ABIDE_fs-6.0.0/0050418/scripts/recon-all.log

Thu Oct 26 21:16:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050418 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 1
subjid 0050418
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-623 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:      65993348   61670368    4322980    2171432          0   59689464
-/+ buffers/cache:    1980904   64012444
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: 2017/10/26-19:16:50-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:51-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-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: ntraut  Machine: tars-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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: 2017/10/26-19:16:53-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-623  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-6.0.0/0050418

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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/UM_2/0050418/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-6.0.0/0050418/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Oct 26 21:16:55 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/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-6.0.0/0050418/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Oct 26 21:17:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/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-623 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
Thu Oct 26 21:17:03 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.9207
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9207/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9207/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.9207/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Oct 26 21:17:05 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.9207/nu0.mnc ./tmp.mri_nu_correct.mni.9207/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9207/0/ -iterations 1000 -distance 50
[ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/] [2017-10-26 21:17:05] 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.9207/0/ ./tmp.mri_nu_correct.mni.9207/nu0.mnc ./tmp.mri_nu_correct.mni.9207/nu1.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 30 
CV of field change: 0.000966525
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.9207/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.9207/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.9207/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...
 
 
Thu Oct 26 21:18:06 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 Thu Oct 26 21:18:06 CEST 2017
Ended   at Thu Oct 26 21:18:49 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Thu Oct 26 21:18:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7729, pval=0.6675 >= 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-6.0.0/0050418/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach_avi.log 

TalAviQA: 0.97571
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Thu Oct 26 21:18:51 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-6.0.0/0050418/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-623 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
Thu Oct 26 21:18:51 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.10482
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10482/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10482/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.10482/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Oct 26 21:18:54 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10482/nu0.mnc ./tmp.mri_nu_correct.mni.10482/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10482/0/
[ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/] [2017-10-26 21:18:54] 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.10482/0/ ./tmp.mri_nu_correct.mni.10482/nu0.mnc ./tmp.mri_nu_correct.mni.10482/nu1.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 23 
CV of field change: 0.000970842
 
 
--------------------------------------------------------
Iteration 2 Thu Oct 26 21:19:39 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10482/nu1.mnc ./tmp.mri_nu_correct.mni.10482/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10482/1/
[ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/] [2017-10-26 21:19:39] 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.10482/1/ ./tmp.mri_nu_correct.mni.10482/nu1.mnc ./tmp.mri_nu_correct.mni.10482/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 11 
CV of field change: 0.000962955
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10482/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-6.0.0/0050418/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10482/ones.mgz 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.10482/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.10482/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.10482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/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.10482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/input.mean.dat 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.10482/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.10482/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10482/ones.mgz --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/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.10482/ones.mgz --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/output.mean.dat 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.10482/ones.mgz
Loading ./tmp.mri_nu_correct.mni.10482/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.10482/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.10482/nu2.mnc ./tmp.mri_nu_correct.mni.10482/nu2.mnc mul 1.02006471169111547311
Saving result to './tmp.mri_nu_correct.mni.10482/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.10482/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.10482/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.10482/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 (18, 98) to ( 3, 110)
 
 
Thu Oct 26 21:21:01 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Oct 26 21:21:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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
 1.04097  -0.04239  -0.06629  -5.29266;
 0.00666   1.05572   0.17579  -1.07414;
 0.07116  -0.20519   1.08700  -8.95361;
 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 = 13
Starting OpenSpline(): npoints = 13
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 90
gm peak at 66 (66), valley at 30 (30)
csf peak at 34, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 19 (19)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 20 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Oct 26 21:23:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 1 == 
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=12.0
skull bounding box = (51, 40, 18) --> (199, 192, 210)
using (100, 91, 114) as brain centroid...
mean wm in atlas = 108, using box (82,72,90) --> (118, 109,137) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 101 +- 7.4
after smoothing, mri peak at 101, scaling input intensities by 1.069
scaling channel 0 by 1.06931
initial log_p = -4.380
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.475875 @ (0.000, 0.000, 0.000)
max log p =    -4.434344 @ (4.545, 4.545, -4.545)
max log p =    -4.386528 @ (2.273, -6.818, 2.273)
max log p =    -4.350627 @ (-3.409, -1.136, 1.136)
max log p =    -4.328517 @ (-0.568, 6.250, -3.977)
max log p =    -4.328517 @ (0.000, 0.000, 0.000)
Found translation: (2.8, 2.8, -5.1): log p = -4.329
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.169, old_max_log_p =-4.329 (thresh=-4.3)
 0.99144  -0.01959   0.12941  -8.40144;
 0.00000   1.22567   0.14032  -37.38474;
-0.14032  -0.15998   1.05669   27.72302;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.169, old_max_log_p =-4.169 (thresh=-4.2)
 0.99144  -0.01959   0.12941  -8.40144;
 0.00000   1.22567   0.14032  -37.38474;
-0.14032  -0.15998   1.05669   27.72302;
 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=-4.093, old_max_log_p =-4.169 (thresh=-4.2)
 1.01829  -0.05325   0.02250   6.74322;
 0.03572   1.16061   0.10545  -32.60637;
-0.04825  -0.12769   1.12894   5.93081;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.093, old_max_log_p =-4.093 (thresh=-4.1)
 1.01829  -0.05325   0.02250   6.74322;
 0.03572   1.16061   0.10545  -32.60637;
-0.04825  -0.12769   1.12894   5.93081;
 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=-4.071, old_max_log_p =-4.093 (thresh=-4.1)
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.071, old_max_log_p =-4.071 (thresh=-4.1)
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 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
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.071 (old=-4.380)
transform before final EM align:
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 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
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.5  tol 0.000000
final transform:
 1.01710  -0.05319   0.02247   7.35184;
 0.03560   1.15653   0.10508  -31.99239;
-0.04836  -0.12799   1.13158   5.68473;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1137.771032
mri_em_register stimesec    1.124829
mri_em_register ru_maxrss   609804
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   160654
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  148912
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    53
mri_em_register ru_nivcsw   3136
registration took 18 minutes and 58 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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=120 y=110 z=112 r=68
      first estimation of the main basin volume: 1353111 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        14 found in the rest of the brain 
      global maximum in x=93, y=104, z=79, Imax=255
      CSF=19, 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=7658985528 voxels, voxel volume =1.000 
                     = 7658985528 mmm3 = 7658985.472 cm3
done.
PostAnalyze...Basin Prior
 284 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
      ambiguous basin, non merged: 1 ambiguous voxels; size: 2913 voxels
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=121,y=116, z=105, r=8954 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 45063
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1035607993
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1045139458
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1087311690
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1066026468
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1079567910
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    3,      4,        35,   56
  after  analyzing :    3,      24,        35,   32
   RIGHT_CER   
  before analyzing :    3,      4,        37,   67
  after  analyzing :    3,      26,        37,   36
   LEFT_CER    
  before analyzing :    3,      5,        41,   57
  after  analyzing :    3,      29,        41,   36
  RIGHT_BRAIN  
  before analyzing :    3,      4,        36,   56
  after  analyzing :    3,      25,        36,   32
  LEFT_BRAIN   
  before analyzing :    3,      4,        33,   56
  after  analyzing :    3,      23,        33,   31
     OTHER     
  before analyzing :    4,      6,        35,   56
  after  analyzing :    4,      25,        35,   32
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...63 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 70.554, std = 7.207

