.146     0.044       14     0.9  G_Ins_lg&S_cent_ins
  733    490   2811  3.993 0.626     0.122     0.033        9     0.9  G_insular_short
 2455   1558   5724  2.823 0.495     0.134     0.029       45     2.7  G_occipital_middle
 1552    986   2979  2.540 0.566     0.140     0.031       23     1.9  G_occipital_sup
 1925   1225   5153  3.151 0.486     0.140     0.032       37     2.3  G_oc-temp_lat-fusifor
 2692   1850   4531  2.103 0.616     0.152     0.041       47     4.7  G_oc-temp_med-Lingual
 1710   1083   4140  2.982 0.736     0.104     0.028       16     1.9  G_oc-temp_med-Parahip
 2560   1765   7359  2.870 0.753     0.154     0.055       67     5.6  G_orbital
 2196   1462   6019  2.996 0.550     0.135     0.028       44     2.2  G_pariet_inf-Angular
 2829   1939   7650  2.941 0.652     0.145     0.032       54     3.8  G_pariet_inf-Supramar
 3811   2397   8151  2.615 0.554     0.124     0.026       60     3.9  G_parietal_sup
 3056   1860   4836  2.103 0.587     0.111     0.028       42     3.6  G_postcentral
 2867   1709   6926  2.952 0.522     0.114     0.031       47     3.2  G_precentral
 3547   2332   8773  2.879 0.601     0.127     0.027       55     3.8  G_precuneus
 1179    760   2741  2.541 0.768     0.142     0.062       29     3.4  G_rectus
  778    422   1058  2.078 1.591     0.115     0.063       19     1.4  G_subcallosal
  444    262    838  2.429 0.509     0.123     0.035        9     0.5  G_temp_sup-G_T_transv
 2042   1295   6905  3.362 0.780     0.130     0.032       36     2.7  G_temp_sup-Lateral
  727    497   1960  3.336 0.485     0.059     0.010        1     0.3  G_temp_sup-Plan_polar
  965    642   2109  2.933 0.633     0.082     0.013        6     0.5  G_temp_sup-Plan_tempo
 3189   2128   9299  2.971 0.861     0.153     0.043       76     6.0  G_temporal_inf
 2545   1703   8314  3.221 0.715     0.142     0.037       59     3.5  G_temporal_middle
  364    251    548  2.317 0.430     0.090     0.011        2     0.1  Lat_Fis-ant-Horizont
  432    306    741  2.689 0.374     0.095     0.019        2     0.3  Lat_Fis-ant-Vertical
 1153    797   1806  2.799 0.567     0.106     0.019        8     0.8  Lat_Fis-post
 2126   1355   3111  2.108 0.525     0.142     0.035       36     3.0  Pole_occipital
 1655   1117   5956  3.688 0.726     0.131     0.032       23     2.0  Pole_temporal
 2220   1764   3372  2.228 0.758     0.124     0.026       21     2.3  S_calcarine
 3305   2258   4185  2.103 0.574     0.093     0.013       18     1.7  S_central
 1203    828   2024  2.649 0.483     0.092     0.012        7     0.6  S_cingul-Marginalis
  549    377   1067  3.129 0.454     0.081     0.014        1     0.3  S_circular_insula_ant
 1349    911   2103  2.843 0.446     0.083     0.013        5     0.8  S_circular_insula_inf
 1705   1180   2781  2.908 0.454     0.102     0.017        8     1.3  S_circular_insula_sup
 1039    707   1708  2.856 0.600     0.096     0.014        6     0.6  S_collat_transv_ant
  553    373    744  2.334 0.294     0.123     0.023        5     0.5  S_collat_transv_post
 2737   1932   4351  2.347 0.502     0.112     0.020       22     2.2  S_front_inf
 1690   1188   2659  2.218 0.573     0.114     0.023       16     1.7  S_front_middle
 3100   2136   5997  2.737 0.511     0.094     0.017       19     1.9  S_front_sup
  291    208    485  2.528 0.471     0.109     0.015        2     0.2  S_interm_prim-Jensen
 3204   2190   5093  2.495 0.435     0.121     0.019       33     2.6  S_intrapariet&P_trans
  984    677   1358  2.241 0.451     0.119     0.023        6     1.0  S_oc_middle&Lunatus
  989    680   1490  2.324 0.391     0.124     0.022       10     0.8  S_oc_sup&transversal
  612    422    992  2.459 0.371     0.082     0.010        3     0.2  S_occipital_ant
 1107    776   1965  2.737 0.502     0.111     0.019        9     0.9  S_oc-temp_lat
 2528   1781   4209  2.711 0.622     0.115     0.020       19     2.1  S_oc-temp_med&Lingual
  432    312    744  2.266 0.537     0.119     0.023        4     0.3  S_orbital_lateral
  746    524   1117  2.583 0.626     0.119     0.025        7     0.8  S_orbital_med-olfact
 1643   1118   3549  3.104 0.675     0.122     0.031       19     2.0  S_orbital-H_Shaped
 2198   1477   3755  2.806 0.478     0.113     0.019       18     1.6  S_parieto_occipital
 1635    987   1432  1.878 0.741     0.109     0.015       21     0.7  S_pericallosal
 2964   2016   4442  2.308 0.408     0.097     0.015       22     1.6  S_postcentral
 1713   1167   2849  2.605 0.420     0.092     0.013       11     0.9  S_precentral-inf-part
 1618   1114   2382  2.475 0.431     0.102     0.016       10     1.1  S_precentral-sup-part
  824    573   1369  2.627 0.666     0.121     0.021        8     0.6  S_suborbital
