ABIDE_fs-6.0.0/0050345/scripts/recon-all.log

Sat Oct  7 23:40:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050345 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050345/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050345
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-610 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    10485760 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked 64 kbytes
maxproc      1024 

             total       used       free     shared    buffers     cached
Mem:      65993848   60871356    5122492    1777140          0   55633236
-/+ buffers/cache:    5238120   60755728
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-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-610  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-6.0.0/0050345

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050345/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050345/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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_1/0050345/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-6.0.0/0050345/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 23:40:23 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/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-6.0.0/0050345/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 23:40:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/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-610 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 23:40:31 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.13692
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13692/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.13692/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.13692/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 23:40:34 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.13692/nu0.mnc ./tmp.mri_nu_correct.mni.13692/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13692/0/ -iterations 1000 -distance 50
[ntraut@tars-610:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/] [2017-10-07 23:40:34] 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.13692/0/ ./tmp.mri_nu_correct.mni.13692/nu0.mnc ./tmp.mri_nu_correct.mni.13692/nu1.imp

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Number of iterations: 55 
CV of field change: 0.000960403
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.13692/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.13692/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.13692/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 23:41:53 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 23:41:53 CEST 2017
Ended   at Sat Oct  7 23:42:30 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 23:42:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.1675, pval=0.0085 >= 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-6.0.0/0050345/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/transforms/talairach_avi.log 

TalAviQA: 0.96150
z-score: -3
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 23:42:32 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-6.0.0/0050345/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-610 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 23:42:33 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.14659
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14659/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.14659/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.14659/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 23:42:35 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.14659/nu0.mnc ./tmp.mri_nu_correct.mni.14659/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14659/0/
[ntraut@tars-610:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/] [2017-10-07 23:42:35] 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.14659/0/ ./tmp.mri_nu_correct.mni.14659/nu0.mnc ./tmp.mri_nu_correct.mni.14659/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00158995
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 23:43:28 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.14659/nu1.mnc ./tmp.mri_nu_correct.mni.14659/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.14659/1/
[ntraut@tars-610:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/] [2017-10-07 23:43:28] 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.14659/1/ ./tmp.mri_nu_correct.mni.14659/nu1.mnc ./tmp.mri_nu_correct.mni.14659/nu2.imp

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Number of iterations: 20 
CV of field change: 0.000991952
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.14659/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14659/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-6.0.0/0050345/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.14659/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14659/ones.mgz 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.14659/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.14659/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.14659/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14659/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.14659/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14659/input.mean.dat 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.14659/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.14659/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14659/ones.mgz --i ./tmp.mri_nu_correct.mni.14659/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14659/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.14659/ones.mgz --i ./tmp.mri_nu_correct.mni.14659/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14659/output.mean.dat 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.14659/ones.mgz
Loading ./tmp.mri_nu_correct.mni.14659/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.14659/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.14659/nu2.mnc ./tmp.mri_nu_correct.mni.14659/nu2.mnc mul 1.02255488163347241938
Saving result to './tmp.mri_nu_correct.mni.14659/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.14659/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.14659/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.14659/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (18, 93) to ( 3, 110)
 
 
Sat Oct  7 23:44:49 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 23:44:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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
 1.05031   0.07585  -0.07810  -140.59451;
-0.06794   1.06574  -0.51379  -101.39873;
 0.03199   0.04719   1.48772  -122.53253;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 16
Starting OpenSpline(): npoints = 16
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 67 (67), valley at 20 (20)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 68 (68), valley at  0 (-1)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 51 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 23:46:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=14.0
skull bounding box = (43, 55, 28) --> (207, 174, 227)
using (98, 95, 128) as brain centroid...
mean wm in atlas = 108, using box (78,80,103) --> (118, 109,152) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 103 +- 8.0
after smoothing, mri peak at 103, scaling input intensities by 1.049
scaling channel 0 by 1.04854
initial log_p = -4.544
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.577523 @ (0.000, 0.000, 0.000)
max log p =    -4.526499 @ (4.545, -4.545, -13.636)
max log p =    -4.463808 @ (-6.818, 2.273, -2.273)
max log p =    -4.458411 @ (1.136, 1.136, 1.136)
max log p =    -4.436737 @ (0.568, -0.568, -1.705)
max log p =    -4.436737 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, -1.7, -16.5): log p = -4.437
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.271, old_max_log_p =-4.437 (thresh=-4.4)
 1.06375   0.00000   0.00000  -8.56520;
 0.00000   1.19413   0.31997  -70.39882;
 0.00000  -0.27532   1.02750   19.63128;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.268, old_max_log_p =-4.271 (thresh=-4.3)
 1.14353   0.00000   0.00000  -18.57324;
 0.00000   1.28369   0.34396  -78.84180;
 0.00000  -0.29597   1.10457   12.78438;
 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=-4.209, old_max_log_p =-4.268 (thresh=-4.3)
 1.06562  -0.09444  -0.16307   24.93066;
 0.10495   1.22471   0.24111  -74.56784;
 0.14097  -0.19793   1.05314  -8.31406;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.201, old_max_log_p =-4.209 (thresh=-4.2)
 1.09259  -0.06035  -0.12373   11.86857;
 0.06645   1.25625   0.21456  -70.95566;
 0.10733  -0.15168   1.04526  -9.69922;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.194, old_max_log_p =-4.201 (thresh=-4.2)
 1.07210  -0.05921  -0.12141   13.98745;
 0.06993   1.25061   0.24864  -74.78819;
 0.10313  -0.18909   1.01822  -2.40651;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.189, old_max_log_p =-4.194 (thresh=-4.2)
 1.05800  -0.03276  -0.04502   2.46664;
 0.03872   1.26887   0.28879  -78.47544;
 0.03103  -0.22977   1.03436   12.25727;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.187, old_max_log_p =-4.189 (thresh=-4.2)
 1.05617  -0.07426  -0.05444   9.75164;
 0.07469   1.29088   0.29255  -86.57243;
 0.03044  -0.22546   1.01496   12.23225;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.170, old_max_log_p =-4.187 (thresh=-4.2)
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.170, old_max_log_p =-4.170 (thresh=-4.2)
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 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
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.170 (old=-4.544)
transform before final EM align:
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 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
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 013: -log(p) =    4.6  tol 0.000000
final transform:
 1.05427  -0.06353  -0.05192   8.62265;
 0.06607   1.29144   0.29298  -85.62514;
 0.03034  -0.22467   1.01140   12.57895;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1711.369832
mri_em_register stimesec    1.554763
mri_em_register ru_maxrss   609824
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157573
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    141
mri_em_register ru_nivcsw   2867
registration took 14 minutes and 43 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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=124 y=115 z=124 r=66
      first estimation of the main basin volume: 1236873 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        16 found in the rest of the brain 
      global maximum in x=144, y=103, z=92, 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=8715299568 voxels, voxel volume =1.000 
                     = 8715299568 mmm3 = 8715299.840 cm3
done.
PostAnalyze...Basin Prior
 64 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=124,y=121, z=118, r=9554 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 44251
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1104195937
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1123018513
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1124401098
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1052650644
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1077757228
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    3,      3,        31,   60
  after  analyzing :    3,      21,        31,   30
   RIGHT_CER   
  before analyzing :    3,      4,        39,   63
  after  analyzing :    3,      27,        39,   36
   LEFT_CER    
  before analyzing :    3,      5,        43,   60
  after  analyzing :    3,      30,        43,   37
  RIGHT_BRAIN  
  before analyzing :    3,      3,        31,   60
  after  analyzing :    3,      21,        31,   30
  LEFT_BRAIN   
  before analyzing :    4,      5,        31,   62
  after  analyzing :    4,      22,        31,   32
     OTHER     
  before analyzing :    3,      5,        66,   91
  after  analyzing :    3,      45,        66,   56
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...68 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 71.405, std = 8.248

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 6.73, sigma = 13.51
      after  rotation: sse = 6.73, sigma = 13.51
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  7.48, its var is 13.08   
      before Erosion-Dilatation  4.80% of inacurate vertices
      after  Erosion-Dilatation  6.31% 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...31 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1575213 voxels, voxel volume = 1.000 mm3
           = 1575213 mmm3 = 1575.213 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    23.064493
mri_watershed stimesec    0.417936
mri_watershed ru_maxrss   818280
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   211187
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  4128
mri_watershed ru_oublock  2456
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1681
mri_watershed ru_nivcsw   63
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct  8 00:01:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

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

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (59, 64, 41) --> (192, 173, 212)
using (103, 100, 127) as brain centroid...
mean wm in atlas = 107, using box (87,87,106) --> (119, 113,148) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 103 +- 5.6
after smoothing, mri peak at 103, scaling input intensities by 1.039
scaling channel 0 by 1.03883
initial log_p = -4.147
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.191320 @ (0.000, 0.000, 0.000)
max log p =    -4.012915 @ (-4.545, -4.545, -13.636)
max log p =    -3.954507 @ (2.273, 2.273, 2.273)
max log p =    -3.935739 @ (3.409, -1.136, -5.682)
max log p =    -3.918092 @ (-1.705, 1.705, 5.114)
max log p =    -3.918092 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, -1.7, -11.9): log p = -3.918
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.856, old_max_log_p =-3.918 (thresh=-3.9)
 1.00000   0.00000   0.00000  -0.56818;
 0.00000   1.11081   0.25882  -52.99171;
 0.00000  -0.27532   0.89348   33.88300;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.833, old_max_log_p =-3.856 (thresh=-3.9)
 0.98296  -0.10936  -0.14941   33.34872;
 0.12941   1.10600   0.24138  -66.77315;
 0.14032  -0.29344   0.95228   11.31111;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.833, old_max_log_p =-3.833 (thresh=-3.8)
 0.98296  -0.10936  -0.14941   33.34872;
 0.12941   1.10600   0.24138  -66.77315;
 0.14032  -0.29344   0.95228   11.31111;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.689, old_max_log_p =-3.833 (thresh=-3.8)
 1.01187  -0.04139  -0.10615   17.61273;
 0.06213   1.15492   0.25160  -63.54146;
 0.10938  -0.28248   0.91982   21.22229;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.677, old_max_log_p =-3.689 (thresh=-3.7)
 0.99447  -0.00383  -0.09506   13.76090;
 0.03253   1.14580   0.28488  -62.52947;
 0.10931  -0.32612   0.92817   25.78332;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.676, old_max_log_p =-3.677 (thresh=-3.7)
 1.01161  -0.04242  -0.10527   17.67460;
 0.06031   1.13345   0.24641  -60.00033;
 0.11238  -0.29387   0.95457   16.39762;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.646, old_max_log_p =-3.676 (thresh=-3.7)
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.646, old_max_log_p =-3.646 (thresh=-3.6)
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 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
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.646 (old=-4.147)
transform before final EM align:
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 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
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.1  tol 0.000000
final transform:
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1373.094257
mri_em_register stimesec    1.442780
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   159464
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    100
mri_em_register ru_nivcsw   2366
registration took 11 minutes and 44 seconds.
#--------------------------------------
#@# CA Normalize Sun Oct  8 00:13:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