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.65, sigma = 3.85
      after  rotation: sse = 2.65, sigma = 3.85
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.85, its var is  3.74   
      before Erosion-Dilatation  0.34% 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...32 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1625863 voxels, voxel volume = 1.000 mm3
           = 1625863 mmm3 = 1625.863 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    21.064797
mri_watershed stimesec    0.482926
mri_watershed ru_maxrss   818700
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   210377
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  7552
mri_watershed ru_oublock  2592
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    154
mri_watershed ru_nivcsw   123
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Oct 26 21:42:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 1 == 
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=28.0
skull bounding box = (52, 57, 33) --> (191, 183, 188)
using (98, 99, 111) as brain centroid...
mean wm in atlas = 107, using box (81,84,92) --> (115, 114,130) to find MRI wm
before smoothing, mri peak at 100
robust fit to distribution - 100 +- 7.5
after smoothing, mri peak at 100, scaling input intensities by 1.070
scaling channel 0 by 1.07
initial log_p = -3.974
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.070300 @ (0.000, 0.000, 0.000)
max log p =    -3.935298 @ (4.545, 4.545, -4.545)
max log p =    -3.921781 @ (-2.273, -2.273, 2.273)
max log p =    -3.861459 @ (1.136, 1.136, -1.136)
max log p =    -3.859510 @ (-0.568, -1.705, 0.568)
max log p =    -3.857513 @ (-0.284, -1.989, -0.284)
Found translation: (2.6, -0.3, -3.1): log p = -3.858
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.858, old_max_log_p =-3.858 (thresh=-3.9)
 1.00000   0.00000   0.00000   2.55682;
 0.00000   1.00000   0.00000  -0.28409;
 0.00000   0.00000   1.00000  -3.12500;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 1 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.764, old_max_log_p =-3.858 (thresh=-3.9)
 1.01803  -0.00377  -0.00461   3.11295;
 0.00424   1.05436   0.07392  -11.76360;
 0.00442  -0.07258   1.03495   3.31443;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.756, old_max_log_p =-3.764 (thresh=-3.8)
 1.05170  -0.08035   0.06030   1.00317;
 0.07334   1.09098   0.08081  -25.21089;
-0.05984  -0.06947   0.99430   15.13697;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.756, old_max_log_p =-3.756 (thresh=-3.8)
 1.05170  -0.08035   0.06030   1.00317;
 0.07334   1.09098   0.08081  -25.21089;
-0.05984  -0.06947   0.99430   15.13697;
 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=-3.729, old_max_log_p =-3.756 (thresh=-3.8)
 1.04673  -0.10560   0.04192   6.97104;
 0.09913   1.08872   0.08160  -28.18139;
-0.04251  -0.07041   0.99401   12.67247;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.728, old_max_log_p =-3.729 (thresh=-3.7)
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 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
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.728 (old=-3.974)
transform before final EM align:
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 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
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.1  tol 0.000000
final transform:
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    954.697863
mri_em_register stimesec    0.732888
mri_em_register ru_maxrss   599032
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158993
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    85
mri_em_register ru_nivcsw   2063
registration took 15 minutes and 55 seconds.
#--------------------------------------
#@# CA Normalize Thu Oct 26 21:58:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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=28.0
skull bounding box = (52, 57, 33) --> (191, 183, 188)
using (98, 99, 111) as brain centroid...
mean wm in atlas = 107, using box (81,84,92) --> (115, 114,130) to find MRI wm
before smoothing, mri peak at 100
robust fit to distribution - 100 +- 7.5
after smoothing, mri peak at 100, scaling input intensities by 1.070
scaling channel 0 by 1.07
using 246344 sample points...
INFO: compute sample coordinates transform
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18139;
-0.04241  -0.07024   0.99168   12.88991;
 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 (120, 54, 28) --> (186, 160, 197)
Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
0 of 251 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (59, 57, 27) --> (122, 166, 196)
Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0
23 of 167 (13.8%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 135, 53) --> (175, 172, 107)
Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 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 (85, 136, 49) --> (127, 175, 108)
Right_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0
0 of 18 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 126, 88) --> (143, 191, 119)
Brain_Stem: limiting intensities to 93.0 --> 132.0
3 of 17 (17.6%) samples deleted
using 462 total control points for intensity normalization...
bias field = 0.963 +- 0.096
0 of 436 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (120, 54, 28) --> (186, 160, 197)
Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
119 of 368 (32.3%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (59, 57, 27) --> (122, 166, 196)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 352 (1.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 135, 53) --> (175, 172, 107)
Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0
37 of 40 (92.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 136, 49) --> (127, 175, 108)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
25 of 54 (46.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 126, 88) --> (143, 191, 119)
Brain_Stem: limiting intensities to 88.0 --> 132.0
79 of 86 (91.9%) samples deleted
using 900 total control points for intensity normalization...
bias field = 1.012 +- 0.068
0 of 636 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (120, 54, 28) --> (186, 160, 197)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
15 of 454 (3.3%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (59, 57, 27) --> (122, 166, 196)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
3 of 422 (0.7%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 135, 53) --> (175, 172, 107)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
64 of 80 (80.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 136, 49) --> (127, 175, 108)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
41 of 53 (77.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 126, 88) --> (143, 191, 119)
Brain_Stem: limiting intensities to 88.0 --> 91.0
129 of 129 (100.0%) samples deleted
using 1138 total control points for intensity normalization...
bias field = 1.043 +- 0.068
0 of 831 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 44 seconds.
#--------------------------------------
#@# CA Reg Thu Oct 26 22:00:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 1 == 
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) = 1.15 (predicted orig area = 7.0)
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=0.940, neg=0, invalid=762
0001: dt=362.101792, rms=0.833 (11.405%), neg=0, invalid=762
0002: dt=262.080903, rms=0.799 (4.070%), neg=0, invalid=762
0003: dt=271.508714, rms=0.787 (1.563%), neg=0, invalid=762
0004: dt=182.436782, rms=0.781 (0.768%), neg=0, invalid=762
0005: dt=517.888000, rms=0.774 (0.826%), neg=0, invalid=762
0006: dt=129.472000, rms=0.772 (0.297%), neg=0, invalid=762
0007: dt=2071.552000, rms=0.763 (1.113%), neg=0, invalid=762
0008: dt=129.472000, rms=0.762 (0.164%), neg=0, invalid=762
0009: dt=129.472000, rms=0.761 (0.109%), neg=0, invalid=762
0010: dt=129.472000, rms=0.760 (0.173%), neg=0, invalid=762
0011: dt=129.472000, rms=0.758 (0.194%), neg=0, invalid=762
0012: dt=129.472000, rms=0.757 (0.193%), neg=0, invalid=762
0013: dt=129.472000, rms=0.755 (0.190%), neg=0, invalid=762
0014: dt=129.472000, rms=0.754 (0.201%), neg=0, invalid=762
0015: dt=129.472000, rms=0.752 (0.214%), neg=0, invalid=762
0016: dt=129.472000, rms=0.751 (0.186%), neg=0, invalid=762
0017: dt=129.472000, rms=0.750 (0.185%), neg=0, invalid=762
0018: dt=129.472000, rms=0.748 (0.198%), neg=0, invalid=762
0019: dt=129.472000, rms=0.747 (0.203%), neg=0, invalid=762
0020: dt=129.472000, rms=0.745 (0.178%), neg=0, invalid=762
0021: dt=129.472000, rms=0.744 (0.142%), neg=0, invalid=762
0022: dt=129.472000, rms=0.743 (0.127%), neg=0, invalid=762
0023: dt=129.472000, rms=0.742 (0.110%), neg=0, invalid=762
0024: dt=129.472000, rms=0.742 (0.096%), neg=0, invalid=762
0025: dt=1183.744000, rms=0.741 (0.125%), neg=0, invalid=762
0026: dt=110.976000, rms=0.740 (0.043%), neg=0, invalid=762
0027: dt=110.976000, rms=0.740 (0.031%), neg=0, invalid=762
0028: dt=110.976000, rms=0.740 (0.032%), neg=0, invalid=762
0029: dt=110.976000, rms=0.740 (0.042%), neg=0, invalid=762
0030: dt=110.976000, rms=0.739 (0.042%), neg=0, invalid=762
0031: dt=110.976000, rms=0.739 (0.048%), neg=0, invalid=762
0032: dt=110.976000, rms=0.739 (0.046%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.739, neg=0, invalid=762
0033: dt=221.952000, rms=0.737 (0.223%), neg=0, invalid=762
0034: dt=517.888000, rms=0.737 (0.097%), neg=0, invalid=762
0035: dt=517.888000, rms=0.737 (-0.034%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.743, neg=0, invalid=762
0036: dt=132.977778, rms=0.736 (0.871%), neg=0, invalid=762
0037: dt=160.619355, rms=0.729 (1.017%), neg=0, invalid=762
0038: dt=67.727121, rms=0.725 (0.589%), neg=0, invalid=762
0039: dt=497.664000, rms=0.715 (1.309%), neg=0, invalid=762
0040: dt=76.000000, rms=0.710 (0.730%), neg=0, invalid=762
0041: dt=94.635071, rms=0.708 (0.281%), neg=0, invalid=762
0042: dt=65.523810, rms=0.707 (0.144%), neg=0, invalid=762
0043: dt=65.523810, rms=0.706 (0.136%), neg=0, invalid=762
0044: dt=65.523810, rms=0.704 (0.220%), neg=0, invalid=762
0045: dt=65.523810, rms=0.702 (0.306%), neg=0, invalid=762
0046: dt=65.523810, rms=0.700 (0.348%), neg=0, invalid=762
0047: dt=65.523810, rms=0.697 (0.379%), neg=0, invalid=762
0048: dt=65.523810, rms=0.694 (0.398%), neg=0, invalid=762
0049: dt=65.523810, rms=0.692 (0.366%), neg=0, invalid=762
0050: dt=65.523810, rms=0.689 (0.351%), neg=0, invalid=762
0051: dt=65.523810, rms=0.687 (0.299%), neg=0, invalid=762
0052: dt=65.523810, rms=0.685 (0.276%), neg=0, invalid=762
0053: dt=65.523810, rms=0.684 (0.237%), neg=0, invalid=762
0054: dt=65.523810, rms=0.682 (0.218%), neg=0, invalid=762
0055: dt=65.523810, rms=0.681 (0.187%), neg=0, invalid=762
0056: dt=65.523810, rms=0.680 (0.154%), neg=0, invalid=762
0057: dt=65.523810, rms=0.679 (0.123%), neg=0, invalid=762
0058: dt=65.523810, rms=0.678 (0.109%), neg=0, invalid=762
0059: dt=124.416000, rms=0.678 (0.040%), neg=0, invalid=762
0060: dt=124.416000, rms=0.678 (-0.112%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.679, neg=0, invalid=762
0061: dt=65.991111, rms=0.677 (0.261%), neg=0, invalid=762
0062: dt=145.152000, rms=0.676 (0.140%), neg=0, invalid=762
0063: dt=145.152000, rms=0.676 (-0.086%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.705, neg=0, invalid=762
0064: dt=4.800000, rms=0.704 (0.132%), neg=0, invalid=762
0065: dt=2.000000, rms=0.704 (0.008%), neg=0, invalid=762
0066: dt=2.000000, rms=0.704 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.705, neg=0, invalid=762
0067: dt=0.175000, rms=0.704 (0.084%), neg=0, invalid=762
0068: dt=0.100000, rms=0.704 (0.001%), neg=0, invalid=762
0069: dt=0.100000, rms=0.704 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.784, neg=0, invalid=762
0070: dt=5.771429, rms=0.761 (2.926%), neg=0, invalid=762
0071: dt=4.666667, rms=0.759 (0.285%), neg=0, invalid=762
0072: dt=1.008000, rms=0.759 (0.005%), neg=0, invalid=762
0073: dt=1.008000, rms=0.758 (0.003%), neg=0, invalid=762
0074: dt=1.008000, rms=0.759 (-0.017%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.759, neg=0, invalid=762
0075: dt=0.000000, rms=0.759 (0.057%), neg=0, invalid=762
0076: dt=0.000000, rms=0.759 (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=0.827, neg=0, invalid=762
0077: dt=0.448000, rms=0.825 (0.134%), neg=0, invalid=762
0078: dt=0.768000, rms=0.824 (0.121%), neg=0, invalid=762
0079: dt=0.768000, rms=0.823 (0.169%), neg=0, invalid=762
0080: dt=0.768000, rms=0.822 (0.132%), neg=0, invalid=762
0081: dt=0.768000, rms=0.822 (-0.096%), neg=0, invalid=762
0082: dt=1.792000, rms=0.820 (0.187%), neg=0, invalid=762
0083: dt=1.536000, rms=0.820 (0.039%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.821, neg=0, invalid=762
0084: dt=1.792000, rms=0.818 (0.275%), neg=0, invalid=762
0085: dt=0.096000, rms=0.818 (-0.001%), neg=0, invalid=762
0086: dt=0.096000, rms=0.818 (0.001%), neg=0, invalid=762
0087: dt=0.096000, rms=0.818 (-0.001%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.760, neg=0, invalid=762
0088: dt=0.953825, rms=0.736 (3.232%), neg=0, invalid=762
0089: dt=0.096000, rms=0.735 (0.159%), neg=0, invalid=762
0090: dt=0.096000, rms=0.735 (-0.115%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.735, neg=0, invalid=762
0091: dt=0.028000, rms=0.734 (0.084%), neg=0, invalid=762
0092: dt=0.016000, rms=0.734 (0.003%), neg=0, invalid=762
0093: dt=0.016000, rms=0.734 (-0.005%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.06770 ( 9)
Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (988 voxels, overlap=0.119)
Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (988 voxels, peak = 10), gca=10.5
gca peak = 0.15565 (16)
mri peak = 0.08798 (16)
Right_Lateral_Ventricle (43): linear fit = 0.81 x + 0.0 (795 voxels, overlap=0.614)
Right_Lateral_Ventricle (43): linear fit = 0.81 x + 0.0 (795 voxels, peak = 13), gca=13.0
gca peak = 0.26829 (96)
mri peak = 0.05663 (91)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (1003 voxels, overlap=0.576)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (1003 voxels, peak = 90), gca=89.8
gca peak = 0.20183 (93)
mri peak = 0.11111 (77)
Left_Pallidum: unreasonable value (74.9/77.0), not in range [75, 135] - rejecting
gca peak = 0.21683 (55)
mri peak = 0.08174 (62)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (621 voxels, overlap=0.841)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (621 voxels, peak = 60), gca=60.2
gca peak = 0.30730 (58)
mri peak = 0.06019 (65)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (589 voxels, overlap=0.893)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (589 voxels, peak = 65), gca=64.7
gca peak = 0.11430 (101)
mri peak = 0.05738 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57291 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57291 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.04838 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57324 voxels, overlap=0.828)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57324 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.03925 (67)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (19919 voxels, overlap=0.905)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (19919 voxels, peak = 65), gca=64.6
gca peak = 0.15082 (58)
mri peak = 0.03607 (61)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (17922 voxels, overlap=0.898)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (17922 voxels, peak = 62), gca=62.4
gca peak = 0.14161 (67)
mri peak = 0.09925 (78)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (831 voxels, overlap=0.100)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (831 voxels, peak = 76), gca=76.0
gca peak = 0.15243 (71)
mri peak = 0.08140 (71)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1033 voxels, overlap=0.960)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1033 voxels, peak = 70), gca=69.9
gca peak = 0.13336 (57)
mri peak = 0.04497 (53)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (20891 voxels, overlap=0.970)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (20891 voxels, peak = 54), gca=53.9
gca peak = 0.13252 (56)
mri peak = 0.03901 (54)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21984 voxels, overlap=0.996)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21984 voxels, peak = 54), gca=54.0
gca peak = 0.18181 (84)
mri peak = 0.03150 (81)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (7659 voxels, overlap=0.874)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (7659 voxels, peak = 83), gca=82.7
gca peak = 0.20573 (83)
mri peak = 0.04090 (82)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7627 voxels, overlap=0.960)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7627 voxels, peak = 83), gca=82.6
gca peak = 0.21969 (57)
mri peak = 0.05170 (69)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (327 voxels, overlap=0.789)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (327 voxels, peak = 69), gca=69.3
gca peak = 0.39313 (56)
mri peak = 0.08808 (60)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (288 voxels, overlap=0.999)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (288 voxels, peak = 59), gca=58.5
gca peak = 0.14181 (85)
mri peak = 0.05563 (92)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5581 voxels, overlap=0.941)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5581 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.04955 (90)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4708 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4708 voxels, peak = 88), gca=87.6
gca peak = 0.13399 (79)
mri peak = 0.03556 (90)
Left_Putamen (12): linear fit = 1.15 x + 0.0 (2402 voxels, overlap=0.828)
Left_Putamen (12): linear fit = 1.15 x + 0.0 (2402 voxels, peak = 91), gca=91.2
gca peak = 0.14159 (79)
mri peak = 0.06441 (73)
Right_Putamen (51): linear fit = 0.98 x + 0.0 (2438 voxels, overlap=0.896)
Right_Putamen (51): linear fit = 0.98 x + 0.0 (2438 voxels, peak = 77), gca=77.0
gca peak = 0.10025 (80)
mri peak = 0.14509 (80)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12111 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12111 voxels, peak = 84), gca=84.4
gca peak = 0.13281 (86)
mri peak = 0.06515 (86)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1506 voxels, overlap=0.729)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1506 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.05971 (86)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1588 voxels, overlap=0.852)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1588 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
mri peak = 0.19056 (51)
Third_Ventricle (14): linear fit = 2.17 x + 0.0 (82 voxels, overlap=0.026)
Third_Ventricle (14): linear fit = 2.17 x + 0.0 (82 voxels, peak = 50), gca=50.0
gca peak = 0.15061 (21)
mri peak = 0.13027 ( 6)
Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (240 voxels, overlap=0.018)
Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (240 voxels, peak =  6), gca=6.0
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Left_Pallidum = 0.20183 (93)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
setting label Left_Pallidum based on Right_Pallidum = 0.94 x +  0: 90
estimating mean gm scale to be 1.11 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.67 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=0.735, neg=0, invalid=762
0094: dt=110.976000, rms=0.728 (0.978%), neg=0, invalid=762
0095: dt=295.936000, rms=0.723 (0.668%), neg=0, invalid=762
0096: dt=129.472000, rms=0.721 (0.181%), neg=0, invalid=762
0097: dt=369.920000, rms=0.719 (0.359%), neg=0, invalid=762
0098: dt=73.984000, rms=0.718 (0.133%), neg=0, invalid=762
0099: dt=443.904000, rms=0.717 (0.102%), neg=0, invalid=762
0100: dt=129.472000, rms=0.716 (0.146%), neg=0, invalid=762
0101: dt=129.472000, rms=0.716 (0.033%), neg=0, invalid=762
0102: dt=129.472000, rms=0.716 (0.050%), neg=0, invalid=762
0103: dt=129.472000, rms=0.715 (0.078%), neg=0, invalid=762
0104: dt=129.472000, rms=0.714 (0.077%), neg=0, invalid=762
0105: dt=129.472000, rms=0.714 (0.076%), neg=0, invalid=762
0106: dt=129.472000, rms=0.713 (0.094%), neg=0, invalid=762
0107: dt=129.472000, rms=0.713 (0.084%), neg=0, invalid=762
0108: dt=129.472000, rms=0.712 (0.062%), neg=0, invalid=762
0109: dt=129.472000, rms=0.712 (0.043%), neg=0, invalid=762
0110: dt=129.472000, rms=0.712 (0.037%), neg=0, invalid=762
0111: dt=129.472000, rms=0.711 (0.033%), neg=0, invalid=762
0112: dt=129.472000, rms=0.711 (0.032%), neg=0, invalid=762
0113: dt=129.472000, rms=0.711 (0.048%), neg=0, invalid=762
0114: dt=129.472000, rms=0.710 (0.056%), neg=0, invalid=762
0115: dt=129.472000, rms=0.710 (0.053%), neg=0, invalid=762
0116: dt=129.472000, rms=0.710 (0.049%), neg=0, invalid=762
0117: dt=129.472000, rms=0.709 (0.047%), neg=0, invalid=762
0118: dt=129.472000, rms=0.709 (0.043%), neg=0, invalid=762
0119: dt=129.472000, rms=0.709 (0.043%), neg=0, invalid=762
0120: dt=129.472000, rms=0.708 (0.045%), neg=0, invalid=762
0121: dt=129.472000, rms=0.708 (0.049%), neg=0, invalid=762
0122: dt=129.472000, rms=0.708 (0.041%), neg=0, invalid=762
0123: dt=129.472000, rms=0.707 (0.045%), neg=0, invalid=762
0124: dt=129.472000, rms=0.707 (0.047%), neg=0, invalid=762
0125: dt=129.472000, rms=0.707 (0.048%), neg=0, invalid=762
0126: dt=129.472000, rms=0.706 (0.045%), neg=0, invalid=762
0127: dt=129.472000, rms=0.706 (0.042%), neg=0, invalid=762
0128: dt=129.472000, rms=0.706 (0.043%), neg=0, invalid=762
0129: dt=129.472000, rms=0.706 (0.046%), neg=0, invalid=762
0130: dt=129.472000, rms=0.705 (0.048%), neg=0, invalid=762
0131: dt=129.472000, rms=0.705 (0.048%), neg=0, invalid=762
0132: dt=129.472000, rms=0.705 (0.043%), neg=0, invalid=762
0133: dt=129.472000, rms=0.704 (0.040%), neg=0, invalid=762
0134: dt=129.472000, rms=0.704 (0.042%), neg=0, invalid=762
0135: dt=129.472000, rms=0.704 (0.044%), neg=0, invalid=762
0136: dt=129.472000, rms=0.703 (0.034%), neg=0, invalid=762
0137: dt=129.472000, rms=0.703 (0.034%), neg=0, invalid=762
0138: dt=129.472000, rms=0.703 (0.030%), neg=0, invalid=762
0139: dt=129.472000, rms=0.703 (0.027%), neg=0, invalid=762
0140: dt=129.472000, rms=0.703 (0.034%), neg=0, invalid=762
0141: dt=129.472000, rms=0.702 (0.030%), neg=0, invalid=762
0142: dt=129.472000, rms=0.702 (0.025%), neg=0, invalid=762
0143: dt=129.472000, rms=0.702 (0.020%), neg=0, invalid=762
0144: dt=517.888000, rms=0.702 (0.003%), neg=0, invalid=762
0145: dt=517.888000, rms=0.702 (0.008%), neg=0, invalid=762
0146: dt=517.888000, rms=0.702 (-0.314%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.702, neg=0, invalid=762
0147: dt=129.472000, rms=0.701 (0.254%), neg=0, invalid=762
0148: dt=369.920000, rms=0.700 (0.123%), neg=0, invalid=762
0149: dt=129.472000, rms=0.699 (0.081%), neg=0, invalid=762
0150: dt=517.888000, rms=0.698 (0.093%), neg=0, invalid=762
0151: dt=129.472000, rms=0.698 (0.056%), neg=0, invalid=762
0152: dt=221.952000, rms=0.698 (0.026%), neg=0, invalid=762
0153: dt=221.952000, rms=0.698 (0.039%), neg=0, invalid=762
0154: dt=221.952000, rms=0.697 (0.067%), neg=0, invalid=762
0155: dt=221.952000, rms=0.697 (0.049%), neg=0, invalid=762
0156: dt=221.952000, rms=0.696 (0.081%), neg=0, invalid=762
0157: dt=221.952000, rms=0.696 (0.058%), neg=0, invalid=762
0158: dt=221.952000, rms=0.695 (0.059%), neg=0, invalid=762
0159: dt=221.952000, rms=0.695 (0.051%), neg=0, invalid=762
0160: dt=221.952000, rms=0.695 (0.051%), neg=0, invalid=762
0161: dt=221.952000, rms=0.694 (0.055%), neg=0, invalid=762
0162: dt=221.952000, rms=0.694 (0.030%), neg=0, invalid=762
0163: dt=221.952000, rms=0.694 (0.049%), neg=0, invalid=762
0164: dt=221.952000, rms=0.694 (0.036%), neg=0, invalid=762
0165: dt=221.952000, rms=0.693 (0.024%), neg=0, invalid=762
0166: dt=221.952000, rms=0.693 (0.047%), neg=0, invalid=762
0167: dt=221.952000, rms=0.693 (0.036%), neg=0, invalid=762
0168: dt=221.952000, rms=0.693 (0.023%), neg=0, invalid=762
0169: dt=221.952000, rms=0.692 (0.027%), neg=0, invalid=762
0170: dt=221.952000, rms=0.692 (0.037%), neg=0, invalid=762
0171: dt=221.952000, rms=0.692 (0.025%), neg=0, invalid=762
0172: dt=221.952000, rms=0.692 (0.011%), neg=0, invalid=762
0173: dt=221.952000, rms=0.692 (0.050%), neg=0, invalid=762
0174: dt=221.952000, rms=0.691 (0.037%), neg=0, invalid=762
0175: dt=221.952000, rms=0.691 (0.016%), neg=0, invalid=762
0176: dt=221.952000, rms=0.691 (0.025%), neg=0, invalid=762
0177: dt=221.952000, rms=0.691 (0.020%), neg=0, invalid=762
0178: dt=32.368000, rms=0.691 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.692, neg=0, invalid=762
0179: dt=36.288000, rms=0.691 (0.229%), neg=0, invalid=762
0180: dt=103.680000, rms=0.689 (0.181%), neg=0, invalid=762
0181: dt=331.776000, rms=0.682 (1.141%), neg=0, invalid=762
0182: dt=55.652174, rms=0.680 (0.260%), neg=0, invalid=762
0183: dt=414.720000, rms=0.674 (0.821%), neg=0, invalid=762
0184: dt=36.288000, rms=0.671 (0.517%), neg=0, invalid=762
0185: dt=36.288000, rms=0.670 (0.141%), neg=0, invalid=762
0186: dt=331.776000, rms=0.668 (0.291%), neg=0, invalid=762
0187: dt=62.208000, rms=0.666 (0.318%), neg=0, invalid=762
0188: dt=82.944000, rms=0.665 (0.100%), neg=0, invalid=762
0189: dt=82.944000, rms=0.664 (0.141%), neg=0, invalid=762
0190: dt=36.288000, rms=0.664 (0.090%), neg=0, invalid=762
0191: dt=580.608000, rms=0.659 (0.653%), neg=0, invalid=762
0192: dt=36.288000, rms=0.659 (0.082%), neg=0, invalid=762
0193: dt=580.608000, rms=0.656 (0.437%), neg=0, invalid=762
0194: dt=64.000000, rms=0.655 (0.100%), neg=0, invalid=762
0195: dt=124.416000, rms=0.655 (0.083%), neg=0, invalid=762
0196: dt=62.208000, rms=0.654 (0.075%), neg=0, invalid=762
0197: dt=103.680000, rms=0.654 (0.057%), neg=0, invalid=762
0198: dt=36.288000, rms=0.653 (0.051%), neg=0, invalid=762
0199: dt=580.608000, rms=0.651 (0.359%), neg=0, invalid=762
0200: dt=36.288000, rms=0.651 (0.041%), neg=0, invalid=762
0201: dt=36.288000, rms=0.651 (0.024%), neg=0, invalid=762
0202: dt=36.288000, rms=0.650 (0.038%), neg=0, invalid=762
0203: dt=36.288000, rms=0.650 (0.051%), neg=0, invalid=762
0204: dt=36.288000, rms=0.650 (0.023%), neg=0, invalid=762
0205: dt=36.288000, rms=0.650 (0.039%), neg=0, invalid=762
0206: dt=18.144000, rms=0.650 (0.010%), neg=0, invalid=762
0207: dt=2.268000, rms=0.650 (0.001%), neg=0, invalid=762
0208: dt=1.944000, rms=0.650 (0.001%), neg=0, invalid=762
0209: dt=0.060750, rms=0.650 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.650, neg=0, invalid=762
0210: dt=0.141750, rms=0.650 (0.097%), neg=0, invalid=762
0211: dt=0.141750, rms=0.650 (0.002%), neg=0, invalid=762
0212: dt=0.070875, rms=0.650 (0.001%), neg=0, invalid=762
0213: dt=0.017719, rms=0.650 (0.000%), neg=0, invalid=762
0214: dt=0.008859, rms=0.650 (0.000%), neg=0, invalid=762
0215: dt=0.005670, rms=0.650 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.657, neg=0, invalid=762
0216: dt=32.000000, rms=0.646 (1.645%), neg=0, invalid=762
0217: dt=2.000000, rms=0.645 (0.077%), neg=0, invalid=762
0218: dt=0.037500, rms=0.645 (0.002%), neg=0, invalid=762
0219: dt=0.002344, rms=0.645 (0.000%), neg=0, invalid=762
0220: dt=0.000146, rms=0.645 (0.000%), neg=0, invalid=762
0221: dt=0.000073, rms=0.645 (0.000%), neg=0, invalid=762
0222: dt=0.000000, rms=0.645 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.646, neg=0, invalid=762
0223: dt=44.800000, rms=0.634 (1.852%), neg=0, invalid=762
0224: dt=2.800000, rms=0.633 (0.111%), neg=0, invalid=762
0225: dt=2.800000, rms=0.633 (0.099%), neg=0, invalid=762
0226: dt=2.000000, rms=0.632 (0.063%), neg=0, invalid=762
0227: dt=0.175000, rms=0.632 (0.007%), neg=0, invalid=762
0228: dt=0.175000, rms=0.632 (0.006%), neg=0, invalid=762
0229: dt=0.021875, rms=0.632 (0.001%), neg=0, invalid=762
0230: dt=0.010937, rms=0.632 (0.000%), neg=0, invalid=762
0231: dt=0.002734, rms=0.632 (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=0.651, neg=0, invalid=762
0232: dt=0.000984, rms=0.651 (0.082%), neg=0, invalid=762
0233: dt=0.000984, rms=0.651 (0.000%), neg=0, invalid=762
0234: dt=0.000123, rms=0.651 (0.000%), neg=0, invalid=762
0235: dt=0.000062, rms=0.651 (0.000%), neg=0, invalid=762
0236: dt=0.000015, rms=0.651 (0.000%), neg=0, invalid=762
0237: dt=0.000000, rms=0.651 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.651, neg=0, invalid=762
0238: dt=25.558101, rms=0.627 (3.656%), neg=0, invalid=762
0239: dt=14.790582, rms=0.617 (1.579%), neg=0, invalid=762
0240: dt=10.249275, rms=0.615 (0.385%), neg=0, invalid=762
0241: dt=30.800000, rms=0.611 (0.676%), neg=0, invalid=762
0242: dt=7.152542, rms=0.609 (0.336%), neg=0, invalid=762
0243: dt=16.128000, rms=0.608 (0.200%), neg=0, invalid=762
0244: dt=21.224490, rms=0.606 (0.208%), neg=0, invalid=762
0245: dt=10.589928, rms=0.605 (0.156%), neg=0, invalid=762
0246: dt=17.739130, rms=0.605 (0.148%), neg=0, invalid=762
0247: dt=9.345133, rms=0.604 (0.108%), neg=0, invalid=762
0248: dt=17.684211, rms=0.603 (0.117%), neg=0, invalid=762
0249: dt=8.677966, rms=0.603 (0.086%), neg=0, invalid=762
0250: dt=16.421053, rms=0.602 (0.107%), neg=0, invalid=762
0251: dt=8.200000, rms=0.602 (0.067%), neg=0, invalid=762
0252: dt=18.285714, rms=0.601 (0.100%), neg=0, invalid=762
0253: dt=7.589744, rms=0.601 (0.064%), neg=0, invalid=762
0254: dt=22.222222, rms=0.600 (0.087%), neg=0, invalid=762
0255: dt=7.917526, rms=0.600 (0.062%), neg=0, invalid=762
0256: dt=16.128000, rms=0.599 (0.074%), neg=0, invalid=762
0257: dt=7.641791, rms=0.599 (0.049%), neg=0, invalid=762
0258: dt=7.641791, rms=0.599 (0.042%), neg=0, invalid=762
0259: dt=7.641791, rms=0.598 (0.063%), neg=0, invalid=762
0260: dt=7.641791, rms=0.598 (0.096%), neg=0, invalid=762
0261: dt=7.641791, rms=0.597 (0.110%), neg=0, invalid=762
0262: dt=7.641791, rms=0.596 (0.149%), neg=0, invalid=762
0263: dt=7.641791, rms=0.595 (0.157%), neg=0, invalid=762
0264: dt=7.641791, rms=0.594 (0.139%), neg=0, invalid=762
0265: dt=7.641791, rms=0.594 (0.125%), neg=0, invalid=762
0266: dt=7.641791, rms=0.593 (0.129%), neg=0, invalid=762
0267: dt=7.641791, rms=0.592 (0.113%), neg=0, invalid=762
0268: dt=7.641791, rms=0.592 (0.106%), neg=0, invalid=762
0269: dt=7.641791, rms=0.591 (0.097%), neg=0, invalid=762
0270: dt=7.641791, rms=0.591 (0.096%), neg=0, invalid=762
0271: dt=7.641791, rms=0.590 (0.078%), neg=0, invalid=762
0272: dt=7.641791, rms=0.590 (0.080%), neg=0, invalid=762
0273: dt=7.641791, rms=0.589 (0.078%), neg=0, invalid=762
0274: dt=7.641791, rms=0.589 (0.078%), neg=0, invalid=762
0275: dt=7.641791, rms=0.588 (0.070%), neg=0, invalid=762
0276: dt=7.641791, rms=0.588 (0.059%), neg=0, invalid=762
0277: dt=7.641791, rms=0.588 (0.049%), neg=0, invalid=762
0278: dt=7.641791, rms=0.587 (0.038%), neg=0, invalid=762
0279: dt=7.641791, rms=0.587 (0.043%), neg=0, invalid=762
0280: dt=7.641791, rms=0.587 (0.043%), neg=0, invalid=762
0281: dt=7.641791, rms=0.587 (0.037%), neg=0, invalid=762
0282: dt=7.641791, rms=0.586 (0.036%), neg=0, invalid=762
0283: dt=7.641791, rms=0.586 (0.039%), neg=0, invalid=762
0284: dt=7.641791, rms=0.586 (0.031%), neg=0, invalid=762
0285: dt=7.641791, rms=0.586 (0.026%), neg=0, invalid=762
0286: dt=7.641791, rms=0.586 (0.036%), neg=0, invalid=762
0287: dt=7.641791, rms=0.586 (0.028%), neg=0, invalid=762
0288: dt=7.641791, rms=0.585 (0.026%), neg=0, invalid=762
0289: dt=7.641791, rms=0.585 (0.020%), neg=0, invalid=762
0290: dt=7.641791, rms=0.585 (0.029%), neg=0, invalid=762
0291: dt=7.641791, rms=0.585 (0.022%), neg=0, invalid=762
0292: dt=7.641791, rms=0.585 (0.020%), neg=0, invalid=762
0293: dt=6.912000, rms=0.585 (0.009%), neg=0, invalid=762
0294: dt=6.912000, rms=0.585 (-0.004%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.601, neg=0, invalid=762
0295: dt=0.000000, rms=0.601 (0.082%), neg=0, invalid=762
0296: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762
0297: dt=0.100000, rms=0.601 (-0.173%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.601, neg=0, invalid=762
0298: dt=0.000000, rms=0.601 (0.082%), neg=0, invalid=762
0299: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762
0300: dt=0.100000, rms=0.601 (-0.156%), 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=0.574, neg=0, invalid=762
0301: dt=0.448000, rms=0.557 (3.029%), neg=0, invalid=762
0302: dt=0.448000, rms=0.553 (0.663%), neg=0, invalid=762
0303: dt=0.448000, rms=0.551 (0.387%), neg=0, invalid=762
0304: dt=0.448000, rms=0.550 (0.194%), neg=0, invalid=762
0305: dt=0.500000, rms=0.549 (0.197%), neg=0, invalid=762
0306: dt=0.448000, rms=0.549 (0.083%), neg=0, invalid=762
0307: dt=0.448000, rms=0.548 (0.112%), neg=0, invalid=762
0308: dt=0.448000, rms=0.548 (0.042%), neg=0, invalid=762
0309: dt=0.448000, rms=0.547 (0.079%), neg=0, invalid=762
0310: dt=0.448000, rms=0.547 (0.087%), neg=0, invalid=762
0311: dt=0.448000, rms=0.546 (0.088%), neg=0, invalid=762
0312: dt=0.448000, rms=0.546 (0.107%), neg=0, invalid=762
0313: dt=0.448000, rms=0.546 (0.015%), neg=0, invalid=762
0314: dt=0.448000, rms=0.546 (-0.005%), neg=0, invalid=762
0315: dt=0.028000, rms=0.546 (0.000%), neg=0, invalid=762
0316: dt=0.028000, rms=0.546 (0.001%), neg=0, invalid=762
0317: dt=0.096000, rms=0.546 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.546, neg=0, invalid=762
0318: dt=0.448000, rms=0.537 (1.596%), neg=0, invalid=762
0319: dt=0.448000, rms=0.536 (0.239%), neg=0, invalid=762
0320: dt=0.448000, rms=0.536 (0.070%), neg=0, invalid=762
0321: dt=0.448000, rms=0.536 (0.041%), neg=0, invalid=762
0322: dt=0.448000, rms=0.536 (-0.006%), 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=0.534, neg=0, invalid=762
0323: dt=0.000000, rms=0.533 (0.108%), neg=0, invalid=762
0324: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.534, neg=0, invalid=762
0325: dt=8.092000, rms=0.533 (0.109%), neg=0, invalid=762
0326: dt=8.092000, rms=0.533 (0.003%), neg=0, invalid=762
0327: dt=8.092000, rms=0.533 (0.001%), neg=0, invalid=762
0328: dt=8.092000, rms=0.533 (0.000%), neg=0, invalid=762
0329: dt=8.092000, rms=0.533 (-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=0.534, neg=0, invalid=762
0330: dt=2.268000, rms=0.533 (0.112%), neg=0, invalid=762
0331: dt=2.268000, rms=0.533 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.534, neg=0, invalid=762
0332: dt=89.342282, rms=0.532 (0.360%), neg=0, invalid=762
0333: dt=62.208000, rms=0.531 (0.112%), neg=0, invalid=762
0334: dt=62.208000, rms=0.531 (-0.010%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.532, neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0335: dt=11.200000, rms=0.530 (0.396%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0336: dt=11.200000, rms=0.529 (0.121%), neg=0, invalid=762
0337: dt=11.200000, rms=0.529 (0.054%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 1 iterations, nbhd size=0, neg = 0
0338: dt=11.200000, rms=0.529 (-0.062%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.529, neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0339: dt=38.400000, rms=0.522 (1.295%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0340: dt=19.912525, rms=0.520 (0.376%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 1 iterations, nbhd size=0, neg = 0
0341: dt=38.400000, rms=0.519 (0.298%), neg=0, invalid=762
0342: dt=11.200000, rms=0.518 (0.172%), neg=0, invalid=762
0343: dt=11.200000, rms=0.517 (0.104%), neg=0, invalid=762
0344: dt=11.200000, rms=0.517 (0.130%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0345: dt=11.200000, rms=0.516 (0.190%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0346: dt=11.200000, rms=0.515 (0.223%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0347: dt=11.200000, rms=0.514 (0.225%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0348: dt=11.200000, rms=0.512 (0.234%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0349: dt=11.200000, rms=0.511 (0.217%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 9 iterations, nbhd size=1, neg = 0
0350: dt=11.200000, rms=0.510 (0.189%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0351: dt=11.200000, rms=0.509 (0.195%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0352: dt=11.200000, rms=0.508 (0.176%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0353: dt=11.200000, rms=0.508 (0.161%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0354: dt=11.200000, rms=0.507 (0.150%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0355: dt=11.200000, rms=0.506 (0.126%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0356: dt=11.200000, rms=0.505 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0357: dt=11.200000, rms=0.505 (0.102%), neg=0, invalid=762
0358: dt=11.200000, rms=0.505 (0.012%), neg=0, invalid=762
0359: dt=11.200000, rms=0.505 (0.008%), neg=0, invalid=762
0360: dt=11.200000, rms=0.505 (0.008%), neg=0, invalid=762
0361: dt=11.200000, rms=0.505 (0.016%), neg=0, invalid=762
0362: dt=11.200000, rms=0.505 (0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.510, neg=0, invalid=762
0363: dt=2.304000, rms=0.509 (0.145%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0364: dt=0.864000, rms=0.509 (0.005%), neg=0, invalid=762
0365: dt=0.864000, rms=0.509 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.510, neg=0, invalid=762
0366: dt=6.933333, rms=0.508 (0.247%), neg=0, invalid=762
0367: dt=10.850575, rms=0.508 (0.114%), neg=0, invalid=762
0368: dt=10.850575, rms=0.507 (0.180%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0369: dt=10.850575, rms=0.506 (0.282%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0370: dt=10.850575, rms=0.504 (0.358%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0371: dt=10.850575, rms=0.501 (0.482%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0372: dt=10.850575, rms=0.498 (0.586%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0373: dt=10.850575, rms=0.496 (0.551%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0374: dt=10.850575, rms=0.494 (0.351%), neg=0, invalid=762
0375: dt=10.850575, rms=0.493 (0.098%), neg=0, invalid=762
0376: dt=10.850575, rms=0.493 (-0.052%), neg=0, invalid=762
0377: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.501, neg=0, invalid=762
0378: dt=0.000000, rms=0.500 (0.138%), neg=0, invalid=762
0379: dt=0.000000, rms=0.500 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.501, neg=0, invalid=762
0380: dt=0.000000, rms=0.500 (0.138%), neg=0, invalid=762
0381: dt=0.000000, rms=0.500 (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=0.490, neg=0, invalid=762
iter 0, gcam->neg = 1171
after 11 iterations, nbhd size=1, neg = 0
0382: dt=1.601331, rms=0.466 (4.780%), neg=0, invalid=762
0383: dt=0.000013, rms=0.466 (0.011%), neg=0, invalid=762
0384: dt=0.000013, rms=0.466 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.467, neg=0, invalid=762
0385: dt=0.096000, rms=0.466 (0.210%), neg=0, invalid=762
0386: dt=0.007000, rms=0.466 (0.000%), neg=0, invalid=762
0387: dt=0.007000, rms=0.466 (0.000%), neg=0, invalid=762
0388: dt=0.007000, rms=0.466 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0389: 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
0390: dt=2.023000, rms=0.457 (0.000%), neg=0, invalid=762
0391: dt=0.289000, rms=0.457 (0.000%), neg=0, invalid=762
0392: dt=0.289000, rms=0.457 (0.000%), neg=0, invalid=762
0393: dt=0.289000, rms=0.457 (-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=0.457, neg=0, invalid=762
0394: 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
0395: dt=9.072000, rms=0.457 (0.007%), neg=0, invalid=762
0396: dt=9.072000, rms=0.457 (0.003%), neg=0, invalid=762
0397: dt=9.072000, rms=0.457 (0.001%), neg=0, invalid=762
0398: dt=9.072000, rms=0.457 (-0.004%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0399: dt=2.800000, rms=0.457 (0.022%), neg=0, invalid=762
0400: dt=1.200000, rms=0.457 (0.002%), neg=0, invalid=762
0401: dt=1.200000, rms=0.457 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0402: dt=44.800000, rms=0.455 (0.411%), neg=0, invalid=762
0403: dt=32.000000, rms=0.454 (0.160%), neg=0, invalid=762
0404: dt=32.000000, rms=0.454 (0.113%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 2 iterations, nbhd size=0, neg = 0
0405: dt=32.000000, rms=0.453 (0.195%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 2 iterations, nbhd size=0, neg = 0
0406: dt=32.000000, rms=0.453 (0.112%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 8 iterations, nbhd size=1, neg = 0
0407: dt=32.000000, rms=0.452 (0.171%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 3 iterations, nbhd size=0, neg = 0
0408: dt=32.000000, rms=0.451 (0.092%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 10 iterations, nbhd size=1, neg = 0
0409: dt=32.000000, rms=0.451 (0.128%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 2 iterations, nbhd size=0, neg = 0
0410: dt=32.000000, rms=0.450 (0.086%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0411: dt=32.000000, rms=0.450 (0.107%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 7 iterations, nbhd size=1, neg = 0
0412: dt=32.000000, rms=0.450 (0.082%), neg=0, invalid=762
0413: dt=25.600000, rms=0.449 (0.046%), neg=0, invalid=762
0414: dt=25.600000, rms=0.449 (0.023%), neg=0, invalid=762
0415: dt=25.600000, rms=0.449 (0.027%), neg=0, invalid=762
0416: dt=25.600000, rms=0.449 (0.038%), neg=0, invalid=762
0417: dt=25.600000, rms=0.449 (0.022%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0418: dt=25.600000, rms=0.449 (0.032%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0419: dt=25.600000, rms=0.449 (0.016%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.452, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0420: dt=0.216000, rms=0.452 (0.000%), neg=0, invalid=762
0421: dt=0.000703, rms=0.452 (0.000%), neg=0, invalid=762
0422: dt=0.000703, rms=0.452 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.452, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0423: dt=10.084034, rms=0.451 (0.145%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0424: dt=25.379310, rms=0.450 (0.248%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0425: dt=24.242424, rms=0.449 (0.232%), neg=0, invalid=762
iter 0, gcam->neg = 22
after 10 iterations, nbhd size=1, neg = 0
0426: dt=24.242424, rms=0.449 (-0.498%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.454, neg=0, invalid=762
0427: dt=0.000050, rms=0.454 (0.000%), neg=0, invalid=762
0428: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.454, neg=0, invalid=762
0429: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.446, neg=0, invalid=762
iter 0, gcam->neg = 372
after 12 iterations, nbhd size=1, neg = 0
0430: dt=1.083179, rms=0.438 (1.716%), neg=0, invalid=762
0431: dt=0.000023, rms=0.438 (0.000%), neg=0, invalid=762
0432: dt=0.000023, rms=0.438 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.438, neg=0, invalid=762
0433: dt=0.320000, rms=0.437 (0.352%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 3 iterations, nbhd size=0, neg = 0
0434: dt=0.583333, rms=0.434 (0.592%), neg=0, invalid=762
0435: dt=0.384000, rms=0.433 (0.168%), neg=0, invalid=762
0436: dt=0.384000, rms=0.432 (0.232%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 3 iterations, nbhd size=0, neg = 0
0437: dt=0.384000, rms=0.432 (0.146%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 1 iterations, nbhd size=0, neg = 0
0438: dt=0.384000, rms=0.432 (0.042%), neg=0, invalid=762
iter 0, gcam->neg = 27
after 8 iterations, nbhd size=1, neg = 0
0439: dt=0.384000, rms=0.432 (-0.030%), neg=0, invalid=762
0440: dt=0.256000, rms=0.431 (0.060%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0441: dt=0.320000, rms=0.431 (0.030%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 19 minutes and 49 seconds.
mri_ca_register utimesec    8385.839158
mri_ca_register stimesec    7.525855
mri_ca_register ru_maxrss   1339828
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4245432
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  64912
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    1256
mri_ca_register ru_nivcsw   20167
FSRUNTIME@ mri_ca_register  2.3303 hours 1 threads
#--------------------------------------
#@# SubCort Seg Fri Oct 27 00:20:12 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-623
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-6.0.0/0050418/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 = 1 == 
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 6.98
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 = 0.08194 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (262 voxels, overlap=0.401)
Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (262 voxels, peak =  9), gca=8.9
gca peak = 0.17677 (13)
mri peak = 0.10423 (10)
Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (355 voxels, overlap=0.558)
Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (355 voxels, peak =  9), gca=9.0
gca peak = 0.28129 (95)
mri peak = 0.06825 (99)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (672 voxels, overlap=1.021)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (672 voxels, peak = 92), gca=91.7
gca peak = 0.16930 (96)
mri peak = 0.12789 (92)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (563 voxels, overlap=0.974)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (563 voxels, peak = 93), gca=92.6
gca peak = 0.24553 (55)
mri peak = 0.07523 (62)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (572 voxels, overlap=1.013)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (572 voxels, peak = 60), gca=60.2
gca peak = 0.30264 (59)
mri peak = 0.06387 (58)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (570 voxels, overlap=1.015)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (570 voxels, peak = 60), gca=60.5
gca peak = 0.07580 (103)
mri peak = 0.05593 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (41078 voxels, overlap=0.784)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (41078 voxels, peak = 106), gca=105.6
gca peak = 0.07714 (104)
mri peak = 0.04577 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43488 voxels, overlap=0.794)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43488 voxels, peak = 109), gca=108.7
gca peak = 0.09712 (58)
mri peak = 0.03751 (62)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28727 voxels, overlap=0.967)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28727 voxels, peak = 61), gca=60.6
gca peak = 0.11620 (58)
mri peak = 0.03770 (61)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (24768 voxels, overlap=0.917)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (24768 voxels, peak = 62), gca=62.4
gca peak = 0.30970 (66)
mri peak = 0.09189 (78)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (880 voxels, overlap=0.241)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (880 voxels, peak = 76), gca=75.6
gca peak = 0.15280 (69)
mri peak = 0.08921 (76)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (825 voxels, overlap=1.003)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (825 voxels, peak = 67), gca=67.3
gca peak = 0.13902 (56)
mri peak = 0.04979 (51)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22467 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22467 voxels, peak = 53), gca=52.9
gca peak = 0.14777 (55)
mri peak = 0.04159 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21138 voxels, overlap=0.998)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21138 voxels, peak = 53), gca=53.1
gca peak = 0.16765 (84)
mri peak = 0.05843 (83)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5964 voxels, overlap=0.986)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5964 voxels, peak = 83), gca=82.7
gca peak = 0.18739 (84)
mri peak = 0.05754 (84)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5089 voxels, overlap=0.911)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5089 voxels, peak = 86), gca=86.1
gca peak = 0.29869 (57)
mri peak = 0.07292 (60)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (296 voxels, overlap=1.044)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (296 voxels, peak = 58), gca=57.9
gca peak = 0.33601 (57)
mri peak = 0.06015 (60)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (283 voxels, overlap=1.040)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (283 voxels, peak = 60), gca=59.6
gca peak = 0.11131 (90)
mri peak = 0.05948 (90)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4428 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4428 voxels, peak = 90), gca=89.6
gca peak = 0.11793 (83)
mri peak = 0.05718 (88)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4026 voxels, overlap=0.980)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4026 voxels, peak = 87), gca=86.7
gca peak = 0.08324 (81)
mri peak = 0.06573 (74)
Left_Putamen (12): linear fit = 0.95 x + 0.0 (3134 voxels, overlap=0.715)
Left_Putamen (12): linear fit = 0.95 x + 0.0 (3134 voxels, peak = 77), gca=77.4
gca peak = 0.10360 (77)
mri peak = 0.07534 (75)
Right_Putamen (51): linear fit = 0.95 x + 0.0 (2232 voxels, overlap=0.820)
Right_Putamen (51): linear fit = 0.95 x + 0.0 (2232 voxels, peak = 74), gca=73.5
gca peak = 0.08424 (78)
mri peak = 0.15709 (80)
Brain_Stem: unreasonable value (79.2/80.0), not in range [80, 110] - rejecting
gca peak = 0.12631 (89)
mri peak = 0.06160 (94)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1034 voxels, overlap=0.830)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1034 voxels, peak = 94), gca=93.9
gca peak = 0.14500 (87)
mri peak = 0.06257 (84)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1203 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1203 voxels, peak = 85), gca=84.8
gca peak = 0.14975 (24)
mri peak = 0.14488 (51)
gca peak = 0.19357 (14)
mri peak = 0.14913 ( 3)
Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (115 voxels, overlap=0.016)
Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (115 voxels, peak =  2), gca=1.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak Brain_Stem = 0.08424 (78)
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 1.05 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.57 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.29497 ( 9)
mri peak = 0.08194 ( 8)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (262 voxels, overlap=0.994)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (262 voxels, peak =  9), gca=9.5
gca peak = 0.27800 ( 9)
mri peak = 0.10423 (10)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (355 voxels, overlap=0.928)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (355 voxels, peak =  9), gca=9.5
gca peak = 0.25179 (91)
mri peak = 0.06825 (99)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (672 voxels, overlap=1.019)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (672 voxels, peak = 91), gca=90.5
gca peak = 0.18582 (93)
mri peak = 0.12789 (92)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (563 voxels, overlap=1.004)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (563 voxels, peak = 93), gca=92.5
gca peak = 0.25839 (61)
mri peak = 0.07523 (62)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (572 voxels, overlap=1.009)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (572 voxels, peak = 61), gca=61.0
gca peak = 0.28192 (58)
mri peak = 0.06387 (58)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (570 voxels, overlap=1.015)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (570 voxels, peak = 58), gca=58.0
gca peak = 0.07614 (105)
mri peak = 0.05593 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41078 voxels, overlap=0.864)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41078 voxels, peak = 104), gca=104.5
gca peak = 0.07799 (109)
mri peak = 0.04577 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43488 voxels, overlap=0.916)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43488 voxels, peak = 109), gca=109.0
gca peak = 0.09240 (60)
mri peak = 0.03751 (62)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28727 voxels, overlap=0.983)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28727 voxels, peak = 62), gca=61.5
gca peak = 0.11117 (62)
mri peak = 0.03770 (61)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24768 voxels, overlap=0.973)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24768 voxels, peak = 64), gca=63.5
gca peak = 0.24573 (76)
mri peak = 0.09189 (78)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (880 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (880 voxels, peak = 77), gca=77.1
gca peak = 0.13720 (67)
mri peak = 0.08921 (76)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (825 voxels, overlap=1.001)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (825 voxels, peak = 67), gca=67.0
gca peak = 0.14851 (53)
mri peak = 0.04979 (51)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (22467 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (22467 voxels, peak = 53), gca=53.0
gca peak = 0.15535 (53)
mri peak = 0.04159 (55)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21138 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21138 voxels, peak = 53), gca=53.0
gca peak = 0.16203 (83)
mri peak = 0.05843 (83)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5964 voxels, overlap=0.977)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5964 voxels, peak = 83), gca=82.6
gca peak = 0.16001 (86)
mri peak = 0.05754 (84)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5089 voxels, overlap=0.966)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5089 voxels, peak = 86), gca=85.6
gca peak = 0.30225 (59)
mri peak = 0.07292 (60)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (296 voxels, overlap=1.036)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (296 voxels, peak = 60), gca=60.5
gca peak = 0.33137 (60)
mri peak = 0.06015 (60)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (283 voxels, overlap=1.039)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (283 voxels, peak = 62), gca=61.5
gca peak = 0.10237 (89)
mri peak = 0.05948 (90)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4428 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4428 voxels, peak = 90), gca=90.3
gca peak = 0.09701 (90)
mri peak = 0.05718 (88)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4026 voxels, overlap=1.000)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4026 voxels, peak = 90), gca=89.6
gca peak = 0.08002 (79)
mri peak = 0.06573 (74)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (3134 voxels, overlap=0.887)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (3134 voxels, peak = 79), gca=78.6
gca peak = 0.11291 (72)
mri peak = 0.07534 (75)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2232 voxels, overlap=0.935)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2232 voxels, peak = 72), gca=71.6
gca peak = 0.08598 (81)
mri peak = 0.15709 (80)
Brain_Stem: unreasonable value (79.8/80.0), not in range [80, 110] - rejecting
gca peak = 0.13330 (94)
mri peak = 0.06160 (94)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1034 voxels, overlap=0.884)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1034 voxels, peak = 93), gca=92.6
gca peak = 0.14445 (85)
mri peak = 0.06257 (84)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1203 voxels, overlap=0.878)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1203 voxels, peak = 91), gca=90.5
gca peak = 0.29549 (15)
mri peak = 0.14488 (51)
gca peak = 0.29582 ( 8)
mri peak = 0.14913 ( 3)
Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (115 voxels, overlap=0.559)
Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (115 voxels, peak =  2), gca=1.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15047 (33)
gca peak Left_Thalamus = 1.00000 (99)
gca peak Third_Ventricle = 0.29549 (15)
gca peak Fourth_Ventricle = 0.29582 ( 8)
gca peak Brain_Stem = 0.08598 (81)
gca peak CSF = 0.26369 (21)
gca peak Left_Accumbens_area = 0.51250 (60)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.20543 (25)
gca peak Right_Accumbens_area = 0.29775 (74)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.89470 (18)
gca peak WM_hypointensities = 0.07030 (78)
gca peak non_WM_hypointensities = 0.08309 (45)
gca peak Optic_Chiasm = 0.71088 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.02 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.05 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
95733 voxels changed in iteration 0 of unlikely voxel relabeling
331 voxels changed in iteration 1 of unlikely voxel relabeling
71 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
51554 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels)
397 hippocampal voxels changed.
4 amygdala voxels changed.
pass 1: 86021 changed. image ll: -2.176, PF=0.500
pass 2: 26135 changed. image ll: -2.176, PF=0.500
pass 3: 8497 changed.
pass 4: 3154 changed.
65461 voxels changed in iteration 0 of unlikely voxel relabeling
255 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
9624 voxels changed in iteration 0 of unlikely voxel relabeling
83 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8292 voxels changed in iteration 0 of unlikely voxel relabeling
86 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
6243 voxels changed in iteration 0 of unlikely voxel relabeling
33 voxels changed in iteration 1 of unlikely voxel relabeling
3 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    3746.111504
mri_ca_label stimesec    1.476775
mri_ca_label ru_maxrss   2116740
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   741966
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  64904
mri_ca_label ru_oublock  480
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    191
mri_ca_label ru_nivcsw   9142
auto-labeling took 62 minutes and 26 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/cc_up.lta 0050418 

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-6.0.0/0050418/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/norm.mgz
55249 voxels in left wm, 53910 in right wm, xrange [115, 127]
searching rotation angles z=[-3 11], y=[-5  9]

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  
searching scale 1 Z rot 7.7  
searching scale 1 Z rot 8.0  
searching scale 1 Z rot 8.2  
searching scale 1 Z rot 8.5  
searching scale 1 Z rot 8.7  
searching scale 1 Z rot 9.0  
searching scale 1 Z rot 9.2  
searching scale 1 Z rot 9.5  
searching scale 1 Z rot 9.7  
searching scale 1 Z rot 10.0  
searching scale 1 Z rot 10.2  
searching scale 1 Z rot 10.5  
searching scale 1 Z rot 10.7  global minimum found at slice 120.4, rotations (1.82, 4.00)
final transformation (x=120.4, yr=1.820, zr=3.997):
 0.99706  -0.06970   0.03168   11.18684;
 0.06967   0.99757   0.00221   23.60376;
-0.03175  -0.00000   0.99950   21.87768;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 127
cc center is found at 127 96 110
eigenvectors:
 0.00339  -0.01445   0.99989;
-0.02829  -0.99950  -0.01435;
 0.99959  -0.02824  -0.00380;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.1 minutes
#--------------------------------------
#@# Merge ASeg Fri Oct 27 01:23:45 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Fri Oct 27 01:23:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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...
1350 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 99
gm peak at 63 (63), valley at 12 (12)
csf peak at 32, setting threshold to 52
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 88 (88), valley at 85 (85)
csf peak at 60, setting threshold to 78
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 15 seconds.
#--------------------------------------------
#@# Mask BFS Fri Oct 27 01:27:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1512859 voxels in mask (pct=  9.02)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Fri Oct 27 01:27:02 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 (104.0): 105.6 +- 6.2 [79.0 --> 125.0]
GM (69.0) : 67.0 +- 10.8 [30.0 --> 95.0]
setting bottom of white matter range to 77.9
setting top of gray matter range to 88.7
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...
10533 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4342 filled
3770 bright non-wm voxels segmented.
4336 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 0.52 minutes
reading wm segmentation from wm.seg.mgz...
438 voxels added to wm to prevent paths from MTL structures to cortex
4776 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 46314 voxels turned on, 16547 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 87   new 87
115,126,128 old 87   new 87
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  34 found -  34 modified     |    TOTAL:  34
pass   2 (xy+):   0 found -  34 modified     |    TOTAL:  34
pass   1 (xy-):  47 found -  47 modified     |    TOTAL:  81
pass   2 (xy-):   0 found -  47 modified     |    TOTAL:  81
pass   1 (yz+):  42 found -  42 modified     |    TOTAL: 123
pass   2 (yz+):   0 found -  42 modified     |    TOTAL: 123
pass   1 (yz-):  45 found -  45 modified     |    TOTAL: 168
pass   2 (yz-):   0 found -  45 modified     |    TOTAL: 168
pass   1 (xz+):  39 found -  39 modified     |    TOTAL: 207
pass   2 (xz+):   0 found -  39 modified     |    TOTAL: 207
pass   1 (xz-):  35 found -  35 modified     |    TOTAL: 242
pass   2 (xz-):   0 found -  35 modified     |    TOTAL: 242
Iteration Number : 1
pass   1 (+++):  34 found -  34 modified     |    TOTAL:  34
pass   2 (+++):   0 found -  34 modified     |    TOTAL:  34
pass   1 (+++):  56 found -  56 modified     |    TOTAL:  90
pass   2 (+++):   0 found -  56 modified     |    TOTAL:  90
pass   1 (+++):  48 found -  48 modified     |    TOTAL: 138
pass   2 (+++):   0 found -  48 modified     |    TOTAL: 138
pass   1 (+++):  65 found -  65 modified     |    TOTAL: 203
pass   2 (+++):   0 found -  65 modified     |    TOTAL: 203
Iteration Number : 1
pass   1 (++): 189 found - 189 modified     |    TOTAL: 189
pass   2 (++):   0 found - 189 modified     |    TOTAL: 189
pass   1 (+-): 192 found - 192 modified     |    TOTAL: 381
pass   2 (+-):   0 found - 192 modified     |    TOTAL: 381
pass   1 (--): 146 found - 146 modified     |    TOTAL: 527
pass   2 (--):   1 found - 147 modified     |    TOTAL: 528
pass   3 (--):   0 found - 147 modified     |    TOTAL: 528
pass   1 (-+): 170 found - 170 modified     |    TOTAL: 698
pass   2 (-+):   0 found - 170 modified     |    TOTAL: 698
Iteration Number : 2
pass   1 (xy+):  13 found -  13 modified     |    TOTAL:  13
pass   2 (xy+):   0 found -  13 modified     |    TOTAL:  13
pass   1 (xy-):   8 found -   8 modified     |    TOTAL:  21
pass   2 (xy-):   0 found -   8 modified     |    TOTAL:  21
pass   1 (yz+):  18 found -  18 modified     |    TOTAL:  39
pass   2 (yz+):   0 found -  18 modified     |    TOTAL:  39
pass   1 (yz-):  16 found -  16 modified     |    TOTAL:  55
pass   2 (yz-):   0 found -  16 modified     |    TOTAL:  55
pass   1 (xz+):   9 found -   9 modified     |    TOTAL:  64
pass   2 (xz+):   0 found -   9 modified     |    TOTAL:  64
pass   1 (xz-):  19 found -  19 modified     |    TOTAL:  83
pass   2 (xz-):   0 found -  19 modified     |    TOTAL:  83
Iteration Number : 2
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   8
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  12
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  12
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  14
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  14
Iteration Number : 2
pass   1 (++):  12 found -  12 modified     |    TOTAL:  12
pass   2 (++):   0 found -  12 modified     |    TOTAL:  12
pass   1 (+-):   9 found -   9 modified     |    TOTAL:  21
pass   2 (+-):   0 found -   9 modified     |    TOTAL:  21
pass   1 (--):   4 found -   4 modified     |    TOTAL:  25
pass   2 (--):   0 found -   4 modified     |    TOTAL:  25
pass   1 (-+):   2 found -   2 modified     |    TOTAL:  27
pass   2 (-+):   0 found -   2 modified     |    TOTAL:  27
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   7
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  10
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  11
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:  11
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 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   2 found -   2 modified     |    TOTAL:   4
pass   2 (--):   0 found -   2 modified     |    TOTAL:   4
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 4
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+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
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
Iteration Number : 5
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 : 5
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 : 5
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 = 1284 (out of 475355: 0.270114)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Fri Oct 27 01:29:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18140;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.04428  -0.10535   0.04182   7.25174;
 0.09913   1.08872   0.08160  -28.18140;
-0.04241  -0.07024   0.99168   12.88991;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1125 (min = 350, max = 1400), aspect = 0.75 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 116, 94), TAL = (2.0, -34.0, 12.0)
talairach voxel to voxel transform
 0.94727   0.08862  -0.04724  -3.76308;
-0.08882   0.90535  -0.07075   27.07001;
 0.03422   0.06792   1.00136  -11.24164;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  116,  94) --> (2.0, -34.0, 12.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (2.00, -34.00, 12.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, -34.00, 12.00) SRC: (104.38, 115.85, 94.46)
search lh wm seed point around talairach space (-16.00, -34.00, 12.00), SRC: (138.48, 112.65, 95.69)
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 Fri Oct 27 01:29:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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