  947    639   1485  2.567 0.475     0.094     0.013        4     0.5  S_subparietal
 1978   1420   3393  2.786 0.501     0.111     0.019       11     1.6  S_temporal_inf
 5281   3602   9976  2.779 0.535     0.107     0.020       50     4.4  S_temporal_sup
  330    243    510  2.470 0.456     0.121     0.014        3     0.2  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050166 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 290970
Total vertex volume 286777 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1044    720   2067  2.442 0.608     0.134     0.032       15     1.6  G&S_frontomargin
 1514    960   3409  2.795 0.500     0.124     0.028       19     1.6  G&S_occipital_inf
 1814   1082   3844  2.666 0.574     0.120     0.040       31     3.2  G&S_paracentral
 1736   1167   3757  2.844 0.558     0.131     0.025       23     1.6  G&S_subcentral
 1328    929   3510  2.766 0.612     0.155     0.039       32     2.3  G&S_transv_frontopol
 3016   2116   7177  2.966 0.743     0.114     0.024       31     3.0  G&S_cingul-Ant
 1259    878   3118  3.039 0.598     0.122     0.027       13     1.2  G&S_cingul-Mid-Ant
 1490   1018   3267  2.802 0.517     0.121     0.028       18     1.7  G&S_cingul-Mid-Post
  540    330   1688  3.370 0.674     0.160     0.046       13     1.0  G_cingul-Post-dorsal
  330    199    883  3.208 0.624     0.176     0.048        9     0.6  G_cingul-Post-ventral
 2413   1591   4167  2.172 0.681     0.147     0.034       42     3.3  G_cuneus
 1902   1269   4735  2.853 0.502     0.134     0.034       34     2.4  G_front_inf-Opercular
  315    210    889  3.104 0.510     0.146     0.037        6     0.4  G_front_inf-Orbital
 1100    781   3027  2.893 0.462     0.149     0.040       26     1.7  G_front_inf-Triangul
 5118   3359  14382  2.984 0.546     0.142     0.036      108     7.2  G_front_middle
 6900   4542  18881  3.068 0.704     0.134     0.035      119    10.3  G_front_sup
  669    465   1883  3.440 0.612     0.136     0.039       12     0.9  G_Ins_lg&S_cent_ins
 1015    682   2728  3.106 1.093     0.142     0.058       25     2.1  G_insular_short
 2254   1431   5690  2.940 0.521     0.139     0.036       40     3.2  G_occipital_middle
 2125   1246   4127  2.720 0.512     0.127     0.028       28     2.3  G_occipital_sup
 1641   1061   4624  3.174 0.504     0.134     0.031       35     1.8  G_oc-temp_lat-fusifor
 2795   1880   4958  2.144 0.685     0.141     0.036       49     3.8  G_oc-temp_med-Lingual
 1330    857   4144  3.339 0.880     0.114     0.027       15     1.3  G_oc-temp_med-Parahip
 2608   1785   7656  2.998 0.749     0.142     0.042       51     4.3  G_orbital
 3213   2139   9631  3.071 0.647     0.144     0.033       68     4.2  G_pariet_inf-Angular
 2477   1673   6606  3.054 0.527     0.134     0.027       40     2.8  G_pariet_inf-Supramar
 3186   2012   7637  2.904 0.568     0.134     0.030       53     3.8  G_parietal_sup
 2634   1463   4158  2.179 0.545     0.104     0.027       36     3.0  G_postcentral
 3020   1737   7280  3.037 0.533     0.108     0.030       37     3.6  G_precentral
 2361   1592   6628  3.012 0.564     0.138     0.030       42     2.9  G_precuneus
  831    581   1943  2.338 0.634     0.168     0.066       22     2.4  G_rectus
  593    344    853  2.143 1.402     0.114     0.055       19     1.3  G_subcallosal
  449    252    844  2.480 0.627     0.130     0.037       10     0.4  G_temp_sup-G_T_transv
 1755   1127   5378  3.457 0.490     0.123     0.031       29     1.9  G_temp_sup-Lateral
  701    466   1806  3.518 0.827     0.081     0.014        2     0.4  G_temp_sup-Plan_polar
  808    566   1799  2.853 0.375     0.077     0.010        4     0.3  G_temp_sup-Plan_tempo
 2841   1841   8551  3.161 0.821     0.138     0.040       59     4.8  G_temporal_inf
 2884   1970   9441  3.445 0.551     0.129     0.030       47     3.5  G_temporal_middle
  438    309    678  2.393 0.481     0.095     0.010        2     0.2  Lat_Fis-ant-Horizont
  174    125    279  2.314 0.378     0.098     0.011        1     0.0  Lat_Fis-ant-Vertical
 1251    861   1934  2.735 0.452     0.087     0.014        5     0.7  Lat_Fis-post
 4004   2472   5931  2.130 0.591     0.141     0.039       60     5.9  Pole_occipital
 1822   1266   6125  3.492 0.700     0.135     0.036       32     2.5  Pole_temporal
 2335   1617   3310  2.313 0.601     0.118     0.020       27     1.9  S_calcarine
 3350   2264   4263  2.129 0.625     0.087     0.013       14     1.8  S_central
 1377    967   2231  2.523 0.426     0.095     0.013        7     0.8  S_cingul-Marginalis
  600    392   1030  3.061 0.514     0.101     0.017        3     0.5  S_circular_insula_ant
 1137    777   1696  2.718 0.624     0.076     0.011        4     0.5  S_circular_insula_inf