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

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (59, 64, 41) --> (192, 173, 212)
using (103, 100, 127) as brain centroid...
mean wm in atlas = 107, using box (87,87,106) --> (119, 113,148) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 103 +- 5.6
after smoothing, mri peak at 103, scaling input intensities by 1.039
scaling channel 0 by 1.03883
using 246344 sample points...
INFO: compute sample coordinates transform
 1.01798  -0.03286  -0.07023   10.62279;
 0.04180   1.13746   0.23166  -56.45664;
 0.08000  -0.27310   0.95915   17.30078;
 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 (121, 69, 40) --> (191, 168, 206)
Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 1437 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 70, 41) --> (129, 167, 208)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 1055 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 148, 68) --> (175, 184, 123)
Left_Cerebellum_White_Matter: limiting intensities to 113.0 --> 132.0
0 of 10 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (83, 148, 69) --> (126, 183, 127)
Right_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0
1 of 18 (5.6%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 135, 106) --> (145, 196, 137)
Brain_Stem: limiting intensities to 110.0 --> 132.0
9 of 11 (81.8%) samples deleted
using 2531 total control points for intensity normalization...
bias field = 0.954 +- 0.055
25 of 2521 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (121, 69, 40) --> (191, 168, 206)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 2035 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 70, 41) --> (129, 167, 208)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 1729 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 148, 68) --> (175, 184, 123)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
17 of 43 (39.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (83, 148, 69) --> (126, 183, 127)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 40 (10.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 135, 106) --> (145, 196, 137)
Brain_Stem: limiting intensities to 88.0 --> 132.0
8 of 77 (10.4%) samples deleted
using 3924 total control points for intensity normalization...
bias field = 1.053 +- 0.066
13 of 3829 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (121, 69, 40) --> (191, 168, 206)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
37 of 2165 (1.7%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 70, 41) --> (129, 167, 208)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
11 of 1793 (0.6%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 148, 68) --> (175, 184, 123)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
17 of 52 (32.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (83, 148, 69) --> (126, 183, 127)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 45 (8.9%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 135, 106) --> (145, 196, 137)
Brain_Stem: limiting intensities to 88.0 --> 132.0
43 of 134 (32.1%) samples deleted
using 4189 total control points for intensity normalization...
bias field = 1.060 +- 0.064
3 of 4003 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 42 seconds.
#--------------------------------------
#@# CA Reg Sun Oct  8 00:15:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 