Iteration Number : 1
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-):   2 found -   2 modified     |    TOTAL:   9
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   9
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  11
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  11
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:  11
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 (++):   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 : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 15 (out of 235604: 0.006367)
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 30: 46 vertices, 55 faces
slice 40: 3221 vertices, 3392 faces
slice 50: 10744 vertices, 11154 faces
slice 60: 20915 vertices, 21358 faces
slice 70: 31610 vertices, 32128 faces
slice 80: 44852 vertices, 45466 faces
slice 90: 58918 vertices, 59594 faces
slice 100: 73167 vertices, 73912 faces
slice 110: 86153 vertices, 86888 faces
slice 120: 98776 vertices, 99590 faces
slice 130: 111420 vertices, 112260 faces
slice 140: 122814 vertices, 123612 faces
slice 150: 132418 vertices, 133212 faces
slice 160: 140984 vertices, 141731 faces
slice 170: 147284 vertices, 147977 faces
slice 180: 152176 vertices, 152844 faces
slice 190: 154050 vertices, 154570 faces
slice 200: 154060 vertices, 154574 faces
slice 210: 154060 vertices, 154574 faces
slice 220: 154060 vertices, 154574 faces
slice 230: 154060 vertices, 154574 faces
slice 240: 154060 vertices, 154574 faces
slice 250: 154060 vertices, 154574 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...
   154060 voxel in cpt #1: X=-514 [v=154060,e=463722,f=309148] located at (-23.236538, -24.180761, 17.568182)
For the whole surface: X=-514 [v=154060,e=463722,f=309148]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Fri Oct 27 01:30:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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


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

Total Number of Modified Voxels = 14 (out of 232763: 0.006015)
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: 932 vertices, 1032 faces
slice 50: 5807 vertices, 6085 faces
slice 60: 14516 vertices, 14941 faces
slice 70: 25035 vertices, 25491 faces
slice 80: 36193 vertices, 36706 faces
slice 90: 48752 vertices, 49306 faces
slice 100: 62606 vertices, 63177 faces
slice 110: 75841 vertices, 76488 faces
slice 120: 88418 vertices, 89031 faces
slice 130: 100765 vertices, 101456 faces
slice 140: 111672 vertices, 112286 faces
slice 150: 121204 vertices, 121808 faces
slice 160: 129891 vertices, 130482 faces
slice 170: 137361 vertices, 137876 faces
slice 180: 142479 vertices, 142943 faces
slice 190: 145226 vertices, 145585 faces
slice 200: 145424 vertices, 145740 faces
slice 210: 145424 vertices, 145740 faces
slice 220: 145424 vertices, 145740 faces
slice 230: 145424 vertices, 145740 faces
slice 240: 145424 vertices, 145740 faces
slice 250: 145424 vertices, 145740 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...
   145424 voxel in cpt #1: X=-316 [v=145424,e=437220,f=291480] located at (36.298618, -19.734886, 15.450806)
For the whole surface: X=-316 [v=145424,e=437220,f=291480]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Fri Oct 27 01:30:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

#--------------------------------------------
#@# Smooth1 rh Fri Oct 27 01:30:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

Waiting for PID 5281 of (5281 5284) to complete...
Waiting for PID 5284 of (5281 5284) 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 (5281 5284) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Fri Oct 27 01:30:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

#--------------------------------------------
#@# Inflation1 rh Fri Oct 27 01:30:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

Waiting for PID 5652 of (5652 5655) to complete...
Waiting for PID 5655 of (5652 5655) 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 = 45.7 mm, total surface area = 77325 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 1.2 minutes

step 000: RMS=0.195 (target=0.015)   
step 005: RMS=0.156 (target=0.015)   
step 010: RMS=0.131 (target=0.015)   
step 015: RMS=0.121 (target=0.015)   
step 020: RMS=0.114 (target=0.015)   
step 025: RMS=0.111 (target=0.015)   
step 030: RMS=0.106 (target=0.015)   
step 035: RMS=0.104 (target=0.015)   
step 040: RMS=0.102 (target=0.015)   
step 045: RMS=0.102 (target=0.015)   
step 050: RMS=0.102 (target=0.015)   
step 055: RMS=0.102 (target=0.015)   
step 060: RMS=0.102 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    36.388468
mris_inflate stimesec    0.068989
mris_inflate ru_maxrss   199188
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   26227
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10864
mris_inflate ru_oublock  10880
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    227
mris_inflate ru_nivcsw   3513

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 45.2 mm, total surface area = 73442 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.1 minutes

step 000: RMS=0.188 (target=0.015)   
step 005: RMS=0.148 (target=0.015)   
step 010: RMS=0.124 (target=0.015)   
step 015: RMS=0.113 (target=0.015)   
step 020: RMS=0.105 (target=0.015)   
step 025: RMS=0.101 (target=0.015)   
step 030: RMS=0.097 (target=0.015)   
step 035: RMS=0.095 (target=0.015)   
step 040: RMS=0.092 (target=0.015)   
step 045: RMS=0.092 (target=0.015)   
step 050: RMS=0.091 (target=0.015)   
step 055: RMS=0.091 (target=0.015)   
step 060: RMS=0.091 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    34.187802
mris_inflate stimesec    0.086986
mris_inflate ru_maxrss   187720
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   24381
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10248
mris_inflate ru_oublock  10264
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    33
mris_inflate ru_nivcsw   3467
PIDs (5652 5655) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Fri Oct 27 01:31:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

#--------------------------------------------
#@# QSphere rh Fri Oct 27 01:31:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

Waiting for PID 7692 of (7692 7695) to complete...
Waiting for PID 7695 of (7692 7695) 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 0.95 +- 0.67 (0.00-->10.69) (max @ vno 66919 --> 68531)
face area 0.03 +- 0.04 (-0.37-->0.92)

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.316...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.828, avgs=0
005/300: dt: 0.9000, rms radial error=176.567, avgs=0
010/300: dt: 0.9000, rms radial error=176.008, avgs=0
015/300: dt: 0.9000, rms radial error=175.274, avgs=0
020/300: dt: 0.9000, rms radial error=174.440, avgs=0
025/300: dt: 0.9000, rms radial error=173.548, avgs=0
030/300: dt: 0.9000, rms radial error=172.624, avgs=0
035/300: dt: 0.9000, rms radial error=171.682, avgs=0
040/300: dt: 0.9000, rms radial error=170.732, avgs=0
045/300: dt: 0.9000, rms radial error=169.785, avgs=0
050/300: dt: 0.9000, rms radial error=168.838, avgs=0
055/300: dt: 0.9000, rms radial error=167.894, avgs=0
060/300: dt: 0.9000, rms radial error=166.954, avgs=0
065/300: dt: 0.9000, rms radial error=166.017, avgs=0
070/300: dt: 0.9000, rms radial error=165.084, avgs=0
075/300: dt: 0.9000, rms radial error=164.157, avgs=0
080/300: dt: 0.9000, rms radial error=163.233, avgs=0
085/300: dt: 0.9000, rms radial error=162.314, avgs=0
090/300: dt: 0.9000, rms radial error=161.401, avgs=0
095/300: dt: 0.9000, rms radial error=160.492, avgs=0
100/300: dt: 0.9000, rms radial error=159.589, avgs=0
105/300: dt: 0.9000, rms radial error=158.694, avgs=0
110/300: dt: 0.9000, rms radial error=157.804, avgs=0
115/300: dt: 0.9000, rms radial error=156.918, avgs=0
120/300: dt: 0.9000, rms radial error=156.039, avgs=0
125/300: dt: 0.9000, rms radial error=155.164, avgs=0
130/300: dt: 0.9000, rms radial error=154.294, avgs=0
135/300: dt: 0.9000, rms radial error=153.429, avgs=0
140/300: dt: 0.9000, rms radial error=152.569, avgs=0
145/300: dt: 0.9000, rms radial error=151.713, avgs=0
150/300: dt: 0.9000, rms radial error=150.861, avgs=0
155/300: dt: 0.9000, rms radial error=150.015, avgs=0
160/300: dt: 0.9000, rms radial error=149.173, avgs=0
165/300: dt: 0.9000, rms radial error=148.335, avgs=0
170/300: dt: 0.9000, rms radial error=147.503, avgs=0
175/300: dt: 0.9000, rms radial error=146.674, avgs=0
180/300: dt: 0.9000, rms radial error=145.850, avgs=0
185/300: dt: 0.9000, rms radial error=145.030, avgs=0
190/300: dt: 0.9000, rms radial error=144.215, avgs=0
195/300: dt: 0.9000, rms radial error=143.404, avgs=0
200/300: dt: 0.9000, rms radial error=142.598, avgs=0
205/300: dt: 0.9000, rms radial error=141.796, avgs=0
210/300: dt: 0.9000, rms radial error=140.999, avgs=0
215/300: dt: 0.9000, rms radial error=140.206, avgs=0
220/300: dt: 0.9000, rms radial error=139.417, avgs=0
225/300: dt: 0.9000, rms radial error=138.633, avgs=0
230/300: dt: 0.9000, rms radial error=137.853, avgs=0
235/300: dt: 0.9000, rms radial error=137.078, avgs=0
240/300: dt: 0.9000, rms radial error=136.307, avgs=0
245/300: dt: 0.9000, rms radial error=135.540, avgs=0
250/300: dt: 0.9000, rms radial error=134.777, avgs=0
255/300: dt: 0.9000, rms radial error=134.019, avgs=0
260/300: dt: 0.9000, rms radial error=133.264, avgs=0
265/300: dt: 0.9000, rms radial error=132.514, avgs=0
270/300: dt: 0.9000, rms radial error=131.769, avgs=0
275/300: dt: 0.9000, rms radial error=131.027, avgs=0
280/300: dt: 0.9000, rms radial error=130.290, avgs=0
285/300: dt: 0.9000, rms radial error=129.557, avgs=0
290/300: dt: 0.9000, rms radial error=128.828, avgs=0
295/300: dt: 0.9000, rms radial error=128.103, avgs=0
300/300: dt: 0.9000, rms radial error=127.383, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18281.77
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00022
epoch 2 (K=40.0), pass 1, starting sse = 3316.91
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/10 = 0.00058
epoch 3 (K=160.0), pass 1, starting sse = 496.83
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00386
epoch 4 (K=640.0), pass 1, starting sse = 99.19
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00693
final distance error %29.18
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.12 hours
mris_sphere utimesec    226.274601
mris_sphere stimesec    0.085986
mris_sphere ru_maxrss   199392
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   26276
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10864
mris_sphere ru_oublock  10904
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    243
mris_sphere ru_nivcsw   21961
FSRUNTIME@ mris_sphere  0.1228 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 0.95 +- 0.64 (0.00-->15.58) (max @ vno 79516 --> 79529)
face area 0.03 +- 0.04 (-0.91-->1.37)

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.323...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.367, avgs=0
005/300: dt: 0.9000, rms radial error=176.106, avgs=0
010/300: dt: 0.9000, rms radial error=175.551, avgs=0
015/300: dt: 0.9000, rms radial error=174.822, avgs=0
020/300: dt: 0.9000, rms radial error=173.991, avgs=0
025/300: dt: 0.9000, rms radial error=173.101, avgs=0
030/300: dt: 0.9000, rms radial error=172.178, avgs=0
035/300: dt: 0.9000, rms radial error=171.239, avgs=0
040/300: dt: 0.9000, rms radial error=170.293, avgs=0
045/300: dt: 0.9000, rms radial error=169.345, avgs=0
050/300: dt: 0.9000, rms radial error=168.399, avgs=0
055/300: dt: 0.9000, rms radial error=167.455, avgs=0
060/300: dt: 0.9000, rms radial error=166.515, avgs=0
065/300: dt: 0.9000, rms radial error=165.579, avgs=0
070/300: dt: 0.9000, rms radial error=164.648, avgs=0
075/300: dt: 0.9000, rms radial error=163.721, avgs=0
080/300: dt: 0.9000, rms radial error=162.800, avgs=0
085/300: dt: 0.9000, rms radial error=161.883, avgs=0
090/300: dt: 0.9000, rms radial error=160.970, avgs=0
095/300: dt: 0.9000, rms radial error=160.062, avgs=0
100/300: dt: 0.9000, rms radial error=159.159, avgs=0
105/300: dt: 0.9000, rms radial error=158.261, avgs=0
110/300: dt: 0.9000, rms radial error=157.369, avgs=0
115/300: dt: 0.9000, rms radial error=156.481, avgs=0
120/300: dt: 0.9000, rms radial error=155.598, avgs=0
125/300: dt: 0.9000, rms radial error=154.720, avgs=0
130/300: dt: 0.9000, rms radial error=153.847, avgs=0
135/300: dt: 0.9000, rms radial error=152.979, avgs=0
140/300: dt: 0.9000, rms radial error=152.115, avgs=0
145/300: dt: 0.9000, rms radial error=151.256, avgs=0
150/300: dt: 0.9000, rms radial error=150.402, avgs=0
155/300: dt: 0.9000, rms radial error=149.553, avgs=0
160/300: dt: 0.9000, rms radial error=148.709, avgs=0
165/300: dt: 0.9000, rms radial error=147.869, avgs=0
170/300: dt: 0.9000, rms radial error=147.035, avgs=0
175/300: dt: 0.9000, rms radial error=146.205, avgs=0
180/300: dt: 0.9000, rms radial error=145.379, avgs=0
185/300: dt: 0.9000, rms radial error=144.558, avgs=0
190/300: dt: 0.9000, rms radial error=143.742, avgs=0
195/300: dt: 0.9000, rms radial error=142.930, avgs=0
200/300: dt: 0.9000, rms radial error=142.123, avgs=0
205/300: dt: 0.9000, rms radial error=141.321, avgs=0
210/300: dt: 0.9000, rms radial error=140.523, avgs=0
215/300: dt: 0.9000, rms radial error=139.729, avgs=0
220/300: dt: 0.9000, rms radial error=138.940, avgs=0
225/300: dt: 0.9000, rms radial error=138.156, avgs=0
230/300: dt: 0.9000, rms radial error=137.376, avgs=0
235/300: dt: 0.9000, rms radial error=136.600, avgs=0
240/300: dt: 0.9000, rms radial error=135.829, avgs=0
245/300: dt: 0.9000, rms radial error=135.063, avgs=0
250/300: dt: 0.9000, rms radial error=134.300, avgs=0
255/300: dt: 0.9000, rms radial error=133.542, avgs=0
260/300: dt: 0.9000, rms radial error=132.789, avgs=0
265/300: dt: 0.9000, rms radial error=132.039, avgs=0
270/300: dt: 0.9000, rms radial error=131.294, avgs=0
275/300: dt: 0.9000, rms radial error=130.553, avgs=0
280/300: dt: 0.9000, rms radial error=129.816, avgs=0
285/300: dt: 0.9000, rms radial error=129.083, avgs=0
290/300: dt: 0.9000, rms radial error=128.355, avgs=0
295/300: dt: 0.9000, rms radial error=127.630, avgs=0
300/300: dt: 0.9000, rms radial error=126.910, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17067.82
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 2 (K=40.0), pass 1, starting sse = 2983.98
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00023
epoch 3 (K=160.0), pass 1, starting sse = 390.23
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/10 = 0.00127
epoch 4 (K=640.0), pass 1, starting sse = 71.06
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00561
final distance error %26.96
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.12 hours
mris_sphere utimesec    215.925174
mris_sphere stimesec    0.078987
mris_sphere ru_maxrss   187916
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   24428
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10248
mris_sphere ru_oublock  10288
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    260
mris_sphere ru_nivcsw   21716
FSRUNTIME@ mris_sphere  0.1199 hours 1 threads
PIDs (7692 7695) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Fri Oct 27 01:38:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Fri Oct 27 01:38:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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


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

#@# Fix Topology lh Fri Oct 27 01:38:53 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 lh 

#@# Fix Topology rh Fri Oct 27 01:38:53 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 rh 

Waiting for PID 20548 of (20548 20551) to complete...
Waiting for PID 20551 of (20548 20551) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 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=-514 (nv=154060, nf=309148, ne=463722, g=258)
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...
54267 ambiguous faces found in tessellation
segmenting defects...
154 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 45 into 35
      -merging segment 56 into 35
      -merging segment 58 into 35
      -merging segment 80 into 35
      -merging segment 103 into 35
      -merging segment 90 into 35
      -merging segment 70 into 62
      -merging segment 68 into 65
      -merging segment 91 into 89
      -merging segment 118 into 99
      -merging segment 114 into 109
      -merging segment 115 into 109
      -merging segment 152 into 149
141 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4716  (-4.7358)
      -vertex     loglikelihood: -6.5776  (-3.2888)
      -normal dot loglikelihood: -3.5519  (-3.5519)
      -quad curv  loglikelihood: -6.2359  (-3.1179)
      Total Loglikelihood : -25.8369

CORRECTING DEFECT 0 (vertices=1852, convex hull=655, v0=82)
XL defect detected...
After retessellation of defect 0 (v0=82), euler #=-131 (123371,361991,238489) : difference with theory (-138) = -7 

CORRECTING DEFECT 1 (vertices=26, convex hull=32, v0=125)
After retessellation of defect 1 (v0=125), euler #=-130 (123374,362009,238505) : difference with theory (-137) = -7 

CORRECTING DEFECT 2 (vertices=52, convex hull=74, v0=1269)
After retessellation of defect 2 (v0=1269), euler #=-129 (123388,362080,238563) : difference with theory (-136) = -7 

CORRECTING DEFECT 3 (vertices=31, convex hull=53, v0=1455)
After retessellation of defect 3 (v0=1455), euler #=-128 (123395,362124,238601) : difference with theory (-135) = -7 

CORRECTING DEFECT 4 (vertices=73, convex hull=57, v0=1747)
After retessellation of defect 4 (v0=1747), euler #=-127 (123403,362168,238638) : difference with theory (-134) = -7 

CORRECTING DEFECT 5 (vertices=20, convex hull=57, v0=1976)
After retessellation of defect 5 (v0=1976), euler #=-126 (123415,362226,238685) : difference with theory (-133) = -7 

CORRECTING DEFECT 6 (vertices=26, convex hull=62, v0=3756)
After retessellation of defect 6 (v0=3756), euler #=-125 (123424,362276,238727) : difference with theory (-132) = -7 

CORRECTING DEFECT 7 (vertices=175, convex hull=168, v0=5442)
After retessellation of defect 7 (v0=5442), euler #=-125 (123500,362595,238970) : difference with theory (-131) = -6 

CORRECTING DEFECT 8 (vertices=48, convex hull=33, v0=5470)
After retessellation of defect 8 (v0=5470), euler #=-124 (123503,362617,238990) : difference with theory (-130) = -6 

CORRECTING DEFECT 9 (vertices=105, convex hull=140, v0=5963)
After retessellation of defect 9 (v0=5963), euler #=-123 (123566,362870,239181) : difference with theory (-129) = -6 

CORRECTING DEFECT 10 (vertices=68, convex hull=95, v0=6999)
After retessellation of defect 10 (v0=6999), euler #=-122 (123590,362979,239267) : difference with theory (-128) = -6 

CORRECTING DEFECT 11 (vertices=172, convex hull=141, v0=7015)
After retessellation of defect 11 (v0=7015), euler #=-122 (123639,363204,239443) : difference with theory (-127) = -5 

CORRECTING DEFECT 12 (vertices=5, convex hull=25, v0=7139)
After retessellation of defect 12 (v0=7139), euler #=-121 (123639,363209,239449) : difference with theory (-126) = -5 

CORRECTING DEFECT 13 (vertices=281, convex hull=138, v0=7227)
After retessellation of defect 13 (v0=7227), euler #=-120 (123709,363481,239652) : difference with theory (-125) = -5 

CORRECTING DEFECT 14 (vertices=32, convex hull=76, v0=7548)
After retessellation of defect 14 (v0=7548), euler #=-119 (123730,363573,239724) : difference with theory (-124) = -5 

CORRECTING DEFECT 15 (vertices=52, convex hull=81, v0=8730)
After retessellation of defect 15 (v0=8730), euler #=-118 (123765,363709,239826) : difference with theory (-123) = -5 

CORRECTING DEFECT 16 (vertices=103, convex hull=34, v0=9334)
After retessellation of defect 16 (v0=9334), euler #=-117 (123773,363743,239853) : difference with theory (-122) = -5 

CORRECTING DEFECT 17 (vertices=50, convex hull=38, v0=9386)
After retessellation of defect 17 (v0=9386), euler #=-116 (123776,363763,239871) : difference with theory (-121) = -5 

CORRECTING DEFECT 18 (vertices=366, convex hull=190, v0=9451)
After retessellation of defect 18 (v0=9451), euler #=-115 (123859,364115,240141) : difference with theory (-120) = -5 

CORRECTING DEFECT 19 (vertices=157, convex hull=108, v0=10502)
After retessellation of defect 19 (v0=10502), euler #=-114 (123886,364246,240246) : difference with theory (-119) = -5 

CORRECTING DEFECT 20 (vertices=35, convex hull=23, v0=10667)
After retessellation of defect 20 (v0=10667), euler #=-113 (123890,364264,240261) : difference with theory (-118) = -5 

CORRECTING DEFECT 21 (vertices=48, convex hull=91, v0=10861)
After retessellation of defect 21 (v0=10861), euler #=-112 (123903,364341,240326) : difference with theory (-117) = -5 

CORRECTING DEFECT 22 (vertices=100, convex hull=87, v0=12285)
After retessellation of defect 22 (v0=12285), euler #=-111 (123943,364496,240442) : difference with theory (-116) = -5 

CORRECTING DEFECT 23 (vertices=36, convex hull=78, v0=12718)
After retessellation of defect 23 (v0=12718), euler #=-110 (123959,364576,240507) : difference with theory (-115) = -5 

CORRECTING DEFECT 24 (vertices=18, convex hull=46, v0=12777)
After retessellation of defect 24 (v0=12777), euler #=-109 (123968,364619,240542) : difference with theory (-114) = -5 

CORRECTING DEFECT 25 (vertices=33, convex hull=63, v0=13514)
After retessellation of defect 25 (v0=13514), euler #=-108 (123990,364708,240610) : difference with theory (-113) = -5 

CORRECTING DEFECT 26 (vertices=52, convex hull=45, v0=14436)
After retessellation of defect 26 (v0=14436), euler #=-107 (123998,364749,240644) : difference with theory (-112) = -5 

CORRECTING DEFECT 27 (vertices=36, convex hull=81, v0=15705)
After retessellation of defect 27 (v0=15705), euler #=-106 (124016,364837,240715) : difference with theory (-111) = -5 

CORRECTING DEFECT 28 (vertices=6, convex hull=25, v0=16080)
After retessellation of defect 28 (v0=16080), euler #=-105 (124016,364846,240725) : difference with theory (-110) = -5 

CORRECTING DEFECT 29 (vertices=332, convex hull=188, v0=16391)
After retessellation of defect 29 (v0=16391), euler #=-104 (124117,365233,241012) : difference with theory (-109) = -5 

CORRECTING DEFECT 30 (vertices=49, convex hull=50, v0=17596)
After retessellation of defect 30 (v0=17596), euler #=-103 (124123,365274,241048) : difference with theory (-108) = -5 

CORRECTING DEFECT 31 (vertices=5, convex hull=26, v0=18681)
After retessellation of defect 31 (v0=18681), euler #=-102 (124123,365280,241055) : difference with theory (-107) = -5 

CORRECTING DEFECT 32 (vertices=44, convex hull=77, v0=18759)
After retessellation of defect 32 (v0=18759), euler #=-101 (124144,365374,241129) : difference with theory (-106) = -5 

CORRECTING DEFECT 33 (vertices=18, convex hull=60, v0=19375)
After retessellation of defect 33 (v0=19375), euler #=-100 (124155,365430,241175) : difference with theory (-105) = -5 

CORRECTING DEFECT 34 (vertices=40, convex hull=36, v0=19673)
After retessellation of defect 34 (v0=19673), euler #=-99 (124159,365459,241201) : difference with theory (-104) = -5 

CORRECTING DEFECT 35 (vertices=13196, convex hull=5172, v0=20537)
XL defect detected...
After retessellation of defect 35 (v0=20537), euler #=-101 (127943,379731,251687) : difference with theory (-103) = -2 

CORRECTING DEFECT 36 (vertices=164, convex hull=166, v0=21399)
After retessellation of defect 36 (v0=21399), euler #=-100 (128010,380009,251899) : difference with theory (-102) = -2 

CORRECTING DEFECT 37 (vertices=25, convex hull=24, v0=21737)
After retessellation of defect 37 (v0=21737), euler #=-99 (128011,380020,251910) : difference with theory (-101) = -2 

CORRECTING DEFECT 38 (vertices=5, convex hull=18, v0=23692)
After retessellation of defect 38 (v0=23692), euler #=-98 (128011,380024,251915) : difference with theory (-100) = -2 

CORRECTING DEFECT 39 (vertices=35, convex hull=69, v0=23838)
After retessellation of defect 39 (v0=23838), euler #=-97 (128029,380102,251976) : difference with theory (-99) = -2 

CORRECTING DEFECT 40 (vertices=107, convex hull=99, v0=24305)
After retessellation of defect 40 (v0=24305), euler #=-96 (128086,380319,252137) : difference with theory (-98) = -2 

CORRECTING DEFECT 41 (vertices=197, convex hull=126, v0=24688)
After retessellation of defect 41 (v0=24688), euler #=-95 (128120,380487,252272) : difference with theory (-97) = -2 

CORRECTING DEFECT 42 (vertices=120, convex hull=147, v0=24935)
After retessellation of defect 42 (v0=24935), euler #=-94 (128172,380705,252439) : difference with theory (-96) = -2 

CORRECTING DEFECT 43 (vertices=22, convex hull=51, v0=25034)
After retessellation of defect 43 (v0=25034), euler #=-93 (128183,380758,252482) : difference with theory (-95) = -2 

CORRECTING DEFECT 44 (vertices=69, convex hull=73, v0=25579)
After retessellation of defect 44 (v0=25579), euler #=-92 (128203,380847,252552) : difference with theory (-94) = -2 

CORRECTING DEFECT 45 (vertices=22, convex hull=24, v0=28815)
After retessellation of defect 45 (v0=28815), euler #=-91 (128208,380871,252572) : difference with theory (-93) = -2 

CORRECTING DEFECT 46 (vertices=153, convex hull=156, v0=29415)
After retessellation of defect 46 (v0=29415), euler #=-90 (128260,381103,252753) : difference with theory (-92) = -2 

CORRECTING DEFECT 47 (vertices=27, convex hull=67, v0=30636)
After retessellation of defect 47 (v0=30636), euler #=-89 (128272,381163,252802) : difference with theory (-91) = -2 

CORRECTING DEFECT 48 (vertices=193, convex hull=67, v0=30886)
After retessellation of defect 48 (v0=30886), euler #=-88 (128294,381257,252875) : difference with theory (-90) = -2 

CORRECTING DEFECT 49 (vertices=37, convex hull=66, v0=31503)
After retessellation of defect 49 (v0=31503), euler #=-87 (128313,381343,252943) : difference with theory (-89) = -2 

CORRECTING DEFECT 50 (vertices=72, convex hull=107, v0=31975)
After retessellation of defect 50 (v0=31975), euler #=-86 (128349,381498,253063) : difference with theory (-88) = -2 

CORRECTING DEFECT 51 (vertices=29, convex hull=73, v0=33178)
After retessellation of defect 51 (v0=33178), euler #=-85 (128366,381578,253127) : difference with theory (-87) = -2 

CORRECTING DEFECT 52 (vertices=78, convex hull=31, v0=33827)
After retessellation of defect 52 (v0=33827), euler #=-84 (128368,381597,253145) : difference with theory (-86) = -2 

CORRECTING DEFECT 53 (vertices=126, convex hull=108, v0=35543)
After retessellation of defect 53 (v0=35543), euler #=-83 (128399,381742,253260) : difference with theory (-85) = -2 

CORRECTING DEFECT 54 (vertices=41, convex hull=69, v0=38998)
After retessellation of defect 54 (v0=38998), euler #=-82 (128412,381810,253316) : difference with theory (-84) = -2 

CORRECTING DEFECT 55 (vertices=187, convex hull=193, v0=43442)
After retessellation of defect 55 (v0=43442), euler #=-81 (128475,382087,253531) : difference with theory (-83) = -2 

CORRECTING DEFECT 56 (vertices=31, convex hull=48, v0=44394)
After retessellation of defect 56 (v0=44394), euler #=-80 (128492,382153,253581) : difference with theory (-82) = -2 

CORRECTING DEFECT 57 (vertices=42, convex hull=55, v0=45218)
After retessellation of defect 57 (v0=45218), euler #=-79 (128514,382241,253648) : difference with theory (-81) = -2 

CORRECTING DEFECT 58 (vertices=18, convex hull=33, v0=45302)
After retessellation of defect 58 (v0=45302), euler #=-78 (128517,382262,253667) : difference with theory (-80) = -2 

CORRECTING DEFECT 59 (vertices=1238, convex hull=639, v0=45521)
XL defect detected...
After retessellation of defect 59 (v0=45521), euler #=-80 (128893,383735,254762) : difference with theory (-79) = 1 

CORRECTING DEFECT 60 (vertices=46, convex hull=37, v0=46122)
After retessellation of defect 60 (v0=46122), euler #=-79 (128898,383764,254787) : difference with theory (-78) = 1 

CORRECTING DEFECT 61 (vertices=25, convex hull=54, v0=46592)
After retessellation of defect 61 (v0=46592), euler #=-78 (128912,383824,254834) : difference with theory (-77) = 1 

CORRECTING DEFECT 62 (vertices=104, convex hull=122, v0=47545)
After retessellation of defect 62 (v0=47545), euler #=-76 (128934,383951,254941) : difference with theory (-76) = 0 

CORRECTING DEFECT 63 (vertices=52, convex hull=34, v0=48329)
After retessellation of defect 63 (v0=48329), euler #=-75 (128942,383989,254972) : difference with theory (-75) = 0 

CORRECTING DEFECT 64 (vertices=38, convex hull=39, v0=48353)
After retessellation of defect 64 (v0=48353), euler #=-74 (128954,384041,255013) : difference with theory (-74) = 0 

CORRECTING DEFECT 65 (vertices=29, convex hull=78, v0=49949)
After retessellation of defect 65 (v0=49949), euler #=-73 (128972,384132,255087) : difference with theory (-73) = 0 

CORRECTING DEFECT 66 (vertices=95, convex hull=164, v0=54082)
After retessellation of defect 66 (v0=54082), euler #=-72 (129001,384292,255219) : difference with theory (-72) = 0 

CORRECTING DEFECT 67 (vertices=21, convex hull=27, v0=55783)
After retessellation of defect 67 (v0=55783), euler #=-71 (129002,384303,255230) : difference with theory (-71) = 0 

CORRECTING DEFECT 68 (vertices=46, convex hull=67, v0=56489)
After retessellation of defect 68 (v0=56489), euler #=-70 (129033,384425,255322) : difference with theory (-70) = 0 

CORRECTING DEFECT 69 (vertices=41, convex hull=66, v0=62822)
After retessellation of defect 69 (v0=62822), euler #=-69 (129049,384497,255379) : difference with theory (-69) = 0 