 1396    978   2276  2.810 0.404     0.094     0.015        5     0.9  S_circular_insula_sup
 1017    739   1806  2.887 0.483     0.108     0.013        6     0.6  S_collat_transv_ant
  485    336    683  2.881 0.556     0.135     0.024        5     0.5  S_collat_transv_post
 2387   1711   4036  2.437 0.442     0.116     0.026       29     2.0  S_front_inf
 2619   1866   4374  2.353 0.514     0.115     0.023       25     2.6  S_front_middle
 3169   2223   5369  2.520 0.466     0.088     0.013       15     1.7  S_front_sup
  532    364    779  2.750 0.331     0.114     0.022        3     0.5  S_interm_prim-Jensen
 3591   2482   5786  2.446 0.408     0.088     0.012       18     1.9  S_intrapariet&P_trans
 1098    740   1551  2.466 0.458     0.120     0.024        7     1.2  S_oc_middle&Lunatus
 1286    895   1864  2.416 0.396     0.106     0.015        8     0.8  S_oc_sup&transversal
  672    492   1272  2.589 0.484     0.117     0.022        6     0.5  S_occipital_ant
 1019    691   1748  2.847 0.475     0.108     0.018        5     0.8  S_oc-temp_lat
 2395   1699   3848  2.696 0.491     0.106     0.016       18     1.5  S_oc-temp_med&Lingual
  359    264    706  2.774 0.539     0.116     0.018        2     0.3  S_orbital_lateral
  655    478   1006  2.428 0.687     0.106     0.020        5     0.4  S_orbital_med-olfact
 1641   1101   3077  2.871 0.720     0.122     0.028       15     1.9  S_orbital-H_Shaped
 2745   1903   4531  2.588 0.479     0.117     0.023       26     2.4  S_parieto_occipital
 1641   1018   1627  1.943 0.790     0.113     0.015       21     0.8  S_pericallosal
 2820   1940   3903  2.282 0.388     0.104     0.016       22     1.9  S_postcentral
 1935   1385   3341  2.570 0.487     0.103     0.017       13     1.4  S_precentral-inf-part
 1262    831   1863  2.663 0.378     0.076     0.009        4     0.5  S_precentral-sup-part
  212    150    359  2.929 0.634     0.136     0.021        2     0.2  S_suborbital
 1043    703   1768  2.649 0.504     0.105     0.017        8     0.7  S_subparietal
 1133    793   1911  2.957 0.428     0.115     0.023        7     1.0  S_temporal_inf
 6581   4537  12162  2.943 0.502     0.096     0.014       43     3.8  S_temporal_sup
  308    228    483  2.763 0.359     0.139     0.015        3     0.2  S_temporal_transverse
PIDs (22744 22747) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 02:04:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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 02:04:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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 22835 of (22835 22838) to complete...
Waiting for PID 22838 of (22835 22838) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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...
1060 labels changed using aseg
relabeling using gibbs priors...
000:   2005 changed, 139581 examined...
001:    410 changed, 9342 examined...
002:     88 changed, 2336 examined...
003:     35 changed, 560 examined...
004:     22 changed, 194 examined...
005:     11 changed, 107 examined...
006:     14 changed, 66 examined...
007:     12 changed, 66 examined...
008:      4 changed, 50 examined...
009:      5 changed, 23 examined...
010:      4 changed, 23 examined...
011:      8 changed, 26 examined...
012:      5 changed, 30 examined...
013:      1 changed, 24 examined...
014:      3 changed, 7 examined...
015:      1 changed, 13 examined...
016:      0 changed, 7 examined...
169 labels changed using aseg
000: 53 total segments, 20 labels (231 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1172 vertices marked for relabeling...
1172 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050166 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...
1168 labels changed using aseg
relabeling using gibbs priors...
000:   2028 changed, 141740 examined...
001:    469 changed, 9466 examined...
002:    129 changed, 2709 examined...
003:     42 changed, 786 examined...
004:     23 changed, 236 examined...
005:     16 changed, 124 examined...
006:     13 changed, 83 examined...
007:      9 changed, 82 examined...
008:      7 changed, 42 examined...
009:      3 changed, 37 examined...
010:      1 changed, 19 examined...
011:      0 changed, 7 examined...
171 labels changed using aseg
000: 58 total segments, 25 labels (167 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
7 filter iterations complete (10 requested, 0 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1116 vertices marked for relabeling...
1116 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.
PIDs (22835 22838) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 02:04:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 02:04:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 rh white 