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

== Number of threads available to mri_ca_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.18 (predicted orig area = 6.8)
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=0.952, neg=0, invalid=762
0001: dt=281.841763, rms=0.893 (6.178%), neg=0, invalid=762
0002: dt=183.663866, rms=0.863 (3.338%), neg=0, invalid=762
0003: dt=265.879195, rms=0.839 (2.766%), neg=0, invalid=762
0004: dt=145.138983, rms=0.827 (1.467%), neg=0, invalid=762
0005: dt=517.888000, rms=0.807 (2.377%), neg=0, invalid=762
0006: dt=115.536105, rms=0.796 (1.372%), neg=0, invalid=762
0007: dt=517.888000, rms=0.781 (1.971%), neg=0, invalid=762
0008: dt=295.936000, rms=0.777 (0.454%), neg=0, invalid=762
0009: dt=155.306667, rms=0.773 (0.521%), neg=0, invalid=762
0010: dt=221.952000, rms=0.771 (0.249%), neg=0, invalid=762
0011: dt=221.952000, rms=0.768 (0.428%), neg=0, invalid=762
0012: dt=221.952000, rms=0.764 (0.528%), neg=0, invalid=762
0013: dt=221.952000, rms=0.761 (0.332%), neg=0, invalid=762
0014: dt=221.952000, rms=0.757 (0.563%), neg=0, invalid=762
0015: dt=221.952000, rms=0.754 (0.347%), neg=0, invalid=762
0016: dt=221.952000, rms=0.751 (0.405%), neg=0, invalid=762
0017: dt=221.952000, rms=0.749 (0.325%), neg=0, invalid=762
0018: dt=221.952000, rms=0.746 (0.354%), neg=0, invalid=762
0019: dt=221.952000, rms=0.744 (0.260%), neg=0, invalid=762
0020: dt=221.952000, rms=0.743 (0.168%), neg=0, invalid=762
0021: dt=221.952000, rms=0.741 (0.226%), neg=0, invalid=762
0022: dt=221.952000, rms=0.738 (0.454%), neg=0, invalid=762
0023: dt=221.952000, rms=0.737 (0.159%), neg=0, invalid=762
0024: dt=221.952000, rms=0.737 (-0.012%), neg=0, invalid=762
0025: dt=129.472000, rms=0.736 (0.071%), neg=0, invalid=762
0026: dt=221.952000, rms=0.736 (0.037%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.736, neg=0, invalid=762
0027: dt=141.575758, rms=0.733 (0.496%), neg=0, invalid=762
0028: dt=0.000000, rms=0.733 (-0.008%), neg=0, invalid=762
0029: dt=0.850000, rms=0.733 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.742, neg=0, invalid=762
0030: dt=9.072000, rms=0.741 (0.118%), neg=0, invalid=762
0031: dt=21.152542, rms=0.741 (0.088%), neg=0, invalid=762
0032: dt=21.152542, rms=0.738 (0.354%), neg=0, invalid=762
0033: dt=21.152542, rms=0.734 (0.588%), neg=0, invalid=762
0034: dt=21.152542, rms=0.729 (0.700%), neg=0, invalid=762
0035: dt=21.152542, rms=0.723 (0.762%), neg=0, invalid=762
0036: dt=21.152542, rms=0.718 (0.743%), neg=0, invalid=762
0037: dt=21.152542, rms=0.713 (0.668%), neg=0, invalid=762
0038: dt=21.152542, rms=0.708 (0.660%), neg=0, invalid=762
0039: dt=21.152542, rms=0.703 (0.676%), neg=0, invalid=762
0040: dt=21.152542, rms=0.699 (0.626%), neg=0, invalid=762
0041: dt=21.152542, rms=0.695 (0.521%), neg=0, invalid=762
0042: dt=21.152542, rms=0.693 (0.388%), neg=0, invalid=762
0043: dt=21.152542, rms=0.691 (0.288%), neg=0, invalid=762
0044: dt=21.152542, rms=0.689 (0.213%), neg=0, invalid=762
0045: dt=21.152542, rms=0.688 (0.235%), neg=0, invalid=762
0046: dt=21.152542, rms=0.685 (0.371%), neg=0, invalid=762
0047: dt=21.152542, rms=0.682 (0.435%), neg=0, invalid=762
0048: dt=21.152542, rms=0.680 (0.228%), neg=0, invalid=762
0049: dt=21.152542, rms=0.680 (0.035%), neg=0, invalid=762
0050: dt=21.152542, rms=0.680 (-0.085%), neg=0, invalid=762
0051: dt=0.486000, rms=0.680 (0.000%), neg=0, invalid=762
0052: dt=0.141750, rms=0.680 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.681, neg=0, invalid=762
0053: dt=25.920000, rms=0.680 (0.153%), neg=0, invalid=762
0054: dt=98.064516, rms=0.678 (0.275%), neg=0, invalid=762
0055: dt=62.208000, rms=0.676 (0.298%), neg=0, invalid=762
0056: dt=0.000000, rms=0.676 (-0.000%), neg=0, invalid=762
0057: dt=0.450000, rms=0.676 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.709, neg=0, invalid=762
0058: dt=2.800000, rms=0.708 (0.116%), neg=0, invalid=762
0059: dt=2.000000, rms=0.708 (0.019%), neg=0, invalid=762
0060: dt=2.000000, rms=0.708 (0.009%), neg=0, invalid=762
0061: dt=2.000000, rms=0.708 (-0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.708, neg=0, invalid=762
0062: dt=0.175000, rms=0.708 (0.096%), neg=0, invalid=762
0063: dt=0.175000, rms=0.708 (0.000%), neg=0, invalid=762
0064: dt=0.175000, rms=0.708 (0.000%), neg=0, invalid=762
0065: dt=0.175000, rms=0.708 (0.001%), neg=0, invalid=762
0066: dt=0.175000, rms=0.708 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.797, neg=0, invalid=762
0067: dt=5.455782, rms=0.779 (2.175%), neg=0, invalid=762
0068: dt=4.032000, rms=0.775 (0.535%), neg=0, invalid=762
0069: dt=0.000000, rms=0.775 (0.002%), neg=0, invalid=762
0070: dt=0.150000, rms=0.775 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.776, neg=0, invalid=762
0071: dt=0.000000, rms=0.775 (0.072%), neg=0, invalid=762
0072: dt=0.000000, rms=0.775 (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=0.880, neg=0, invalid=762
0073: dt=0.448000, rms=0.878 (0.164%), neg=0, invalid=762
0074: dt=1.280000, rms=0.876 (0.205%), neg=0, invalid=762
0075: dt=1.792000, rms=0.870 (0.679%), neg=0, invalid=762
0076: dt=1.280000, rms=0.870 (0.069%), neg=0, invalid=762
0077: dt=1.280000, rms=0.867 (0.324%), neg=0, invalid=762
0078: dt=1.280000, rms=0.865 (0.217%), neg=0, invalid=762
0079: dt=1.280000, rms=0.865 (0.047%), neg=0, invalid=762
0080: dt=1.280000, rms=0.865 (0.006%), neg=0, invalid=762
0081: dt=3.225806, rms=0.860 (0.534%), neg=0, invalid=762
0082: dt=0.448000, rms=0.860 (0.046%), neg=0, invalid=762
0083: dt=0.448000, rms=0.859 (0.040%), neg=0, invalid=762
0084: dt=0.448000, rms=0.859 (0.056%), neg=0, invalid=762
0085: dt=0.448000, rms=0.858 (0.070%), neg=0, invalid=762
0086: dt=0.448000, rms=0.857 (0.111%), neg=0, invalid=762
0087: dt=0.448000, rms=0.856 (0.145%), neg=0, invalid=762
0088: dt=0.448000, rms=0.855 (0.140%), neg=0, invalid=762
0089: dt=0.448000, rms=0.854 (0.112%), neg=0, invalid=762
0090: dt=0.448000, rms=0.853 (0.082%), neg=0, invalid=762
0091: dt=-0.000916, rms=0.853 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.854, neg=0, invalid=762
0092: dt=1.280000, rms=0.852 (0.159%), neg=0, invalid=762
0093: dt=-0.000793, rms=0.852 (0.001%), neg=0, invalid=762
0094: dt=-0.000793, rms=0.852 (0.000%), neg=0, invalid=762
0095: dt=-0.000793, rms=0.852 (0.000%), neg=0, invalid=762
0096: dt=-0.000793, rms=0.852 (0.000%), neg=0, invalid=762
0097: dt=-0.000793, rms=0.852 (0.000%), neg=0, invalid=762
0098: dt=-0.000793, rms=0.852 (0.000%), 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=0.799, neg=0, invalid=762
0099: dt=0.995816, rms=0.775 (3.093%), neg=0, invalid=762
0100: dt=0.096000, rms=0.773 (0.171%), neg=0, invalid=762
0101: dt=0.096000, rms=0.773 (-0.067%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.774, neg=0, invalid=762
0102: dt=0.028000, rms=0.773 (0.080%), neg=0, invalid=762
0103: dt=0.024000, rms=0.773 (0.006%), neg=0, invalid=762
0104: dt=0.024000, rms=0.773 (-0.007%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.10974 (16)
Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (804 voxels, overlap=0.416)
Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (804 voxels, peak = 12), gca=12.1
gca peak = 0.15565 (16)
mri peak = 0.11666 (16)
Right_Lateral_Ventricle (43): linear fit = 0.74 x + 0.0 (912 voxels, overlap=0.665)
Right_Lateral_Ventricle (43): linear fit = 0.74 x + 0.0 (912 voxels, peak = 12), gca=11.8
gca peak = 0.26829 (96)
mri peak = 0.08993 (93)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (916 voxels, overlap=0.984)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (916 voxels, peak = 92), gca=91.7
gca peak = 0.20183 (93)
mri peak = 0.07661 (93)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (828 voxels, overlap=0.944)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (828 voxels, peak = 89), gca=88.8
gca peak = 0.21683 (55)
mri peak = 0.08039 (61)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (786 voxels, overlap=0.998)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (786 voxels, peak = 56), gca=56.4
gca peak = 0.30730 (58)
mri peak = 0.07195 (61)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (830 voxels, overlap=1.002)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (830 voxels, peak = 61), gca=60.6
gca peak = 0.11430 (101)
mri peak = 0.07295 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (59742 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (59742 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.08109 (101)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63208 voxels, overlap=0.943)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63208 voxels, peak = 103), gca=102.5
gca peak = 0.14995 (59)
mri peak = 0.02983 (60)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24332 voxels, overlap=0.973)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24332 voxels, peak = 60), gca=60.5
gca peak = 0.15082 (58)
mri peak = 0.03174 (65)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22938 voxels, overlap=0.919)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22938 voxels, peak = 64), gca=63.5
gca peak = 0.14161 (67)
mri peak = 0.06522 (72)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (789 voxels, overlap=0.774)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (789 voxels, peak = 71), gca=71.4
gca peak = 0.15243 (71)
mri peak = 0.06616 (76)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (962 voxels, overlap=0.973)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (962 voxels, peak = 73), gca=73.5
gca peak = 0.13336 (57)
mri peak = 0.05097 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (9014 voxels, overlap=0.903)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (9014 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.05603 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (9922 voxels, overlap=0.758)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (9922 voxels, peak = 62), gca=62.4
gca peak = 0.18181 (84)
mri peak = 0.03664 (67)
Left_Cerebellum_White_Matter (7): linear fit = 0.81 x + 0.0 (4329 voxels, overlap=0.262)
Left_Cerebellum_White_Matter (7): linear fit = 0.81 x + 0.0 (4329 voxels, peak = 68), gca=67.6
gca peak = 0.20573 (83)
mri peak = 0.05014 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3301 voxels, overlap=0.600)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3301 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.10268 (63)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (425 voxels, overlap=0.703)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (425 voxels, peak = 62), gca=62.4
gca peak = 0.39313 (56)
mri peak = 0.09153 (64)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (323 voxels, overlap=0.432)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (323 voxels, peak = 63), gca=63.0
gca peak = 0.14181 (85)
mri peak = 0.05897 (80)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5555 voxels, overlap=0.969)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5555 voxels, peak = 81), gca=81.2
gca peak = 0.11978 (83)
mri peak = 0.09034 (78)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4422 voxels, overlap=0.870)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4422 voxels, peak = 79), gca=79.3
gca peak = 0.13399 (79)
mri peak = 0.04956 (79)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2499 voxels, overlap=0.973)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2499 voxels, peak = 78), gca=77.8
gca peak = 0.14159 (79)
mri peak = 0.06654 (77)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (2514 voxels, overlap=0.962)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (2514 voxels, peak = 76), gca=76.2
gca peak = 0.10025 (80)
mri peak = 0.07449 (85)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8310 voxels, overlap=0.403)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8310 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.07030 (95)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1297 voxels, overlap=0.646)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1297 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.06671 (94)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1734 voxels, overlap=0.671)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1734 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.06920 (49)
Fourth_Ventricle (15): linear fit = 2.54 x + 0.0 (137 voxels, overlap=0.021)
Fourth_Ventricle (15): linear fit = 2.54 x + 0.0 (137 voxels, peak = 53), gca=53.2
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.07 x + 0.0
estimating mean wm scale to be 1.01 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=0.770, neg=0, invalid=762
0105: dt=230.446886, rms=0.739 (4.083%), neg=0, invalid=762
0106: dt=129.472000, rms=0.732 (0.943%), neg=0, invalid=762
0107: dt=43.428571, rms=0.730 (0.224%), neg=0, invalid=762
0108: dt=8.092000, rms=0.730 (0.036%), neg=0, invalid=762
0109: dt=8.092000, rms=0.729 (0.035%), neg=0, invalid=762
0110: dt=4.046000, rms=0.729 (0.018%), neg=0, invalid=762
0111: dt=2.023000, rms=0.729 (0.009%), neg=0, invalid=762
0112: dt=0.505750, rms=0.729 (0.002%), neg=0, invalid=762
0113: dt=0.252875, rms=0.729 (0.001%), neg=0, invalid=762
0114: dt=0.063219, rms=0.729 (0.000%), neg=0, invalid=762
0115: dt=0.000988, rms=0.729 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.730, neg=0, invalid=762
0116: dt=0.000000, rms=0.729 (0.094%), neg=0, invalid=762
0117: dt=0.000000, rms=0.729 (0.000%), neg=0, invalid=762
0118: dt=0.000830, rms=0.729 (0.000%), neg=0, invalid=762
0119: dt=0.000415, rms=0.729 (0.000%), neg=0, invalid=762
0120: dt=0.000208, rms=0.729 (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=0.730, neg=0, invalid=762
0121: dt=0.000000, rms=0.729 (0.094%), neg=0, invalid=762
0122: dt=0.000000, rms=0.729 (0.000%), neg=0, invalid=762
0123: dt=0.000003, rms=0.729 (0.000%), neg=0, invalid=762
0124: dt=0.000000, rms=0.729 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.730, neg=0, invalid=762
0125: dt=0.000000, rms=0.729 (0.094%), neg=0, invalid=762
0126: dt=0.000000, rms=0.729 (0.000%), neg=0, invalid=762
0127: dt=0.000001, rms=0.729 (0.000%), neg=0, invalid=762
0128: dt=0.000000, rms=0.729 (-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=0.730, neg=0, invalid=762
0129: dt=2.800000, rms=0.724 (0.859%), neg=0, invalid=762
0130: dt=2.800000, rms=0.719 (0.728%), neg=0, invalid=762
0131: dt=2.800000, rms=0.714 (0.692%), neg=0, invalid=762
0132: dt=0.700000, rms=0.713 (0.166%), neg=0, invalid=762
0133: dt=0.700000, rms=0.711 (0.164%), neg=0, invalid=762
0134: dt=0.010937, rms=0.711 (0.004%), neg=0, invalid=762
0135: dt=0.010937, rms=0.711 (0.003%), neg=0, invalid=762
0136: dt=0.005469, rms=0.711 (0.001%), neg=0, invalid=762
0137: dt=0.001367, rms=0.711 (0.000%), neg=0, invalid=762
0138: dt=0.000684, rms=0.711 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.712, neg=0, invalid=762
0139: dt=0.000000, rms=0.711 (0.087%), neg=0, invalid=762
0140: dt=0.000000, rms=0.711 (0.000%), neg=0, invalid=762
0141: dt=0.000244, rms=0.711 (0.000%), neg=0, invalid=762
0142: dt=0.000031, rms=0.711 (0.000%), neg=0, invalid=762
0143: dt=0.000015, rms=0.711 (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=0.713, neg=0, invalid=762
0144: dt=4.032000, rms=0.689 (3.369%), neg=0, invalid=762
0145: dt=1.008000, rms=0.685 (0.679%), neg=0, invalid=762
0146: dt=1.008000, rms=0.680 (0.657%), neg=0, invalid=762
0147: dt=0.252000, rms=0.679 (0.160%), neg=0, invalid=762
0148: dt=0.063000, rms=0.679 (0.040%), neg=0, invalid=762
0149: dt=0.063000, rms=0.679 (0.039%), neg=0, invalid=762
0150: dt=0.031500, rms=0.678 (0.019%), neg=0, invalid=762
0151: dt=0.007875, rms=0.678 (0.005%), neg=0, invalid=762
0152: dt=0.003938, rms=0.678 (0.003%), neg=0, invalid=762
0153: dt=0.000984, rms=0.678 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.679, neg=0, invalid=762
0154: dt=4.032000, rms=0.665 (2.031%), neg=0, invalid=762
0155: dt=4.032000, rms=0.655 (1.564%), neg=0, invalid=762
0156: dt=4.032000, rms=0.647 (1.242%), neg=0, invalid=762
0157: dt=4.032000, rms=0.640 (1.010%), neg=0, invalid=762
0158: dt=4.032000, rms=0.635 (0.833%), neg=0, invalid=762
0159: dt=2.880000, rms=0.632 (0.497%), neg=0, invalid=762
0160: dt=0.252000, rms=0.631 (0.041%), neg=0, invalid=762
0161: dt=0.252000, rms=0.631 (0.039%), neg=0, invalid=762
0162: dt=0.063000, rms=0.631 (0.010%), neg=0, invalid=762
0163: dt=0.015750, rms=0.631 (0.002%), neg=0, invalid=762
0164: dt=0.011250, rms=0.631 (0.002%), neg=0, invalid=762
0165: dt=0.000703, rms=0.631 (0.000%), neg=0, invalid=762
0166: dt=0.000088, rms=0.631 (0.000%), neg=0, invalid=762
0167: dt=0.000022, rms=0.631 (0.000%), neg=0, invalid=762
0168: dt=0.000001, rms=0.631 (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=0.642, neg=0, invalid=762
0169: dt=0.000000, rms=0.641 (0.091%), neg=0, invalid=762
0170: dt=0.000000, rms=0.641 (0.000%), neg=0, invalid=762