CORRECTING DEFECT 70 (vertices=29, convex hull=31, v0=62930)
After retessellation of defect 70 (v0=62930), euler #=-68 (129052,384519,255399) : difference with theory (-68) = 0 

CORRECTING DEFECT 71 (vertices=34, convex hull=33, v0=63183)
After retessellation of defect 71 (v0=63183), euler #=-67 (129055,384538,255416) : difference with theory (-67) = 0 

CORRECTING DEFECT 72 (vertices=46, convex hull=94, v0=63224)
After retessellation of defect 72 (v0=63224), euler #=-66 (129086,384670,255518) : difference with theory (-66) = 0 

CORRECTING DEFECT 73 (vertices=135, convex hull=74, v0=64348)
After retessellation of defect 73 (v0=64348), euler #=-66 (129111,384782,255605) : difference with theory (-65) = 1 

CORRECTING DEFECT 74 (vertices=43, convex hull=53, v0=69405)
After retessellation of defect 74 (v0=69405), euler #=-65 (129124,384840,255651) : difference with theory (-64) = 1 

CORRECTING DEFECT 75 (vertices=22, convex hull=17, v0=72847)
After retessellation of defect 75 (v0=72847), euler #=-64 (129127,384854,255663) : difference with theory (-63) = 1 

CORRECTING DEFECT 76 (vertices=41, convex hull=82, v0=73101)
After retessellation of defect 76 (v0=73101), euler #=-63 (129139,384932,255730) : difference with theory (-62) = 1 

CORRECTING DEFECT 77 (vertices=96, convex hull=102, v0=73351)
After retessellation of defect 77 (v0=73351), euler #=-62 (129192,385137,255883) : difference with theory (-61) = 1 

CORRECTING DEFECT 78 (vertices=29, convex hull=63, v0=73833)
After retessellation of defect 78 (v0=73833), euler #=-61 (129209,385215,255945) : difference with theory (-60) = 1 

CORRECTING DEFECT 79 (vertices=33, convex hull=68, v0=73866)
After retessellation of defect 79 (v0=73866), euler #=-60 (129231,385307,256016) : difference with theory (-59) = 1 

CORRECTING DEFECT 80 (vertices=98, convex hull=48, v0=74595)
After retessellation of defect 80 (v0=74595), euler #=-59 (129240,385356,256057) : difference with theory (-58) = 1 

CORRECTING DEFECT 81 (vertices=10, convex hull=18, v0=76584)
After retessellation of defect 81 (v0=76584), euler #=-58 (129241,385366,256067) : difference with theory (-57) = 1 

CORRECTING DEFECT 82 (vertices=108, convex hull=135, v0=78474)
After retessellation of defect 82 (v0=78474), euler #=-57 (129251,385457,256149) : difference with theory (-56) = 1 

CORRECTING DEFECT 83 (vertices=41, convex hull=53, v0=81006)
After retessellation of defect 83 (v0=81006), euler #=-55 (129260,385507,256192) : difference with theory (-55) = 0 

CORRECTING DEFECT 84 (vertices=48, convex hull=61, v0=84591)
After retessellation of defect 84 (v0=84591), euler #=-54 (129285,385609,256270) : difference with theory (-54) = 0 

CORRECTING DEFECT 85 (vertices=39, convex hull=44, v0=87157)
After retessellation of defect 85 (v0=87157), euler #=-53 (129291,385642,256298) : difference with theory (-53) = 0 

CORRECTING DEFECT 86 (vertices=56, convex hull=106, v0=88480)
After retessellation of defect 86 (v0=88480), euler #=-52 (129318,385777,256407) : difference with theory (-52) = 0 

CORRECTING DEFECT 87 (vertices=113, convex hull=110, v0=88544)
After retessellation of defect 87 (v0=88544), euler #=-51 (129359,385960,256550) : difference with theory (-51) = 0 

CORRECTING DEFECT 88 (vertices=40, convex hull=61, v0=88576)
After retessellation of defect 88 (v0=88576), euler #=-50 (129381,386046,256615) : difference with theory (-50) = 0 

CORRECTING DEFECT 89 (vertices=166, convex hull=49, v0=89740)
After retessellation of defect 89 (v0=89740), euler #=-49 (129399,386121,256673) : difference with theory (-49) = 0 

CORRECTING DEFECT 90 (vertices=129, convex hull=206, v0=90255)
After retessellation of defect 90 (v0=90255), euler #=-48 (129490,386497,256959) : difference with theory (-48) = 0 

CORRECTING DEFECT 91 (vertices=1101, convex hull=275, v0=92246)
After retessellation of defect 91 (v0=92246), euler #=-48 (129746,387426,257632) : difference with theory (-47) = 1 

CORRECTING DEFECT 92 (vertices=21, convex hull=55, v0=94279)
After retessellation of defect 92 (v0=94279), euler #=-47 (129756,387477,257674) : difference with theory (-46) = 1 

CORRECTING DEFECT 93 (vertices=66, convex hull=102, v0=94848)
After retessellation of defect 93 (v0=94848), euler #=-46 (129794,387636,257796) : difference with theory (-45) = 1 

CORRECTING DEFECT 94 (vertices=24, convex hull=66, v0=96667)
After retessellation of defect 94 (v0=96667), euler #=-45 (129803,387686,257838) : difference with theory (-44) = 1 

CORRECTING DEFECT 95 (vertices=72, convex hull=95, v0=99039)
After retessellation of defect 95 (v0=99039), euler #=-44 (129826,387797,257927) : difference with theory (-43) = 1 

CORRECTING DEFECT 96 (vertices=2594, convex hull=529, v0=99867)
XL defect detected...
After retessellation of defect 96 (v0=99867), euler #=-44 (130271,389439,259124) : difference with theory (-42) = 2 

CORRECTING DEFECT 97 (vertices=38, convex hull=62, v0=102000)
After retessellation of defect 97 (v0=102000), euler #=-43 (130281,389494,259170) : difference with theory (-41) = 2 

CORRECTING DEFECT 98 (vertices=100, convex hull=37, v0=103995)
After retessellation of defect 98 (v0=103995), euler #=-42 (130292,389544,259210) : difference with theory (-40) = 2 

CORRECTING DEFECT 99 (vertices=5, convex hull=15, v0=106471)
After retessellation of defect 99 (v0=106471), euler #=-41 (130293,389551,259217) : difference with theory (-39) = 2 

CORRECTING DEFECT 100 (vertices=243, convex hull=260, v0=107059)
After retessellation of defect 100 (v0=107059), euler #=-38 (130386,389954,259530) : difference with theory (-38) = 0 

CORRECTING DEFECT 101 (vertices=38, convex hull=59, v0=109721)
After retessellation of defect 101 (v0=109721), euler #=-37 (130395,390006,259574) : difference with theory (-37) = 0 

CORRECTING DEFECT 102 (vertices=125, convex hull=43, v0=109975)
After retessellation of defect 102 (v0=109975), euler #=-36 (130404,390048,259608) : difference with theory (-36) = 0 

CORRECTING DEFECT 103 (vertices=19, convex hull=25, v0=110007)
After retessellation of defect 103 (v0=110007), euler #=-35 (130406,390061,259620) : difference with theory (-35) = 0 

CORRECTING DEFECT 104 (vertices=44, convex hull=71, v0=111755)
After retessellation of defect 104 (v0=111755), euler #=-34 (130441,390198,259723) : difference with theory (-34) = 0 

CORRECTING DEFECT 105 (vertices=38, convex hull=60, v0=113772)
After retessellation of defect 105 (v0=113772), euler #=-33 (130460,390277,259784) : difference with theory (-33) = 0 

CORRECTING DEFECT 106 (vertices=26, convex hull=34, v0=114689)
After retessellation of defect 106 (v0=114689), euler #=-32 (130464,390300,259804) : difference with theory (-32) = 0 

CORRECTING DEFECT 107 (vertices=555, convex hull=128, v0=116310)
After retessellation of defect 107 (v0=116310), euler #=-32 (130566,390670,260072) : difference with theory (-31) = 1 

CORRECTING DEFECT 108 (vertices=51, convex hull=96, v0=119588)
After retessellation of defect 108 (v0=119588), euler #=-31 (130598,390808,260179) : difference with theory (-30) = 1 

CORRECTING DEFECT 109 (vertices=73, convex hull=79, v0=120388)
After retessellation of defect 109 (v0=120388), euler #=-30 (130631,390939,260278) : difference with theory (-29) = 1 

CORRECTING DEFECT 110 (vertices=102, convex hull=39, v0=122413)
After retessellation of defect 110 (v0=122413), euler #=-29 (130644,390994,260321) : difference with theory (-28) = 1 

CORRECTING DEFECT 111 (vertices=40, convex hull=22, v0=124223)
After retessellation of defect 111 (v0=124223), euler #=-28 (130648,391011,260335) : difference with theory (-27) = 1 

CORRECTING DEFECT 112 (vertices=59, convex hull=33, v0=124257)
After retessellation of defect 112 (v0=124257), euler #=-27 (130654,391040,260359) : difference with theory (-26) = 1 

CORRECTING DEFECT 113 (vertices=28, convex hull=25, v0=125545)
After retessellation of defect 113 (v0=125545), euler #=-26 (130656,391055,260373) : difference with theory (-25) = 1 

CORRECTING DEFECT 114 (vertices=477, convex hull=65, v0=125835)
After retessellation of defect 114 (v0=125835), euler #=-25 (130673,391132,260434) : difference with theory (-24) = 1 

CORRECTING DEFECT 115 (vertices=159, convex hull=136, v0=128208)
After retessellation of defect 115 (v0=128208), euler #=-24 (130737,391388,260627) : difference with theory (-23) = 1 

CORRECTING DEFECT 116 (vertices=85, convex hull=134, v0=130564)
After retessellation of defect 116 (v0=130564), euler #=-23 (130774,391559,260762) : difference with theory (-22) = 1 

CORRECTING DEFECT 117 (vertices=13, convex hull=23, v0=131053)
After retessellation of defect 117 (v0=131053), euler #=-22 (130775,391568,260771) : difference with theory (-21) = 1 

CORRECTING DEFECT 118 (vertices=317, convex hull=107, v0=133167)
After retessellation of defect 118 (v0=133167), euler #=-21 (130813,391733,260899) : difference with theory (-20) = 1 

CORRECTING DEFECT 119 (vertices=36, convex hull=20, v0=133217)
After retessellation of defect 119 (v0=133217), euler #=-20 (130813,391741,260908) : difference with theory (-19) = 1 

CORRECTING DEFECT 120 (vertices=158, convex hull=97, v0=136084)
After retessellation of defect 120 (v0=136084), euler #=-19 (130825,391817,260973) : difference with theory (-18) = 1 

CORRECTING DEFECT 121 (vertices=46, convex hull=34, v0=137485)
After retessellation of defect 121 (v0=137485), euler #=-18 (130830,391844,260996) : difference with theory (-17) = 1 

CORRECTING DEFECT 122 (vertices=360, convex hull=176, v0=138259)
After retessellation of defect 122 (v0=138259), euler #=-17 (130933,392236,261286) : difference with theory (-16) = 1 

CORRECTING DEFECT 123 (vertices=40, convex hull=75, v0=139330)
After retessellation of defect 123 (v0=139330), euler #=-16 (130948,392311,261347) : difference with theory (-15) = 1 

CORRECTING DEFECT 124 (vertices=41, convex hull=65, v0=140290)
After retessellation of defect 124 (v0=140290), euler #=-15 (130970,392404,261419) : difference with theory (-14) = 1 

CORRECTING DEFECT 125 (vertices=85, convex hull=89, v0=140650)
After retessellation of defect 125 (v0=140650), euler #=-14 (131005,392544,261525) : difference with theory (-13) = 1 

CORRECTING DEFECT 126 (vertices=33, convex hull=69, v0=141039)
After retessellation of defect 126 (v0=141039), euler #=-13 (131018,392611,261580) : difference with theory (-12) = 1 

CORRECTING DEFECT 127 (vertices=44, convex hull=94, v0=142386)
After retessellation of defect 127 (v0=142386), euler #=-12 (131047,392741,261682) : difference with theory (-11) = 1 

CORRECTING DEFECT 128 (vertices=51, convex hull=108, v0=142527)
After retessellation of defect 128 (v0=142527), euler #=-11 (131065,392840,261764) : difference with theory (-10) = 1 

CORRECTING DEFECT 129 (vertices=43, convex hull=77, v0=142873)
After retessellation of defect 129 (v0=142873), euler #=-10 (131077,392905,261818) : difference with theory (-9) = 1 

CORRECTING DEFECT 130 (vertices=30, convex hull=18, v0=143060)
After retessellation of defect 130 (v0=143060), euler #=-9 (131077,392910,261824) : difference with theory (-8) = 1 

CORRECTING DEFECT 131 (vertices=34, convex hull=27, v0=145650)
After retessellation of defect 131 (v0=145650), euler #=-8 (131078,392924,261838) : difference with theory (-7) = 1 

CORRECTING DEFECT 132 (vertices=58, convex hull=106, v0=147022)
After retessellation of defect 132 (v0=147022), euler #=-7 (131102,393048,261939) : difference with theory (-6) = 1 

CORRECTING DEFECT 133 (vertices=34, convex hull=84, v0=147314)
After retessellation of defect 133 (v0=147314), euler #=-6 (131116,393125,262003) : difference with theory (-5) = 1 

CORRECTING DEFECT 134 (vertices=63, convex hull=50, v0=147590)
After retessellation of defect 134 (v0=147590), euler #=-5 (131122,393161,262034) : difference with theory (-4) = 1 

CORRECTING DEFECT 135 (vertices=179, convex hull=48, v0=150295)
After retessellation of defect 135 (v0=150295), euler #=-4 (131132,393212,262076) : difference with theory (-3) = 1 

CORRECTING DEFECT 136 (vertices=23, convex hull=71, v0=151271)
After retessellation of defect 136 (v0=151271), euler #=-3 (131144,393272,262125) : difference with theory (-2) = 1 

CORRECTING DEFECT 137 (vertices=64, convex hull=60, v0=151636)
After retessellation of defect 137 (v0=151636), euler #=-1 (131150,393312,262161) : difference with theory (-1) = 0 

CORRECTING DEFECT 138 (vertices=291, convex hull=145, v0=151952)
After retessellation of defect 138 (v0=151952), euler #=0 (131214,393571,262357) : difference with theory (0) = 0 

CORRECTING DEFECT 139 (vertices=60, convex hull=87, v0=152760)
After retessellation of defect 139 (v0=152760), euler #=1 (131237,393678,262442) : difference with theory (1) = 0 

CORRECTING DEFECT 140 (vertices=95, convex hull=63, v0=153708)
After retessellation of defect 140 (v0=153708), euler #=2 (131248,393738,262492) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.91 +- 0.38 (0.01-->19.97) (max @ vno 57431 --> 132570)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.91 +- 0.38 (0.01-->19.97) (max @ vno 57431 --> 132570)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
441 mutations (36.2%), 777 crossovers (63.8%), 1846 vertices were eliminated
building final representation...
22812 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=131248, nf=262492, ne=393738, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 3066.3 minutes
0 defective edges
removing intersecting faces
000: 3001 intersecting
001: 458 intersecting
002: 214 intersecting
003: 180 intersecting
004: 172 intersecting
005: 129 intersecting
006: 119 intersecting
007: 102 intersecting
expanding nbhd size to 2
008: 109 intersecting
009: 78 intersecting
010: 45 intersecting
011: 35 intersecting
012: 27 intersecting
013: 16 intersecting
expanding nbhd size to 3
014: 30 intersecting
015: 6 intersecting
expanding nbhd size to 4
016: 7 intersecting
017: 3 intersecting
018: 2 intersecting
expanding nbhd size to 5
019: 2 intersecting
mris_fix_topology utimesec    173119.689806
mris_fix_topology stimesec    17.504338
mris_fix_topology ru_maxrss   2641484
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   567349
mris_fix_topology ru_majflt   19
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  77160
mris_fix_topology ru_oublock  13712
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    484
mris_fix_topology ru_nivcsw   1468749
FSRUNTIME@ mris_fix_topology lh 51.1058 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 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=-316 (nv=145424, nf=291480, ne=437220, g=159)
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...
35363 ambiguous faces found in tessellation
segmenting defects...
120 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 1 into 0
      -merging segment 6 into 3
      -merging segment 8 into 5
      -merging segment 14 into 7
      -merging segment 22 into 7
      -merging segment 17 into 15
      -merging segment 24 into 15
      -merging segment 46 into 38
      -merging segment 73 into 72
      -merging segment 90 into 72
      -merging segment 94 into 72
      -merging segment 86 into 77
108 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5619  (-4.7809)
      -vertex     loglikelihood: -6.6352  (-3.3176)
      -normal dot loglikelihood: -3.5189  (-3.5189)
      -quad curv  loglikelihood: -6.2410  (-3.1205)
      Total Loglikelihood : -25.9569

CORRECTING DEFECT 0 (vertices=512, convex hull=292, v0=0)
After retessellation of defect 0 (v0=0), euler #=-110 (125182,370015,244723) : difference with theory (-105) = 5 

CORRECTING DEFECT 1 (vertices=35, convex hull=72, v0=348)
After retessellation of defect 1 (v0=348), euler #=-109 (125203,370109,244797) : difference with theory (-104) = 5 

CORRECTING DEFECT 2 (vertices=234, convex hull=215, v0=515)
After retessellation of defect 2 (v0=515), euler #=-107 (125288,370482,245087) : difference with theory (-103) = 4 

CORRECTING DEFECT 3 (vertices=35, convex hull=53, v0=600)
After retessellation of defect 3 (v0=600), euler #=-106 (125291,370510,245113) : difference with theory (-102) = 4 

CORRECTING DEFECT 4 (vertices=805, convex hull=557, v0=1187)
L defect detected...
After retessellation of defect 4 (v0=1187), euler #=-104 (125433,371248,245711) : difference with theory (-101) = 3 

CORRECTING DEFECT 5 (vertices=338, convex hull=245, v0=5539)
After retessellation of defect 5 (v0=5539), euler #=-101 (125492,371553,245960) : difference with theory (-100) = 1 

CORRECTING DEFECT 6 (vertices=123, convex hull=84, v0=6150)
After retessellation of defect 6 (v0=6150), euler #=-100 (125525,371689,246064) : difference with theory (-99) = 1 

CORRECTING DEFECT 7 (vertices=103, convex hull=96, v0=6408)
After retessellation of defect 7 (v0=6408), euler #=-99 (125568,371859,246192) : difference with theory (-98) = 1 

CORRECTING DEFECT 8 (vertices=85, convex hull=108, v0=7633)
After retessellation of defect 8 (v0=7633), euler #=-98 (125584,371955,246273) : difference with theory (-97) = 1 

CORRECTING DEFECT 9 (vertices=41, convex hull=101, v0=8130)
After retessellation of defect 9 (v0=8130), euler #=-97 (125610,372071,246364) : difference with theory (-96) = 1 

CORRECTING DEFECT 10 (vertices=34, convex hull=76, v0=8262)
After retessellation of defect 10 (v0=8262), euler #=-96 (125619,372129,246414) : difference with theory (-95) = 1 

CORRECTING DEFECT 11 (vertices=599, convex hull=340, v0=10567)
After retessellation of defect 11 (v0=10567), euler #=-94 (125853,373042,247095) : difference with theory (-94) = 0 

CORRECTING DEFECT 12 (vertices=225, convex hull=164, v0=10571)
After retessellation of defect 12 (v0=10571), euler #=-93 (125967,373462,247402) : difference with theory (-93) = 0 

CORRECTING DEFECT 13 (vertices=401, convex hull=75, v0=11189)
After retessellation of defect 13 (v0=11189), euler #=-92 (126000,373595,247503) : difference with theory (-92) = 0 

CORRECTING DEFECT 14 (vertices=111, convex hull=90, v0=13953)
After retessellation of defect 14 (v0=13953), euler #=-91 (126032,373732,247609) : difference with theory (-91) = 0 

CORRECTING DEFECT 15 (vertices=71, convex hull=90, v0=15117)
After retessellation of defect 15 (v0=15117), euler #=-90 (126049,373822,247683) : difference with theory (-90) = 0 

CORRECTING DEFECT 16 (vertices=15, convex hull=34, v0=15361)
After retessellation of defect 16 (v0=15361), euler #=-89 (126052,373842,247701) : difference with theory (-89) = 0 

CORRECTING DEFECT 17 (vertices=106, convex hull=99, v0=16392)
After retessellation of defect 17 (v0=16392), euler #=-88 (126105,374044,247851) : difference with theory (-88) = 0 

CORRECTING DEFECT 18 (vertices=15, convex hull=17, v0=18878)
After retessellation of defect 18 (v0=18878), euler #=-87 (126106,374052,247859) : difference with theory (-87) = 0 

CORRECTING DEFECT 19 (vertices=67, convex hull=84, v0=20010)
After retessellation of defect 19 (v0=20010), euler #=-86 (126138,374181,247957) : difference with theory (-86) = 0 

CORRECTING DEFECT 20 (vertices=21, convex hull=57, v0=21225)
After retessellation of defect 20 (v0=21225), euler #=-85 (126149,374236,248002) : difference with theory (-85) = 0 

CORRECTING DEFECT 21 (vertices=86, convex hull=55, v0=21526)
After retessellation of defect 21 (v0=21526), euler #=-84 (126158,374287,248045) : difference with theory (-84) = 0 

CORRECTING DEFECT 22 (vertices=5, convex hull=18, v0=22310)
After retessellation of defect 22 (v0=22310), euler #=-83 (126158,374291,248050) : difference with theory (-83) = 0 

CORRECTING DEFECT 23 (vertices=96, convex hull=124, v0=23786)
After retessellation of defect 23 (v0=23786), euler #=-83 (126198,374483,248202) : difference with theory (-82) = 1 

CORRECTING DEFECT 24 (vertices=126, convex hull=127, v0=24075)
After retessellation of defect 24 (v0=24075), euler #=-82 (126268,374752,248402) : difference with theory (-81) = 1 

CORRECTING DEFECT 25 (vertices=51, convex hull=116, v0=24324)
After retessellation of defect 25 (v0=24324), euler #=-81 (126298,374888,248509) : difference with theory (-80) = 1 

CORRECTING DEFECT 26 (vertices=153, convex hull=181, v0=25006)
After retessellation of defect 26 (v0=25006), euler #=-80 (126390,375251,248781) : difference with theory (-79) = 1 

CORRECTING DEFECT 27 (vertices=185, convex hull=134, v0=25129)
After retessellation of defect 27 (v0=25129), euler #=-80 (126469,375566,249017) : difference with theory (-78) = 2 

CORRECTING DEFECT 28 (vertices=31, convex hull=73, v0=28119)
After retessellation of defect 28 (v0=28119), euler #=-79 (126490,375659,249090) : difference with theory (-77) = 2 

CORRECTING DEFECT 29 (vertices=94, convex hull=113, v0=29627)
After retessellation of defect 29 (v0=29627), euler #=-78 (126533,375839,249228) : difference with theory (-76) = 2 

CORRECTING DEFECT 30 (vertices=84, convex hull=72, v0=29822)
After retessellation of defect 30 (v0=29822), euler #=-77 (126556,375937,249304) : difference with theory (-75) = 2 

CORRECTING DEFECT 31 (vertices=2168, convex hull=564, v0=30155)
XL defect detected...
After retessellation of defect 31 (v0=30155), euler #=-75 (126870,377169,250224) : difference with theory (-74) = 1 

CORRECTING DEFECT 32 (vertices=62, convex hull=57, v0=33561)
After retessellation of defect 32 (v0=33561), euler #=-74 (126877,377214,250263) : difference with theory (-73) = 1 

CORRECTING DEFECT 33 (vertices=130, convex hull=51, v0=33633)
After retessellation of defect 33 (v0=33633), euler #=-73 (126900,377304,250331) : difference with theory (-72) = 1 

CORRECTING DEFECT 34 (vertices=29, convex hull=38, v0=36016)
After retessellation of defect 34 (v0=36016), euler #=-72 (126904,377330,250354) : difference with theory (-71) = 1 

CORRECTING DEFECT 35 (vertices=69, convex hull=97, v0=36148)
After retessellation of defect 35 (v0=36148), euler #=-71 (126934,377457,250452) : difference with theory (-70) = 1 

CORRECTING DEFECT 36 (vertices=23, convex hull=46, v0=36203)
After retessellation of defect 36 (v0=36203), euler #=-70 (126945,377506,250491) : difference with theory (-69) = 1 

CORRECTING DEFECT 37 (vertices=34, convex hull=26, v0=38980)
After retessellation of defect 37 (v0=38980), euler #=-69 (126948,377524,250507) : difference with theory (-68) = 1 

CORRECTING DEFECT 38 (vertices=38, convex hull=77, v0=45209)
After retessellation of defect 38 (v0=45209), euler #=-68 (126972,377629,250589) : difference with theory (-67) = 1 

CORRECTING DEFECT 39 (vertices=18, convex hull=36, v0=46065)
After retessellation of defect 39 (v0=46065), euler #=-67 (126972,377640,250601) : difference with theory (-66) = 1 

CORRECTING DEFECT 40 (vertices=93, convex hull=95, v0=46212)
After retessellation of defect 40 (v0=46212), euler #=-66 (127018,377819,250735) : difference with theory (-65) = 1 

CORRECTING DEFECT 41 (vertices=40, convex hull=31, v0=48255)
After retessellation of defect 41 (v0=48255), euler #=-65 (127021,377837,250751) : difference with theory (-64) = 1 

CORRECTING DEFECT 42 (vertices=517, convex hull=247, v0=48285)
After retessellation of defect 42 (v0=48285), euler #=-65 (127277,378739,251397) : difference with theory (-63) = 2 

CORRECTING DEFECT 43 (vertices=86, convex hull=127, v0=48373)
After retessellation of defect 43 (v0=48373), euler #=-64 (127331,378956,251561) : difference with theory (-62) = 2 

CORRECTING DEFECT 44 (vertices=113, convex hull=121, v0=48476)
After retessellation of defect 44 (v0=48476), euler #=-63 (127368,379122,251691) : difference with theory (-61) = 2 

CORRECTING DEFECT 45 (vertices=68, convex hull=107, v0=48805)
After retessellation of defect 45 (v0=48805), euler #=-62 (127411,379298,251825) : difference with theory (-60) = 2 

CORRECTING DEFECT 46 (vertices=52, convex hull=71, v0=50418)
After retessellation of defect 46 (v0=50418), euler #=-61 (127437,379402,251904) : difference with theory (-59) = 2 

CORRECTING DEFECT 47 (vertices=95, convex hull=109, v0=52119)
After retessellation of defect 47 (v0=52119), euler #=-60 (127486,379598,252052) : difference with theory (-58) = 2 

CORRECTING DEFECT 48 (vertices=13, convex hull=30, v0=54176)
After retessellation of defect 48 (v0=54176), euler #=-59 (127487,379611,252065) : difference with theory (-57) = 2 

CORRECTING DEFECT 49 (vertices=58, convex hull=28, v0=54483)
After retessellation of defect 49 (v0=54483), euler #=-58 (127493,379639,252088) : difference with theory (-56) = 2 

CORRECTING DEFECT 50 (vertices=29, convex hull=39, v0=55697)
After retessellation of defect 50 (v0=55697), euler #=-57 (127500,379674,252117) : difference with theory (-55) = 2 

CORRECTING DEFECT 51 (vertices=49, convex hull=63, v0=55973)
After retessellation of defect 51 (v0=55973), euler #=-56 (127509,379727,252162) : difference with theory (-54) = 2 

CORRECTING DEFECT 52 (vertices=111, convex hull=120, v0=55995)
After retessellation of defect 52 (v0=55995), euler #=-55 (127525,379825,252245) : difference with theory (-53) = 2 

CORRECTING DEFECT 53 (vertices=48, convex hull=30, v0=58016)
After retessellation of defect 53 (v0=58016), euler #=-54 (127529,379847,252264) : difference with theory (-52) = 2 

CORRECTING DEFECT 54 (vertices=32, convex hull=26, v0=60670)
After retessellation of defect 54 (v0=60670), euler #=-53 (127530,379859,252276) : difference with theory (-51) = 2 

CORRECTING DEFECT 55 (vertices=65, convex hull=69, v0=63467)
After retessellation of defect 55 (v0=63467), euler #=-52 (127555,379959,252352) : difference with theory (-50) = 2 

CORRECTING DEFECT 56 (vertices=103, convex hull=51, v0=63725)
After retessellation of defect 56 (v0=63725), euler #=-51 (127564,380004,252389) : difference with theory (-49) = 2 

CORRECTING DEFECT 57 (vertices=26, convex hull=42, v0=64960)
After retessellation of defect 57 (v0=64960), euler #=-50 (127570,380032,252412) : difference with theory (-48) = 2 

CORRECTING DEFECT 58 (vertices=83, convex hull=45, v0=65243)
After retessellation of defect 58 (v0=65243), euler #=-49 (127577,380073,252447) : difference with theory (-47) = 2 

CORRECTING DEFECT 59 (vertices=122, convex hull=32, v0=65841)
After retessellation of defect 59 (v0=65841), euler #=-48 (127588,380117,252481) : difference with theory (-46) = 2 

CORRECTING DEFECT 60 (vertices=1215, convex hull=306, v0=66443)
L defect detected...
After retessellation of defect 60 (v0=66443), euler #=-47 (127787,380881,253047) : difference with theory (-45) = 2 

CORRECTING DEFECT 61 (vertices=23, convex hull=58, v0=66630)
After retessellation of defect 61 (v0=66630), euler #=-46 (127798,380936,253092) : difference with theory (-44) = 2 

CORRECTING DEFECT 62 (vertices=62, convex hull=76, v0=66851)
After retessellation of defect 62 (v0=66851), euler #=-45 (127840,381091,253206) : difference with theory (-43) = 2 

CORRECTING DEFECT 63 (vertices=15, convex hull=19, v0=67069)
After retessellation of defect 63 (v0=67069), euler #=-44 (127841,381098,253213) : difference with theory (-42) = 2 

CORRECTING DEFECT 64 (vertices=4032, convex hull=1514, v0=71524)
XL defect detected...
After retessellation of defect 64 (v0=71524), euler #=-40 (128215,383019,254764) : difference with theory (-41) = -1 

CORRECTING DEFECT 65 (vertices=62, convex hull=128, v0=73354)
After retessellation of defect 65 (v0=73354), euler #=-39 (128261,383210,254910) : difference with theory (-40) = -1 

CORRECTING DEFECT 66 (vertices=6, convex hull=15, v0=79212)
After retessellation of defect 66 (v0=79212), euler #=-38 (128262,383219,254919) : difference with theory (-39) = -1 

CORRECTING DEFECT 67 (vertices=29, convex hull=31, v0=82932)
After retessellation of defect 67 (v0=82932), euler #=-37 (128266,383241,254938) : difference with theory (-38) = -1 

CORRECTING DEFECT 68 (vertices=228, convex hull=188, v0=89101)
After retessellation of defect 68 (v0=89101), euler #=-35 (128385,383693,255273) : difference with theory (-37) = -2 

CORRECTING DEFECT 69 (vertices=12, convex hull=24, v0=92689)
After retessellation of defect 69 (v0=92689), euler #=-34 (128387,383707,255286) : difference with theory (-36) = -2 

CORRECTING DEFECT 70 (vertices=62, convex hull=84, v0=92787)
After retessellation of defect 70 (v0=92787), euler #=-33 (128418,383834,255383) : difference with theory (-35) = -2 

CORRECTING DEFECT 71 (vertices=19, convex hull=22, v0=94049)
After retessellation of defect 71 (v0=94049), euler #=-32 (128419,383842,255391) : difference with theory (-34) = -2 

CORRECTING DEFECT 72 (vertices=766, convex hull=302, v0=94066)
After retessellation of defect 72 (v0=94066), euler #=-31 (128582,384486,255873) : difference with theory (-33) = -2 

CORRECTING DEFECT 73 (vertices=48, convex hull=36, v0=94920)
After retessellation of defect 73 (v0=94920), euler #=-30 (128588,384514,255896) : difference with theory (-32) = -2 

CORRECTING DEFECT 74 (vertices=45, convex hull=56, v0=95067)
After retessellation of defect 74 (v0=95067), euler #=-29 (128597,384563,255937) : difference with theory (-31) = -2 

CORRECTING DEFECT 75 (vertices=27, convex hull=61, v0=97120)
After retessellation of defect 75 (v0=97120), euler #=-28 (128614,384637,255995) : difference with theory (-30) = -2 

CORRECTING DEFECT 76 (vertices=30, convex hull=39, v0=100711)
After retessellation of defect 76 (v0=100711), euler #=-27 (128617,384657,256013) : difference with theory (-29) = -2 

CORRECTING DEFECT 77 (vertices=67, convex hull=25, v0=101808)
After retessellation of defect 77 (v0=101808), euler #=-26 (128621,384677,256030) : difference with theory (-28) = -2 

CORRECTING DEFECT 78 (vertices=38, convex hull=43, v0=102645)
After retessellation of defect 78 (v0=102645), euler #=-25 (128628,384714,256061) : difference with theory (-27) = -2 

CORRECTING DEFECT 79 (vertices=61, convex hull=101, v0=102790)
After retessellation of defect 79 (v0=102790), euler #=-24 (128666,384870,256180) : difference with theory (-26) = -2 

CORRECTING DEFECT 80 (vertices=621, convex hull=306, v0=108281)
After retessellation of defect 80 (v0=108281), euler #=-24 (128799,385425,256602) : difference with theory (-25) = -1 

CORRECTING DEFECT 81 (vertices=337, convex hull=118, v0=108330)
After retessellation of defect 81 (v0=108330), euler #=-23 (128842,385607,256742) : difference with theory (-24) = -1 

CORRECTING DEFECT 82 (vertices=193, convex hull=38, v0=108582)
After retessellation of defect 82 (v0=108582), euler #=-22 (128858,385669,256789) : difference with theory (-23) = -1 

CORRECTING DEFECT 83 (vertices=22, convex hull=48, v0=112052)
After retessellation of defect 83 (v0=112052), euler #=-21 (128863,385703,256819) : difference with theory (-22) = -1 

CORRECTING DEFECT 84 (vertices=179, convex hull=48, v0=114362)
After retessellation of defect 84 (v0=114362), euler #=-20 (128878,385766,256868) : difference with theory (-21) = -1 