Waiting for PID 22901 of (22901 22904) to complete...
Waiting for PID 22904 of (22901 22904) 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 0050166 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 288391
Total vertex volume 284396 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1515   1058   3057  2.826 0.720     0.119     0.016       19     0.9  caudalanteriorcingulate
 3772   2548   8112  2.822 0.544     0.106     0.019       32     2.8  caudalmiddlefrontal
 3144   2079   5624  2.400 0.610     0.135     0.029       43     3.6  cuneus
  713    468   1844  3.219 0.711     0.114     0.034        7     1.0  entorhinal
 4465   2946   9657  2.972 0.554     0.127     0.027       58     4.5  fusiform
 5911   3990  13472  2.833 0.558     0.125     0.024       94     5.7  inferiorparietal
 5890   3998  15098  2.981 0.789     0.130     0.032       91     8.1  inferiortemporal
 1493    967   2722  2.554 0.969     0.126     0.026       22     1.6  isthmuscingulate
 7483   4888  13163  2.411 0.539     0.135     0.029      105     8.3  lateraloccipital
 4603   3129  11143  2.988 0.741     0.140     0.045       88     8.3  lateralorbitofrontal
 4244   3030   6800  2.199 0.642     0.142     0.033       62     6.2  lingual
 2682   1724   4960  2.423 0.998     0.123     0.043       47     4.6  medialorbitofrontal
 6147   4202  15300  3.004 0.653     0.123     0.026       88     6.2  middletemporal
 1439    916   3021  2.851 0.709     0.092     0.018        9     1.1  parahippocampal
 2258   1499   4611  2.780 0.554     0.103     0.019       17     1.6  paracentral
 2855   1941   6346  2.837 0.467     0.129     0.028       45     3.0  parsopercularis
 1125    758   2898  2.969 0.598     0.120     0.023       14     1.1  parsorbitalis
 2851   1983   6278  2.606 0.590     0.130     0.030       46     3.5  parstriangularis
 1794   1388   2565  1.949 0.521     0.125     0.029       18     1.9  pericalcarine
 7992   5165  12637  2.196 0.641     0.106     0.022       85     7.0  postcentral
 2175   1473   4497  2.677 0.865     0.126     0.025       31     2.0  posteriorcingulate
 7743   5009  15089  2.725 0.527     0.110     0.023       87     7.3  precentral
 6243   4137  13592  2.869 0.560     0.120     0.023       78     5.7  precuneus
 1947   1291   4683  3.127 0.773     0.137     0.036       36     2.7  rostralanteriorcingulate
 6560   4621  14845  2.564 0.653     0.137     0.034      111     9.1  rostralmiddlefrontal
12221   8489  31188  2.981 0.624     0.126     0.029      173    14.1  superiorfrontal
 7525   4905  14168  2.512 0.510     0.117     0.021       95     6.4  superiorparietal
 7137   4753  18061  3.066 0.734     0.102     0.023       75     6.8  superiortemporal
 5055   3478  11194  2.784 0.622     0.131     0.027       69     5.4  supramarginal
  700    443   1152  2.472 0.481     0.131     0.029       11     0.7  transversetemporal
 2723   1882   6621  3.323 0.686     0.109     0.024       26     2.6  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 0050166 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 290970
Total vertex volume 286777 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1252    836   2925  2.784 0.857     0.135     0.025       20     1.1  caudalanteriorcingulate
 4249   2820   9218  2.839 0.577     0.114     0.023       48     3.8  caudalmiddlefrontal
 3165   2081   5412  2.303 0.593     0.138     0.031       48     3.7  cuneus
  526    372   2035  3.665 0.764     0.126     0.026        6     0.5  entorhinal
 3897   2645   8613  3.034 0.514     0.121     0.024       52     3.6  fusiform
 8173   5561  19307  2.901 0.578     0.120     0.025      110     8.3  inferiorparietal
 5266   3516  13814  3.114 0.736     0.125     0.032       81     7.0  inferiortemporal
 1299    816   2533  2.652 0.910     0.142     0.033       27     1.4  isthmuscingulate
 8508   5308  14951  2.479 0.572     0.131     0.032      112    10.3  lateraloccipital
 4443   3069   9630  2.801 0.792     0.137     0.040       68     6.9  lateralorbitofrontal
 4729   3235   7717  2.210 0.603     0.138     0.032       74     5.9  lingual
 2445   1624   5103  2.492 0.895     0.129     0.047       58     5.1  medialorbitofrontal
 6065   4162  15917  3.275 0.568     0.118     0.024       77     5.7  middletemporal
 1206    780   2596  2.965 0.698     0.096     0.020       10     0.9  parahippocampal
 2533   1693   5359  2.774 0.542     0.113     0.018       23     1.9  paracentral
 2702   1869   6090  2.759 0.477     0.122     0.028       38     2.8  parsopercularis
  996    657   2619  2.951 0.574     0.118     0.026       13     1.0  parsorbitalis
 2430   1692   5227  2.680 0.546     0.129     0.029       42     2.7  parstriangularis
 2198   1506   2585  1.919 0.586     0.119     0.023       20     2.1  pericalcarine
 7825   4899  12434  2.244 0.651     0.103     0.023       87     7.4  postcentral
 2088   1376   4274  2.593 0.854     0.127     0.028       31     2.5  posteriorcingulate
 7880   4947  15411  2.791 0.526     0.102     0.024       73     7.5  precentral
 5844   4005  12658  2.789 0.539     0.123     0.025       75     5.6  precuneus
 1303    896   3618  3.211 0.870     0.129     0.034       21     1.9  rostralanteriorcingulate
 6904   4816  15161  2.607 0.590     0.132     0.031      108     8.8  rostralmiddlefrontal
13510   9263  31549  2.854 0.678     0.122     0.028      176    15.6  superiorfrontal
 7743   5099  15142  2.654 0.545     0.112     0.021       82     6.5  superiorparietal
 6935   4675  16578  3.139 0.655     0.101     0.019       62     5.2  superiortemporal
 4870   3324  10370  2.823 0.517     0.116     0.022       55     4.5  supramarginal
  558    341    934  2.439 0.547     0.142     0.036       12     0.5  transversetemporal
 2956   2033   6997  3.245 0.635     0.115     0.027       34     3.0  insula
PIDs (22901 22904) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 02:05:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 pctsurfcon --s 0050166 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 02:05:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts

 pctsurfcon --s 0050166 --rh-only 

Waiting for PID 22971 of (22971 22982) to complete...
Waiting for PID 22982 of (22971 22982) to complete...

 pctsurfcon --s 0050166 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts/pctsurfcon.log
Sun Oct  8 02:05:31 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-6.0.0/0050166/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-960 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-6.0.0/0050166/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22971/lh.wm.mgh --regheader 0050166 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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   0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 71693
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22971/lh.wm.mgh
Dim: 139581 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22971/lh.gm.mgh --projfrac 0.3 --regheader 0050166 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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   0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 88754
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22971/lh.gm.mgh
Dim: 139581 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22971/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22971/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.w-g.pct.mgh --annot 0050166 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/lh.w-g.pct.mgh --annot 0050166 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/lh.w-g.pct.mgh
Vertex Area is 0.672307 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 0050166 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/scripts/pctsurfcon.log
Sun Oct  8 02:05:31 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-6.0.0/0050166/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-960 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-6.0.0/0050166/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22982/rh.wm.mgh --regheader 0050166 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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   0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 73050
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22982/rh.wm.mgh
Dim: 141740 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22982/rh.gm.mgh --projfrac 0.3 --regheader 0050166 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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   0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 90082
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22982/rh.gm.mgh
Dim: 141740 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22982/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/tmp.pctsurfcon.22982/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.w-g.pct.mgh --annot 0050166 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.w-g.pct.mgh --annot 0050166 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.w-g.pct.mgh
Vertex Area is 0.668873 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 (22971 22982) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 02:05:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1040 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1082 voxels changed to hypointensity...
2090 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 02:06:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166

 mri_aparc2aseg --s 0050166 --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 02:06:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166

 mri_aparc2aseg --s 0050166 --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 02:06:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166

 mri_aparc2aseg --s 0050166 --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 23140 of (23140 23143 23146) to complete...
Waiting for PID 23143 of (23140 23143 23146) to complete...
Waiting for PID 23146 of (23140 23143 23146) to complete...

 mri_aparc2aseg --s 0050166 --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 0050166
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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-6.0.0/0050166/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 6.23
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 59
rescaling Left_Lateral_Ventricle from 13 --> 12
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 76
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 88
rescaling Third_Ventricle from 25 --> 22
rescaling Fourth_Ventricle from 22 --> 17
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 30
rescaling Left_Accumbens_area from 62 --> 61
rescaling Left_VentralDC from 87 --> 92
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 10
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 72
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 70
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 27
rescaling WM_hypointensities from 78 --> 77
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 = 566925
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 86 changed.
pass 2: 5 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050166 --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 0050166
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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-6.0.0/0050166/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 6.23
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 59
rescaling Left_Lateral_Ventricle from 13 --> 12
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 76
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 88
rescaling Third_Ventricle from 25 --> 22
rescaling Fourth_Ventricle from 22 --> 17
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 30
rescaling Left_Accumbens_area from 62 --> 61
rescaling Left_VentralDC from 87 --> 92
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 10
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 72
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 70
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 27
rescaling WM_hypointensities from 78 --> 77
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 = 566981
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 86 changed.
pass 2: 5 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050166 --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 0050166
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/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-6.0.0/0050166/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 6.23
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 59
rescaling Left_Lateral_Ventricle from 13 --> 12
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 76
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 88
rescaling Third_Ventricle from 25 --> 22
rescaling Fourth_Ventricle from 22 --> 17
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 30
rescaling Left_Accumbens_area from 62 --> 61
rescaling Left_VentralDC from 87 --> 92
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 10
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 72
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 70
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 27
rescaling WM_hypointensities from 78 --> 77
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 = 566981
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 86 changed.
pass 2: 5 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (23140 23143 23146) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 02:14:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri

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

Sun Oct  8 02:14:14 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-6.0.0/0050166/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-960 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-6.0.0/0050166/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-960
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 02:14:14 CEST 2017 
Ended   at Sun Oct  8 02:14:21 CEST 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 02:14:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166