0171: dt=0.100000, rms=0.641 (-0.046%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.642, neg=0, invalid=762
0172: dt=0.000000, rms=0.641 (0.091%), neg=0, invalid=762
0173: dt=0.000000, rms=0.641 (0.000%), neg=0, invalid=762
0174: dt=0.100000, rms=0.641 (-0.030%), 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=0.625, neg=0, invalid=762
0175: dt=0.448000, rms=0.607 (2.864%), neg=0, invalid=762
0176: dt=0.448000, rms=0.601 (0.876%), neg=0, invalid=762
0177: dt=0.448000, rms=0.598 (0.510%), neg=0, invalid=762
0178: dt=0.448000, rms=0.597 (0.299%), neg=0, invalid=762
0179: dt=0.448000, rms=0.595 (0.237%), neg=0, invalid=762
0180: dt=0.448000, rms=0.594 (0.156%), neg=0, invalid=762
0181: dt=0.448000, rms=0.593 (0.149%), neg=0, invalid=762
0182: dt=0.448000, rms=0.593 (0.098%), neg=0, invalid=762
0183: dt=0.448000, rms=0.592 (0.107%), neg=0, invalid=762
0184: dt=0.384000, rms=0.592 (0.067%), neg=0, invalid=762
0185: dt=0.384000, rms=0.591 (0.081%), neg=0, invalid=762
0186: dt=0.384000, rms=0.591 (0.055%), neg=0, invalid=762
0187: dt=0.384000, rms=0.591 (0.058%), neg=0, invalid=762
0188: dt=0.320000, rms=0.590 (0.039%), neg=0, invalid=762
0189: dt=0.320000, rms=0.590 (0.056%), neg=0, invalid=762
0190: dt=0.320000, rms=0.590 (0.083%), neg=0, invalid=762
0191: dt=0.320000, rms=0.589 (0.094%), neg=0, invalid=762
0192: dt=0.320000, rms=0.588 (0.117%), neg=0, invalid=762
0193: dt=0.320000, rms=0.588 (0.120%), neg=0, invalid=762
0194: dt=0.320000, rms=0.587 (0.103%), neg=0, invalid=762
0195: dt=0.160000, rms=0.587 (0.005%), neg=0, invalid=762
0196: dt=0.160000, rms=0.587 (0.008%), neg=0, invalid=762
0197: dt=0.160000, rms=0.587 (0.009%), neg=0, invalid=762
0198: dt=0.160000, rms=0.587 (0.010%), neg=0, invalid=762
0199: dt=0.160000, rms=0.587 (0.012%), neg=0, invalid=762
0200: dt=0.160000, rms=0.587 (0.016%), neg=0, invalid=762
0201: dt=0.160000, rms=0.587 (0.017%), neg=0, invalid=762
0202: dt=0.160000, rms=0.586 (0.019%), neg=0, invalid=762
0203: dt=0.160000, rms=0.586 (0.021%), neg=0, invalid=762
0204: dt=0.160000, rms=0.586 (0.024%), neg=0, invalid=762
0205: dt=0.160000, rms=0.586 (0.021%), neg=0, invalid=762
0206: dt=0.112000, rms=0.586 (0.004%), neg=0, invalid=762
0207: dt=0.112000, rms=0.586 (0.004%), neg=0, invalid=762
0208: dt=0.112000, rms=0.586 (0.003%), neg=0, invalid=762
0209: dt=0.112000, rms=0.586 (0.006%), neg=0, invalid=762
0210: dt=0.112000, rms=0.586 (0.008%), neg=0, invalid=762
0211: dt=0.112000, rms=0.586 (0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.587, neg=0, invalid=762
0212: dt=0.384000, rms=0.580 (1.068%), neg=0, invalid=762
0213: dt=0.448000, rms=0.579 (0.274%), neg=0, invalid=762
0214: dt=0.448000, rms=0.578 (0.061%), neg=0, invalid=762
0215: dt=0.112000, rms=0.578 (0.007%), neg=0, invalid=762
0216: dt=0.112000, rms=0.578 (0.007%), neg=0, invalid=762
0217: dt=0.112000, rms=0.578 (0.003%), neg=0, invalid=762
0218: dt=0.112000, rms=0.578 (0.003%), neg=0, invalid=762
0219: dt=0.112000, rms=0.578 (0.004%), neg=0, invalid=762
0220: dt=0.112000, rms=0.578 (-0.002%), 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=0.575, neg=0, invalid=762
0221: dt=8.092000, rms=0.575 (0.117%), neg=0, invalid=762
0222: dt=8.092000, rms=0.575 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.575, neg=0, invalid=762
0223: dt=129.472000, rms=0.574 (0.252%), neg=0, invalid=762
0224: dt=221.952000, rms=0.573 (0.129%), neg=0, invalid=762
0225: dt=221.952000, rms=0.573 (-0.515%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.574, neg=0, invalid=762
0226: dt=36.288000, rms=0.572 (0.397%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 7 iterations, nbhd size=1, neg = 0
0227: dt=80.271186, rms=0.570 (0.229%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 9 iterations, nbhd size=1, neg = 0
0228: dt=80.271186, rms=0.569 (0.159%), neg=0, invalid=762
iter 0, gcam->neg = 79
after 11 iterations, nbhd size=1, neg = 0
0229: dt=80.271186, rms=0.569 (-0.057%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 4 iterations, nbhd size=0, neg = 0
0230: dt=25.920000, rms=0.569 (0.034%), neg=0, invalid=762
iter 0, gcam->neg = 19
after 9 iterations, nbhd size=1, neg = 0
0231: dt=36.288000, rms=0.569 (0.028%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.570, neg=0, invalid=762
0232: dt=69.284404, rms=0.566 (0.568%), neg=0, invalid=762
0233: dt=124.416000, rms=0.565 (0.291%), neg=0, invalid=762
0234: dt=36.288000, rms=0.564 (0.120%), neg=0, invalid=762
0235: dt=36.288000, rms=0.564 (0.045%), neg=0, invalid=762
0236: dt=36.288000, rms=0.563 (0.077%), neg=0, invalid=762
0237: dt=36.288000, rms=0.563 (0.110%), neg=0, invalid=762
0238: dt=36.288000, rms=0.562 (0.128%), neg=0, invalid=762
0239: dt=36.288000, rms=0.561 (0.128%), neg=0, invalid=762
0240: dt=36.288000, rms=0.561 (0.125%), neg=0, invalid=762
0241: dt=36.288000, rms=0.560 (0.114%), neg=0, invalid=762
0242: dt=36.288000, rms=0.559 (0.113%), neg=0, invalid=762
0243: dt=414.720000, rms=0.559 (0.116%), neg=0, invalid=762
0244: dt=36.288000, rms=0.559 (0.036%), neg=0, invalid=762
0245: dt=36.288000, rms=0.558 (0.023%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0246: dt=36.288000, rms=0.558 (0.030%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0247: dt=36.288000, rms=0.558 (0.037%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 9 iterations, nbhd size=1, neg = 0
0248: dt=36.288000, rms=0.558 (0.053%), neg=0, invalid=762
0249: dt=36.288000, rms=0.557 (0.059%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0250: dt=36.288000, rms=0.557 (0.051%), neg=0, invalid=762
0251: dt=36.288000, rms=0.557 (0.042%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.559, neg=0, invalid=762
iter 0, gcam->neg = 72
after 12 iterations, nbhd size=1, neg = 0
0252: dt=25.600000, rms=0.555 (0.572%), neg=0, invalid=762
iter 0, gcam->neg = 66
after 12 iterations, nbhd size=1, neg = 0
0253: dt=66.153846, rms=0.553 (0.503%), neg=0, invalid=762
iter 0, gcam->neg = 99
after 15 iterations, nbhd size=1, neg = 0
0254: dt=32.000000, rms=0.551 (0.336%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0255: dt=11.200000, rms=0.550 (0.157%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 9 iterations, nbhd size=1, neg = 0
0256: dt=11.200000, rms=0.549 (0.126%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 1 iterations, nbhd size=0, neg = 0
0257: dt=11.200000, rms=0.548 (0.202%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 8 iterations, nbhd size=1, neg = 0
0258: dt=11.200000, rms=0.547 (0.242%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0259: dt=11.200000, rms=0.545 (0.256%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 2 iterations, nbhd size=0, neg = 0
0260: dt=11.200000, rms=0.544 (0.244%), neg=0, invalid=762
iter 0, gcam->neg = 17
after 11 iterations, nbhd size=1, neg = 0
0261: dt=11.200000, rms=0.543 (0.221%), neg=0, invalid=762
iter 0, gcam->neg = 22
after 10 iterations, nbhd size=1, neg = 0
0262: dt=11.200000, rms=0.542 (0.207%), neg=0, invalid=762
iter 0, gcam->neg = 31
after 8 iterations, nbhd size=1, neg = 0
0263: dt=11.200000, rms=0.541 (0.180%), neg=0, invalid=762
iter 0, gcam->neg = 47
after 12 iterations, nbhd size=1, neg = 0
0264: dt=11.200000, rms=0.540 (0.129%), neg=0, invalid=762
iter 0, gcam->neg = 44
after 11 iterations, nbhd size=1, neg = 0
0265: dt=11.200000, rms=0.539 (0.148%), neg=0, invalid=762
iter 0, gcam->neg = 37
after 12 iterations, nbhd size=1, neg = 0
0266: dt=11.200000, rms=0.538 (0.206%), neg=0, invalid=762
iter 0, gcam->neg = 34
after 13 iterations, nbhd size=1, neg = 0
0267: dt=11.200000, rms=0.537 (0.171%), neg=0, invalid=762
iter 0, gcam->neg = 56
after 16 iterations, nbhd size=1, neg = 0
0268: dt=11.200000, rms=0.537 (0.061%), neg=0, invalid=762
iter 0, gcam->neg = 43
after 18 iterations, nbhd size=1, neg = 0
0269: dt=11.200000, rms=0.537 (0.037%), neg=0, invalid=762
iter 0, gcam->neg = 51
after 14 iterations, nbhd size=1, neg = 0
0270: dt=32.000000, rms=0.536 (0.175%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 6 iterations, nbhd size=1, neg = 0
0271: dt=6.400000, rms=0.536 (0.011%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0272: dt=6.400000, rms=0.536 (0.029%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0273: dt=6.400000, rms=0.535 (0.049%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 8 iterations, nbhd size=1, neg = 0
0274: dt=6.400000, rms=0.535 (0.045%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 1 iterations, nbhd size=0, neg = 0
0275: dt=6.400000, rms=0.535 (0.042%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.536, neg=0, invalid=762
iter 0, gcam->neg = 12
after 5 iterations, nbhd size=0, neg = 0
0276: dt=44.800000, rms=0.532 (0.734%), neg=0, invalid=762
iter 0, gcam->neg = 71
after 23 iterations, nbhd size=1, neg = 0
0277: dt=25.600000, rms=0.530 (0.384%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0278: dt=11.200000, rms=0.529 (0.067%), neg=0, invalid=762
0279: dt=11.200000, rms=0.529 (0.067%), neg=0, invalid=762
0280: dt=11.200000, rms=0.528 (0.117%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0281: dt=11.200000, rms=0.528 (0.135%), neg=0, invalid=762
0282: dt=11.200000, rms=0.527 (0.093%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0283: dt=11.200000, rms=0.527 (0.073%), neg=0, invalid=762
iter 0, gcam->neg = 137
after 22 iterations, nbhd size=1, neg = 0
0284: dt=44.800000, rms=0.525 (0.252%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0285: dt=6.400000, rms=0.525 (0.012%), neg=0, invalid=762
0286: dt=6.400000, rms=0.525 (0.010%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0287: dt=6.400000, rms=0.525 (0.014%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 8 iterations, nbhd size=1, neg = 0
0288: dt=6.400000, rms=0.525 (0.012%), neg=0, invalid=762
0289: dt=6.400000, rms=0.525 (0.034%), neg=0, invalid=762
0290: dt=6.400000, rms=0.525 (0.053%), neg=0, invalid=762
0291: dt=6.400000, rms=0.524 (0.035%), neg=0, invalid=762
0292: dt=8.000000, rms=0.524 (0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.536, neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0293: dt=2.545455, rms=0.536 (0.168%), neg=0, invalid=762
0294: dt=0.576000, rms=0.536 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.536, neg=0, invalid=762
0295: dt=2.571429, rms=0.535 (0.162%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 3 iterations, nbhd size=0, neg = 0
0296: dt=3.456000, rms=0.535 (0.047%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0297: dt=3.456000, rms=0.535 (0.032%), neg=0, invalid=762
0298: dt=3.456000, rms=0.535 (-0.021%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.552, neg=0, invalid=762
0299: dt=0.448000, rms=0.551 (0.158%), neg=0, invalid=762
0300: dt=0.448000, rms=0.551 (0.014%), neg=0, invalid=762
0301: dt=0.448000, rms=0.551 (-0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.552, neg=0, invalid=762
iter 0, gcam->neg = 23
after 1 iterations, nbhd size=0, neg = 0
0302: dt=1.792000, rms=0.550 (0.404%), neg=0, invalid=762
iter 0, gcam->neg = 19
after 2 iterations, nbhd size=0, neg = 0
0303: dt=1.536000, rms=0.549 (0.104%), neg=0, invalid=762
iter 0, gcam->neg = 19
after 8 iterations, nbhd size=1, neg = 0
0304: dt=1.536000, rms=0.549 (0.029%), neg=0, invalid=762
iter 0, gcam->neg = 20
after 1 iterations, nbhd size=0, neg = 0
0305: dt=1.536000, rms=0.549 (-0.067%), 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=0.535, neg=0, invalid=762
iter 0, gcam->neg = 2567
after 16 iterations, nbhd size=1, neg = 0
0306: dt=1.878408, rms=0.498 (6.908%), neg=0, invalid=762
0307: dt=0.000013, rms=0.498 (0.008%), neg=0, invalid=762
0308: dt=0.000013, rms=0.498 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.499, neg=0, invalid=762
0309: dt=0.064000, rms=0.498 (0.203%), neg=0, invalid=762
0310: dt=0.000000, rms=0.498 (-0.002%), 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=0.484, neg=0, invalid=762
0311: dt=0.000000, rms=0.484 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
0312: dt=32.368000, rms=0.483 (0.006%), neg=0, invalid=762
0313: dt=23.120000, rms=0.483 (0.001%), neg=0, invalid=762
0314: dt=23.120000, rms=0.483 (-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=0.484, neg=0, invalid=762
0315: dt=9.072000, rms=0.484 (0.010%), neg=0, invalid=762
0316: dt=4.666667, rms=0.484 (0.002%), neg=0, invalid=762
0317: dt=4.666667, rms=0.484 (0.001%), neg=0, invalid=762
0318: dt=4.666667, rms=0.484 (-0.006%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0319: dt=82.944000, rms=0.483 (0.143%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 10 iterations, nbhd size=1, neg = 0
0320: dt=82.944000, rms=0.483 (0.081%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 10 iterations, nbhd size=1, neg = 0
0321: dt=82.944000, rms=0.482 (0.184%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 8 iterations, nbhd size=1, neg = 0
0322: dt=82.944000, rms=0.481 (0.174%), neg=0, invalid=762
iter 0, gcam->neg = 28
after 9 iterations, nbhd size=1, neg = 0
0323: dt=82.944000, rms=0.480 (0.082%), neg=0, invalid=762
iter 0, gcam->neg = 53
after 12 iterations, nbhd size=1, neg = 0
0324: dt=82.944000, rms=0.480 (0.036%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0325: dt=36.288000, rms=0.480 (0.018%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0326: dt=36.288000, rms=0.480 (0.017%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 9 iterations, nbhd size=1, neg = 0
0327: dt=36.288000, rms=0.480 (0.026%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 1 iterations, nbhd size=0, neg = 0
0328: dt=36.288000, rms=0.480 (0.028%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 9 iterations, nbhd size=1, neg = 0
0329: dt=36.288000, rms=0.480 (0.026%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 9 iterations, nbhd size=1, neg = 0
0330: dt=36.288000, rms=0.480 (0.022%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.480, neg=0, invalid=762
iter 0, gcam->neg = 15
after 12 iterations, nbhd size=1, neg = 0
0331: dt=11.200000, rms=0.480 (0.132%), neg=0, invalid=762
iter 0, gcam->neg = 66
after 11 iterations, nbhd size=1, neg = 0
0332: dt=23.418994, rms=0.479 (0.080%), neg=0, invalid=762
iter 0, gcam->neg = 58
after 13 iterations, nbhd size=1, neg = 0
0333: dt=23.418994, rms=0.479 (0.035%), neg=0, invalid=762
iter 0, gcam->neg = 140
after 12 iterations, nbhd size=1, neg = 0
0334: dt=23.418994, rms=0.479 (-0.105%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
iter 0, gcam->neg = 44
after 10 iterations, nbhd size=1, neg = 0
0335: dt=44.800000, rms=0.475 (0.869%), neg=0, invalid=762
iter 0, gcam->neg = 23
after 12 iterations, nbhd size=1, neg = 0
0336: dt=38.400000, rms=0.473 (0.441%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0337: dt=11.200000, rms=0.473 (0.062%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0338: dt=11.200000, rms=0.472 (0.089%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 3 iterations, nbhd size=0, neg = 0
0339: dt=11.200000, rms=0.472 (0.122%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 8 iterations, nbhd size=1, neg = 0
0340: dt=11.200000, rms=0.471 (0.123%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 4 iterations, nbhd size=0, neg = 0
0341: dt=11.200000, rms=0.470 (0.142%), neg=0, invalid=762
iter 0, gcam->neg = 25
after 10 iterations, nbhd size=1, neg = 0
0342: dt=11.200000, rms=0.470 (0.169%), neg=0, invalid=762
iter 0, gcam->neg = 50
after 12 iterations, nbhd size=1, neg = 0
0343: dt=11.200000, rms=0.469 (0.170%), neg=0, invalid=762
iter 0, gcam->neg = 27
after 11 iterations, nbhd size=0, neg = 0
0344: dt=11.200000, rms=0.468 (0.160%), neg=0, invalid=762
iter 0, gcam->neg = 35
after 13 iterations, nbhd size=1, neg = 0
0345: dt=11.200000, rms=0.467 (0.125%), neg=0, invalid=762
iter 0, gcam->neg = 28
after 17 iterations, nbhd size=1, neg = 0
0346: dt=11.200000, rms=0.467 (0.088%), neg=0, invalid=762
iter 0, gcam->neg = 26
after 17 iterations, nbhd size=1, neg = 0
0347: dt=11.200000, rms=0.467 (0.017%), neg=0, invalid=762
0348: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0349: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0350: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0351: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0352: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0353: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0354: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0355: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0356: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0357: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0358: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0359: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0360: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0361: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0362: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0363: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0364: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0365: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0366: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0367: dt=-0.003472, rms=0.467 (0.000%), neg=0, invalid=762