CORRECTING DEFECT 85 (vertices=32, convex hull=43, v0=116208)
After retessellation of defect 85 (v0=116208), euler #=-19 (128879,385783,256885) : difference with theory (-20) = -1 

CORRECTING DEFECT 86 (vertices=92, convex hull=51, v0=117716)
After retessellation of defect 86 (v0=117716), euler #=-18 (128894,385851,256939) : difference with theory (-19) = -1 

CORRECTING DEFECT 87 (vertices=97, convex hull=113, v0=118086)
After retessellation of defect 87 (v0=118086), euler #=-17 (128958,386096,257121) : difference with theory (-18) = -1 

CORRECTING DEFECT 88 (vertices=464, convex hull=298, v0=121139)
After retessellation of defect 88 (v0=121139), euler #=-16 (129070,386593,257507) : difference with theory (-17) = -1 

CORRECTING DEFECT 89 (vertices=283, convex hull=62, v0=124090)
After retessellation of defect 89 (v0=124090), euler #=-15 (129086,386674,257573) : difference with theory (-16) = -1 

CORRECTING DEFECT 90 (vertices=805, convex hull=286, v0=124779)
After retessellation of defect 90 (v0=124779), euler #=-14 (129271,387380,258095) : difference with theory (-15) = -1 

CORRECTING DEFECT 91 (vertices=73, convex hull=75, v0=126820)
After retessellation of defect 91 (v0=126820), euler #=-13 (129308,387523,258202) : difference with theory (-14) = -1 

CORRECTING DEFECT 92 (vertices=104, convex hull=100, v0=130295)
After retessellation of defect 92 (v0=130295), euler #=-13 (129357,387719,258349) : difference with theory (-13) = 0 

CORRECTING DEFECT 93 (vertices=57, convex hull=76, v0=131631)
After retessellation of defect 93 (v0=131631), euler #=-12 (129396,387870,258462) : difference with theory (-12) = 0 

CORRECTING DEFECT 94 (vertices=8, convex hull=23, v0=132792)
After retessellation of defect 94 (v0=132792), euler #=-11 (129397,387883,258475) : difference with theory (-11) = 0 

CORRECTING DEFECT 95 (vertices=37, convex hull=70, v0=133803)
After retessellation of defect 95 (v0=133803), euler #=-10 (129409,387951,258532) : difference with theory (-10) = 0 

CORRECTING DEFECT 96 (vertices=82, convex hull=118, v0=134505)
After retessellation of defect 96 (v0=134505), euler #=-9 (129451,388121,258661) : difference with theory (-9) = 0 

CORRECTING DEFECT 97 (vertices=31, convex hull=14, v0=138199)
After retessellation of defect 97 (v0=138199), euler #=-8 (129451,388124,258665) : difference with theory (-8) = 0 

CORRECTING DEFECT 98 (vertices=87, convex hull=38, v0=138876)
After retessellation of defect 98 (v0=138876), euler #=-7 (129456,388153,258690) : difference with theory (-7) = 0 

CORRECTING DEFECT 99 (vertices=43, convex hull=90, v0=139211)
After retessellation of defect 99 (v0=139211), euler #=-6 (129484,388273,258783) : difference with theory (-6) = 0 

CORRECTING DEFECT 100 (vertices=28, convex hull=28, v0=139881)
After retessellation of defect 100 (v0=139881), euler #=-5 (129487,388294,258802) : difference with theory (-5) = 0 

CORRECTING DEFECT 101 (vertices=17, convex hull=58, v0=141619)
After retessellation of defect 101 (v0=141619), euler #=-4 (129495,388337,258838) : difference with theory (-4) = 0 

CORRECTING DEFECT 102 (vertices=6, convex hull=18, v0=142438)
After retessellation of defect 102 (v0=142438), euler #=-3 (129495,388342,258844) : difference with theory (-3) = 0 

CORRECTING DEFECT 103 (vertices=48, convex hull=43, v0=143247)
After retessellation of defect 103 (v0=143247), euler #=-2 (129498,388365,258865) : difference with theory (-2) = 0 

CORRECTING DEFECT 104 (vertices=48, convex hull=75, v0=143358)
After retessellation of defect 104 (v0=143358), euler #=-1 (129510,388429,258918) : difference with theory (-1) = 0 

CORRECTING DEFECT 105 (vertices=99, convex hull=31, v0=144159)
After retessellation of defect 105 (v0=144159), euler #=0 (129515,388453,258938) : difference with theory (0) = 0 

CORRECTING DEFECT 106 (vertices=223, convex hull=155, v0=144210)
After retessellation of defect 106 (v0=144210), euler #=1 (129551,388631,259081) : difference with theory (1) = 0 

CORRECTING DEFECT 107 (vertices=125, convex hull=48, v0=144653)
After retessellation of defect 107 (v0=144653), euler #=2 (129560,388674,259116) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.90 +- 0.36 (0.04-->27.30) (max @ vno 69448 --> 92233)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.90 +- 0.36 (0.04-->27.30) (max @ vno 69448 --> 92233)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
295 mutations (32.9%), 602 crossovers (67.1%), 2096 vertices were eliminated
building final representation...
15864 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=129560, nf=259116, ne=388674, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 364.5 minutes
0 defective edges
removing intersecting faces
000: 1754 intersecting
001: 106 intersecting
002: 64 intersecting
expanding nbhd size to 2
003: 67 intersecting
004: 62 intersecting
005: 59 intersecting
expanding nbhd size to 3
006: 64 intersecting
007: 54 intersecting
008: 43 intersecting
009: 33 intersecting
expanding nbhd size to 4
010: 50 intersecting
011: 31 intersecting
012: 15 intersecting
013: 14 intersecting
014: 10 intersecting
expanding nbhd size to 5
015: 12 intersecting
016: 9 intersecting
mris_fix_topology utimesec    10936.256436
mris_fix_topology stimesec    3.080531
mris_fix_topology ru_maxrss   613132
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   88702
mris_fix_topology ru_majflt   3
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  20592
mris_fix_topology ru_oublock  13344
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    258
mris_fix_topology ru_nivcsw   1096571
FSRUNTIME@ mris_fix_topology rh  6.0743 hours 1 threads
PIDs (20548 20551) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 131248 - 393738 + 262492 = 2 --> 0 holes
      F =2V-4:          262492 = 262496-4 (0)
      2E=3F:            787476 = 787476 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 129560 - 388674 + 259116 = 2 --> 0 holes
      F =2V-4:          259116 = 259120-4 (0)
      2E=3F:            777348 = 777348 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 1267 intersecting
001: 333 intersecting
002: 225 intersecting
003: 196 intersecting
004: 155 intersecting
005: 130 intersecting
006: 107 intersecting
expanding nbhd size to 2
007: 113 intersecting
008: 83 intersecting
009: 58 intersecting
010: 47 intersecting
011: 37 intersecting
012: 28 intersecting
013: 12 intersecting
014: 4 intersecting
015: 2 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 485 intersecting
001: 95 intersecting
002: 73 intersecting
003: 67 intersecting
expanding nbhd size to 2
004: 67 intersecting
005: 56 intersecting
expanding nbhd size to 3
006: 60 intersecting
007: 51 intersecting
008: 45 intersecting
009: 35 intersecting
expanding nbhd size to 4
010: 38 intersecting
011: 34 intersecting
expanding nbhd size to 5
012: 42 intersecting
013: 17 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct 29 03:45:45 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct 29 03:45:45 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 rh 

Waiting for PID 25638 of (25638 25641) to complete...
Waiting for PID 25641 of (25638 25641) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 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-6.0.0/0050418/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
23908 bright wm thresholded.
4134 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig...
computing class statistics...
border white:    256030 voxels (1.53%)
border gray      340019 voxels (2.03%)
WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0]
GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70)
setting MAX_BORDER_WHITE to 104.9 (was 105)
setting MIN_BORDER_WHITE to 63.0 (was 85)
setting MAX_CSF to 40.8 (was 40)
setting MAX_GRAY to 87.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.29 (0.01-->11.21) (max @ vno 57431 --> 125716)
face area 0.28 +- 0.19 (0.00-->16.27)
mean absolute distance = 0.75 +- 0.96
3886 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=96+-8.7,    GM=63+-8.7
mean inside = 89.3, mean outside = 71.5
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=75.7, 527 (527) missing vertices, mean dist 0.3 [0.7 (%33.2)->0.8 (%66.8))]
%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 0.93 +- 0.33 (0.04-->11.60) (max @ vno 57431 --> 125716)
face area 0.28 +- 0.18 (0.00-->14.20)
mean absolute distance = 0.38 +- 0.68
3992 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3414600.5, rms=10.249
001: dt: 0.5000, sse=2057774.0, rms=7.684 (25.031%)
002: dt: 0.5000, sse=1523707.0, rms=6.203 (19.269%)
003: dt: 0.5000, sse=1247211.4, rms=5.289 (14.742%)
004: dt: 0.5000, sse=1112542.5, rms=4.771 (9.780%)
005: dt: 0.5000, sse=1042551.9, rms=4.465 (6.416%)
006: dt: 0.5000, sse=1006678.9, rms=4.297 (3.760%)
007: dt: 0.5000, sse=978989.6, rms=4.181 (2.710%)
008: dt: 0.5000, sse=968210.2, rms=4.130 (1.205%)
009: dt: 0.5000, sse=965118.4, rms=4.072 (1.412%)
rms = 4.04, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=955012.9, rms=4.040 (0.795%)
011: dt: 0.2500, sse=786997.6, rms=3.052 (24.442%)
012: dt: 0.2500, sse=761400.9, rms=2.819 (7.654%)
013: dt: 0.2500, sse=744242.4, rms=2.755 (2.248%)
rms = 2.72, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=744245.8, rms=2.724 (1.141%)
015: dt: 0.1250, sse=729110.2, rms=2.656 (2.492%)
rms = 2.64, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=728576.2, rms=2.641 (0.572%)
positioning took 3.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=78.2, 524 (141) missing vertices, mean dist -0.2 [0.4 (%66.3)->0.3 (%33.7))]
%78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.93 +- 0.32 (0.04-->11.66) (max @ vno 57431 --> 125716)
face area 0.36 +- 0.24 (0.00-->18.43)
mean absolute distance = 0.29 +- 0.50
3219 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1170418.9, rms=4.311
017: dt: 0.5000, sse=1021326.6, rms=3.351 (22.255%)
rms = 3.51, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=894051.3, rms=2.739 (18.267%)
019: dt: 0.2500, sse=877563.2, rms=2.426 (11.433%)
020: dt: 0.2500, sse=847438.1, rms=2.322 (4.300%)
rms = 2.29, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=847790.2, rms=2.289 (1.409%)
022: dt: 0.1250, sse=828879.2, rms=2.215 (3.241%)
rms = 2.20, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=826171.1, rms=2.196 (0.837%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.5, 626 (99) missing vertices, mean dist -0.1 [0.3 (%59.2)->0.3 (%40.8))]
%81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.32 (0.06-->11.60) (max @ vno 57431 --> 125716)
face area 0.35 +- 0.24 (0.00-->18.33)
mean absolute distance = 0.28 +- 0.43
3470 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=903947.8, rms=2.864
rms = 2.92, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=841668.8, rms=2.376 (17.031%)
025: dt: 0.2500, sse=812065.6, rms=2.093 (11.907%)
rms = 2.06, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=806732.8, rms=2.060 (1.568%)
027: dt: 0.1250, sse=794903.2, rms=1.970 (4.369%)
rms = 1.95, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=803366.7, rms=1.948 (1.146%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=80.1, 662 (84) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))]
%83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=821219.4, rms=2.149
rms = 2.22, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=779452.2, rms=1.825 (15.046%)
030: dt: 0.2500, sse=772902.9, rms=1.655 (9.312%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
rms = 1.63, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=762235.4, rms=1.632 (1.440%)
positioning took 0.9 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 6516 vertices
erasing segment 0 (vno[0] = 31021)
erasing segment 1 (vno[0] = 34449)
erasing segment 2 (vno[0] = 36478)
erasing segment 3 (vno[0] = 37545)
erasing segment 5 (vno[0] = 81973)
erasing segment 6 (vno[0] = 82914)
erasing segment 7 (vno[0] = 88867)
erasing segment 8 (vno[0] = 94720)
erasing segment 9 (vno[0] = 96228)
erasing segment 10 (vno[0] = 105551)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.area
vertex spacing 0.92 +- 0.32 (0.02-->11.65) (max @ vno 57431 --> 125716)
face area 0.35 +- 0.23 (0.00-->18.31)
refinement took 9.4 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 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-6.0.0/0050418/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
23908 bright wm thresholded.
4134 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig...
computing class statistics...
border white:    256030 voxels (1.53%)
border gray      340019 voxels (2.03%)
WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0]
GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70)
setting MAX_BORDER_WHITE to 104.9 (was 105)
setting MIN_BORDER_WHITE to 63.0 (was 85)
setting MAX_CSF to 40.8 (was 40)
setting MAX_GRAY to 87.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.26 (0.02-->9.64) (max @ vno 69448 --> 92233)
face area 0.28 +- 0.16 (0.00-->13.62)
mean absolute distance = 0.72 +- 0.88
3795 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=96+-9.6,    GM=63+-9.6
mean inside = 89.8, mean outside = 71.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=76.0, 224 (224) missing vertices, mean dist 0.3 [0.6 (%33.0)->0.8 (%67.0))]
%73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.30 (0.06-->9.84) (max @ vno 69448 --> 92233)
face area 0.28 +- 0.16 (0.00-->10.88)
mean absolute distance = 0.36 +- 0.63
3486 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3459371.0, rms=10.663
001: dt: 0.5000, sse=2028926.6, rms=7.805 (26.802%)
002: dt: 0.5000, sse=1434236.0, rms=6.094 (21.914%)
003: dt: 0.5000, sse=1148175.0, rms=5.059 (16.998%)
004: dt: 0.5000, sse=1015404.9, rms=4.479 (11.456%)
005: dt: 0.5000, sse=947584.1, rms=4.175 (6.787%)
006: dt: 0.5000, sse=916542.9, rms=4.012 (3.896%)
007: dt: 0.5000, sse=911968.5, rms=3.924 (2.208%)
008: dt: 0.5000, sse=887991.9, rms=3.860 (1.634%)
rms = 3.83, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=883283.9, rms=3.827 (0.835%)
010: dt: 0.2500, sse=718156.4, rms=2.754 (28.051%)
011: dt: 0.2500, sse=687600.1, rms=2.480 (9.925%)
012: dt: 0.2500, sse=677312.6, rms=2.419 (2.490%)
rms = 2.38, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=676274.1, rms=2.383 (1.474%)
014: dt: 0.1250, sse=663993.9, rms=2.309 (3.105%)
rms = 2.30, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=662009.2, rms=2.296 (0.561%)
positioning took 2.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=78.7, 272 (43) missing vertices, mean dist -0.2 [0.4 (%67.3)->0.3 (%32.7))]
%78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.30 (0.06-->9.87) (max @ vno 69448 --> 92233)
face area 0.36 +- 0.20 (0.00-->14.46)
mean absolute distance = 0.29 +- 0.47
3436 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1149162.4, rms=4.365
016: dt: 0.5000, sse=942952.4, rms=3.164 (27.509%)
rms = 3.35, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=835394.2, rms=2.488 (21.381%)
018: dt: 0.2500, sse=794215.7, rms=2.141 (13.945%)
019: dt: 0.2500, sse=782259.4, rms=2.008 (6.199%)
rms = 1.98, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=776670.8, rms=1.975 (1.627%)
021: dt: 0.1250, sse=768080.9, rms=1.904 (3.625%)
rms = 1.89, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=766807.1, rms=1.891 (0.648%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=80.2, 364 (26) missing vertices, mean dist -0.1 [0.3 (%59.6)->0.3 (%40.4))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.29 (0.05-->9.82) (max @ vno 69448 --> 92233)
face area 0.35 +- 0.20 (0.00-->14.35)
mean absolute distance = 0.27 +- 0.42
3074 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=842306.8, rms=2.655
rms = 2.74, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=778524.1, rms=2.105 (20.714%)
024: dt: 0.2500, sse=755053.1, rms=1.781 (15.396%)
rms = 1.74, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=752048.2, rms=1.736 (2.500%)
026: dt: 0.1250, sse=739136.0, rms=1.667 (3.992%)
rms = 1.66, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=736909.9, rms=1.658 (0.547%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=80.8, 418 (17) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))]
%84 local maxima, %10 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-6.0.0/0050418/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=750256.2, rms=1.867
rms = 1.95, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=717741.4, rms=1.493 (20.041%)
029: dt: 0.2500, sse=707741.9, rms=1.300 (12.945%)
rms = 1.31, time step reduction 2 of 3 to 0.125...
rms = 1.29, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=703833.9, rms=1.285 (1.142%)
positioning took 0.8 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 6313 vertices
erasing segment 0 (vno[0] = 31921)
erasing segment 2 (vno[0] = 82688)
erasing segment 3 (vno[0] = 86120)
erasing segment 4 (vno[0] = 87128)
erasing segment 5 (vno[0] = 93751)
erasing segment 6 (vno[0] = 95923)
erasing segment 7 (vno[0] = 96633)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.area
vertex spacing 0.91 +- 0.30 (0.02-->9.81) (max @ vno 69448 --> 92233)
face area 0.35 +- 0.20 (0.00-->14.27)
refinement took 9.2 minutes
PIDs (25638 25641) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct 29 03:55:09 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct 29 03:55:09 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

Waiting for PID 26001 of (26001 26004) to complete...
Waiting for PID 26004 of (26001 26004) 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 (26001 26004) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct 29 03:55:19 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct 29 03:55:19 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 26043 of (26043 26046) to complete...
Waiting for PID 26046 of (26043 26046) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 45.2 mm, total surface area = 82010 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.201 (target=0.015)   
step 005: RMS=0.145 (target=0.015)   
step 010: RMS=0.119 (target=0.015)   
step 015: RMS=0.101 (target=0.015)   
step 020: RMS=0.088 (target=0.015)   
step 025: RMS=0.076 (target=0.015)   
step 030: RMS=0.065 (target=0.015)   
step 035: RMS=0.058 (target=0.015)   
step 040: RMS=0.052 (target=0.015)   
step 045: RMS=0.048 (target=0.015)   
step 050: RMS=0.044 (target=0.015)   
step 055: RMS=0.041 (target=0.015)   
step 060: RMS=0.039 (target=0.015)   
inflation complete.
inflation took 1.1 minutes
mris_inflate utimesec    32.000135
mris_inflate stimesec    0.073988
mris_inflate ru_maxrss   170560
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   22772
mris_inflate ru_majflt   3
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12280
mris_inflate ru_oublock  10288
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    293
mris_inflate ru_nivcsw   3423

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 44.7 mm, total surface area = 80296 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.198 (target=0.015)   
step 005: RMS=0.142 (target=0.015)   
step 010: RMS=0.116 (target=0.015)   
step 015: RMS=0.098 (target=0.015)   
step 020: RMS=0.086 (target=0.015)   
step 025: RMS=0.075 (target=0.015)   
step 030: RMS=0.065 (target=0.015)   
step 035: RMS=0.060 (target=0.015)   
step 040: RMS=0.053 (target=0.015)   
step 045: RMS=0.048 (target=0.015)   
step 050: RMS=0.046 (target=0.015)   
step 055: RMS=0.042 (target=0.015)   
step 060: RMS=0.042 (target=0.015)   
inflation complete.
inflation took 1.0 minutes
mris_inflate utimesec    31.209255
mris_inflate stimesec    0.067989
mris_inflate ru_maxrss   167968
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   22126
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10152
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    216
mris_inflate ru_nivcsw   3206
PIDs (26043 26046) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct 29 03:56:23 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct 29 03:56:23 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 26163 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26166 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26169 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26172 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26175 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26178 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26181 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26184 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26187 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26190 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26193 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...
Waiting for PID 26196 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 31.877*4pi (400.582) --> -31 handles
ICI = 255.1, FI = 2114.2, variation=34772.835
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
166 vertices thresholded to be in k1 ~ [-0.47 1.68], k2 ~ [-0.30 0.16]
total integrated curvature = -0.095*4pi (-1.193) --> 1 handles
ICI = 1.4, FI = 8.2, variation=153.681
149 vertices thresholded to be in [-0.12 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
109 vertices thresholded to be in [-0.18 0.61]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.024
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 29.682*4pi (372.993) --> -29 handles
ICI = 241.7, FI = 1990.7, variation=32771.932
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.

 rm -f rh.white.H


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


 rm -f rh.white.K


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


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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
171 vertices thresholded to be in k1 ~ [-0.64 1.70], k2 ~ [-0.34 0.19]
total integrated curvature = 0.110*4pi (1.376) --> 1 handles
ICI = 1.3, FI = 9.9, variation=166.955
154 vertices thresholded to be in [-0.12 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = -0.000, std = 0.003
97 vertices thresholded to be in [-0.25 0.49]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.025
done.
PIDs (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct 29 03:59:09 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050418 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      [ 0050418/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                      [ 278 ]
Gb_filter = 0

WARN:    S lookup   min:                          -1.325662
WARN:    S explicit min:                          0.000000	vertex = 684

#-----------------------------------------
#@# Curvature Stats rh Sun Oct 29 03:59:13 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050418 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      [ 0050418/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                      [ 253 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.038302
WARN:    S explicit min:                          0.000000	vertex = 1
#--------------------------------------------
#@# Sphere lh Sun Oct 29 03:59:16 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct 29 03:59:16 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 26369 of (26369 26372) to complete...
Waiting for PID 26372 of (26369 26372) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 1 == 
scaling brain by 0.299...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %22.35
pass 1: epoch 2 of 3 starting distance error %22.26
unfolding complete - removing small folds...
starting distance error %21.82
removing remaining folds...
final distance error %21.87
MRISunfold() return, current seed 1234
-01: dt=0.0000, 471 negative triangles
381: dt=0.9900, 471 negative triangles
382: dt=0.9900, 206 negative triangles
383: dt=0.9900, 140 negative triangles
384: dt=0.9900, 130 negative triangles
385: dt=0.9900, 108 negative triangles
386: dt=0.9900, 107 negative triangles
387: dt=0.9900, 95 negative triangles
388: dt=0.9900, 80 negative triangles
389: dt=0.9900, 87 negative triangles
390: dt=0.9900, 79 negative triangles
391: dt=0.9900, 66 negative triangles
392: dt=0.9900, 71 negative triangles
393: dt=0.9900, 71 negative triangles
394: dt=0.9900, 67 negative triangles
395: dt=0.9900, 67 negative triangles
396: dt=0.9900, 67 negative triangles
397: dt=0.9900, 61 negative triangles
398: dt=0.9900, 61 negative triangles
399: dt=0.9900, 60 negative triangles
400: dt=0.9900, 55 negative triangles
401: dt=0.9900, 52 negative triangles
402: dt=0.9900, 48 negative triangles
403: dt=0.9900, 54 negative triangles
404: dt=0.9900, 48 negative triangles
405: dt=0.9900, 50 negative triangles
406: dt=0.9900, 54 negative triangles
407: dt=0.9900, 47 negative triangles
408: dt=0.9900, 48 negative triangles
409: dt=0.9900, 45 negative triangles
410: dt=0.9900, 44 negative triangles
411: dt=0.9900, 49 negative triangles
412: dt=0.9900, 51 negative triangles
413: dt=0.9900, 44 negative triangles
414: dt=0.9900, 44 negative triangles
415: dt=0.9900, 42 negative triangles
416: dt=0.9900, 45 negative triangles
417: dt=0.9900, 46 negative triangles
418: dt=0.9900, 36 negative triangles
419: dt=0.9900, 43 negative triangles
420: dt=0.9900, 42 negative triangles
421: dt=0.9900, 36 negative triangles
422: dt=0.9900, 38 negative triangles
423: dt=0.9900, 39 negative triangles
424: dt=0.9900, 37 negative triangles
425: dt=0.9900, 43 negative triangles
426: dt=0.9900, 41 negative triangles
427: dt=0.9900, 38 negative triangles
428: dt=0.9405, 38 negative triangles
429: dt=0.9405, 33 negative triangles
430: dt=0.9405, 40 negative triangles
431: dt=0.9405, 37 negative triangles
432: dt=0.9405, 32 negative triangles
433: dt=0.9405, 32 negative triangles
434: dt=0.9405, 32 negative triangles
435: dt=0.9405, 29 negative triangles
436: dt=0.9405, 27 negative triangles
437: dt=0.9405, 30 negative triangles
438: dt=0.9405, 27 negative triangles
439: dt=0.9405, 29 negative triangles
440: dt=0.9405, 29 negative triangles
441: dt=0.9405, 26 negative triangles
442: dt=0.9405, 23 negative triangles
443: dt=0.9405, 22 negative triangles
444: dt=0.9405, 22 negative triangles
445: dt=0.9405, 22 negative triangles
446: dt=0.9405, 22 negative triangles
447: dt=0.9405, 19 negative triangles
448: dt=0.9405, 16 negative triangles
449: dt=0.9405, 18 negative triangles
450: dt=0.9405, 15 negative triangles
451: dt=0.9405, 15 negative triangles
452: dt=0.9405, 15 negative triangles
453: dt=0.9405, 12 negative triangles
454: dt=0.9405, 13 negative triangles
455: dt=0.9405, 13 negative triangles
456: dt=0.9405, 10 negative triangles
457: dt=0.9405, 8 negative triangles
458: dt=0.9405, 9 negative triangles
459: dt=0.9405, 10 negative triangles
460: dt=0.9405, 11 negative triangles
461: dt=0.9405, 10 negative triangles
462: dt=0.9405, 8 negative triangles
463: dt=0.9405, 9 negative triangles
464: dt=0.9405, 7 negative triangles
465: dt=0.9405, 7 negative triangles
466: dt=0.9405, 6 negative triangles
467: dt=0.9405, 8 negative triangles
468: dt=0.9405, 5 negative triangles
469: dt=0.9405, 4 negative triangles
470: dt=0.9405, 1 negative triangles
471: dt=0.9405, 2 negative triangles
472: dt=0.9405, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.97 hours
mris_sphere utimesec    3898.742301
mris_sphere stimesec    0.197969
mris_sphere ru_maxrss   234000
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   38741
mris_sphere ru_majflt   3
mris_sphere ru_nswap    0
mris_sphere ru_inblock  12512
mris_sphere ru_oublock  9328
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    361
mris_sphere ru_nivcsw   323023
FSRUNTIME@ mris_sphere  1.9669 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 1 == 
scaling brain by 0.306...
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 %22.00
pass 1: epoch 2 of 3 starting distance error %21.86
unfolding complete - removing small folds...
starting distance error %21.46
removing remaining folds...
final distance error %21.52
MRISunfold() return, current seed 1234
-01: dt=0.0000, 379 negative triangles
286: dt=0.9900, 379 negative triangles
287: dt=0.9900, 164 negative triangles
288: dt=0.9900, 116 negative triangles
289: dt=0.9900, 109 negative triangles
290: dt=0.9900, 88 negative triangles
291: dt=0.9900, 83 negative triangles
292: dt=0.9900, 85 negative triangles
293: dt=0.9900, 73 negative triangles
294: dt=0.9900, 70 negative triangles
295: dt=0.9900, 59 negative triangles
296: dt=0.9900, 60 negative triangles
297: dt=0.9900, 50 negative triangles
298: dt=0.9900, 46 negative triangles
299: dt=0.9900, 48 negative triangles
300: dt=0.9900, 33 negative triangles
301: dt=0.9900, 35 negative triangles
302: dt=0.9900, 35 negative triangles
303: dt=0.9900, 37 negative triangles
304: dt=0.9900, 24 negative triangles
305: dt=0.9900, 23 negative triangles
306: dt=0.9900, 18 negative triangles
307: dt=0.9900, 29 negative triangles
308: dt=0.9900, 18 negative triangles
309: dt=0.9900, 15 negative triangles
310: dt=0.9900, 13 negative triangles
311: dt=0.9900, 11 negative triangles
312: dt=0.9900, 13 negative triangles
313: dt=0.9900, 7 negative triangles
314: dt=0.9900, 4 negative triangles
315: dt=0.9900, 7 negative triangles
316: dt=0.9900, 4 negative triangles
317: dt=0.9900, 3 negative triangles
318: dt=0.9900, 2 negative triangles
319: dt=0.9900, 3 negative triangles
320: dt=0.9900, 1 negative triangles
321: dt=0.9900, 1 negative triangles
322: dt=0.9900, 3 negative triangles
323: dt=0.9900, 1 negative triangles
324: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.77 hours
mris_sphere utimesec    3185.240769
mris_sphere stimesec    0.217966
mris_sphere ru_maxrss   230624
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   37913
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9192
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    90
mris_sphere ru_nivcsw   321031
FSRUNTIME@ mris_sphere  1.7688 hours 1 threads
PIDs (26369 26372) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct 29 05:57:18 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct 29 05:57:18 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 31117 of (31117 31120) to complete...
Waiting for PID 31120 of (31117 31120) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 5.615
curvature mean = 0.025, std = 0.812
curvature mean = 0.011, std = 0.863
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 8.00) sse = 288392.7, tmin=4.0424
  d=16.00 min @ (4.00, 4.00, -4.00) sse = 267206.1, tmin=6.1104
  d=8.00 min @ (0.00, 0.00, 2.00) sse = 265042.0, tmin=8.2699
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 264453.8, tmin=10.4455
  d=2.00 min @ (0.50, 0.00, -0.50) sse = 264361.6, tmin=12.6226
  d=1.00 min @ (-0.25, 0.00, 0.25) sse = 264325.9, tmin=14.7681
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 264310.7, tmin=16.9017
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  16.90 min
curvature mean = -0.000, std = 0.839
curvature mean = 0.004, std = 0.948
curvature mean = -0.002, std = 0.850
curvature mean = 0.001, std = 0.979
curvature mean = -0.002, std = 0.853
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.043, std = 0.423
curvature mean = 0.039, std = 0.244
curvature mean = 0.065, std = 0.243
curvature mean = 0.034, std = 0.306
curvature mean = 0.056, std = 0.360
curvature mean = 0.032, std = 0.333
curvature mean = 0.036, std = 0.475
curvature mean = 0.031, std = 0.344
curvature mean = 0.016, std = 0.584
MRISregister() return, current seed 0
-01: dt=0.0000, 380 negative triangles
137: dt=0.9900, 380 negative triangles
expanding nbhd size to 1
138: dt=0.9900, 458 negative triangles
139: dt=0.9900, 399 negative triangles
140: dt=0.9405, 406 negative triangles
141: dt=0.9405, 389 negative triangles
142: dt=0.9405, 391 negative triangles
143: dt=0.9405, 374 negative triangles
144: dt=0.9405, 371 negative triangles
145: dt=0.9405, 358 negative triangles
146: dt=0.9405, 346 negative triangles
147: dt=0.9405, 323 negative triangles
148: dt=0.9405, 300 negative triangles
149: dt=0.9405, 286 negative triangles
150: dt=0.9405, 273 negative triangles
151: dt=0.9405, 262 negative triangles
152: dt=0.9405, 262 negative triangles
153: dt=0.9405, 250 negative triangles
154: dt=0.9405, 236 negative triangles
155: dt=0.9405, 211 negative triangles
156: dt=0.9405, 216 negative triangles
157: dt=0.9405, 209 negative triangles
158: dt=0.9405, 198 negative triangles
159: dt=0.9405, 202 negative triangles
160: dt=0.9405, 189 negative triangles
161: dt=0.9405, 179 negative triangles
162: dt=0.9405, 171 negative triangles
163: dt=0.9405, 164 negative triangles
164: dt=0.9405, 161 negative triangles
165: dt=0.9405, 149 negative triangles
166: dt=0.9405, 147 negative triangles
167: dt=0.9405, 142 negative triangles
168: dt=0.9405, 151 negative triangles
169: dt=0.9405, 131 negative triangles
170: dt=0.9405, 128 negative triangles
171: dt=0.9405, 130 negative triangles
172: dt=0.9405, 119 negative triangles
173: dt=0.9405, 109 negative triangles
174: dt=0.9405, 97 negative triangles
175: dt=0.9405, 90 negative triangles
176: dt=0.9405, 80 negative triangles
177: dt=0.9405, 74 negative triangles
178: dt=0.9405, 78 negative triangles
179: dt=0.9405, 67 negative triangles
180: dt=0.9405, 65 negative triangles
181: dt=0.9405, 58 negative triangles
182: dt=0.9405, 58 negative triangles
183: dt=0.9405, 47 negative triangles
184: dt=0.9405, 45 negative triangles
185: dt=0.9405, 47 negative triangles
186: dt=0.9405, 43 negative triangles
187: dt=0.9405, 47 negative triangles
188: dt=0.9405, 38 negative triangles
189: dt=0.9405, 37 negative triangles
190: dt=0.9405, 34 negative triangles
191: dt=0.9405, 32 negative triangles
192: dt=0.9405, 31 negative triangles
193: dt=0.9405, 27 negative triangles
194: dt=0.9405, 25 negative triangles
195: dt=0.9405, 24 negative triangles
196: dt=0.9405, 26 negative triangles
197: dt=0.9405, 19 negative triangles
198: dt=0.9405, 16 negative triangles
199: dt=0.9405, 15 negative triangles
200: dt=0.9405, 14 negative triangles
201: dt=0.9405, 11 negative triangles
202: dt=0.9405, 11 negative triangles
203: dt=0.9405, 10 negative triangles
204: dt=0.9405, 10 negative triangles
205: dt=0.9405, 10 negative triangles
206: dt=0.9405, 10 negative triangles
207: dt=0.9405, 10 negative triangles
208: dt=0.9405, 10 negative triangles
209: dt=0.9405, 9 negative triangles
210: dt=0.9405, 8 negative triangles
211: dt=0.9405, 8 negative triangles
212: dt=0.9405, 8 negative triangles
213: dt=0.9405, 12 negative triangles
214: dt=0.9405, 10 negative triangles
215: dt=0.9405, 8 negative triangles
216: dt=0.9405, 8 negative triangles
217: dt=0.9405, 7 negative triangles
218: dt=0.9405, 10 negative triangles
219: dt=0.9405, 9 negative triangles
220: dt=0.9405, 8 negative triangles
221: dt=0.9405, 4 negative triangles
222: dt=0.9405, 5 negative triangles
223: dt=0.9405, 4 negative triangles
224: dt=0.9405, 4 negative triangles
225: dt=0.9405, 5 negative triangles
226: dt=0.9405, 5 negative triangles
227: dt=0.9405, 4 negative triangles
228: dt=0.9405, 3 negative triangles
229: dt=0.9405, 2 negative triangles
230: dt=0.9405, 2 negative triangles
231: dt=0.9405, 2 negative triangles
232: dt=0.9405, 2 negative triangles
233: dt=0.9405, 2 negative triangles
234: dt=0.9405, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.82 hours
mris_register utimesec    3507.351801
mris_register stimesec    0.635903
mris_register ru_maxrss   225856
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   31888
mris_register ru_majflt   3
mris_register ru_nswap    0
mris_register ru_inblock  18120
mris_register ru_oublock  9336
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    390
mris_register ru_nivcsw   308047
FSRUNTIME@ mris_register  1.8192 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 5.640
curvature mean = 0.027, std = 0.812
curvature mean = 0.010, std = 0.870
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 314626.8, tmin=1.9876
  d=32.00 min @ (8.00, 8.00, -8.00) sse = 246616.2, tmin=4.0327
  d=16.00 min @ (-4.00, -4.00, 0.00) sse = 229902.5, tmin=6.1086
  d=8.00 min @ (0.00, 2.00, 2.00) sse = 218453.6, tmin=8.1946
  d=4.00 min @ (-1.00, -1.00, 0.00) sse = 218045.2, tmin=10.2961
  d=2.00 min @ (0.50, 0.50, 0.00) sse = 217782.4, tmin=12.4060
  d=1.00 min @ (0.00, -0.25, -0.25) sse = 217608.5, tmin=14.5096
  d=0.50 min @ (0.12, 0.12, 0.00) sse = 217580.7, tmin=16.6252
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  16.63 min
curvature mean = -0.004, std = 0.826
curvature mean = 0.005, std = 0.950
curvature mean = -0.008, std = 0.834
curvature mean = 0.003, std = 0.979
curvature mean = -0.009, std = 0.836
curvature mean = 0.001, std = 0.991
2 Reading smoothwm
curvature mean = -0.045, std = 0.419
curvature mean = 0.033, std = 0.237
curvature mean = 0.072, std = 0.251
curvature mean = 0.026, std = 0.298
curvature mean = 0.059, std = 0.367
curvature mean = 0.025, std = 0.325
curvature mean = 0.037, std = 0.482
curvature mean = 0.024, std = 0.337
curvature mean = 0.015, std = 0.591
MRISregister() return, current seed 0
-01: dt=0.0000, 347 negative triangles
131: dt=0.9900, 347 negative triangles
expanding nbhd size to 1
132: dt=0.9900, 461 negative triangles
133: dt=0.9900, 357 negative triangles
134: dt=0.9900, 362 negative triangles
135: dt=0.9900, 363 negative triangles
136: dt=0.9900, 353 negative triangles
137: dt=0.9900, 351 negative triangles
138: dt=0.9900, 331 negative triangles
139: dt=0.9900, 311 negative triangles
140: dt=0.9900, 306 negative triangles
141: dt=0.9900, 283 negative triangles
142: dt=0.9900, 263 negative triangles
143: dt=0.9900, 255 negative triangles
144: dt=0.9900, 243 negative triangles
145: dt=0.9900, 236 negative triangles
146: dt=0.9900, 232 negative triangles
147: dt=0.9900, 217 negative triangles
148: dt=0.9900, 201 negative triangles
149: dt=0.9900, 188 negative triangles
150: dt=0.9900, 171 negative triangles
151: dt=0.9900, 160 negative triangles
152: dt=0.9900, 164 negative triangles
153: dt=0.9900, 149 negative triangles
154: dt=0.9900, 148 negative triangles
155: dt=0.9900, 138 negative triangles
156: dt=0.9900, 132 negative triangles
157: dt=0.9900, 124 negative triangles
158: dt=0.9900, 124 negative triangles
159: dt=0.9900, 121 negative triangles
160: dt=0.9900, 109 negative triangles
161: dt=0.9900, 99 negative triangles
162: dt=0.9900, 102 negative triangles
163: dt=0.9900, 96 negative triangles
164: dt=0.9900, 91 negative triangles
165: dt=0.9900, 94 negative triangles
166: dt=0.9900, 87 negative triangles
167: dt=0.9900, 80 negative triangles
168: dt=0.9900, 77 negative triangles
169: dt=0.9900, 71 negative triangles
170: dt=0.9900, 65 negative triangles
171: dt=0.9900, 66 negative triangles
172: dt=0.9900, 66 negative triangles
173: dt=0.9900, 68 negative triangles
174: dt=0.9900, 73 negative triangles
175: dt=0.9900, 74 negative triangles
176: dt=0.9900, 67 negative triangles
177: dt=0.9900, 61 negative triangles
178: dt=0.9900, 55 negative triangles
179: dt=0.9900, 52 negative triangles
180: dt=0.9900, 49 negative triangles
181: dt=0.9900, 43 negative triangles
182: dt=0.9900, 41 negative triangles
183: dt=0.9900, 43 negative triangles
184: dt=0.9900, 44 negative triangles
185: dt=0.9900, 42 negative triangles
186: dt=0.9900, 42 negative triangles
187: dt=0.9900, 38 negative triangles
188: dt=0.9900, 43 negative triangles
189: dt=0.9900, 48 negative triangles
190: dt=0.9900, 43 negative triangles
191: dt=0.9900, 42 negative triangles
192: dt=0.9900, 42 negative triangles
193: dt=0.9900, 31 negative triangles
194: dt=0.9900, 31 negative triangles
195: dt=0.9900, 31 negative triangles
196: dt=0.9900, 27 negative triangles
197: dt=0.9900, 28 negative triangles
198: dt=0.9900, 29 negative triangles
199: dt=0.9900, 26 negative triangles
200: dt=0.9900, 24 negative triangles
201: dt=0.9900, 23 negative triangles
202: dt=0.9900, 27 negative triangles
203: dt=0.9900, 30 negative triangles
204: dt=0.9900, 25 negative triangles
205: dt=0.9900, 22 negative triangles
206: dt=0.9900, 19 negative triangles
207: dt=0.9900, 20 negative triangles
208: dt=0.9900, 21 negative triangles
209: dt=0.9900, 19 negative triangles
210: dt=0.9900, 22 negative triangles
211: dt=0.9900, 23 negative triangles
212: dt=0.9900, 17 negative triangles
213: dt=0.9900, 18 negative triangles
214: dt=0.9900, 19 negative triangles
215: dt=0.9900, 17 negative triangles
216: dt=0.9900, 17 negative triangles
217: dt=0.9900, 20 negative triangles
218: dt=0.9900, 22 negative triangles
219: dt=0.9900, 17 negative triangles
220: dt=0.9900, 16 negative triangles
221: dt=0.9900, 15 negative triangles
222: dt=0.9900, 15 negative triangles
223: dt=0.9900, 15 negative triangles
224: dt=0.9900, 16 negative triangles
225: dt=0.9900, 18 negative triangles
226: dt=0.9900, 16 negative triangles
227: dt=0.9900, 15 negative triangles
228: dt=0.9900, 15 negative triangles
229: dt=0.9900, 15 negative triangles
230: dt=0.9900, 14 negative triangles
231: dt=0.9900, 13 negative triangles
232: dt=0.9900, 14 negative triangles
233: dt=0.9900, 14 negative triangles
234: dt=0.9900, 13 negative triangles
235: dt=0.9900, 12 negative triangles
236: dt=0.9900, 12 negative triangles
237: dt=0.9900, 12 negative triangles
238: dt=0.9900, 11 negative triangles
239: dt=0.9900, 11 negative triangles
240: dt=0.9900, 11 negative triangles
241: dt=0.9900, 11 negative triangles
242: dt=0.9900, 10 negative triangles
243: dt=0.9900, 10 negative triangles
244: dt=0.9900, 8 negative triangles
245: dt=0.9900, 8 negative triangles
246: dt=0.9900, 7 negative triangles
247: dt=0.9900, 7 negative triangles
248: dt=0.9900, 7 negative triangles
249: dt=0.9900, 6 negative triangles
250: dt=0.9900, 6 negative triangles
251: dt=0.9900, 4 negative triangles
252: dt=0.9900, 1 negative triangles
253: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.69 hours
mris_register utimesec    3043.867261
mris_register stimesec    0.287956
mris_register ru_maxrss   221236
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   30207
mris_register ru_majflt   1
mris_register ru_nswap    0
mris_register ru_inblock  8168
mris_register ru_oublock  9248
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    472
mris_register ru_nivcsw   306417
FSRUNTIME@ mris_register  1.6904 hours 1 threads
PIDs (31117 31120) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct 29 07:46:27 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct 29 07:46:27 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