 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 0050166 


$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 0050166 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1507855 mm^3    (det: 1.291971 )
Computing euler number
orig.nofix lheno =  -38, rheno = -54
orig.nofix lhholes =   20, rhholes = 28
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
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 02:16:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166

 mri_aparc2aseg --s 0050166 --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 0050166
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-6.0.0/0050166/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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-6.0.0/0050166/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7174 vertices from left hemi
Ripped 7246 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-6.0.0/0050166/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 = 957568
Used brute-force search on 64 voxels
Fixing Parahip LH WM
  Found 14 clusters
     0 k 2.000000
     1 k 1.000000
     2 k 5.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1.000000
     9 k 4.000000
     10 k 24.000000
     11 k 3.000000
     12 k 1836.000000
     13 k 2.000000
Fixing Parahip RH WM
  Found 10 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 2.000000
     3 k 2.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 11.000000
     8 k 1380.000000
     9 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050166 --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 0050166 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1507855 mm^3    (det: 1.291971 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
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-6.0.0/0050166/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 02:27:08 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 25092 of (25092 25098 25104 25109 25114) to complete...
Waiting for PID 25098 of (25092 25098 25104 25109 25114) to complete...
Waiting for PID 25104 of (25092 25098 25104 25109 25114) to complete...
Waiting for PID 25109 of (25092 25098 25104 25109 25114) to complete...
Waiting for PID 25114 of (25092 25098 25104 25109 25114) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 539
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4668
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 857
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8766
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 162
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4239
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 344
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6327
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 378
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6162
mri_label2label: Done

PIDs (25092 25098 25104 25109 25114) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 25207 of (25207 25213 25219 25224) to complete...
Waiting for PID 25213 of (25207 25213 25219 25224) to complete...
Waiting for PID 25219 of (25207 25213 25219 25224) to complete...
Waiting for PID 25224 of (25207 25213 25219 25224) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 274
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4344
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 1291
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14880
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 596
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4777
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 1188
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4610
mri_label2label: Done

PIDs (25207 25213 25219 25224) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 25270 of (25270 25276 25282 25288 25292) to complete...
Waiting for PID 25276 of (25270 25276 25282 25288 25292) to complete...
Waiting for PID 25282 of (25270 25276 25282 25288 25292) to complete...
Waiting for PID 25288 of (25270 25276 25282 25288 25292) to complete...
Waiting for PID 25292 of (25270 25276 25282 25288 25292) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 1207
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5848
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 2568
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10682
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 430
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2448
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 164
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1454
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 153
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1352
mri_label2label: Done

PIDs (25270 25276 25282 25288 25292) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 25359 of (25359 25365 25371 25377 25383) to complete...
Waiting for PID 25365 of (25359 25365 25371 25377 25383) to complete...
Waiting for PID 25371 of (25359 25365 25371 25377 25383) to complete...
Waiting for PID 25377 of (25359 25365 25371 25377 25383) to complete...
Waiting for PID 25383 of (25359 25365 25371 25377 25383) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 116
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1130
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 276
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2368
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 54
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1558
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2101
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 126
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2445
mri_label2label: Done

PIDs (25359 25365 25371 25377 25383) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 25477 of (25477 25483 25489 25494) to complete...
Waiting for PID 25483 of (25477 25483 25489 25494) to complete...
Waiting for PID 25489 of (25477 25483 25489 25494) to complete...
Waiting for PID 25494 of (25477 25483 25489 25494) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 78
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1627
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 492
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7527
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 280
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2192
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 411
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1562
mri_label2label: Done

PIDs (25477 25483 25489 25494) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 25543 of (25543 25549 25555 25559 25565) to complete...
Waiting for PID 25549 of (25543 25549 25555 25559 25565) to complete...
Waiting for PID 25555 of (25543 25549 25555 25559 25565) to complete...
Waiting for PID 25559 of (25543 25549 25555 25559 25565) to complete...
Waiting for PID 25565 of (25543 25549 25555 25559 25565) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 814
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4219
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 1204
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4538
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 111
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 624
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 54
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 524
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 139581
Number of reverse mapping hits = 51
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 501
mri_label2label: Done

PIDs (25543 25549 25555 25559 25565) completed and logs appended.

 mris_label2annot --s 0050166 --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-6.0.0/0050166/label
cmdline mris_label2annot --s 0050166 --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-960
machine  x86_64
user     ntraut

subject 0050166
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-6.0.0/0050166/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 96432 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050166 --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-6.0.0/0050166/label
cmdline mris_label2annot --s 0050166 --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-960
machine  x86_64
user     ntraut