0368: dt=-0.003472, rms=0.467 (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=0.472, neg=0, invalid=762
iter 0, gcam->neg = 30
after 11 iterations, nbhd size=0, neg = 0
0369: dt=4.666667, rms=0.472 (0.117%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 4 iterations, nbhd size=0, neg = 0
0370: dt=2.000000, rms=0.472 (0.005%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 0 iterations, nbhd size=0, neg = 0
0371: dt=2.000000, rms=0.472 (-0.018%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
iter 0, gcam->neg = 39
after 21 iterations, nbhd size=1, neg = 0
0372: dt=6.666667, rms=0.471 (0.071%), neg=0, invalid=762
iter 0, gcam->neg = 272
after 17 iterations, nbhd size=1, neg = 0
0373: dt=10.494624, rms=0.469 (0.405%), neg=0, invalid=762
iter 0, gcam->neg = 25
after 4 iterations, nbhd size=0, neg = 0
0374: dt=3.333333, rms=0.469 (0.027%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 4 iterations, nbhd size=0, neg = 0
0375: dt=3.333333, rms=0.469 (0.046%), neg=0, invalid=762
iter 0, gcam->neg = 16
after 3 iterations, nbhd size=0, neg = 0
0376: dt=3.333333, rms=0.469 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0377: dt=0.000050, rms=0.477 (0.000%), neg=0, invalid=762
0378: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0379: dt=0.000000, rms=0.477 (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=0.463, neg=0, invalid=762
iter 0, gcam->neg = 1233
after 18 iterations, nbhd size=1, neg = 0
0380: dt=0.896819, rms=0.453 (2.359%), neg=0, invalid=762
0381: dt=0.005000, rms=0.453 (0.000%), neg=0, invalid=762
0382: dt=0.005000, rms=0.453 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.453, neg=0, invalid=762
iter 0, gcam->neg = 26
after 3 iterations, nbhd size=0, neg = 0
0383: dt=0.256000, rms=0.451 (0.291%), neg=0, invalid=762
iter 0, gcam->neg = 123
after 3 iterations, nbhd size=0, neg = 0
0384: dt=0.384000, rms=0.450 (0.357%), neg=0, invalid=762
iter 0, gcam->neg = 94
after 2 iterations, nbhd size=0, neg = 0
0385: dt=0.384000, rms=0.449 (0.201%), neg=0, invalid=762
iter 0, gcam->neg = 78
after 2 iterations, nbhd size=0, neg = 0
0386: dt=0.384000, rms=0.449 (0.047%), neg=0, invalid=762
iter 0, gcam->neg = 102
after 2 iterations, nbhd size=0, neg = 0
0387: dt=0.384000, rms=0.448 (0.138%), neg=0, invalid=762
iter 0, gcam->neg = 183
after 10 iterations, nbhd size=1, neg = 0
0388: dt=0.384000, rms=0.447 (0.116%), neg=0, invalid=762
iter 0, gcam->neg = 183
after 11 iterations, nbhd size=1, neg = 0
0389: dt=0.384000, rms=0.447 (0.035%), neg=0, invalid=762
0390: dt=0.112000, rms=0.447 (0.038%), neg=0, invalid=762
0391: dt=0.112000, rms=0.447 (0.018%), neg=0, invalid=762
0392: dt=0.112000, rms=0.447 (0.027%), neg=0, invalid=762
0393: dt=0.112000, rms=0.447 (0.035%), neg=0, invalid=762
0394: dt=0.112000, rms=0.447 (0.027%), neg=0, invalid=762
0395: dt=0.112000, rms=0.446 (0.016%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 2 minutes and 15 seconds.
mri_ca_register utimesec    8182.067136
mri_ca_register stimesec    9.772514
mri_ca_register ru_maxrss   1341980
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4989126
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  65328
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3979
mri_ca_register ru_nivcsw   11332
FSRUNTIME@ mri_ca_register  2.0375 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 02:17:29 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-610
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-6.0.0/0050345/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.76
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 = 0.11664 (16)
Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (1849 voxels, overlap=0.446)
Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (1849 voxels, peak = 15), gca=15.3
gca peak = 0.17677 (13)
mri peak = 0.07405 (16)
Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (1788 voxels, overlap=0.662)
Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (1788 voxels, peak =  9), gca=9.0
gca peak = 0.28129 (95)
mri peak = 0.09738 (93)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (688 voxels, overlap=1.017)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (688 voxels, peak = 92), gca=91.7
gca peak = 0.16930 (96)
mri peak = 0.08244 (91)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (654 voxels, overlap=1.014)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (654 voxels, peak = 92), gca=91.7
gca peak = 0.24553 (55)
mri peak = 0.08814 (57)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (853 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (853 voxels, peak = 56), gca=56.4
gca peak = 0.30264 (59)
mri peak = 0.07476 (58)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (935 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (935 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.06979 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (46650 voxels, overlap=0.824)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (46650 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.07708 (101)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49924 voxels, overlap=0.873)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49924 voxels, peak = 103), gca=103.5
gca peak = 0.09712 (58)
mri peak = 0.03262 (61)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28968 voxels, overlap=0.946)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28968 voxels, peak = 61), gca=60.6
gca peak = 0.11620 (58)
mri peak = 0.03183 (59)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (27971 voxels, overlap=0.917)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (27971 voxels, peak = 64), gca=63.5
gca peak = 0.30970 (66)
mri peak = 0.07045 (76)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1276 voxels, overlap=0.917)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1276 voxels, peak = 74), gca=74.2
gca peak = 0.15280 (69)
mri peak = 0.07402 (76)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1389 voxels, overlap=1.003)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1389 voxels, peak = 69), gca=69.0
gca peak = 0.13902 (56)
mri peak = 0.04354 (61)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (7621 voxels, overlap=0.721)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (7621 voxels, peak = 60), gca=59.6
gca peak = 0.14777 (55)
mri peak = 0.05131 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (8052 voxels, overlap=0.721)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (8052 voxels, peak = 64), gca=63.5
gca peak = 0.16765 (84)
mri peak = 0.05712 (66)
Left_Cerebellum_White_Matter (7): linear fit = 0.77 x + 0.0 (1920 voxels, overlap=0.043)
Left_Cerebellum_White_Matter (7): linear fit = 0.77 x + 0.0 (1920 voxels, peak = 65), gca=65.1
gca peak = 0.18739 (84)
mri peak = 0.08662 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (1392 voxels, overlap=0.672)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (1392 voxels, peak = 89), gca=89.5
gca peak = 0.29869 (57)
mri peak = 0.10377 (63)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (421 voxels, overlap=1.007)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (421 voxels, peak = 62), gca=62.4
gca peak = 0.33601 (57)
mri peak = 0.08984 (64)
Right_Amygdala (54): linear fit = 1.09 x + 0.0 (430 voxels, overlap=1.023)
Right_Amygdala (54): linear fit = 1.09 x + 0.0 (430 voxels, peak = 62), gca=61.8
gca peak = 0.11131 (90)
mri peak = 0.08628 (80)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (4916 voxels, overlap=0.722)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (4916 voxels, peak = 85), gca=85.1
gca peak = 0.11793 (83)
mri peak = 0.09414 (78)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4762 voxels, overlap=0.926)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4762 voxels, peak = 81), gca=80.9
gca peak = 0.08324 (81)
mri peak = 0.06305 (76)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (2345 voxels, overlap=0.827)
Left_Putamen (12): linear fit = 0.96 x + 0.0 (2345 voxels, peak = 78), gca=78.2
gca peak = 0.10360 (77)
mri peak = 0.06577 (75)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (2482 voxels, overlap=0.834)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (2482 voxels, peak = 74), gca=74.3
gca peak = 0.08424 (78)
mri peak = 0.07807 (88)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (6697 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (6697 voxels, peak = 88), gca=87.8
gca peak = 0.12631 (89)
mri peak = 0.06395 (88)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1384 voxels, overlap=0.742)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1384 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.06022 (97)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1566 voxels, overlap=0.684)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1566 voxels, peak = 94), gca=93.5
gca peak = 0.14975 (24)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.19357 (14)
mri peak = 0.02342 ( 3)
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.07 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.73 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.18489 (14)
mri peak = 0.11664 (16)
Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1849 voxels, overlap=0.918)
Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1849 voxels, peak = 13), gca=12.9
gca peak = 0.28597 ( 9)
mri peak = 0.07405 (16)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1788 voxels, overlap=0.948)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1788 voxels, peak =  9), gca=9.5
gca peak = 0.25037 (90)
mri peak = 0.09738 (93)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (688 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (688 voxels, peak = 90), gca=89.6
gca peak = 0.19950 (92)
mri peak = 0.08244 (91)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (654 voxels, overlap=1.009)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (654 voxels, peak = 92), gca=91.5
gca peak = 0.29186 (57)
mri peak = 0.08814 (57)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (853 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (853 voxels, peak = 56), gca=56.1
gca peak = 0.29362 (59)
mri peak = 0.07476 (58)
Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (935 voxels, overlap=1.004)
Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (935 voxels, peak = 57), gca=56.9
gca peak = 0.07777 (104)
mri peak = 0.06979 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46650 voxels, overlap=0.867)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46650 voxels, peak = 103), gca=103.5
gca peak = 0.08042 (104)
mri peak = 0.07708 (101)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49924 voxels, overlap=0.858)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49924 voxels, peak = 103), gca=103.5
gca peak = 0.09232 (61)
mri peak = 0.03262 (61)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28968 voxels, overlap=0.975)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28968 voxels, peak = 63), gca=62.5
gca peak = 0.10555 (64)
mri peak = 0.03183 (59)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (27971 voxels, overlap=0.954)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (27971 voxels, peak = 63), gca=63.0
gca peak = 0.25480 (75)
mri peak = 0.07045 (76)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1276 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1276 voxels, peak = 75), gca=75.0
gca peak = 0.15279 (69)
mri peak = 0.07402 (76)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1389 voxels, overlap=1.003)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1389 voxels, peak = 69), gca=69.0
gca peak = 0.13461 (60)
mri peak = 0.04354 (61)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7621 voxels, overlap=0.925)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7621 voxels, peak = 62), gca=61.5
gca peak = 0.13028 (63)
mri peak = 0.05131 (62)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (8052 voxels, overlap=0.995)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (8052 voxels, peak = 62), gca=62.1
gca peak = 0.20155 (65)
mri peak = 0.05712 (66)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (1920 voxels, overlap=0.944)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (1920 voxels, peak = 69), gca=68.6
gca peak = 0.15241 (90)
mri peak = 0.08662 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (1392 voxels, overlap=0.941)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (1392 voxels, peak = 90), gca=89.6
gca peak = 0.28520 (62)
mri peak = 0.10377 (63)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (421 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (421 voxels, peak = 62), gca=62.0
gca peak = 0.34769 (62)
mri peak = 0.08984 (64)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (430 voxels, overlap=1.018)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (430 voxels, peak = 62), gca=62.0
gca peak = 0.10582 (85)
mri peak = 0.08628 (80)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4916 voxels, overlap=0.930)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4916 voxels, peak = 85), gca=85.0
gca peak = 0.11372 (79)
mri peak = 0.09414 (78)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4762 voxels, overlap=0.913)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4762 voxels, peak = 79), gca=79.0
gca peak = 0.08891 (78)
mri peak = 0.06305 (76)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2345 voxels, overlap=0.937)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2345 voxels, peak = 77), gca=76.8
gca peak = 0.09183 (72)
mri peak = 0.06577 (75)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2482 voxels, overlap=0.992)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2482 voxels, peak = 71), gca=70.9
gca peak = 0.07798 (88)
mri peak = 0.07807 (88)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (6697 voxels, overlap=0.796)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (6697 voxels, peak = 87), gca=86.7
gca peak = 0.11370 (97)
mri peak = 0.06395 (88)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1384 voxels, overlap=0.865)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1384 voxels, peak = 97), gca=96.5
gca peak = 0.15908 (92)
mri peak = 0.06022 (97)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1566 voxels, overlap=0.910)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1566 voxels, peak = 93), gca=93.4
gca peak = 0.21250 (19)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.21959 (12)
mri peak = 0.02342 ( 3)
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16507 (28)
gca peak Left_Thalamus = 0.63354 (100)
gca peak Third_Ventricle = 0.21250 (19)
gca peak Fourth_Ventricle = 0.21959 (12)
gca peak CSF = 0.22310 (26)
gca peak Left_Accumbens_area = 0.70436 (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 = 0.18682 (24)
gca peak Right_Accumbens_area = 0.29951 (73)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.89778 (23)
gca peak WM_hypointensities = 0.07884 (76)
gca peak non_WM_hypointensities = 0.07897 (44)
gca peak Optic_Chiasm = 0.70596 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.99 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
83277 voxels changed in iteration 0 of unlikely voxel relabeling
379 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
60683 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels)
685 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 82721 changed. image ll: -2.143, PF=0.500
pass 2: 24250 changed. image ll: -2.143, PF=0.500
pass 3: 7540 changed.
pass 4: 2896 changed.
61023 voxels changed in iteration 0 of unlikely voxel relabeling
499 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
9307 voxels changed in iteration 0 of unlikely voxel relabeling
157 voxels changed in iteration 1 of unlikely voxel relabeling
11 voxels changed in iteration 2 of unlikely voxel relabeling
10 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
8890 voxels changed in iteration 0 of unlikely voxel relabeling
99 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7166 voxels changed in iteration 0 of unlikely voxel relabeling
28 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3944.779302
mri_ca_label stimesec    1.560762
mri_ca_label ru_maxrss   2100612
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   736593
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  65320
mri_ca_label ru_oublock  488
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    302
mri_ca_label ru_nivcsw   5961
auto-labeling took 64 minutes and 58 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/transforms/cc_up.lta 0050345 