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

Waiting for PID 3325 of (3325 3328) to complete...
Waiting for PID 3328 of (3325 3328) 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 (3325 3328) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct 29 07:46:30 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 29 07:46:30 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 3367 of (3367 3370) to complete...
Waiting for PID 3370 of (3367 3370) 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 (3367 3370) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct 29 07:46:34 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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 29 07:46:34 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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 3413 of (3413 3416) to complete...
Waiting for PID 3416 of (3413 3416) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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...
1175 labels changed using aseg
relabeling using gibbs priors...
000:   3029 changed, 131248 examined...
001:    740 changed, 12883 examined...
002:    173 changed, 4062 examined...
003:     72 changed, 1049 examined...
004:     35 changed, 443 examined...
005:     13 changed, 190 examined...
006:      8 changed, 78 examined...
007:      4 changed, 51 examined...
008:      1 changed, 22 examined...
009:      0 changed, 7 examined...
225 labels changed using aseg
000: 126 total segments, 83 labels (515 vertices) changed
001: 43 total segments, 1 labels (2 vertices) changed
002: 42 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1447 vertices marked for relabeling...
1447 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 33 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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...
1026 labels changed using aseg
relabeling using gibbs priors...
000:   2646 changed, 129560 examined...
001:    600 changed, 11404 examined...
002:    157 changed, 3458 examined...
003:     64 changed, 918 examined...
004:     33 changed, 368 examined...
005:     13 changed, 207 examined...
006:      5 changed, 77 examined...
007:      0 changed, 27 examined...
130 labels changed using aseg
000: 96 total segments, 57 labels (219 vertices) changed
001: 40 total segments, 1 labels (1 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1307 vertices marked for relabeling...
1307 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 37 seconds.
PIDs (3413 3416) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct 29 07:47:10 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct 29 07:47:10 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 rh 

Waiting for PID 3478 of (3478 3481) to complete...
Waiting for PID 3481 of (3478 3481) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 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-6.0.0/0050418/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
23908 bright wm thresholded.
4134 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig...
computing class statistics...
border white:    256030 voxels (1.53%)
border gray      340019 voxels (2.03%)
WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0]
GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70)
setting MAX_BORDER_WHITE to 104.9 (was 105)
setting MIN_BORDER_WHITE to 63.0 (was 85)
setting MAX_CSF to 40.8 (was 40)
setting MAX_GRAY to 87.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=96+-8.7,    GM=63+-8.7
mean inside = 89.3, mean outside = 71.5
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 0.92 +- 0.32 (0.02-->11.65) (max @ vno 57431 --> 125716)
face area 0.35 +- 0.23 (0.00-->18.31)
mean absolute distance = 0.57 +- 0.92
3553 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 178 points - only 0.00% unknown
deleting segment 1 with 20 points - only 0.00% unknown
deleting segment 2 with 38 points - only 0.00% unknown
deleting segment 3 with 83 points - only 0.00% unknown
deleting segment 4 with 110 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 81 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 21 points - only 0.00% unknown
deleting segment 12 with 35 points - only 0.00% unknown
deleting segment 13 with 35 points - only 0.00% unknown
deleting segment 14 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 15 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
deleting segment 17 with 62 points - only 0.00% unknown
deleting segment 18 with 11 points - only 0.00% unknown
deleting segment 19 with 5 points - only 0.00% unknown
deleting segment 20 with 7 points - only 0.00% unknown
deleting segment 21 with 11 points - only 0.00% unknown
deleting segment 22 with 24 points - only 0.00% unknown
deleting segment 23 with 126 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 24 with 2 points - only 0.00% unknown
deleting segment 26 with 40 points - only 0.00% unknown
deleting segment 27 with 96 points - only 0.00% unknown
mean border=75.4, 419 (418) missing vertices, mean dist 0.2 [0.8 (%19.8)->0.5 (%80.2))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.94 +- 0.33 (0.05-->11.61) (max @ vno 57431 --> 125716)
face area 0.35 +- 0.23 (0.00-->17.67)
mean absolute distance = 0.38 +- 0.68
3711 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1784046.5, rms=6.571
001: dt: 0.5000, sse=1211239.4, rms=4.467 (32.020%)
002: dt: 0.5000, sse=1081838.9, rms=3.922 (12.207%)
rms = 3.98, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=966111.8, rms=3.285 (16.234%)
004: dt: 0.2500, sse=925156.8, rms=3.008 (8.421%)
005: dt: 0.2500, sse=916870.3, rms=2.892 (3.870%)
006: dt: 0.2500, sse=910641.8, rms=2.841 (1.776%)
007: dt: 0.2500, sse=899266.7, rms=2.790 (1.773%)
rms = 2.75, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=891174.9, rms=2.754 (1.294%)
009: dt: 0.1250, sse=880523.9, rms=2.690 (2.326%)
rms = 2.67, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=877732.5, rms=2.667 (0.867%)
positioning took 2.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 188 points - only 0.00% unknown
deleting segment 1 with 18 points - only 0.00% unknown
deleting segment 2 with 34 points - only 0.00% unknown
deleting segment 3 with 107 points - only 0.00% unknown
deleting segment 4 with 83 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 71 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 21 points - only 0.00% unknown
deleting segment 12 with 27 points - only 0.00% unknown
deleting segment 13 with 31 points - only 0.00% unknown
deleting segment 14 with 21 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 15 with 2 points - only 0.00% unknown
deleting segment 16 with 7 points - only 0.00% unknown
deleting segment 17 with 11 points - only 0.00% unknown
deleting segment 18 with 27 points - only 0.00% unknown
deleting segment 19 with 47 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 20 with 2 points - only 0.00% unknown
deleting segment 21 with 33 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 22 with 3 points - only 0.00% unknown
deleting segment 23 with 103 points - only 0.00% unknown
mean border=78.0, 541 (171) missing vertices, mean dist -0.2 [0.4 (%67.8)->0.3 (%32.2))]
%78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.93 +- 0.33 (0.07-->11.58) (max @ vno 57431 --> 125716)
face area 0.37 +- 0.24 (0.00-->18.79)
mean absolute distance = 0.29 +- 0.49
3131 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1166963.6, rms=4.199
011: dt: 0.5000, sse=1007663.9, rms=3.214 (23.467%)
rms = 3.41, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=903943.8, rms=2.623 (18.366%)
013: dt: 0.2500, sse=865633.2, rms=2.342 (10.725%)
014: dt: 0.2500, sse=860791.3, rms=2.255 (3.715%)
rms = 2.23, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=859675.4, rms=2.229 (1.155%)
016: dt: 0.1250, sse=845289.5, rms=2.160 (3.100%)
rms = 2.15, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=840518.4, rms=2.146 (0.627%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 69 points - only 0.00% unknown
deleting segment 1 with 18 points - only 0.00% unknown
deleting segment 2 with 34 points - only 0.00% unknown
deleting segment 3 with 135 points - only 0.00% unknown
deleting segment 4 with 107 points - only 0.00% unknown
deleting segment 5 with 83 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 71 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
deleting segment 12 with 26 points - only 0.00% unknown
deleting segment 13 with 28 points - only 0.00% unknown
deleting segment 14 with 27 points - only 0.00% unknown
deleting segment 15 with 25 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 16 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 17 with 1 points - only 0.00% unknown
deleting segment 18 with 7 points - only 0.00% unknown
deleting segment 19 with 16 points - only 0.00% unknown
deleting segment 20 with 17 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 21 with 4 points - only 0.00% unknown
deleting segment 22 with 10 points - only 0.00% unknown
deleting segment 23 with 27 points - only 0.00% unknown
deleting segment 24 with 75 points - only 0.00% unknown
deleting segment 25 with 9 points - only 0.00% unknown
deleting segment 26 with 31 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 27 with 3 points - only 0.00% unknown
deleting segment 28 with 105 points - only 0.00% unknown
mean border=79.3, 695 (118) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.3 (%40.6))]
%81 local maxima, %13 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 0.93 +- 0.33 (0.06-->11.54) (max @ vno 57431 --> 125716)
face area 0.36 +- 0.24 (0.00-->18.16)
mean absolute distance = 0.28 +- 0.43
3434 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=911837.9, rms=2.823
rms = 2.88, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=850959.4, rms=2.320 (17.810%)
019: dt: 0.2500, sse=829013.2, rms=2.028 (12.583%)
rms = 2.01, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=830651.0, rms=2.014 (0.733%)
021: dt: 0.1250, sse=806100.6, rms=1.919 (4.720%)
rms = 1.90, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=803037.6, rms=1.900 (0.952%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 68 points - only 0.00% unknown
deleting segment 1 with 18 points - only 0.00% unknown
deleting segment 2 with 34 points - only 0.00% unknown
deleting segment 3 with 117 points - only 0.00% unknown
deleting segment 4 with 107 points - only 0.00% unknown
deleting segment 5 with 83 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 71 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 27 points - only 0.00% unknown
deleting segment 11 with 28 points - only 0.00% unknown
deleting segment 12 with 28 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
deleting segment 14 with 25 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 15 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
deleting segment 17 with 7 points - only 0.00% unknown
deleting segment 18 with 16 points - only 0.00% unknown
deleting segment 19 with 13 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 20 with 4 points - only 0.00% unknown
deleting segment 21 with 11 points - only 0.00% unknown
deleting segment 22 with 27 points - only 0.00% unknown
deleting segment 23 with 82 points - only 0.00% unknown
deleting segment 24 with 9 points - only 0.00% unknown
deleting segment 25 with 32 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 26 with 3 points - only 0.00% unknown
deleting segment 27 with 105 points - only 0.00% unknown
mean border=80.0, 769 (103) missing vertices, mean dist -0.0 [0.3 (%52.7)->0.3 (%47.3))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=820344.4, rms=2.111
rms = 2.17, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=785463.9, rms=1.771 (16.115%)
024: dt: 0.2500, sse=771739.7, rms=1.596 (9.881%)
rms = 1.62, time step reduction 2 of 3 to 0.125...
rms = 1.57, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=767655.4, rms=1.570 (1.612%)
positioning took 0.9 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 6519 vertices
erasing segment 0 (vno[0] = 31010)
erasing segment 1 (vno[0] = 32161)
erasing segment 2 (vno[0] = 36478)
erasing segment 4 (vno[0] = 54109)
erasing segment 5 (vno[0] = 81973)
erasing segment 6 (vno[0] = 82913)
erasing segment 7 (vno[0] = 86065)
erasing segment 8 (vno[0] = 88867)
erasing segment 9 (vno[0] = 94720)
erasing segment 10 (vno[0] = 96228)
erasing segment 11 (vno[0] = 105551)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.area
vertex spacing 0.92 +- 0.33 (0.02-->11.46) (max @ vno 57431 --> 125716)
face area 0.36 +- 0.24 (0.00-->18.14)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 59 points - only 0.00% unknown
deleting segment 1 with 32 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 5 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=51.2, 400 (400) missing vertices, mean dist 1.4 [1.0 (%0.0)->3.0 (%100.0))]
% 8 local maxima, %37 large gradients and %51 min vals, 965 gradients ignored
perforing initial smooth deformation to move away from white surface
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=22523430.0, rms=29.506
001: dt: 0.0500, sse=19921118.0, rms=27.691 (6.152%)
002: dt: 0.0500, sse=18041402.0, rms=26.301 (5.017%)
003: dt: 0.0500, sse=16590684.0, rms=25.176 (4.277%)
004: dt: 0.0500, sse=15412776.0, rms=24.225 (3.781%)
005: dt: 0.0500, sse=14422604.0, rms=23.394 (3.427%)
006: dt: 0.0500, sse=13568109.0, rms=22.653 (3.167%)
007: dt: 0.0500, sse=12815069.0, rms=21.980 (2.974%)
008: dt: 0.0500, sse=12144431.0, rms=21.362 (2.812%)
009: dt: 0.0500, sse=11538691.0, rms=20.788 (2.687%)
010: dt: 0.0500, sse=10988115.0, rms=20.252 (2.578%)
positioning took 1.8 minutes
mean border=51.0, 401 (216) missing vertices, mean dist 1.2 [0.2 (%0.2)->2.6 (%99.8))]
% 9 local maxima, %37 large gradients and %49 min vals, 922 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=11914375.0, rms=21.141
011: dt: 0.0500, sse=11400633.0, rms=20.650 (2.320%)
012: dt: 0.0500, sse=10929284.0, rms=20.190 (2.230%)
013: dt: 0.0500, sse=10493866.0, rms=19.754 (2.155%)
014: dt: 0.0500, sse=10093185.0, rms=19.345 (2.071%)
015: dt: 0.0500, sse=9721563.0, rms=18.958 (2.003%)
016: dt: 0.0500, sse=9378128.0, rms=18.593 (1.927%)
017: dt: 0.0500, sse=9060223.0, rms=18.248 (1.854%)
018: dt: 0.0500, sse=8765371.0, rms=17.922 (1.785%)
019: dt: 0.0500, sse=8490959.0, rms=17.613 (1.723%)
020: dt: 0.0500, sse=8235264.0, rms=17.321 (1.662%)
positioning took 1.8 minutes
mean border=50.9, 466 (165) missing vertices, mean dist 1.1 [0.1 (%2.1)->2.3 (%97.9))]
% 9 local maxima, %38 large gradients and %49 min vals, 914 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=8358297.5, rms=17.468
021: dt: 0.0500, sse=8111856.5, rms=17.183 (1.628%)
022: dt: 0.0500, sse=7883419.0, rms=16.915 (1.559%)
023: dt: 0.0500, sse=7669262.0, rms=16.660 (1.509%)
024: dt: 0.0500, sse=7470349.5, rms=16.419 (1.445%)
025: dt: 0.0500, sse=7284163.5, rms=16.191 (1.392%)
026: dt: 0.0500, sse=7110500.5, rms=15.975 (1.336%)
027: dt: 0.0500, sse=6947347.0, rms=15.769 (1.289%)
028: dt: 0.0500, sse=6792784.0, rms=15.571 (1.254%)
029: dt: 0.0500, sse=6646514.0, rms=15.381 (1.218%)
030: dt: 0.0500, sse=6507681.0, rms=15.199 (1.185%)
positioning took 1.8 minutes
mean border=50.9, 546 (139) missing vertices, mean dist 1.0 [0.1 (%11.0)->2.2 (%89.0))]
% 9 local maxima, %38 large gradients and %48 min vals, 809 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=6568624.5, rms=15.279
031: dt: 0.5000, sse=5568462.0, rms=13.907 (8.978%)
032: dt: 0.5000, sse=4921412.5, rms=12.934 (7.000%)
033: dt: 0.5000, sse=4449370.0, rms=12.175 (5.867%)
034: dt: 0.5000, sse=4104504.0, rms=11.582 (4.867%)
035: dt: 0.5000, sse=3809564.5, rms=11.053 (4.567%)
036: dt: 0.5000, sse=3554665.8, rms=10.572 (4.352%)
037: dt: 0.5000, sse=3306390.0, rms=10.086 (4.597%)
038: dt: 0.5000, sse=3079537.2, rms=9.621 (4.615%)
039: dt: 0.5000, sse=2870288.2, rms=9.173 (4.654%)
040: dt: 0.5000, sse=2698777.8, rms=8.787 (4.206%)
041: dt: 0.5000, sse=2548886.8, rms=8.438 (3.973%)
042: dt: 0.5000, sse=2440727.8, rms=8.175 (3.116%)
043: dt: 0.5000, sse=2350467.0, rms=7.951 (2.740%)
044: dt: 0.5000, sse=2289422.0, rms=7.793 (1.991%)
045: dt: 0.5000, sse=2241339.0, rms=7.668 (1.599%)
046: dt: 0.5000, sse=2209147.0, rms=7.580 (1.148%)
047: dt: 0.5000, sse=2179584.0, rms=7.502 (1.034%)
048: dt: 0.5000, sse=2158639.8, rms=7.443 (0.787%)
049: dt: 0.5000, sse=2139878.0, rms=7.392 (0.683%)
rms = 7.35, time step reduction 1 of 3 to 0.250...
050: dt: 0.5000, sse=2125075.5, rms=7.349 (0.578%)
051: dt: 0.2500, sse=2047654.8, rms=7.109 (3.270%)
052: dt: 0.2500, sse=2015584.5, rms=7.018 (1.283%)
rms = 7.03, time step reduction 2 of 3 to 0.125...
rms = 6.98, time step reduction 3 of 3 to 0.062...
053: dt: 0.1250, sse=2002416.9, rms=6.978 (0.567%)
positioning took 6.1 minutes
mean border=50.0, 3860 (56) missing vertices, mean dist 0.2 [0.2 (%47.2)->1.0 (%52.8))]
%17 local maxima, %31 large gradients and %45 min vals, 407 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=2241410.2, rms=6.947
054: dt: 0.5000, sse=2162338.0, rms=6.725 (3.188%)
055: dt: 0.5000, sse=2067294.0, rms=6.459 (3.964%)
rms = 6.53, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1973017.1, rms=6.133 (5.040%)
057: dt: 0.2500, sse=1960439.1, rms=6.082 (0.840%)
rms = 6.10, time step reduction 2 of 3 to 0.125...
058: dt: 0.1250, sse=1942388.6, rms=6.018 (1.043%)
059: dt: 0.1250, sse=1919217.4, rms=5.936 (1.364%)
rms = 5.90, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1908110.8, rms=5.899 (0.627%)
positioning took 2.5 minutes
mean border=49.4, 4485 (48) missing vertices, mean dist 0.2 [0.2 (%47.5)->0.8 (%52.5))]
%24 local maxima, %23 large gradients and %45 min vals, 465 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=1964299.2, rms=6.034
rms = 6.36, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1931356.9, rms=5.922 (1.856%)
rms = 5.90, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1921573.0, rms=5.898 (0.404%)
063: dt: 0.1250, sse=1900245.1, rms=5.821 (1.309%)
064: dt: 0.1250, sse=1883896.8, rms=5.769 (0.899%)
rms = 5.75, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1876085.2, rms=5.745 (0.409%)
positioning took 1.9 minutes
mean border=48.9, 7941 (45) missing vertices, mean dist 0.1 [0.2 (%46.7)->0.6 (%53.3))]
%27 local maxima, %19 large gradients and %43 min vals, 534 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-6.0.0/0050418/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1901558.1, rms=5.791
rms = 5.98, time step reduction 1 of 3 to 0.250...
066: dt: 0.2500, sse=1872328.4, rms=5.691 (1.724%)
067: dt: 0.2500, sse=1841534.6, rms=5.602 (1.558%)
rms = 5.59, time step reduction 2 of 3 to 0.125...
068: dt: 0.2500, sse=1833290.4, rms=5.585 (0.305%)
069: dt: 0.1250, sse=1785044.2, rms=5.405 (3.225%)
070: dt: 0.1250, sse=1764686.2, rms=5.335 (1.308%)
rms = 5.31, time step reduction 3 of 3 to 0.062...
071: dt: 0.1250, sse=1757149.4, rms=5.310 (0.456%)
positioning took 2.3 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.area.pial
vertex spacing 1.09 +- 0.55 (0.06-->11.53) (max @ vno 57431 --> 125716)
face area 0.46 +- 0.46 (0.00-->20.37)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 131248 vertices processed
25000 of 131248 vertices processed
50000 of 131248 vertices processed
75000 of 131248 vertices processed
100000 of 131248 vertices processed
125000 of 131248 vertices processed
0 of 131248 vertices processed
25000 of 131248 vertices processed
50000 of 131248 vertices processed
75000 of 131248 vertices processed
100000 of 131248 vertices processed
125000 of 131248 vertices processed
thickness calculation complete, 527:2302 truncations.
21477 vertices at 0 distance
72580 vertices at 1 distance
81694 vertices at 2 distance
46447 vertices at 3 distance
18195 vertices at 4 distance
6328 vertices at 5 distance
2281 vertices at 6 distance
1000 vertices at 7 distance
482 vertices at 8 distance
274 vertices at 9 distance
136 vertices at 10 distance
138 vertices at 11 distance
105 vertices at 12 distance
62 vertices at 13 distance
60 vertices at 14 distance
35 vertices at 15 distance
49 vertices at 16 distance
26 vertices at 17 distance
31 vertices at 18 distance
40 vertices at 19 distance
48 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.thickness
positioning took 30.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 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-6.0.0/0050418/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
23908 bright wm thresholded.
4134 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig...
computing class statistics...
border white:    256030 voxels (1.53%)
border gray      340019 voxels (2.03%)
WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0]
GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70)
setting MAX_BORDER_WHITE to 104.9 (was 105)
setting MIN_BORDER_WHITE to 63.0 (was 85)
setting MAX_CSF to 40.8 (was 40)
setting MAX_GRAY to 87.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=96+-9.6,    GM=63+-9.6
mean inside = 89.8, mean outside = 71.7
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 0.91 +- 0.30 (0.02-->9.81) (max @ vno 69448 --> 92233)
face area 0.35 +- 0.20 (0.00-->14.24)
mean absolute distance = 0.55 +- 0.85
3418 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
deleting segment 1 with 41 points - only 0.00% unknown
deleting segment 2 with 8 points - only 0.00% unknown
deleting segment 3 with 21 points - only 0.00% unknown
deleting segment 5 with 50 points - only 0.00% unknown
deleting segment 6 with 111 points - only 0.00% unknown
deleting segment 7 with 11 points - only 0.00% unknown
deleting segment 8 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
deleting segment 11 with 134 points - only 0.00% unknown
deleting segment 12 with 46 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 33 points - only 0.00% unknown
deleting segment 15 with 113 points - only 0.00% unknown
deleting segment 16 with 43 points - only 0.00% unknown
deleting segment 17 with 5 points - only 0.00% unknown
deleting segment 18 with 11 points - only 0.00% unknown
deleting segment 19 with 13 points - only 0.00% unknown
deleting segment 20 with 83 points - only 0.00% unknown
mean border=75.6, 261 (261) missing vertices, mean dist 0.3 [0.7 (%18.5)->0.5 (%81.5))]
%70 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 0.93 +- 0.30 (0.07-->9.82) (max @ vno 69448 --> 92233)
face area 0.35 +- 0.20 (0.00-->13.90)
mean absolute distance = 0.36 +- 0.63
3303 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1842870.9, rms=6.894
001: dt: 0.5000, sse=1161472.9, rms=4.459 (35.313%)
002: dt: 0.5000, sse=1015373.3, rms=3.785 (15.121%)
rms = 3.79, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=899215.8, rms=3.091 (18.338%)
004: dt: 0.2500, sse=851830.9, rms=2.733 (11.575%)
005: dt: 0.2500, sse=835550.0, rms=2.580 (5.613%)
006: dt: 0.2500, sse=824682.8, rms=2.512 (2.622%)
rms = 2.46, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=817734.1, rms=2.464 (1.924%)
008: dt: 0.1250, sse=810242.3, rms=2.402 (2.507%)
rms = 2.38, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=807976.6, rms=2.379 (0.942%)
positioning took 1.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 13 points - only 0.00% unknown
deleting segment 1 with 37 points - only 0.00% unknown
deleting segment 2 with 23 points - only 0.00% unknown
deleting segment 3 with 15 points - only 0.00% unknown
deleting segment 4 with 51 points - only 0.00% unknown
deleting segment 5 with 99 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
deleting segment 10 with 92 points - only 0.00% unknown
deleting segment 11 with 39 points - only 0.00% unknown
deleting segment 12 with 36 points - only 0.00% unknown
deleting segment 13 with 87 points - only 0.00% unknown
deleting segment 14 with 10 points - only 0.00% unknown
deleting segment 15 with 38 points - only 0.00% unknown
deleting segment 16 with 11 points - only 0.00% unknown
deleting segment 17 with 9 points - only 0.00% unknown
deleting segment 18 with 59 points - only 0.00% unknown
mean border=78.6, 278 (84) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.3 (%31.2))]
%78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.30 (0.05-->9.83) (max @ vno 69448 --> 92233)
face area 0.36 +- 0.21 (0.00-->15.04)
mean absolute distance = 0.29 +- 0.48
3346 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1151385.6, rms=4.285
010: dt: 0.5000, sse=938254.7, rms=3.041 (29.026%)
rms = 3.23, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=840086.6, rms=2.373 (21.954%)
012: dt: 0.2500, sse=803540.1, rms=2.024 (14.709%)
013: dt: 0.2500, sse=794332.7, rms=1.907 (5.788%)
rms = 1.88, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=787078.1, rms=1.880 (1.421%)
015: dt: 0.1250, sse=780082.1, rms=1.818 (3.317%)
rms = 1.81, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=777120.0, rms=1.810 (0.434%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 13 points - only 0.00% unknown
deleting segment 1 with 37 points - only 0.00% unknown
deleting segment 2 with 23 points - only 0.00% unknown
deleting segment 3 with 18 points - only 0.00% unknown
deleting segment 4 with 51 points - only 0.00% unknown
deleting segment 5 with 100 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
deleting segment 8 with 93 points - only 0.00% unknown
deleting segment 9 with 39 points - only 0.00% unknown
deleting segment 10 with 37 points - only 0.00% unknown
deleting segment 11 with 91 points - only 0.00% unknown
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 45 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
deleting segment 15 with 12 points - only 0.00% unknown
deleting segment 16 with 62 points - only 0.00% unknown
deleting segment 17 with 9 points - only 0.00% unknown
mean border=80.1, 317 (51) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.3 (%40.1))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.30 (0.07-->9.82) (max @ vno 69448 --> 92233)
face area 0.36 +- 0.21 (0.00-->14.88)
mean absolute distance = 0.28 +- 0.42
3104 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=848647.4, rms=2.607
rms = 2.70, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=783880.3, rms=2.041 (21.714%)
018: dt: 0.2500, sse=756800.9, rms=1.709 (16.252%)
rms = 1.67, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=752885.9, rms=1.665 (2.552%)
020: dt: 0.1250, sse=745662.1, rms=1.600 (3.919%)
rms = 1.60, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=750865.8, rms=1.595 (0.302%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 13 points - only 0.00% unknown
deleting segment 1 with 37 points - only 0.00% unknown
deleting segment 2 with 20 points - only 0.00% unknown
deleting segment 3 with 18 points - only 0.00% unknown
deleting segment 4 with 51 points - only 0.00% unknown
deleting segment 5 with 100 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
deleting segment 8 with 98 points - only 0.00% unknown
deleting segment 9 with 40 points - only 0.00% unknown
deleting segment 10 with 37 points - only 0.00% unknown
deleting segment 11 with 104 points - only 0.00% unknown
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 45 points - only 0.00% unknown
deleting segment 14 with 5 points - only 0.00% unknown
deleting segment 15 with 11 points - only 0.00% unknown
deleting segment 16 with 64 points - only 0.00% unknown
deleting segment 17 with 9 points - only 0.00% unknown
mean border=80.7, 384 (35) missing vertices, mean dist -0.0 [0.3 (%52.6)->0.3 (%47.4))]
%85 local maxima, %10 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-6.0.0/0050418/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=765798.4, rms=1.833
rms = 1.91, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=727234.6, rms=1.444 (21.238%)
023: dt: 0.2500, sse=714266.5, rms=1.239 (14.224%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
rms = 1.22, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=710467.0, rms=1.224 (1.180%)
positioning took 0.8 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 6313 vertices
erasing segment 0 (vno[0] = 31939)
erasing segment 1 (vno[0] = 32998)
erasing segment 3 (vno[0] = 76597)
erasing segment 4 (vno[0] = 82670)
erasing segment 5 (vno[0] = 82688)
erasing segment 6 (vno[0] = 86088)
erasing segment 7 (vno[0] = 86120)
erasing segment 8 (vno[0] = 87128)
erasing segment 9 (vno[0] = 93751)
erasing segment 10 (vno[0] = 95923)
erasing segment 11 (vno[0] = 96633)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.area
vertex spacing 0.92 +- 0.30 (0.02-->9.82) (max @ vno 69448 --> 92233)
face area 0.35 +- 0.21 (0.00-->14.70)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 10 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=50.8, 281 (281) missing vertices, mean dist 1.5 [1.7 (%0.0)->3.1 (%100.0))]
% 8 local maxima, %39 large gradients and %49 min vals, 792 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=23946122.0, rms=30.663
001: dt: 0.0500, sse=21225300.0, rms=28.815 (6.026%)
002: dt: 0.0500, sse=19254408.0, rms=27.399 (4.916%)
003: dt: 0.0500, sse=17732704.0, rms=26.252 (4.183%)
004: dt: 0.0500, sse=16497728.0, rms=25.284 (3.689%)
005: dt: 0.0500, sse=15456960.0, rms=24.438 (3.346%)
006: dt: 0.0500, sse=14556396.0, rms=23.682 (3.095%)
007: dt: 0.0500, sse=13762728.0, rms=22.994 (2.903%)
008: dt: 0.0500, sse=13052958.0, rms=22.362 (2.752%)
009: dt: 0.0500, sse=12412531.0, rms=21.775 (2.624%)
010: dt: 0.0500, sse=11828569.0, rms=21.226 (2.522%)
positioning took 1.8 minutes
mean border=50.5, 271 (153) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.6 (%99.9))]
% 9 local maxima, %39 large gradients and %47 min vals, 723 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=12756315.0, rms=22.088
011: dt: 0.0500, sse=12211216.0, rms=21.584 (2.283%)
012: dt: 0.0500, sse=11710493.0, rms=21.110 (2.196%)
013: dt: 0.0500, sse=11248806.0, rms=20.663 (2.116%)
014: dt: 0.0500, sse=10821538.0, rms=20.241 (2.044%)
015: dt: 0.0500, sse=10426159.0, rms=19.842 (1.971%)
016: dt: 0.0500, sse=10060004.0, rms=19.465 (1.899%)
017: dt: 0.0500, sse=9720089.0, rms=19.109 (1.832%)
018: dt: 0.0500, sse=9404538.0, rms=18.772 (1.764%)
019: dt: 0.0500, sse=9111062.0, rms=18.453 (1.700%)
020: dt: 0.0500, sse=8837338.0, rms=18.150 (1.641%)
positioning took 1.7 minutes
mean border=50.4, 332 (127) missing vertices, mean dist 1.2 [0.1 (%1.9)->2.4 (%98.1))]
% 9 local maxima, %40 large gradients and %47 min vals, 766 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=8960727.0, rms=18.293
021: dt: 0.0500, sse=8695920.0, rms=17.997 (1.615%)
022: dt: 0.0500, sse=8450954.0, rms=17.719 (1.544%)
023: dt: 0.0500, sse=8222297.0, rms=17.456 (1.487%)
024: dt: 0.0500, sse=8009258.0, rms=17.207 (1.427%)
025: dt: 0.0500, sse=7810915.0, rms=16.972 (1.368%)
026: dt: 0.0500, sse=7625615.5, rms=16.749 (1.314%)
027: dt: 0.0500, sse=7451650.5, rms=16.537 (1.267%)
028: dt: 0.0500, sse=7286212.5, rms=16.332 (1.236%)
029: dt: 0.0500, sse=7129248.0, rms=16.136 (1.203%)
030: dt: 0.0500, sse=6979744.0, rms=15.946 (1.174%)
positioning took 1.8 minutes
mean border=50.3, 360 (107) missing vertices, mean dist 1.1 [0.1 (%9.8)->2.3 (%90.2))]
% 9 local maxima, %40 large gradients and %46 min vals, 733 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=7095884.5, rms=16.093
031: dt: 0.5000, sse=6008925.0, rms=14.659 (8.907%)
032: dt: 0.5000, sse=5277125.0, rms=13.601 (7.221%)
033: dt: 0.5000, sse=4723056.5, rms=12.741 (6.318%)
034: dt: 0.5000, sse=4308263.0, rms=12.052 (5.414%)
035: dt: 0.5000, sse=3961887.0, rms=11.446 (5.025%)
036: dt: 0.5000, sse=3667347.0, rms=10.903 (4.746%)
037: dt: 0.5000, sse=3392727.8, rms=10.374 (4.845%)
038: dt: 0.5000, sse=3151102.0, rms=9.885 (4.715%)
039: dt: 0.5000, sse=2920770.2, rms=9.398 (4.931%)
040: dt: 0.5000, sse=2726265.0, rms=8.965 (4.611%)
041: dt: 0.5000, sse=2560496.0, rms=8.580 (4.287%)
042: dt: 0.5000, sse=2437306.5, rms=8.280 (3.497%)
043: dt: 0.5000, sse=2338877.5, rms=8.034 (2.969%)
044: dt: 0.5000, sse=2269841.8, rms=7.855 (2.228%)
045: dt: 0.5000, sse=2222293.0, rms=7.731 (1.578%)
046: dt: 0.5000, sse=2182498.5, rms=7.623 (1.401%)
047: dt: 0.5000, sse=2152504.2, rms=7.543 (1.050%)
048: dt: 0.5000, sse=2130155.8, rms=7.479 (0.847%)
rms = 7.44, time step reduction 1 of 3 to 0.250...
049: dt: 0.5000, sse=2113989.0, rms=7.435 (0.591%)
050: dt: 0.2500, sse=2020713.0, rms=7.148 (3.859%)
051: dt: 0.2500, sse=1981788.5, rms=7.037 (1.560%)
rms = 7.03, time step reduction 2 of 3 to 0.125...
052: dt: 0.2500, sse=1981517.2, rms=7.034 (0.034%)
053: dt: 0.1250, sse=1948269.6, rms=6.933 (1.437%)
rms = 6.90, time step reduction 3 of 3 to 0.062...
054: dt: 0.1250, sse=1938483.1, rms=6.904 (0.422%)
positioning took 6.0 minutes
mean border=49.4, 3039 (49) missing vertices, mean dist 0.2 [0.2 (%46.0)->0.9 (%54.0))]
%17 local maxima, %32 large gradients and %44 min vals, 408 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=2201920.0, rms=6.937
055: dt: 0.5000, sse=2119293.2, rms=6.707 (3.316%)
056: dt: 0.5000, sse=2018386.1, rms=6.417 (4.312%)
rms = 6.47, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1907407.2, rms=6.030 (6.042%)
058: dt: 0.2500, sse=1886914.1, rms=5.950 (1.327%)
rms = 5.95, time step reduction 2 of 3 to 0.125...
059: dt: 0.1250, sse=1867749.1, rms=5.880 (1.163%)
060: dt: 0.1250, sse=1840041.1, rms=5.780 (1.702%)
rms = 5.75, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1830576.5, rms=5.747 (0.582%)
positioning took 2.5 minutes
mean border=48.7, 3640 (35) missing vertices, mean dist 0.2 [0.2 (%47.4)->0.7 (%52.6))]
%26 local maxima, %24 large gradients and %44 min vals, 427 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=1899533.0, rms=5.921
rms = 6.33, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1860729.8, rms=5.785 (2.289%)
rms = 5.78, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1855363.8, rms=5.775 (0.170%)
064: dt: 0.1250, sse=1828287.9, rms=5.677 (1.698%)
065: dt: 0.1250, sse=1812861.4, rms=5.626 (0.896%)
rms = 5.60, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1805326.9, rms=5.603 (0.415%)
positioning took 1.9 minutes
mean border=48.1, 7068 (33) missing vertices, mean dist 0.1 [0.2 (%47.5)->0.5 (%52.5))]
%28 local maxima, %20 large gradients and %42 min vals, 458 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-6.0.0/0050418/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1840456.1, rms=5.683
rms = 5.95, time step reduction 1 of 3 to 0.250...
067: dt: 0.2500, sse=1809995.1, rms=5.577 (1.878%)
068: dt: 0.2500, sse=1783617.8, rms=5.502 (1.332%)
rms = 5.52, time step reduction 2 of 3 to 0.125...
rms = 5.45, time step reduction 3 of 3 to 0.062...
069: dt: 0.1250, sse=1771089.5, rms=5.454 (0.882%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.area.pial
vertex spacing 1.09 +- 0.54 (0.04-->10.27) (max @ vno 52019 --> 127268)
face area 0.47 +- 0.44 (0.00-->15.86)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 129560 vertices processed
25000 of 129560 vertices processed
50000 of 129560 vertices processed
75000 of 129560 vertices processed
100000 of 129560 vertices processed
125000 of 129560 vertices processed
0 of 129560 vertices processed
25000 of 129560 vertices processed
50000 of 129560 vertices processed
75000 of 129560 vertices processed
100000 of 129560 vertices processed
125000 of 129560 vertices processed
thickness calculation complete, 578:2581 truncations.
21298 vertices at 0 distance
70949 vertices at 1 distance
80118 vertices at 2 distance
45914 vertices at 3 distance
18358 vertices at 4 distance
6532 vertices at 5 distance
2418 vertices at 6 distance
1054 vertices at 7 distance
482 vertices at 8 distance
263 vertices at 9 distance
219 vertices at 10 distance
153 vertices at 11 distance
92 vertices at 12 distance
68 vertices at 13 distance
61 vertices at 14 distance
44 vertices at 15 distance
35 vertices at 16 distance
22 vertices at 17 distance
26 vertices at 18 distance
26 vertices at 19 distance
34 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.thickness
positioning took 29.9 minutes
PIDs (3478 3481) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct 29 08:17:53 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label
Total face volume 275133
Total vertex volume 271693 (mask=0)
#@# 0050418 lh 271693
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct 29 08:17:57 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label
Total face volume 276809
Total vertex volume 274048 (mask=0)
#@# 0050418 rh 274048
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct 29 08:18:00 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 