subject 0050166
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-6.0.0/0050166/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 114900 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 288391
Total vertex volume 284396 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1400    797   2212  2.130 0.591     0.136     0.046       28     2.5  BA1_exvivo
 4409   2889   7645  2.408 0.500     0.102     0.017       43     2.9  BA2_exvivo
 1103    762   1236  2.040 0.421     0.118     0.017        8     0.7  BA3a_exvivo
 2499   1656   3754  1.911 0.659     0.098     0.017       22     1.8  BA3b_exvivo
 1592    981   3502  2.898 0.462     0.108     0.022       18     1.4  BA4a_exvivo
 1308    860   2318  2.754 0.372     0.084     0.014        7     0.7  BA4p_exvivo
 9469   6245  22460  2.958 0.596     0.116     0.026      110     9.6  BA6_exvivo
 2709   1863   5533  2.718 0.446     0.116     0.024       36     2.3  BA44_exvivo
 3689   2576   8545  2.639 0.605     0.136     0.033       66     4.9  BA45_exvivo
 3244   2471   4698  1.848 0.460     0.137     0.036       42     4.6  V1_exvivo
 8165   5382  13463  2.332 0.608     0.143     0.033      124    11.0  V2_exvivo
 2085   1380   3996  2.609 0.475     0.109     0.018       21     1.4  MT_exvivo
  690    441   1939  3.138 0.711     0.094     0.029        6     0.9  perirhinal_exvivo
  787    547   1919  3.291 0.624     0.119     0.022        6     0.7  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 0050166 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 288391
Total vertex volume 284396 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
  814    466   1425  2.187 0.526     0.142     0.046       17     1.3  BA1_exvivo
 1804   1160   2945  2.332 0.477     0.093     0.014       15     1.0  BA2_exvivo
  954    652    985  2.011 0.378     0.120     0.018        7     0.6  BA3a_exvivo
 1513   1041   1723  1.595 0.383     0.078     0.012        7     0.8  BA3b_exvivo
 1526    961   3251  2.911 0.433     0.090     0.016       10     0.9  BA4a_exvivo
 1076    716   1889  2.730 0.381     0.094     0.015        7     0.6  BA4p_exvivo
 4908   3154  11442  2.973 0.635     0.117     0.029       62     5.6  BA6_exvivo
 1786   1245   3951  2.794 0.468     0.124     0.026       28     1.8  BA44_exvivo
 1428   1019   3873  2.774 0.575     0.145     0.038       30     2.1  BA45_exvivo
 3436   2599   4939  1.839 0.450     0.135     0.035       44     4.6  V1_exvivo
 4147   2731   6525  2.222 0.574     0.153     0.038       72     6.7  V2_exvivo
  543    358   1359  2.859 0.460     0.108     0.019        6     0.4  MT_exvivo
  342    220   1079  3.349 0.642     0.074     0.014        1     0.2  perirhinal_exvivo
  404    288    973  3.302 0.451     0.103     0.013        2     0.2  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 02:30:31 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 25733 of (25733 25739 25745 25751 25757) to complete...
Waiting for PID 25739 of (25733 25739 25745 25751 25757) to complete...
Waiting for PID 25745 of (25733 25739 25745 25751 25757) to complete...
Waiting for PID 25751 of (25733 25739 25745 25751 25757) to complete...
Waiting for PID 25757 of (25733 25739 25745 25751 25757) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 599
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4561
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 687
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7374
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 198
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4178
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 530
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5052
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 387
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6134
mri_label2label: Done

PIDs (25733 25739 25745 25751 25757) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 25799 of (25799 25805 25811 25817) to complete...
Waiting for PID 25805 of (25799 25805 25811 25817) to complete...
Waiting for PID 25811 of (25799 25805 25811 25817) to complete...
Waiting for PID 25817 of (25799 25805 25811 25817) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 238
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4711
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 1028
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13284
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 1174
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8086
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 1076
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6431
mri_label2label: Done

PIDs (25799 25805 25811 25817) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 25867 of (25867 25873 25879 25884 25890) to complete...
Waiting for PID 25873 of (25867 25873 25879 25884 25890) to complete...
Waiting for PID 25879 of (25867 25873 25879 25884 25890) to complete...
Waiting for PID 25884 of (25867 25873 25879 25884 25890) to complete...
Waiting for PID 25890 of (25867 25873 25879 25884 25890) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 1527
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6254
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 3336
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11352
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 379
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2311
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 96
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1134
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 53
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 805
mri_label2label: Done

PIDs (25867 25873 25879 25884 25890) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 25947 of (25947 25953 25959 25964 25971) to complete...
Waiting for PID 25953 of (25947 25953 25959 25964 25971) to complete...
Waiting for PID 25959 of (25947 25953 25959 25964 25971) to complete...
Waiting for PID 25964 of (25947 25953 25959 25964 25971) to complete...
Waiting for PID 25971 of (25947 25953 25959 25964 25971) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 167
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1043
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 65
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1763
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 188
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2371
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1473
mri_label2label: Done

PIDs (25947 25953 25959 25964 25971) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 26017 of (26017 26023 26029 26034) to complete...
Waiting for PID 26023 of (26017 26023 26029 26034) to complete...
Waiting for PID 26029 of (26017 26023 26029 26034) to complete...
Waiting for PID 26034 of (26017 26023 26029 26034) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 62
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1551
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 459
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7418
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 238
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1250
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1412
mri_label2label: Done

PIDs (26017 26023 26029 26034) 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 0050166 --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 0050166 --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 0050166 --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 0050166 --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 0050166 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 26095 of (26095 26101 26107 26110 26117) to complete...
Waiting for PID 26101 of (26095 26101 26107 26110 26117) to complete...
Waiting for PID 26107 of (26095 26101 26107 26110 26117) to complete...
Waiting for PID 26110 of (26095 26101 26107 26110 26117) to complete...
Waiting for PID 26117 of (26095 26101 26107 26110 26117) 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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 954
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4186
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 1425
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4862
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 24
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 292
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 61
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 755
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 0050166 --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 = 0050166
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-6.0.0/0050166/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 141740
Number of reverse mapping hits = 12
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 303
mri_label2label: Done