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-6.0.0/0050345/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/norm.mgz
74674 voxels in left wm, 74491 in right wm, xrange [117, 133]
searching rotation angles z=[-5  9], y=[-12  2]

searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.9  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.4  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.9  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.4  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.9  
searching scale 1 Z rot 9.1  global minimum found at slice 124.0, rotations (-4.62, 2.38)
final transformation (x=124.0, yr=-4.620, zr=2.381):
 0.99589  -0.04154  -0.08048   18.21458;
 0.04141   0.99914  -0.00335   19.34548;
 0.08054  -0.00000   0.99675   2.39334;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 104 116
eigenvectors:
 0.00042   0.00586   0.99998;
-0.02210  -0.99974   0.00587;
 0.99976  -0.02210  -0.00030;
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.7 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 03:24:08 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 03:24:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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...
1155 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 109
gm peak at 67 (67), valley at 22 (22)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 64 (64), valley at 21 (21)
csf peak at 33, setting threshold to 53
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 57 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 03:27:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1487767 voxels in mask (pct=  8.87)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 03:27:08 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (103.0): 104.5 +- 5.3 [79.0 --> 125.0]
GM (71.0) : 69.0 +- 10.3 [30.0 --> 95.0]
setting bottom of white matter range to 79.3
setting top of gray matter range to 89.6
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...
5854 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3226 filled
1806 bright non-wm voxels segmented.
2793 diagonally connected voxels added...
white matter segmentation took 1.5 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 0.71 minutes
reading wm segmentation from wm.seg.mgz...
1606 voxels added to wm to prevent paths from MTL structures to cortex
4439 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 65445 voxels turned on, 12457 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+):  37 found -  37 modified     |    TOTAL:  37
pass   2 (xy+):   0 found -  37 modified     |    TOTAL:  37
pass   1 (xy-):  41 found -  41 modified     |    TOTAL:  78
pass   2 (xy-):   0 found -  41 modified     |    TOTAL:  78
pass   1 (yz+):  38 found -  38 modified     |    TOTAL: 116
pass   2 (yz+):   0 found -  38 modified     |    TOTAL: 116
pass   1 (yz-):  44 found -  44 modified     |    TOTAL: 160
pass   2 (yz-):   0 found -  44 modified     |    TOTAL: 160
pass   1 (xz+):  27 found -  27 modified     |    TOTAL: 187
pass   2 (xz+):   0 found -  27 modified     |    TOTAL: 187
pass   1 (xz-):  42 found -  42 modified     |    TOTAL: 229
pass   2 (xz-):   0 found -  42 modified     |    TOTAL: 229
Iteration Number : 1
pass   1 (+++):  26 found -  26 modified     |    TOTAL:  26
pass   2 (+++):   0 found -  26 modified     |    TOTAL:  26
pass   1 (+++):  41 found -  41 modified     |    TOTAL:  67
pass   2 (+++):   0 found -  41 modified     |    TOTAL:  67
pass   1 (+++):  41 found -  41 modified     |    TOTAL: 108
pass   2 (+++):   0 found -  41 modified     |    TOTAL: 108
pass   1 (+++):  34 found -  34 modified     |    TOTAL: 142
pass   2 (+++):   0 found -  34 modified     |    TOTAL: 142
Iteration Number : 1
pass   1 (++): 114 found - 114 modified     |    TOTAL: 114
pass   2 (++):   0 found - 114 modified     |    TOTAL: 114
pass   1 (+-):  95 found -  95 modified     |    TOTAL: 209
pass   2 (+-):   1 found -  96 modified     |    TOTAL: 210
pass   3 (+-):   0 found -  96 modified     |    TOTAL: 210
pass   1 (--):  92 found -  92 modified     |    TOTAL: 302
pass   2 (--):   0 found -  92 modified     |    TOTAL: 302
pass   1 (-+):  65 found -  65 modified     |    TOTAL: 367
pass   2 (-+):   0 found -  65 modified     |    TOTAL: 367
Iteration Number : 2
pass   1 (xy+):  10 found -  10 modified     |    TOTAL:  10
pass   2 (xy+):   0 found -  10 modified     |    TOTAL:  10
pass   1 (xy-):  10 found -  10 modified     |    TOTAL:  20
pass   2 (xy-):   0 found -  10 modified     |    TOTAL:  20
pass   1 (yz+):   7 found -   7 modified     |    TOTAL:  27
pass   2 (yz+):   0 found -   7 modified     |    TOTAL:  27
pass   1 (yz-):  15 found -  15 modified     |    TOTAL:  42
pass   2 (yz-):   0 found -  15 modified     |    TOTAL:  42
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  46
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  46
pass   1 (xz-):  12 found -  12 modified     |    TOTAL:  58
pass   2 (xz-):   0 found -  12 modified     |    TOTAL:  58
Iteration Number : 2
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   7
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  11
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  11
Iteration Number : 2
pass   1 (++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   7
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   7
pass   1 (--):   6 found -   6 modified     |    TOTAL:  13
pass   2 (--):   0 found -   6 modified     |    TOTAL:  13
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  17
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  17
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 827 (out of 572202: 0.144529)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 03:29:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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
 1.01798  -0.03286  -0.07023   10.62282;
 0.04180   1.13746   0.23166  -56.45665;
 0.08000  -0.27310   0.95915   17.30079;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.01798  -0.03286  -0.07023   10.62282;
 0.04180   1.13746   0.23166  -56.45665;
 0.08000  -0.27310   0.95915   17.30079;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1157 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75)
no need to search
using seed (126, 126, 149), TAL = (2.0, 21.0, 2.0)
talairach voxel to voxel transform
 0.97577   0.04286   0.06110  -9.00299;
-0.01823   0.83016  -0.20184   50.55385;
-0.08658   0.23280   0.98002  -2.89224;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  126,  149) --> (2.0, 21.0, 2.0)
done.
writing output to filled.mgz...
filling took 0.6 minutes
talairach cc position changed to (2.00, 21.00, 2.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 21.00, 2.00) SRC: (110.88, 123.11, 163.11)
search lh wm seed point around talairach space (-16.00, 21.00, 2.00), SRC: (146.01, 122.46, 160.00)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 03:30:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   8 found -   8 modified     |    TOTAL:  11
pass   2 (yz-):   0 found -   8 modified     |    TOTAL:  11
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  13
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  13
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  14
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  14
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (--):   4 found -   4 modified     |    TOTAL:   6
pass   2 (--):   0 found -   4 modified     |    TOTAL:   6
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   8
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 = 22 (out of 281482: 0.007816)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 2784 vertices, 2989 faces
slice 60: 12757 vertices, 13211 faces
slice 70: 25964 vertices, 26455 faces
slice 80: 38943 vertices, 39471 faces
slice 90: 51567 vertices, 52020 faces
slice 100: 63392 vertices, 63860 faces
slice 110: 76174 vertices, 76685 faces
slice 120: 88199 vertices, 88672 faces
slice 130: 99251 vertices, 99759 faces
slice 140: 110451 vertices, 110956 faces
slice 150: 121492 vertices, 121979 faces
slice 160: 129681 vertices, 130125 faces
slice 170: 137301 vertices, 137701 faces
slice 180: 143684 vertices, 144059 faces
slice 190: 148721 vertices, 149034 faces
slice 200: 152250 vertices, 152516 faces
slice 210: 153782 vertices, 153971 faces
slice 220: 153808 vertices, 153986 faces
slice 230: 153808 vertices, 153986 faces
slice 240: 153808 vertices, 153986 faces
slice 250: 153808 vertices, 153986 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...
   153808 voxel in cpt #1: X=-178 [v=153808,e=461958,f=307972] located at (-25.396955, -15.209072, 8.170959)
For the whole surface: X=-178 [v=153808,e=461958,f=307972]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 03:30:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz-):   7 found -   7 modified     |    TOTAL:  11
pass   2 (yz-):   0 found -   7 modified     |    TOTAL:  11
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  12
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  12
pass   1 (xz-):   4 found -   4 modified     |    TOTAL:  16
pass   2 (xz-):   0 found -   4 modified     |    TOTAL:  16
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 (++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (--):   1 found -   1 modified     |    TOTAL:   5
pass   2 (--):   0 found -   1 modified     |    TOTAL:   5
pass   1 (-+):   0 found -   0 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 = 21 (out of 277428: 0.007570)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 2453 vertices, 2594 faces
slice 60: 10831 vertices, 11177 faces
slice 70: 22485 vertices, 23039 faces
slice 80: 35337 vertices, 35809 faces
slice 90: 47417 vertices, 47890 faces
slice 100: 59197 vertices, 59663 faces
slice 110: 71550 vertices, 72083 faces
slice 120: 83833 vertices, 84360 faces
slice 130: 96246 vertices, 96768 faces
slice 140: 107664 vertices, 108220 faces
slice 150: 119263 vertices, 119789 faces
slice 160: 129859 vertices, 130386 faces
slice 170: 138223 vertices, 138680 faces
slice 180: 145181 vertices, 145590 faces
slice 190: 150579 vertices, 150975 faces
slice 200: 154848 vertices, 155164 faces
slice 210: 156632 vertices, 156842 faces
slice 220: 156632 vertices, 156842 faces
slice 230: 156632 vertices, 156842 faces
slice 240: 156632 vertices, 156842 faces
slice 250: 156632 vertices, 156842 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...
   156632 voxel in cpt #1: X=-210 [v=156632,e=470526,f=313684] located at (32.284119, -11.784150, 6.376072)
For the whole surface: X=-210 [v=156632,e=470526,f=313684]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 03:30:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 03:30:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