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 = 298
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz
mris_volmask took 13.03 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct 29 08:31:01 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 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 0050418 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct 29 08:31:01 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 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 0050418 rh pial 

Waiting for PID 5447 of (5447 5450 5453 5456) to complete...
Waiting for PID 5450 of (5447 5450 5453 5456) to complete...
Waiting for PID 5453 of (5447 5450 5453 5456) to complete...
Waiting for PID 5456 of (5447 5450 5453 5456) 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 0050418 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 275133
Total vertex volume 271693 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1312   1031   2467  2.521 0.637     0.135     0.036       16     2.3  bankssts
  914    585   1643  2.375 0.803     0.112     0.022       10     0.7  caudalanteriorcingulate
 3389   2343   8045  2.885 0.710     0.117     0.026       33     3.3  caudalmiddlefrontal
 2601   1917   4343  2.058 0.534     0.171     0.056       49     6.3  cuneus
  584    365   1372  2.760 1.016     0.150     0.067       13     1.7  entorhinal
 4059   2961   8583  2.409 0.761     0.147     0.051       71     9.7  fusiform
 5422   3982  12617  2.554 0.702     0.146     0.043       93     9.9  inferiorparietal
 4301   3173   9122  2.529 0.849     0.146     0.047       74     9.5  inferiortemporal
 1406    972   3079  2.495 1.109     0.135     0.041       20     2.2  isthmuscingulate
 6621   4794  14180  2.350 0.718     0.165     0.054      128    14.8  lateraloccipital
 3791   2585   7592  2.536 0.744     0.139     0.051      126     8.0  lateralorbitofrontal
 3711   2774   6964  2.126 0.688     0.164     0.057       74     8.9  lingual
 2269   1608   5307  2.734 0.799     0.156     0.051       51     4.9  medialorbitofrontal
 4222   3269  10257  2.624 0.847     0.161     0.048       82     9.3  middletemporal
 1075    725   2280  2.580 0.945     0.126     0.042       16     1.7  parahippocampal
 2105   1502   3881  2.469 0.624     0.134     0.037       28     3.3  paracentral
 1866   1419   4745  2.860 0.667     0.151     0.046       31     4.4  parsopercularis
  840    664   2443  2.634 0.815     0.152     0.054       13     1.7  parsorbitalis
 1517   1065   3958  2.869 0.602     0.128     0.035       27     2.6  parstriangularis
 1987   1446   2535  1.843 0.605     0.157     0.055       36     4.7  pericalcarine
 6891   4808  11539  2.176 0.805     0.138     0.041       90    12.4  postcentral
 1513   1090   3424  2.757 0.858     0.135     0.029       21     1.8  posteriorcingulate
 8689   5922  16727  2.481 0.795     0.135     0.041      129    15.6  precentral
 6191   4476  13835  2.730 0.737     0.152     0.042      111    11.8  precuneus
  999    711   2913  2.972 1.003     0.145     0.042       15     1.8  rostralanteriorcingulate
 9292   6441  22617  2.790 0.698     0.137     0.042      159    16.6  rostralmiddlefrontal
10868   7872  28951  3.026 0.730     0.141     0.041      159    18.9  superiorfrontal
 8232   5792  18058  2.548 0.671     0.142     0.038      116    13.0  superiorparietal
 6020   4934  14149  2.532 0.912     0.153     0.052      137    15.3  superiortemporal
 6155   4324  12308  2.623 0.739     0.144     0.045       99    11.9  supramarginal
  417    287   1282  2.921 0.666     0.174     0.062       10     1.1  frontalpole
  714    492   2402  3.264 0.889     0.144     0.051       14     1.7  temporalpole
  463    417   1257  2.687 0.630     0.171     0.048        7     0.8  transversetemporal
 3539   2359   6813  2.862 0.699     0.136     0.046       43     6.5  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 0050418 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 275133
Total vertex volume 271693 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1312    954   2467  2.521 0.637     0.162     0.053       45     2.8  bankssts
  914    724   1643  2.375 0.803     0.153     0.040       14     1.7  caudalanteriorcingulate
 3389   3119   8045  2.885 0.710     0.158     0.040       52     6.5  caudalmiddlefrontal
 2601   2463   4343  2.058 0.534     0.179     0.050       53     5.9  cuneus
  584    626   1372  2.760 1.016     0.194     0.057       10     1.5  entorhinal
 4059   4033   8583  2.409 0.761     0.198     0.072       86    14.4  fusiform
 5422   5874  12617  2.554 0.702     0.202     0.049       93    13.3  inferiorparietal
 4301   4059   9122  2.529 0.849     0.188     0.057       81    12.0  inferiortemporal
 1406   1341   3079  2.495 1.109     0.178     0.065       30     4.8  isthmuscingulate
 6621   7033  14180  2.350 0.718     0.201     0.051      117    16.2  lateraloccipital
 3791   3408   7592  2.536 0.744     0.189     0.059       66    10.6  lateralorbitofrontal
 3711   3764   6964  2.126 0.688     0.196     0.055       67     9.7  lingual
 2269   2240   5307  2.734 0.799     0.191     0.055       46     5.8  medialorbitofrontal
 4222   4459  10257  2.624 0.847     0.187     0.044       66     9.2  middletemporal
 1075   1060   2280  2.580 0.945     0.205     0.059       19     3.1  parahippocampal
 2105   1663   3881  2.469 0.624     0.141     0.043       30     4.2  paracentral
 1866   1978   4745  2.860 0.667     0.203     0.051       36     4.7  parsopercularis
  840   1096   2443  2.634 0.815     0.238     0.064       14     2.5  parsorbitalis
 1517   1657   3958  2.869 0.602     0.205     0.049       28     3.9  parstriangularis
 1987   1415   2535  1.843 0.605     0.167     0.114      266    13.4  pericalcarine
 6891   5702  11539  2.176 0.805     0.149     0.040      136    12.7  postcentral
 1513   1316   3424  2.757 0.858     0.171     0.041       37     2.8  posteriorcingulate
 8689   7255  16727  2.481 0.795     0.145     0.038      133    15.9  precentral
 6191   5530  13835  2.730 0.737     0.179     0.048      132    14.3  precuneus
  999   1202   2913  2.972 1.003     0.240     0.073       22     4.1  rostralanteriorcingulate
 9292   9416  22617  2.790 0.698     0.186     0.047      175    20.6  rostralmiddlefrontal
10868  10978  28951  3.026 0.730     0.183     0.047      192    24.0  superiorfrontal
 8232   8082  18058  2.548 0.671     0.177     0.045      139    17.1  superiorparietal
 6020   6221  14149  2.532 0.912     0.179     0.047      101    13.0  superiortemporal
 6155   5136  12308  2.623 0.739     0.167     0.051      144    13.8  supramarginal
  417    584   1282  2.921 0.666     0.245     0.047       10     1.1  frontalpole
  714    965   2402  3.264 0.889     0.233     0.066       15     2.2  temporalpole
  463    485   1257  2.687 0.630     0.170     0.043        8     0.8  transversetemporal
 3539   2462   6813  2.862 0.699     0.162     0.053       96     7.9  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050418 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 276809
Total vertex volume 274048 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1032    694   1842  2.524 0.680     0.091     0.020        5     0.7  bankssts
 1056    706   2865  3.159 1.014     0.127     0.028       12     1.3  caudalanteriorcingulate
 3248   2311   8682  3.121 0.647     0.129     0.032       36     4.4  caudalmiddlefrontal
 2374   1715   4002  2.129 0.505     0.167     0.054       41     6.0  cuneus
  370    305   1494  3.082 0.895     0.157     0.046        5     0.6  entorhinal
 4019   2907   8171  2.225 0.728     0.154     0.049       72     8.6  fusiform
 6721   4876  15078  2.527 0.776     0.147     0.042      105    12.4  inferiorparietal
 3661   2700   8904  2.691 0.818     0.144     0.057       68     9.5  inferiortemporal
 1165    792   2849  2.800 0.978     0.153     0.056       27     2.6  isthmuscingulate
 7374   5205  15358  2.304 0.679     0.157     0.054      127    17.5  lateraloccipital
 3893   2560   7440  2.570 0.843     0.144     0.052       58     8.8  lateralorbitofrontal
 3272   2519   7511  2.511 0.695     0.163     0.051       56     6.7  lingual
 2926   1990   6257  2.855 0.878     0.123     0.038       40     3.7  medialorbitofrontal
 4903   3365  13051  3.029 0.780     0.130     0.041       71     8.4  middletemporal
  819    574   1828  2.558 0.763     0.125     0.041       11     1.2  parahippocampal
 1935   1353   3876  2.588 0.644     0.124     0.031       20     2.4  paracentral
 1864   1335   3942  2.709 0.694     0.135     0.037       27     2.8  parsopercularis
 1567   1102   4365  2.825 0.740     0.167     0.067       37     4.7  parsorbitalis
 2125   1470   5238  2.863 0.718     0.134     0.044       33     3.6  parstriangularis
 1786   1287   2873  2.259 0.641     0.151     0.048       24     3.1  pericalcarine
 5903   3979   8673  1.950 0.603     0.117     0.033       64     7.4  postcentral
 1622   1202   4147  2.928 0.878     0.155     0.040       28     2.6  posteriorcingulate
 7728   5161  15839  2.700 0.735     0.125     0.041       95    14.2  precentral
 5725   4025  11594  2.661 0.686     0.153     0.046      101    12.1  precuneus
  997    706   2917  3.196 0.853     0.149     0.048       21     2.0  rostralanteriorcingulate
 8971   6391  20914  2.688 0.702     0.153     0.051      175    20.3  rostralmiddlefrontal
11537   7997  29761  3.116 0.704     0.135     0.036      141    16.6  superiorfrontal
 8491   5936  18250  2.480 0.686     0.138     0.038      126    14.1  superiorparietal
 4951   3741  11632  2.705 0.766     0.134     0.042       69     9.1  superiortemporal
 5980   4206  13587  2.800 0.686     0.142     0.041       89     9.9  supramarginal
  626    392   1369  2.157 0.847     0.196     0.115       23     3.0  frontalpole
  643    456   1558  2.554 0.910     0.177     0.079       14     2.1  temporalpole
  477    318    904  2.622 0.655     0.158     0.055       10     1.0  transversetemporal
 2903   2143   7225  3.029 0.994     0.127     0.037       29     4.3  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 0050418 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 276809
Total vertex volume 274048 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1032    690   1842  2.524 0.680     0.146     0.047       18     2.2  bankssts
 1056   1012   2865  3.159 1.014     0.183     0.046       26     2.1  caudalanteriorcingulate
 3248   3070   8682  3.121 0.647     0.160     0.041       59     5.9  caudalmiddlefrontal
 2374   2216   4002  2.129 0.505     0.193     0.051       44     5.8  cuneus
  370    608   1494  3.082 0.895     0.240     0.061        5     0.9  entorhinal
 4019   4217   8171  2.225 0.728     0.209     0.069       84    11.5  fusiform
 6721   6625  15078  2.527 0.776     0.193     0.051      117    16.3  inferiorparietal
 3661   3771   8904  2.691 0.818     0.188     0.062       78     9.9  inferiortemporal
 1165   1102   2849  2.800 0.978     0.199     0.074       54     4.4  isthmuscingulate
 7374   7848  15358  2.304 0.679     0.202     0.056      132    18.8  lateraloccipital
 3893   3215   7440  2.570 0.843     0.186     0.058       88    10.5  lateralorbitofrontal
 3272   3558   7511  2.511 0.695     0.192     0.048       50     7.5  lingual
 2926   2542   6257  2.855 0.878     0.171     0.049       67     6.3  medialorbitofrontal
 4903   5145  13051  3.029 0.780     0.182     0.044       88    10.0  middletemporal
  819    857   1828  2.558 0.763     0.207     0.061       13     2.3  parahippocampal
 1935   1611   3876  2.588 0.644     0.149     0.039       35     3.2  paracentral
 1864   1688   3942  2.709 0.694     0.162     0.045       48     3.7  parsopercularis
 1567   1931   4365  2.825 0.740     0.215     0.052       39     3.9  parsorbitalis
 2125   2141   5238  2.863 0.718     0.180     0.044       44     4.4  parstriangularis
 1786   1252   2873  2.259 0.641     0.148     0.051      135     4.2  pericalcarine
 5903   4860   8673  1.950 0.603     0.145     0.036       71     9.5  postcentral
 1622   1499   4147  2.928 0.878     0.186     0.050       45     3.4  posteriorcingulate
 7728   6256  15839  2.700 0.735     0.141     0.038      168    13.7  precentral
 5725   4731  11594  2.661 0.686     0.180     0.059      178    13.5  precuneus
  997   1051   2917  3.196 0.853     0.228     0.558       62    39.4  rostralanteriorcingulate
 8971   9033  20914  2.688 0.702     0.196     0.054      190    23.5  rostralmiddlefrontal
11537  10848  29761  3.116 0.704     0.174     0.044      233    23.7  superiorfrontal
 8491   8482  18250  2.480 0.686     0.183     0.048      144    20.3  superiorparietal
 4951   5002  11632  2.705 0.766     0.182     0.064      110    17.0  superiortemporal
 5980   5477  13587  2.800 0.686     0.166     0.043      103    12.3  supramarginal
  626    725   1369  2.157 0.847     0.194     0.082       18     3.2  frontalpole
  643    751   1558  2.554 0.910     0.241     0.075       15     2.1  temporalpole
  477    352    904  2.622 0.655     0.138     0.338      165     1.6  transversetemporal
 2903   2342   7225  3.029 0.994     0.187     0.061       88     8.1  insula
PIDs (5447 5450 5453 5456) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct 29 08:34:05 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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 29 08:34:05 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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 5599 of (5599 5602) to complete...
Waiting for PID 5602 of (5599 5602) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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...
39 labels changed using aseg
relabeling using gibbs priors...
000:   8713 changed, 131248 examined...
001:   2078 changed, 34314 examined...
002:    610 changed, 10810 examined...
003:    253 changed, 3448 examined...
004:    110 changed, 1421 examined...
005:     55 changed, 644 examined...
006:     32 changed, 329 examined...
007:     10 changed, 187 examined...
008:      1 changed, 68 examined...
009:      1 changed, 7 examined...
010:      1 changed, 8 examined...
011:      1 changed, 7 examined...
012:      1 changed, 7 examined...
013:      0 changed, 8 examined...
0 labels changed using aseg
000: 285 total segments, 201 labels (2389 vertices) changed
001: 90 total segments, 7 labels (22 vertices) changed
002: 84 total segments, 1 labels (1 vertices) changed
003: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 31 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1172 vertices marked for relabeling...
1172 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 47 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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...
5 labels changed using aseg
relabeling using gibbs priors...
000:   8535 changed, 129560 examined...
001:   1941 changed, 33460 examined...
002:    541 changed, 10353 examined...
003:    190 changed, 3080 examined...
004:     89 changed, 1163 examined...
005:     55 changed, 493 examined...
006:     28 changed, 299 examined...
007:     14 changed, 152 examined...
008:     10 changed, 70 examined...
009:      4 changed, 54 examined...
010:      5 changed, 25 examined...
011:      4 changed, 26 examined...
012:      2 changed, 20 examined...
013:      0 changed, 6 examined...
1 labels changed using aseg
000: 262 total segments, 177 labels (2619 vertices) changed
001: 94 total segments, 9 labels (29 vertices) changed
002: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 36 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1073 vertices marked for relabeling...
1073 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 46 seconds.
PIDs (5599 5602) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct 29 08:34:52 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct 29 08:34:52 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 rh white 