PIDs (26095 26101 26107 26110 26117) completed and logs appended.

 mris_label2annot --s 0050166 --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-6.0.0/0050166/label
cmdline mris_label2annot --s 0050166 --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-960
machine  x86_64
user     ntraut

subject 0050166
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-6.0.0/0050166/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 98132 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050166 --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-6.0.0/0050166/label
cmdline mris_label2annot --s 0050166 --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-960
machine  x86_64
user     ntraut

subject 0050166
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-6.0.0/0050166/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 118001 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/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 0050166 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 290970
Total vertex volume 286777 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
 1209    603   2042  2.355 0.464     0.116     0.031       22     1.3  BA1_exvivo
 3612   2348   5860  2.354 0.458     0.105     0.022       41     3.3  BA2_exvivo
 1169    799   1265  2.036 0.446     0.118     0.023        8     1.0  BA3a_exvivo
 2278   1483   3044  1.794 0.542     0.089     0.016       16     1.5  BA3b_exvivo
 1596    975   3308  2.774 0.548     0.094     0.029       13     1.9  BA4a_exvivo
 1293    860   2327  2.733 0.385     0.092     0.014        8     0.7  BA4p_exvivo
 7953   5057  18302  2.987 0.618     0.109     0.026       88     8.6  BA6_exvivo
 4348   2989   8725  2.671 0.511     0.119     0.023       49     4.2  BA44_exvivo
 4487   3138  10421  2.731 0.541     0.133     0.032       77     5.3  BA45_exvivo
 3858   2619   5184  1.889 0.561     0.130     0.033       49     4.8  V1_exvivo
 8888   5672  14701  2.324 0.597     0.140     0.033      135    11.5  V2_exvivo
 1939   1338   3969  2.732 0.504     0.121     0.026       21     1.9  MT_exvivo
  603    407   2154  3.518 0.734     0.111     0.030        6     0.6  perirhinal_exvivo
  375    281   1057  3.368 0.679     0.142     0.034        6     0.6  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 0050166 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050166/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 290970
Total vertex volume 286777 (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) = 1507855 mm^3    (det: 1.291971 )
lhCtxGM: 283343.200 282680.000  diff=  663.2  pctdiff= 0.234
rhCtxGM: 285669.487 285054.000  diff=  615.5  pctdiff= 0.215
lhCtxWM: 195621.769 196089.000  diff= -467.2  pctdiff=-0.239
rhCtxWM: 195715.777 196025.000  diff= -309.2  pctdiff=-0.158
SubCortGMVol  60491.000
SupraTentVol  1036723.234 (1034274.000) diff=2449.234 pctdiff=0.236
SupraTentVolNotVent  1022802.234 (1020353.000) diff=2449.234 pctdiff=0.239
BrainSegVol  1183198.000 (1180938.000) diff=2260.000 pctdiff=0.191
BrainSegVolNotVent  1166158.000 (1166500.234) diff=-342.234 pctdiff=-0.029
BrainSegVolNotVent  1166158.000
CerebellumVol 145645.000
VentChorVol   13921.000
3rd4th5thCSF   3119.000
CSFVol   859.000, OptChiasmVol   160.000
MaskVol 1535456.000
  811    401   1296  2.236 0.515     0.115     0.028       14     0.9  BA1_exvivo
 2026   1286   3297  2.327 0.412     0.090     0.021       20     1.9  BA2_exvivo
 1040    709   1042  2.075 0.420     0.119     0.022        6     1.0  BA3a_exvivo
 1764   1179   1932  1.593 0.381     0.074     0.011        7     0.8  BA3b_exvivo
  932    564   2096  2.796 0.663     0.116     0.043       12     1.6  BA4a_exvivo
 1031    694   1821  2.724 0.396     0.085     0.013        4     0.5  BA4p_exvivo
 4939   3136  11234  2.967 0.574     0.108     0.025       50     5.1  BA6_exvivo
 1074    744   2593  2.818 0.468     0.140     0.036       18     1.5  BA44_exvivo
 1188    871   2966  2.696 0.479     0.136     0.039       21     1.7  BA45_exvivo
 3649   2481   4862  1.903 0.577     0.124     0.029       39     4.2  V1_exvivo
 4458   2899   6604  2.119 0.585     0.153     0.039       84     6.8  V2_exvivo
  219    160    436  2.457 0.505     0.139     0.026        3     0.3  MT_exvivo
  378    239   1329  3.515 0.727     0.098     0.020        3     0.3  perirhinal_exvivo
  230    193    659  3.309 0.598     0.134     0.023        2     0.2  entorhinal_exvivo

Started at Sat Oct 7 18:00:46 CEST 2017 
Ended   at Sun Oct 8 02:33:54 CEST 2017
#@#%# recon-all-run-time-hours 8.552
recon-all -s 0050166 finished without error at Sun Oct  8 02:33:54 CEST 2017