Waiting for PID 27465 of (27465 27468) to complete...
Waiting for PID 27468 of (27465 27468) 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 (27465 27468) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 03:30:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 03:30:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

Waiting for PID 27511 of (27511 27514) to complete...
Waiting for PID 27514 of (27511 27514) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 49.3 mm, total surface area = 80158 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.168 (target=0.015)   
step 005: RMS=0.130 (target=0.015)   
step 010: RMS=0.103 (target=0.015)   
step 015: RMS=0.092 (target=0.015)   
step 020: RMS=0.084 (target=0.015)   
step 025: RMS=0.078 (target=0.015)   
step 030: RMS=0.072 (target=0.015)   
step 035: RMS=0.068 (target=0.015)   
step 040: RMS=0.065 (target=0.015)   
step 045: RMS=0.064 (target=0.015)   
step 050: RMS=0.063 (target=0.015)   
step 055: RMS=0.063 (target=0.015)   
step 060: RMS=0.063 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    48.488628
mris_inflate stimesec    0.103984
mris_inflate ru_maxrss   224768
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32111
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10832
mris_inflate ru_oublock  10848
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2317
mris_inflate ru_nivcsw   3530

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.3 mm, total surface area = 81071 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.174 (target=0.015)   
step 005: RMS=0.135 (target=0.015)   
step 010: RMS=0.109 (target=0.015)   
step 015: RMS=0.098 (target=0.015)   
step 020: RMS=0.090 (target=0.015)   
step 025: RMS=0.083 (target=0.015)   
step 030: RMS=0.079 (target=0.015)   
step 035: RMS=0.075 (target=0.015)   
step 040: RMS=0.073 (target=0.015)   
step 045: RMS=0.072 (target=0.015)   
step 050: RMS=0.072 (target=0.015)   
step 055: RMS=0.072 (target=0.015)   
step 060: RMS=0.072 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.000550
mris_inflate stimesec    0.111982
mris_inflate ru_maxrss   228980
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33163
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11032
mris_inflate ru_oublock  11048
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2247
mris_inflate ru_nivcsw   4311
PIDs (27511 27514) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 03:31:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 03:31:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

Waiting for PID 27587 of (27587 27591) to complete...
Waiting for PID 27591 of (27587 27591) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.60 (0.00-->8.02) (max @ vno 108944 --> 108945)
face area 0.02 +- 0.03 (-0.22-->0.67)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.293...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.841, avgs=0
005/300: dt: 0.9000, rms radial error=176.583, avgs=0
010/300: dt: 0.9000, rms radial error=176.028, avgs=0
015/300: dt: 0.9000, rms radial error=175.300, avgs=0
020/300: dt: 0.9000, rms radial error=174.470, avgs=0
025/300: dt: 0.9000, rms radial error=173.582, avgs=0
030/300: dt: 0.9000, rms radial error=172.663, avgs=0
035/300: dt: 0.9000, rms radial error=171.727, avgs=0
040/300: dt: 0.9000, rms radial error=170.784, avgs=0
045/300: dt: 0.9000, rms radial error=169.838, avgs=0
050/300: dt: 0.9000, rms radial error=168.892, avgs=0
055/300: dt: 0.9000, rms radial error=167.948, avgs=0
060/300: dt: 0.9000, rms radial error=167.007, avgs=0
065/300: dt: 0.9000, rms radial error=166.070, avgs=0
070/300: dt: 0.9000, rms radial error=165.137, avgs=0
075/300: dt: 0.9000, rms radial error=164.209, avgs=0
080/300: dt: 0.9000, rms radial error=163.285, avgs=0
085/300: dt: 0.9000, rms radial error=162.365, avgs=0
090/300: dt: 0.9000, rms radial error=161.451, avgs=0
095/300: dt: 0.9000, rms radial error=160.541, avgs=0
100/300: dt: 0.9000, rms radial error=159.636, avgs=0
105/300: dt: 0.9000, rms radial error=158.735, avgs=0
110/300: dt: 0.9000, rms radial error=157.840, avgs=0
115/300: dt: 0.9000, rms radial error=156.950, avgs=0
120/300: dt: 0.9000, rms radial error=156.064, avgs=0
125/300: dt: 0.9000, rms radial error=155.183, avgs=0
130/300: dt: 0.9000, rms radial error=154.307, avgs=0
135/300: dt: 0.9000, rms radial error=153.436, avgs=0
140/300: dt: 0.9000, rms radial error=152.569, avgs=0
145/300: dt: 0.9000, rms radial error=151.707, avgs=0
150/300: dt: 0.9000, rms radial error=150.849, avgs=0
155/300: dt: 0.9000, rms radial error=149.996, avgs=0
160/300: dt: 0.9000, rms radial error=149.147, avgs=0
165/300: dt: 0.9000, rms radial error=148.303, avgs=0
170/300: dt: 0.9000, rms radial error=147.463, avgs=0
175/300: dt: 0.9000, rms radial error=146.634, avgs=0
180/300: dt: 0.9000, rms radial error=145.809, avgs=0
185/300: dt: 0.9000, rms radial error=144.988, avgs=0
190/300: dt: 0.9000, rms radial error=144.172, avgs=0
195/300: dt: 0.9000, rms radial error=143.361, avgs=0
200/300: dt: 0.9000, rms radial error=142.554, avgs=0
205/300: dt: 0.9000, rms radial error=141.751, avgs=0
210/300: dt: 0.9000, rms radial error=140.953, avgs=0
215/300: dt: 0.9000, rms radial error=140.160, avgs=0
220/300: dt: 0.9000, rms radial error=139.370, avgs=0
225/300: dt: 0.9000, rms radial error=138.585, avgs=0
230/300: dt: 0.9000, rms radial error=137.804, avgs=0
235/300: dt: 0.9000, rms radial error=137.028, avgs=0
240/300: dt: 0.9000, rms radial error=136.255, avgs=0
245/300: dt: 0.9000, rms radial error=135.488, avgs=0
250/300: dt: 0.9000, rms radial error=134.724, avgs=0
255/300: dt: 0.9000, rms radial error=133.964, avgs=0
260/300: dt: 0.9000, rms radial error=133.209, avgs=0
265/300: dt: 0.9000, rms radial error=132.458, avgs=0
270/300: dt: 0.9000, rms radial error=131.711, avgs=0
275/300: dt: 0.9000, rms radial error=130.970, avgs=0
280/300: dt: 0.9000, rms radial error=130.232, avgs=0
285/300: dt: 0.9000, rms radial error=129.499, avgs=0
290/300: dt: 0.9000, rms radial error=128.771, avgs=0
295/300: dt: 0.9000, rms radial error=128.046, avgs=0
300/300: dt: 0.9000, rms radial error=127.326, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18445.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 3318.22
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
epoch 3 (K=160.0), pass 1, starting sse = 400.19
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00391
epoch 4 (K=640.0), pass 1, starting sse = 37.67
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00395
final distance error %28.32
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    269.273064
mris_sphere stimesec    0.167974
mris_sphere ru_maxrss   227016
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   32672
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10872
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8208
mris_sphere ru_nivcsw   21460
FSRUNTIME@ mris_sphere  0.0748 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 0.91 +- 0.59 (0.00-->8.99) (max @ vno 63269 --> 64525)
face area 0.02 +- 0.03 (-0.09-->0.79)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.284...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.443, avgs=0
005/300: dt: 0.9000, rms radial error=177.186, avgs=0
010/300: dt: 0.9000, rms radial error=176.634, avgs=0
015/300: dt: 0.9000, rms radial error=175.909, avgs=0
020/300: dt: 0.9000, rms radial error=175.082, avgs=0
025/300: dt: 0.9000, rms radial error=174.197, avgs=0
030/300: dt: 0.9000, rms radial error=173.280, avgs=0
035/300: dt: 0.9000, rms radial error=172.345, avgs=0
040/300: dt: 0.9000, rms radial error=171.401, avgs=0
045/300: dt: 0.9000, rms radial error=170.449, avgs=0
050/300: dt: 0.9000, rms radial error=169.498, avgs=0
055/300: dt: 0.9000, rms radial error=168.548, avgs=0
060/300: dt: 0.9000, rms radial error=167.606, avgs=0
065/300: dt: 0.9000, rms radial error=166.666, avgs=0
070/300: dt: 0.9000, rms radial error=165.729, avgs=0
075/300: dt: 0.9000, rms radial error=164.797, avgs=0
080/300: dt: 0.9000, rms radial error=163.870, avgs=0
085/300: dt: 0.9000, rms radial error=162.948, avgs=0
090/300: dt: 0.9000, rms radial error=162.032, avgs=0
095/300: dt: 0.9000, rms radial error=161.121, avgs=0
100/300: dt: 0.9000, rms radial error=160.216, avgs=0
105/300: dt: 0.9000, rms radial error=159.319, avgs=0
110/300: dt: 0.9000, rms radial error=158.420, avgs=0
115/300: dt: 0.9000, rms radial error=157.529, avgs=0
120/300: dt: 0.9000, rms radial error=156.641, avgs=0
125/300: dt: 0.9000, rms radial error=155.765, avgs=0
130/300: dt: 0.9000, rms radial error=154.890, avgs=0
135/300: dt: 0.9000, rms radial error=154.016, avgs=0
140/300: dt: 0.9000, rms radial error=153.150, avgs=0
145/300: dt: 0.9000, rms radial error=152.294, avgs=0
150/300: dt: 0.9000, rms radial error=151.434, avgs=0
155/300: dt: 0.9000, rms radial error=150.584, avgs=0
160/300: dt: 0.9000, rms radial error=149.739, avgs=0
165/300: dt: 0.9000, rms radial error=148.898, avgs=0
170/300: dt: 0.9000, rms radial error=148.059, avgs=0
175/300: dt: 0.9000, rms radial error=147.226, avgs=0
180/300: dt: 0.9000, rms radial error=146.398, avgs=0
185/300: dt: 0.9000, rms radial error=145.576, avgs=0
190/300: dt: 0.9000, rms radial error=144.756, avgs=0
195/300: dt: 0.9000, rms radial error=143.942, avgs=0
200/300: dt: 0.9000, rms radial error=143.133, avgs=0
205/300: dt: 0.9000, rms radial error=142.327, avgs=0
210/300: dt: 0.9000, rms radial error=141.522, avgs=0
215/300: dt: 0.9000, rms radial error=140.725, avgs=0
220/300: dt: 0.9000, rms radial error=139.935, avgs=0
225/300: dt: 0.9000, rms radial error=139.146, avgs=0
230/300: dt: 0.9000, rms radial error=138.362, avgs=0
235/300: dt: 0.9000, rms radial error=137.583, avgs=0
240/300: dt: 0.9000, rms radial error=136.814, avgs=0
245/300: dt: 0.9000, rms radial error=136.048, avgs=0
250/300: dt: 0.9000, rms radial error=135.283, avgs=0
255/300: dt: 0.9000, rms radial error=134.531, avgs=0
260/300: dt: 0.9000, rms radial error=133.753, avgs=0
265/300: dt: 0.9000, rms radial error=133.003, avgs=0
270/300: dt: 0.9000, rms radial error=132.249, avgs=0
275/300: dt: 0.9000, rms radial error=131.504, avgs=0
280/300: dt: 0.9000, rms radial error=130.763, avgs=0
285/300: dt: 0.9000, rms radial error=130.026, avgs=0
290/300: dt: 0.9000, rms radial error=129.293, avgs=0
295/300: dt: 0.9000, rms radial error=128.570, avgs=0
300/300: dt: 0.9000, rms radial error=127.839, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18915.27
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
epoch 2 (K=40.0), pass 1, starting sse = 3418.93
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 437.09
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00492
epoch 4 (K=640.0), pass 1, starting sse = 49.49
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/10 = 0.00555
final distance error %27.69
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    274.562260
mris_sphere stimesec    0.153976
mris_sphere ru_maxrss   229180
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33215
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11032
mris_sphere ru_oublock  11072
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8260
mris_sphere ru_nivcsw   20499
FSRUNTIME@ mris_sphere  0.0758 hours 1 threads
PIDs (27587 27591) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 03:35:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 03:35:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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