Waiting for PID 5664 of (5664 5667) to complete...
Waiting for PID 5667 of (5664 5667) 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 0050418 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 275133
Total vertex volume 271693 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1307    888   2738  2.586 0.785     0.143     0.051       23     2.7  G&S_frontomargin
 1211    957   3518  2.625 0.824     0.168     0.052       24     2.5  G&S_occipital_inf
 1713   1205   3272  2.273 0.726     0.151     0.049       46     3.9  G&S_paracentral
 2484   1663   4286  2.368 0.802     0.149     0.058       41     6.2  G&S_subcentral
 1008    736   2981  2.826 0.651     0.156     0.054       25     2.4  G&S_transv_frontopol
 2422   1728   5918  2.945 0.739     0.136     0.037       32     4.0  G&S_cingul-Ant
 1312    911   2687  2.842 0.673     0.105     0.021        8     1.3  G&S_cingul-Mid-Ant
 1223    902   2881  3.119 0.492     0.127     0.030       11     1.5  G&S_cingul-Mid-Post
  441    341   1658  3.427 0.795     0.191     0.065        9     1.2  G_cingul-Post-dorsal
  264    192    942  3.236 1.025     0.163     0.050        5     0.5  G_cingul-Post-ventral
 2319   1747   4274  2.025 0.622     0.182     0.063       52     6.1  G_cuneus
 1358   1010   3549  2.540 0.747     0.169     0.061       27     4.4  G_front_inf-Opercular
  458    339   1640  3.173 0.541     0.171     0.062       15     1.4  G_front_inf-Orbital
  678    496   2438  3.087 0.673     0.152     0.044       16     1.3  G_front_inf-Triangul
 5553   3883  18223  3.122 0.733     0.153     0.047      114    11.0  G_front_middle
 7300   5365  22124  3.073 0.798     0.164     0.053      153    16.6  G_front_sup
  843    509   1552  2.696 0.843     0.136     0.058       12     1.7  G_Ins_lg&S_cent_ins
  763    491   2020  3.047 0.727     0.159     0.065       14     2.0  G_insular_short
 2102   1479   5202  2.516 0.714     0.174     0.060       48     5.3  G_occipital_middle
 1548   1117   3117  2.202 0.623     0.171     0.057       31     3.6  G_occipital_sup
 1560   1150   3641  2.535 0.757     0.163     0.054       34     4.1  G_oc-temp_lat-fusifor
 2746   2069   5787  2.141 0.754     0.188     0.070       66     8.2  G_oc-temp_med-Lingual
 1700   1094   3667  2.648 0.965     0.136     0.055       30     3.7  G_oc-temp_med-Parahip
 2602   1793   5997  2.430 0.804     0.162     0.077      129     8.4  G_orbital
 1903   1420   5850  2.796 0.758     0.171     0.059       52     4.6  G_pariet_inf-Angular
 3395   2367   7525  2.511 0.796     0.160     0.059       72     8.9  G_pariet_inf-Supramar
 3625   2587  10171  2.799 0.730     0.151     0.041       64     6.1  G_parietal_sup
 2306   1625   4406  2.128 0.846     0.150     0.048       36     4.8  G_postcentral
 3083   2126   7672  2.726 0.925     0.149     0.048       51     6.3  G_precentral
 2941   2233   8822  2.901 0.787     0.183     0.056       73     7.4  G_precuneus
  807    591   2301  2.749 0.775     0.176     0.071       22     2.3  G_rectus
  158    107    397  2.776 0.818     0.171     0.074        5     0.4  G_subcallosal
  384    446   1439  2.986 0.681     0.204     0.047        9     0.7  G_temp_sup-G_T_transv
 2056   1753   5844  2.634 1.056     0.186     0.070       50     6.8  G_temp_sup-Lateral
  802    620   2437  2.861 1.068     0.148     0.046       12     1.5  G_temp_sup-Plan_polar
 1071    786   2244  2.573 0.658     0.129     0.037       13     1.7  G_temp_sup-Plan_tempo
 2163   1583   5161  2.606 0.843     0.159     0.055       45     5.8  G_temporal_inf
 2715   1926   6874  2.588 0.891     0.172     0.062       70     7.5  G_temporal_middle
  200    135    372  2.567 0.525     0.109     0.019        1     0.2  Lat_Fis-ant-Horizont
  260    187    468  2.949 0.651     0.088     0.016        1     0.1  Lat_Fis-ant-Vertical
 1399    967   2002  2.584 0.685     0.124     0.032       11     2.1  Lat_Fis-post
 2021   1474   4038  2.133 0.681     0.184     0.071       49     5.9  Pole_occipital
 1441   1024   4366  3.021 0.861     0.161     0.071       32     4.6  Pole_temporal
 2413   1837   3424  2.035 0.670     0.142     0.046       36     4.9  S_calcarine
 3143   2185   3773  1.959 0.525     0.119     0.026       24     3.7  S_central
 1144    775   1793  2.471 0.463     0.095     0.015        6     0.8  S_cingul-Marginalis
  519    342    849  2.822 0.568     0.099     0.024        3     0.5  S_circular_insula_ant
 1182    921   1962  2.415 0.858     0.140     0.058       52     4.1  S_circular_insula_inf
 1694   1163   2688  2.991 0.504     0.109     0.022        9     1.7  S_circular_insula_sup
  905    652   1551  2.237 0.719     0.109     0.023        7     0.9  S_collat_transv_ant
  371    256    580  2.514 0.605     0.138     0.042        4     0.6  S_collat_transv_post
 1584   1082   2702  2.601 0.519     0.104     0.021       10     1.5  S_front_inf
 1975   1335   3155  2.721 0.481     0.107     0.022       14     1.9  S_front_middle
 2731   1928   5124  2.724 0.536     0.111     0.024       21     2.4  S_front_sup
  326    222    469  2.510 0.554     0.124     0.022        2     0.4  S_interm_prim-Jensen
 2608   1769   3862  2.370 0.493     0.114     0.026       20     3.0  S_intrapariet&P_trans
  863    626   1305  2.063 0.539     0.141     0.036       10     1.3  S_oc_middle&Lunatus
 1214    822   2013  2.365 0.607     0.116     0.027       10     1.3  S_oc_sup&transversal
  872    592   1126  2.157 0.460     0.105     0.023        6     0.9  S_occipital_ant
 1124    753   1467  2.015 0.651     0.111     0.040       15     2.2  S_oc-temp_lat
 1439   1104   2746  2.367 0.670     0.131     0.035       18     2.0  S_oc-temp_med&Lingual
  365    277    539  2.038 0.490     0.112     0.019        2     0.3  S_orbital_lateral
  487    352    958  2.959 0.694     0.131     0.028        7     0.4  S_orbital_med-olfact
 1278    901   2218  2.410 0.653     0.120     0.029       12     1.5  S_orbital-H_Shaped
 2282   1574   3455  2.424 0.624     0.122     0.028       29     2.8  S_parieto_occipital
 1287    766   1005  1.561 0.627     0.110     0.025       20     1.0  S_pericallosal
 2793   1910   4580  2.546 0.677     0.129     0.028       27     3.2  S_postcentral
 2188   1567   4079  2.683 0.568     0.105     0.023       16     2.0  S_precentral-inf-part
 1362    917   2096  2.510 0.671     0.100     0.018        8     1.0  S_precentral-sup-part
  518    367    964  2.778 0.752     0.121     0.022        5     0.5  S_suborbital
 1196    822   1860  2.789 0.638     0.132     0.031       11     1.6  S_subparietal
 1148    960   2322  2.785 0.761     0.142     0.028       11     1.6  S_temporal_inf
 4852   3983   9873  2.503 0.679     0.135     0.030       54     6.7  S_temporal_sup
  463    314    652  2.426 0.568     0.093     0.023        3     0.5  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 0050418 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 276809
Total vertex volume 274048 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1110    721   1951  2.316 0.753     0.171     0.086       37     4.3  G&S_frontomargin
 1237    873   2452  2.155 0.735     0.145     0.050       18     2.6  G&S_occipital_inf
 1411    976   3050  2.436 0.699     0.135     0.044       20     2.3  G&S_paracentral
 1492   1019   3179  2.469 0.698     0.129     0.039       19     2.2  G&S_subcentral
 1246    881   3477  2.882 0.670     0.166     0.049       29     2.3  G&S_transv_frontopol
 3418   2400   7759  2.989 0.701     0.126     0.033       42     4.9  G&S_cingul-Ant
 1468    993   3414  3.259 0.594     0.113     0.024       11     1.5  G&S_cingul-Mid-Ant
 1416   1029   3479  2.932 0.717     0.143     0.041       21     2.2  G&S_cingul-Mid-Post
  340    270   1460  3.568 0.622     0.199     0.074        9     1.0  G_cingul-Post-dorsal
  312    199    869  3.118 1.102     0.162     0.091       10     1.5  G_cingul-Post-ventral
 2076   1551   3778  2.066 0.511     0.185     0.060       42     5.9  G_cuneus
 1245    938   3055  2.552 0.802     0.165     0.051       26     2.8  G_front_inf-Opercular
  452    314   1467  3.091 0.545     0.182     0.097       15     1.9  G_front_inf-Orbital
  895    609   2811  3.125 0.676     0.161     0.054       21     1.9  G_front_inf-Triangul
 4407   3230  14105  2.993 0.772     0.177     0.061      109    12.4  G_front_middle
 7414   5108  22063  3.239 0.727     0.150     0.046      120    13.3  G_front_sup
  641    471   1848  3.243 1.189     0.145     0.053        8     1.3  G_Ins_lg&S_cent_ins
  542    365   1938  3.424 0.905     0.143     0.052        9     1.0  G_insular_short
 2859   2000   7431  2.538 0.731     0.168     0.061       66     8.0  G_occipital_middle
 1301    895   2965  2.425 0.657     0.140     0.038       20     2.0  G_occipital_sup
 1856   1389   4417  2.354 0.792     0.163     0.052       35     4.4  G_oc-temp_lat-fusifor
 2042   1597   5367  2.580 0.701     0.180     0.058       43     4.8  G_oc-temp_med-Lingual
  929    682   2729  2.774 0.855     0.159     0.059       17     1.8  G_oc-temp_med-Parahip
 3353   2202   8101  2.560 0.916     0.163     0.072       77    10.4  G_orbital
 2257   1670   7036  3.009 0.787     0.174     0.059       54     5.8  G_pariet_inf-Angular
 3095   2184   8079  2.757 0.684     0.158     0.053       61     6.7  G_pariet_inf-Supramar
 3415   2489   9315  2.731 0.759     0.166     0.050       76     7.7  G_parietal_sup
 2050   1371   3129  1.900 0.548     0.141     0.049       33     4.1  G_postcentral
 3360   2214   8546  2.824 0.856     0.146     0.062       64     9.6  G_precentral
 2696   1943   7097  2.827 0.639     0.176     0.062       66     7.9  G_precuneus
  833    546   2339  3.065 0.819     0.155     0.053       16     2.0  G_rectus
  589    380    942  2.522 1.223     0.101     0.058        7     1.1  G_subcallosal
  436    291    975  2.807 0.784     0.154     0.052        9     0.9  G_temp_sup-G_T_transv
 1880   1316   4796  2.765 0.793     0.156     0.062       37     5.0  G_temp_sup-Lateral
  646    558   1911  2.862 0.930     0.156     0.046       11     1.2  G_temp_sup-Plan_polar
  793    573   1509  2.449 0.531     0.109     0.025        7     0.8  G_temp_sup-Plan_tempo
 2137   1568   6347  2.822 0.854     0.165     0.068       54     6.2  G_temporal_inf
 2864   1878   9003  3.277 0.739     0.140     0.054       57     6.2  G_temporal_middle
  334    239    548  2.405 0.636     0.096     0.017        1     0.2  Lat_Fis-ant-Horizont
  345    226    482  2.469 0.646     0.097     0.024        1     0.3  Lat_Fis-ant-Vertical
 1350    886   2011  2.787 0.820     0.105     0.021        8     1.2  Lat_Fis-post
 3095   2289   7119  2.367 0.690     0.173     0.067       61     8.5  Pole_occipital
 1356   1128   3812  2.512 0.776     0.183     0.066       29     3.9  Pole_temporal
 2021   1440   3074  2.477 0.667     0.135     0.035       24     2.8  S_calcarine
 2865   1921   3574  2.013 0.647     0.097     0.018       17     2.0  S_central
 1103    774   1586  2.373 0.711     0.118     0.023        8     1.1  S_cingul-Marginalis
  571    378   1066  3.089 0.666     0.109     0.026        3     0.6  S_circular_insula_ant
  766    791   2005  2.684 0.971     0.112     0.021        4     0.7  S_circular_insula_inf
 1137    793   2078  2.895 0.668     0.109     0.025        7     1.2  S_circular_insula_sup
  833    608   1280  2.148 0.571     0.113     0.024        6     1.0  S_collat_transv_ant
  426    304    505  2.089 0.567     0.135     0.033        4     0.7  S_collat_transv_post
 1823   1313   3757  2.825 0.693     0.116     0.025       14     2.1  S_front_inf
 2327   1634   3987  2.629 0.553     0.123     0.032       21     3.0  S_front_middle
 2452   1712   5003  2.814 0.632     0.108     0.023       16     2.2  S_front_sup
  559    407   1034  2.988 0.584     0.134     0.027        5     0.7  S_interm_prim-Jensen
 3225   2215   5373  2.395 0.512     0.107     0.023       20     3.0  S_intrapariet&P_trans
  975    682   1236  1.993 0.461     0.120     0.030        7     1.3  S_oc_middle&Lunatus
 1104    728   1419  1.987 0.447     0.118     0.029        9     1.3  S_oc_sup&transversal
  728    506    982  2.016 0.531     0.125     0.037        9     1.4  S_occipital_ant
  506    385   1144  2.463 0.821     0.120     0.030        4     0.5  S_oc-temp_lat
 1523   1045   2457  2.151 0.639     0.119     0.036       18     2.4  S_oc-temp_med&Lingual
  566    403    957  2.657 0.736     0.108     0.024        3     0.5  S_orbital_lateral
  469    330    782  2.563 0.682     0.128     0.027        4     0.5  S_orbital_med-olfact
 1521   1042   2657  2.611 0.730     0.129     0.039       16     2.4  S_orbital-H_Shaped
 2454   1657   3657  2.439 0.695     0.127     0.030       27     3.1  S_parieto_occipital
 1321    875   1821  2.232 0.912     0.125     0.021       17     0.9  S_pericallosal
 2743   1856   3917  2.241 0.536     0.112     0.025       21     2.6  S_postcentral
 1553   1048   2890  2.859 0.485     0.109     0.020       11     1.2  S_precentral-inf-part
 1601   1112   2575  2.793 0.491     0.104     0.021        8     1.5  S_precentral-sup-part
  330    228    520  2.935 0.900     0.136     0.024        3     0.3  S_suborbital
 1049    754   1966  2.618 0.578     0.148     0.042       16     1.8  S_subparietal
 1224    875   2003  2.679 0.654     0.120     0.036       11     2.3  S_temporal_inf
 5721   3988  10146  2.516 0.726     0.115     0.029       52     7.1  S_temporal_sup
  221    181    436  3.027 0.675     0.149     0.019        2     0.2  S_temporal_transverse
PIDs (5664 5667) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct 29 08:36:10 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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 29 08:36:10 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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 5757 of (5757 5760) to complete...
Waiting for PID 5760 of (5757 5760) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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...
1006 labels changed using aseg
relabeling using gibbs priors...
000:   1922 changed, 131248 examined...
001:    434 changed, 9152 examined...
002:    126 changed, 2545 examined...
003:     48 changed, 724 examined...
004:     21 changed, 270 examined...
005:     12 changed, 120 examined...
006:     10 changed, 73 examined...
007:      7 changed, 56 examined...
008:      6 changed, 38 examined...
009:      5 changed, 33 examined...
010:      6 changed, 24 examined...
011:      2 changed, 30 examined...
012:      3 changed, 12 examined...
013:      1 changed, 17 examined...
014:      2 changed, 11 examined...
015:      2 changed, 14 examined...
016:      1 changed, 12 examined...
017:      0 changed, 7 examined...
109 labels changed using aseg
000: 71 total segments, 38 labels (395 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
812 vertices marked for relabeling...
812 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 26 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 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...
1154 labels changed using aseg
relabeling using gibbs priors...
000:   1939 changed, 129560 examined...
001:    446 changed, 9005 examined...
002:    114 changed, 2442 examined...
003:     41 changed, 695 examined...
004:     17 changed, 261 examined...
005:     11 changed, 110 examined...
006:      5 changed, 69 examined...
007:      1 changed, 35 examined...
008:      0 changed, 6 examined...
86 labels changed using aseg
000: 60 total segments, 27 labels (182 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
839 vertices marked for relabeling...
839 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 26 seconds.
PIDs (5757 5760) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct 29 08:36:36 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct 29 08:36:36 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 rh white 

Waiting for PID 5818 of (5818 5821) to complete...
Waiting for PID 5821 of (5818 5821) 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 0050418 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 275133
Total vertex volume 271693 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1779   1216   3660  2.561 0.793     0.127     0.033       23     2.4  caudalanteriorcingulate
 3588   2482   8548  2.875 0.717     0.116     0.025       34     3.4  caudalmiddlefrontal
 3483   2561   5985  2.112 0.572     0.165     0.052       65     7.7  cuneus
  716    441   1581  2.646 0.964     0.153     0.070       17     2.1  entorhinal
 3584   2637   7251  2.354 0.738     0.146     0.047       62     7.7  fusiform
 5453   3985  12607  2.572 0.699     0.144     0.042       92     9.6  inferiorparietal
 4233   3140   9513  2.576 0.854     0.145     0.049       74    10.3  inferiortemporal
 1356    938   3063  2.551 1.107     0.140     0.043       21     2.2  isthmuscingulate
 6627   4814  14102  2.318 0.707     0.165     0.054      127    14.7  lateraloccipital
 4475   3011   9057  2.500 0.811     0.147     0.060      150    11.1  lateralorbitofrontal
 3821   2867   7323  2.150 0.710     0.165     0.057       73     9.2  lingual
 1649   1201   4032  2.760 0.757     0.155     0.050       32     3.4  medialorbitofrontal
 5828   4414  12860  2.559 0.806     0.153     0.046      102    11.7  middletemporal
 1086    719   2259  2.589 0.930     0.120     0.040       14     1.7  parahippocampal
 2460   1749   4943  2.549 0.685     0.136     0.040       56     4.4  paracentral
 1809   1369   4474  2.854 0.658     0.152     0.046       30     4.3  parsopercularis
  770    608   2287  2.870 0.663     0.135     0.041        9     1.3  parsorbitalis
 1684   1183   4205  2.841 0.620     0.127     0.035       29     2.7  parstriangularis
 1947   1406   2476  1.858 0.622     0.154     0.054       34     4.7  pericalcarine
 7680   5343  12883  2.231 0.804     0.138     0.041      100    13.5  postcentral
 1679   1222   3703  2.749 0.826     0.132     0.028       22     1.9  posteriorcingulate
 8598   5865  16339  2.481 0.786     0.134     0.040      105    15.1  precentral
 5946   4323  13654  2.764 0.724     0.154     0.043      108    11.4  precuneus
 1396    977   3736  3.037 0.930     0.149     0.044       22     2.7  rostralanteriorcingulate
 6266   4343  14968  2.772 0.668     0.134     0.039      103    10.4  rostralmiddlefrontal
12749   9153  34311  2.989 0.737     0.144     0.042      208    23.1  superiorfrontal
 6704   4674  14979  2.582 0.681     0.140     0.037       93    10.2  superiorparietal
 7644   6140  18475  2.616 0.911     0.154     0.052      168    19.2  superiortemporal
 5649   3970  11420  2.615 0.754     0.145     0.046       92    11.3  supramarginal
  474    444   1334  2.688 0.628     0.172     0.047        7     0.8  transversetemporal
 2838   1905   5664  2.881 0.682     0.130     0.040       29     4.7  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050418 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 276809
Total vertex volume 274048 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1154    776   3069  3.135 1.025     0.126     0.028       13     1.4  caudalanteriorcingulate
 3397   2407   8842  3.106 0.644     0.129     0.031       37     4.6  caudalmiddlefrontal
 2794   2027   4733  2.120 0.515     0.160     0.049       44     6.5  cuneus
  323    267   1288  3.059 0.941     0.151     0.039        3     0.4  entorhinal
 3527   2571   7293  2.243 0.741     0.151     0.048       60     7.4  fusiform
 6864   4953  15517  2.545 0.797     0.149     0.043      113    13.1  inferiorparietal
 4191   3094  10000  2.595 0.833     0.147     0.055       78     9.9  inferiortemporal
 1139    782   2763  2.770 0.980     0.153     0.047       24     1.9  isthmuscingulate
 7288   5155  15142  2.307 0.669     0.157     0.054      124    17.1  lateraloccipital
 4687   3060   8911  2.447 0.859     0.154     0.066       92    13.6  lateralorbitofrontal
 3227   2496   7377  2.495 0.692     0.162     0.051       55     6.6  lingual
 1971   1323   4447  2.927 0.978     0.129     0.040       26     2.9  medialorbitofrontal
 5756   3901  14442  2.960 0.798     0.127     0.043       83    10.8  middletemporal
  856    596   1878  2.546 0.745     0.126     0.045       12     1.3  parahippocampal
 2036   1438   4261  2.614 0.671     0.125     0.031       22     2.5  paracentral
 2096   1491   4320  2.693 0.693     0.132     0.036       31     3.1  parsopercularis
 1257    857   3035  2.836 0.665     0.162     0.073       28     4.1  parsorbitalis
 2035   1438   5113  2.889 0.696     0.132     0.037       27     2.7  parstriangularis
 1794   1277   2889  2.265 0.648     0.152     0.050       26     3.3  pericalcarine
 6572   4404   9736  1.982 0.610     0.120     0.033       73     8.6  postcentral
 1695   1267   4304  2.916 0.854     0.158     0.042       29     2.9  posteriorcingulate
 7467   4986  15449  2.687 0.743     0.125     0.042       93    13.9  precentral
 5902   4154  12093  2.669 0.694     0.153     0.048      106    13.1  precuneus
 1374    955   3499  3.071 0.828     0.135     0.044       24     2.4  rostralanteriorcingulate
 6201   4485  14936  2.681 0.718     0.152     0.051      116    14.3  rostralmiddlefrontal
14837  10276  37644  3.045 0.701     0.139     0.039      212    22.9  superiorfrontal
 7316   5113  16307  2.540 0.680     0.139     0.038      113    12.4  superiorparietal
 6205   4696  14319  2.656 0.760     0.137     0.043       85    11.4  superiortemporal
 5577   3941  12659  2.789 0.680     0.139     0.040       79     8.9  supramarginal
  469    312    901  2.634 0.656     0.158     0.054       10     1.0  transversetemporal
 2703   1951   6880  3.116 0.969     0.121     0.035       26     3.8  insula
PIDs (5818 5821) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct 29 08:37:44 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 pctsurfcon --s 0050418 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct 29 08:37:44 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts

 pctsurfcon --s 0050418 --rh-only 

Waiting for PID 5991 of (5991 5994) to complete...
Waiting for PID 5994 of (5991 5994) to complete...

 pctsurfcon --s 0050418 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts/pctsurfcon.log
Sun Oct 29 08:37:44 CET 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-623 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-6.0.0/0050418/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.wm.mgh --regheader 0050418 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 62946
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.wm.mgh
Dim: 131248 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.gm.mgh --projfrac 0.3 --regheader 0050418 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 75606
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.gm.mgh
Dim: 131248 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.w-g.pct.mgh --annot 0050418 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/lh.w-g.pct.mgh --annot 0050418 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/lh.w-g.pct.mgh
Vertex Area is 0.713875 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 0050418 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts/pctsurfcon.log
Sun Oct 29 08:37:44 CET 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-623 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-6.0.0/0050418/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.wm.mgh --regheader 0050418 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 62076
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.wm.mgh
Dim: 129560 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.gm.mgh --projfrac 0.3 --regheader 0050418 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 74786
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.gm.mgh
Dim: 129560 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.w-g.pct.mgh --annot 0050418 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.w-g.pct.mgh --annot 0050418 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.w-g.pct.mgh
Vertex Area is 0.703019 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 (5991 5994) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct 29 08:37:55 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
3159 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1930 voxels changed to hypointensity...
5601 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct 29 08:38:16 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418

 mri_aparc2aseg --s 0050418 --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 29 08:38:16 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418

 mri_aparc2aseg --s 0050418 --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 29 08:38:16 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418

 mri_aparc2aseg --s 0050418 --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 6141 of (6141 6144 6147) to complete...
Waiting for PID 6144 of (6141 6144 6147) to complete...
Waiting for PID 6147 of (6141 6144 6147) to complete...

 mri_aparc2aseg --s 0050418 --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 0050418
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/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-6.0.0/0050418/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 6.98
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 109
rescaling Left_Cerebral_Cortex from 61 --> 62
rescaling Left_Lateral_Ventricle from 13 -->  9
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 83
rescaling Left_Cerebellum_Cortex from 60 --> 53
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 67
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 16
rescaling Fourth_Ventricle from 22 -->  8
rescaling Brain_Stem from 81 --> 81
rescaling Left_Hippocampus from 57 --> 58
rescaling Left_Amygdala from 56 --> 60
rescaling CSF from 32 --> 22
rescaling Left_Accumbens_area from 62 --> 60
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 64
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 53
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 77
rescaling Right_Putamen from 80 --> 72
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 75
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 19
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 538226
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 100 changed.
pass 2: 9 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050418 --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 0050418
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/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-6.0.0/0050418/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 6.98
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 109
rescaling Left_Cerebral_Cortex from 61 --> 62
rescaling Left_Lateral_Ventricle from 13 -->  9
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 83
rescaling Left_Cerebellum_Cortex from 60 --> 53
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 67
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 16
rescaling Fourth_Ventricle from 22 -->  8
rescaling Brain_Stem from 81 --> 81
rescaling Left_Hippocampus from 57 --> 58
rescaling Left_Amygdala from 56 --> 60
rescaling CSF from 32 --> 22
rescaling Left_Accumbens_area from 62 --> 60
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 64
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 53
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 77
rescaling Right_Putamen from 80 --> 72
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 75
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 19
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 538261
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 100 changed.
pass 2: 9 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050418 --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 0050418
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/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-6.0.0/0050418/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 6.98
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 109
rescaling Left_Cerebral_Cortex from 61 --> 62
rescaling Left_Lateral_Ventricle from 13 -->  9
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 83
rescaling Left_Cerebellum_Cortex from 60 --> 53
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 67
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 16
rescaling Fourth_Ventricle from 22 -->  8
rescaling Brain_Stem from 81 --> 81
rescaling Left_Hippocampus from 57 --> 58
rescaling Left_Amygdala from 56 --> 60
rescaling CSF from 32 --> 22
rescaling Left_Accumbens_area from 62 --> 60
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 64
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 53
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 77
rescaling Right_Putamen from 80 --> 72
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 75
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 19
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 538261
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 100 changed.
pass 2: 9 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (6141 6144 6147) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct 29 08:53:37 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri

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

Sun Oct 29 08:53:37 CET 2017

setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-623 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-6.0.0/0050418/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-623
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 29 08:53:37 CET 2017 
Ended   at Sun Oct 29 08:53:44 CET 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct 29 08:53:44 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418

 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 0050418 


$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 0050418 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1574874 mm^3    (det: 1.236991 )
Computing euler number
orig.nofix lheno = -514, rheno = -316
orig.nofix lhholes =  258, rhholes = 159
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
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 29 08:56:44 CET 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418

 mri_aparc2aseg --s 0050418 --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 0050418
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-6.0.0/0050418/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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-6.0.0/0050418/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7273 vertices from left hemi
Ripped 6896 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-6.0.0/0050418/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 = 951163
Used brute-force search on 163 voxels
Fixing Parahip LH WM
  Found 7 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1478.000000
     5 k 2.000000
     6 k 14.000000
Fixing Parahip RH WM
  Found 9 clusters
     0 k 1096.000000
     1 k 1.000000
     2 k 1.000000
     3 k 3.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 49.000000
     8 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 0050418 --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 0050418 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-623
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1574874 mm^3    (det: 1.236991 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
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-6.0.0/0050418/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct 29 09:05:49 CET 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 7625 of (7625 7628 7631 7639 7649) to complete...
Waiting for PID 7628 of (7625 7628 7631 7639 7649) to complete...
Waiting for PID 7631 of (7625 7628 7631 7639 7649) to complete...
Waiting for PID 7639 of (7625 7628 7631 7639 7649) to complete...
Waiting for PID 7649 of (7625 7628 7631 7639 7649) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 361
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4490
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 663
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8572
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 261
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4338
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 692
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6675
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 582
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6366
mri_label2label: Done

PIDs (7625 7628 7631 7639 7649) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 7706 of (7706 7712 7718 7724) to complete...
Waiting for PID 7712 of (7706 7712 7718 7724) to complete...
Waiting for PID 7718 of (7706 7712 7718 7724) to complete...
Waiting for PID 7724 of (7706 7712 7718 7724) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 248
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4318
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 1493
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15082
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 664
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4845
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 336
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 3758
mri_label2label: Done

PIDs (7706 7712 7718 7724) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 7762 of (7762 7768 7774 7780 7784) to complete...
Waiting for PID 7768 of (7762 7768 7774 7780 7784) to complete...
Waiting for PID 7774 of (7762 7768 7774 7780 7784) to complete...
Waiting for PID 7780 of (7762 7768 7774 7780 7784) to complete...
Waiting for PID 7784 of (7762 7768 7774 7780 7784) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 1380
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6021
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 2606
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10720
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 417
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2435
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 250
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1540
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 229
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1428
mri_label2label: Done

PIDs (7762 7768 7774 7780 7784) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 7838 of (7838 7844 7850 7856 7861) to complete...
Waiting for PID 7844 of (7838 7844 7850 7856 7861) to complete...
Waiting for PID 7850 of (7838 7844 7850 7856 7861) to complete...
Waiting for PID 7856 of (7838 7844 7850 7856 7861) to complete...
Waiting for PID 7861 of (7838 7844 7850 7856 7861) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 107
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1121
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 89
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2181
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1567
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 102
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2098
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 233
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2552
mri_label2label: Done

PIDs (7838 7844 7850 7856 7861) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 7921 of (7921 7927 7933 7939) to complete...
Waiting for PID 7927 of (7921 7927 7933 7939) to complete...
Waiting for PID 7933 of (7921 7927 7933 7939) to complete...
Waiting for PID 7939 of (7921 7927 7933 7939) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 77
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1626
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 592
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7627
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 201
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2113
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 112
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1263
mri_label2label: Done

PIDs (7921 7927 7933 7939) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 7992 of (7992 7998 8004 8010 8016) to complete...
Waiting for PID 7998 of (7992 7998 8004 8010 8016) to complete...
Waiting for PID 8004 of (7992 7998 8004 8010 8016) to complete...
Waiting for PID 8010 of (7992 7998 8004 8010 8016) to complete...
Waiting for PID 8016 of (7992 7998 8004 8010 8016) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 950
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4355
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 1172
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4506
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 106
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 619
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 129
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 599
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 131248
Number of reverse mapping hits = 113
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 563
mri_label2label: Done

PIDs (7992 7998 8004 8010 8016) completed and logs appended.

 mris_label2annot --s 0050418 --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-6.0.0/0050418/label
cmdline mris_label2annot --s 0050418 --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-623
machine  x86_64
user     ntraut

subject 0050418
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-6.0.0/0050418/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 90918 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050418 --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-6.0.0/0050418/label
cmdline mris_label2annot --s 0050418 --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-623
machine  x86_64
user     ntraut

subject 0050418
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-6.0.0/0050418/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 108003 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 275133
Total vertex volume 271693 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
 1107    783   2058  2.064 0.745     0.167     0.057       23     2.8  BA1_exvivo
 3776   2614   6883  2.473 0.718     0.133     0.036       44     5.6  BA2_exvivo
 1133    718   1108  1.993 0.407     0.146     0.042       36     2.1  BA3a_exvivo
 2747   1840   3374  1.745 0.564     0.127     0.041       33     5.0  BA3b_exvivo
 1781   1234   3112  2.276 0.603     0.145     0.045       25     3.6  BA4a_exvivo
 1289    926   1880  2.127 0.556     0.122     0.031        9     2.0  BA4p_exvivo
 9463   6696  24724  2.974 0.832     0.137     0.040      130    15.7  BA6_exvivo
 2399   1750   5664  2.692 0.690     0.140     0.041       34     4.6  BA44_exvivo
 2191   1619   6224  2.880 0.656     0.147     0.043       50     4.3  BA45_exvivo
 3382   2521   5167  1.893 0.627     0.166     0.061       66     8.7  V1_exvivo
 7637   5665  14638  2.178 0.677     0.176     0.062      162    19.9  V2_exvivo
 1940   1438   4375  2.455 0.629     0.142     0.040       29     2.9  MT_exvivo
  710    416   1457  2.618 0.924     0.127     0.054       13     1.5  perirhinal_exvivo
  775    552   2057  2.925 1.045     0.144     0.048       13     1.6  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 0050418 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 275133
Total vertex volume 271693 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
  685    466   1343  2.115 0.768     0.191     0.073       17     2.1  BA1_exvivo
 1356    974   2875  2.506 0.812     0.129     0.032       15     1.7  BA2_exvivo
  908    584    885  2.029 0.381     0.155     0.044       33     1.8  BA3a_exvivo
 1396   1036   1734  1.565 0.369     0.099     0.020        9     1.1  BA3b_exvivo
 1702   1193   3108  2.355 0.594     0.134     0.036       17     2.8  BA4a_exvivo
 1048    758   1461  2.117 0.551     0.120     0.030        7     1.5  BA4p_exvivo
 5094   3558  13107  2.960 0.877     0.142     0.043       72     8.8  BA6_exvivo
 1392   1060   3398  2.680 0.663     0.144     0.044       23     3.2  BA44_exvivo
  889    678   2888  3.032 0.676     0.164     0.042       19     1.9  BA45_exvivo
 3575   2666   5483  1.886 0.614     0.167     0.063       70     9.9  V1_exvivo
 3866   2949   7436  2.113 0.692     0.186     0.065       91    10.9  V2_exvivo
  527    361    874  2.401 0.599     0.141     0.043        9     0.9  MT_exvivo
  355    226    764  2.353 0.826     0.109     0.050        5     0.7  perirhinal_exvivo
  452    321   1013  2.840 1.129     0.141     0.057        8     1.0  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct 29 09:10:34 CET 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 8123 of (8123 8129 8135 8141 8147) to complete...
Waiting for PID 8129 of (8123 8129 8135 8141 8147) to complete...
Waiting for PID 8135 of (8123 8129 8135 8141 8147) to complete...
Waiting for PID 8141 of (8123 8129 8135 8141 8147) to complete...
Waiting for PID 8147 of (8123 8129 8135 8141 8147) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 373
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4335
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 416
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7103
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 115
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4095
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 243
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4765
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 405
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6152
mri_label2label: Done

PIDs (8123 8129 8135 8141 8147) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 8203 of (8203 8209 8215 8221) to complete...
Waiting for PID 8209 of (8203 8209 8215 8221) to complete...
Waiting for PID 8215 of (8203 8209 8215 8221) to complete...
Waiting for PID 8221 of (8203 8209 8215 8221) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 259
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4732
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 1657
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13913
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 743
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7655
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 1027
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6382
mri_label2label: Done

PIDs (8203 8209 8215 8221) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 8288 of (8288 8294 8300 8306 8312) to complete...
Waiting for PID 8294 of (8288 8294 8300 8306 8312) to complete...
Waiting for PID 8300 of (8288 8294 8300 8306 8312) to complete...
Waiting for PID 8306 of (8288 8294 8300 8306 8312) to complete...
Waiting for PID 8312 of (8288 8294 8300 8306 8312) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 1254
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 5981
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 1989
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10005
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 793
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2725
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1142
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 110
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 862
mri_label2label: Done

PIDs (8288 8294 8300 8306 8312) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 8371 of (8371 8377 8383 8389 8393) to complete...
Waiting for PID 8377 of (8371 8377 8383 8389 8393) to complete...
Waiting for PID 8383 of (8371 8377 8383 8389 8393) to complete...
Waiting for PID 8389 of (8371 8377 8383 8389 8393) to complete...
Waiting for PID 8393 of (8371 8377 8383 8389 8393) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 111
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 987
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 129
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2817
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 42
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1740
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 99
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2282
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 27
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1415
mri_label2label: Done

PIDs (8371 8377 8383 8389 8393) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 8432 of (8432 8438 8444 8450) to complete...
Waiting for PID 8438 of (8432 8438 8444 8450) to complete...
Waiting for PID 8444 of (8432 8438 8444 8450) to complete...
Waiting for PID 8450 of (8432 8438 8444 8450) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 123
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1612
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 791
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7750
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 152
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1164
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 205
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1383
mri_label2label: Done

PIDs (8432 8438 8444 8450) 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 0050418 --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 0050418 --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 0050418 --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 0050418 --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 0050418 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 8517 of (8517 8523 8529 8535 8539) to complete...
Waiting for PID 8523 of (8517 8523 8529 8535 8539) to complete...
Waiting for PID 8529 of (8517 8523 8529 8535 8539) to complete...
Waiting for PID 8535 of (8517 8523 8529 8535 8539) to complete...
Waiting for PID 8539 of (8517 8523 8529 8535 8539) 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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 788
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4020
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 941
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4378
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 139
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 407
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 35
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 729
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 0050418 --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 = 0050418
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-6.0.0/0050418/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 129560
Number of reverse mapping hits = 23
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 314
mri_label2label: Done

PIDs (8517 8523 8529 8535 8539) completed and logs appended.

 mris_label2annot --s 0050418 --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-6.0.0/0050418/label
cmdline mris_label2annot --s 0050418 --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-623
machine  x86_64
user     ntraut

subject 0050418
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-6.0.0/0050418/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 90399 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050418 --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-6.0.0/0050418/label
cmdline mris_label2annot --s 0050418 --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-623
machine  x86_64
user     ntraut

subject 0050418
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-6.0.0/0050418/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 108204 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 0050418 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 276809
Total vertex volume 274048 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
  965    594   1442  1.907 0.542     0.152     0.061       18     2.5  BA1_exvivo
 3051   2069   4420  2.142 0.559     0.119     0.031       31     3.6  BA2_exvivo
 1074    702   1119  1.934 0.510     0.128     0.025       10     1.0  BA3a_exvivo
 1836   1273   2559  1.741 0.573     0.101     0.029       15     2.0  BA3b_exvivo
 1267    924   2915  2.686 0.660     0.126     0.040       11     2.0  BA4a_exvivo
 1167    788   1877  2.392 0.588     0.103     0.027       14     1.3  BA4p_exvivo
 8952   6098  22173  2.979 0.707     0.130     0.040      108    15.6  BA6_exvivo
 3402   2382   7151  2.782 0.694     0.128     0.035       44     5.0  BA44_exvivo
 4042   2802  10192  2.826 0.716     0.141     0.049       67     8.1  BA45_exvivo
 3305   2506   6812  2.307 0.663     0.170     0.060       58     8.3  V1_exvivo
 6828   4981  13845  2.357 0.680     0.166     0.053      122    15.4  V2_exvivo
 2434   1770   4704  2.242 0.620     0.156     0.050       46     5.9  MT_exvivo
  459    363   1805  3.165 0.913     0.152     0.043        6     0.7  perirhinal_exvivo
  379    265    838  2.486 0.694     0.173     0.064        8     1.0  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 0050418 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 276809
Total vertex volume 274048 (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) = 1574874 mm^3    (det: 1.236991 )
lhCtxGM: 269017.890 269026.000  diff=   -8.1  pctdiff=-0.003
rhCtxGM: 270588.895 270359.000  diff=  229.9  pctdiff= 0.085
lhCtxWM: 206072.430 206920.000  diff= -847.6  pctdiff=-0.411
rhCtxWM: 206417.922 207270.000  diff= -852.1  pctdiff=-0.413
SubCortGMVol  59871.000
SupraTentVol  1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215
SupraTentVolNotVent  1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217
BrainSegVol  1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188
BrainSegVolNotVent  1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134
BrainSegVolNotVent  1163718.000
CerebellumVol 150171.000
VentChorVol    7630.000
3rd4th5thCSF   2870.000
CSFVol   668.000, OptChiasmVol    84.000
MaskVol 1524796.000
  645    403    939  1.880 0.522     0.166     0.063       13     1.9  BA1_exvivo
 1656   1129   2328  1.977 0.516     0.107     0.027       14     1.7  BA2_exvivo
  949    615    921  1.929 0.480     0.128     0.023        9     0.9  BA3a_exvivo
 1409   1002   1735  1.573 0.476     0.088     0.021        8     1.2  BA3b_exvivo
  721    516   1820  2.880 0.559     0.121     0.032        7     0.9  BA4a_exvivo
 1025    679   1567  2.394 0.612     0.101     0.027       13     1.2  BA4p_exvivo
 5444   3728  13486  2.942 0.698     0.127     0.039       62     9.1  BA6_exvivo
  822    653   1808  2.392 0.735     0.167     0.047       18     1.7  BA44_exvivo
 1025    714   2888  2.895 0.711     0.152     0.051       21     1.8  BA45_exvivo
 3157   2380   6310  2.314 0.659     0.169     0.060       54     8.0  V1_exvivo
 3658   2700   8094  2.405 0.713     0.171     0.053       69     8.0  V2_exvivo
  383    249    998  2.673 0.606     0.153     0.064        9     1.1  MT_exvivo
  253    201   1055  3.172 0.994     0.127     0.036        2     0.3  perirhinal_exvivo
  209    175    622  2.816 0.667     0.166     0.047        3     0.4  entorhinal_exvivo

Started at Thu Oct 26 21:16:50 CEST 2017 
Ended   at Sun Oct 29 09:15:14 CET 2017
#@#%# recon-all-run-time-hours 60.973
recon-all -s 0050418 finished without error at Sun Oct 29 09:15:14 CET 2017