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

#@# Fix Topology lh Sun Oct  8 03:35:45 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050345 lh 

#@# Fix Topology rh Sun Oct  8 03:35:45 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050345 rh 

Waiting for PID 27782 of (27782 27785) to complete...
Waiting for PID 27785 of (27782 27785) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050345 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=-178 (nv=153808, nf=307972, ne=461958, g=90)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
14924 ambiguous faces found in tessellation
segmenting defects...
93 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 6 into 1
      -merging segment 4 into 3
      -merging segment 13 into 7
      -merging segment 20 into 19
      -merging segment 56 into 53
      -merging segment 76 into 73
      -merging segment 77 into 80
      -merging segment 83 into 81
85 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1462  (-4.5731)
      -vertex     loglikelihood: -6.3591  (-3.1796)
      -normal dot loglikelihood: -3.5760  (-3.5760)
      -quad curv  loglikelihood: -6.1822  (-3.0911)
      Total Loglikelihood : -25.2636

CORRECTING DEFECT 0 (vertices=475, convex hull=136, v0=0)
After retessellation of defect 0 (v0=0), euler #=-87 (144971,431953,286895) : difference with theory (-82) = 5 

CORRECTING DEFECT 1 (vertices=994, convex hull=355, v0=13)
After retessellation of defect 1 (v0=13), euler #=-85 (145145,432661,287431) : difference with theory (-81) = 4 

CORRECTING DEFECT 2 (vertices=228, convex hull=160, v0=562)
After retessellation of defect 2 (v0=562), euler #=-84 (145173,432826,287569) : difference with theory (-80) = 4 

CORRECTING DEFECT 3 (vertices=213, convex hull=123, v0=713)
After retessellation of defect 3 (v0=713), euler #=-82 (145211,433006,287713) : difference with theory (-79) = 3 

CORRECTING DEFECT 4 (vertices=23, convex hull=83, v0=3600)
After retessellation of defect 4 (v0=3600), euler #=-81 (145228,433086,287777) : difference with theory (-78) = 3 

CORRECTING DEFECT 5 (vertices=214, convex hull=110, v0=4134)
After retessellation of defect 5 (v0=4134), euler #=-79 (145245,433186,287862) : difference with theory (-77) = 2 

CORRECTING DEFECT 6 (vertices=32, convex hull=70, v0=6787)
After retessellation of defect 6 (v0=6787), euler #=-78 (145264,433269,287927) : difference with theory (-76) = 2 

CORRECTING DEFECT 7 (vertices=44, convex hull=15, v0=7629)
After retessellation of defect 7 (v0=7629), euler #=-77 (145264,433272,287931) : difference with theory (-75) = 2 

CORRECTING DEFECT 8 (vertices=69, convex hull=72, v0=7649)
After retessellation of defect 8 (v0=7649), euler #=-76 (145288,433374,288010) : difference with theory (-74) = 2 

CORRECTING DEFECT 9 (vertices=19, convex hull=21, v0=9156)
After retessellation of defect 9 (v0=9156), euler #=-75 (145288,433378,288015) : difference with theory (-73) = 2 

CORRECTING DEFECT 10 (vertices=359, convex hull=236, v0=10028)
After retessellation of defect 10 (v0=10028), euler #=-75 (145405,433859,288379) : difference with theory (-72) = 3 

CORRECTING DEFECT 11 (vertices=88, convex hull=108, v0=12758)
After retessellation of defect 11 (v0=12758), euler #=-74 (145448,434043,288521) : difference with theory (-71) = 3 

CORRECTING DEFECT 12 (vertices=78, convex hull=89, v0=13901)
After retessellation of defect 12 (v0=13901), euler #=-73 (145481,434181,288627) : difference with theory (-70) = 3 

CORRECTING DEFECT 13 (vertices=14, convex hull=27, v0=15121)
After retessellation of defect 13 (v0=15121), euler #=-72 (145482,434189,288635) : difference with theory (-69) = 3 

CORRECTING DEFECT 14 (vertices=6, convex hull=19, v0=17510)
After retessellation of defect 14 (v0=17510), euler #=-71 (145483,434199,288645) : difference with theory (-68) = 3 

CORRECTING DEFECT 15 (vertices=44, convex hull=37, v0=17578)
After retessellation of defect 15 (v0=17578), euler #=-70 (145484,434216,288662) : difference with theory (-67) = 3 

CORRECTING DEFECT 16 (vertices=158, convex hull=125, v0=17729)
After retessellation of defect 16 (v0=17729), euler #=-68 (145514,434369,288787) : difference with theory (-66) = 2 

CORRECTING DEFECT 17 (vertices=63, convex hull=77, v0=20972)
After retessellation of defect 17 (v0=20972), euler #=-67 (145542,434489,288880) : difference with theory (-65) = 2 

CORRECTING DEFECT 18 (vertices=84, convex hull=79, v0=23058)
After retessellation of defect 18 (v0=23058), euler #=-66 (145568,434602,288968) : difference with theory (-64) = 2 

CORRECTING DEFECT 19 (vertices=242, convex hull=140, v0=24270)
After retessellation of defect 19 (v0=24270), euler #=-65 (145600,434765,289100) : difference with theory (-63) = 2 

CORRECTING DEFECT 20 (vertices=39, convex hull=62, v0=24620)
After retessellation of defect 20 (v0=24620), euler #=-64 (145619,434845,289162) : difference with theory (-62) = 2 

CORRECTING DEFECT 21 (vertices=49, convex hull=28, v0=26258)
After retessellation of defect 21 (v0=26258), euler #=-63 (145621,434859,289175) : difference with theory (-61) = 2 

CORRECTING DEFECT 22 (vertices=60, convex hull=88, v0=27148)
After retessellation of defect 22 (v0=27148), euler #=-63 (145632,434935,289240) : difference with theory (-60) = 3 

CORRECTING DEFECT 23 (vertices=29, convex hull=76, v0=29896)
After retessellation of defect 23 (v0=29896), euler #=-62 (145641,434994,289291) : difference with theory (-59) = 3 

CORRECTING DEFECT 24 (vertices=23, convex hull=49, v0=30773)
After retessellation of defect 24 (v0=30773), euler #=-61 (145653,435048,289334) : difference with theory (-58) = 3 

CORRECTING DEFECT 25 (vertices=27, convex hull=88, v0=33224)
After retessellation of defect 25 (v0=33224), euler #=-60 (145662,435107,289385) : difference with theory (-57) = 3 

CORRECTING DEFECT 26 (vertices=34, convex hull=49, v0=34186)
After retessellation of defect 26 (v0=34186), euler #=-59 (145669,435147,289419) : difference with theory (-56) = 3 

CORRECTING DEFECT 27 (vertices=29, convex hull=58, v0=34361)
After retessellation of defect 27 (v0=34361), euler #=-58 (145685,435220,289477) : difference with theory (-55) = 3 

CORRECTING DEFECT 28 (vertices=37, convex hull=71, v0=36473)
After retessellation of defect 28 (v0=36473), euler #=-57 (145700,435292,289535) : difference with theory (-54) = 3 

CORRECTING DEFECT 29 (vertices=18, convex hull=23, v0=37434)
After retessellation of defect 29 (v0=37434), euler #=-56 (145701,435301,289544) : difference with theory (-53) = 3 

CORRECTING DEFECT 30 (vertices=176, convex hull=62, v0=47440)
After retessellation of defect 30 (v0=47440), euler #=-55 (145721,435387,289611) : difference with theory (-52) = 3 

CORRECTING DEFECT 31 (vertices=22, convex hull=60, v0=49265)
After retessellation of defect 31 (v0=49265), euler #=-54 (145732,435440,289654) : difference with theory (-51) = 3 

CORRECTING DEFECT 32 (vertices=21, convex hull=74, v0=50309)
After retessellation of defect 32 (v0=50309), euler #=-53 (145745,435507,289709) : difference with theory (-50) = 3 

CORRECTING DEFECT 33 (vertices=41, convex hull=33, v0=58654)
After retessellation of defect 33 (v0=58654), euler #=-52 (145749,435528,289727) : difference with theory (-49) = 3 

CORRECTING DEFECT 34 (vertices=59, convex hull=91, v0=59577)
After retessellation of defect 34 (v0=59577), euler #=-51 (145762,435606,289793) : difference with theory (-48) = 3 

CORRECTING DEFECT 35 (vertices=993, convex hull=480, v0=63129)
L defect detected...
After retessellation of defect 35 (v0=63129), euler #=-50 (146000,436574,290524) : difference with theory (-47) = 3 

CORRECTING DEFECT 36 (vertices=16, convex hull=36, v0=65361)
After retessellation of defect 36 (v0=65361), euler #=-49 (146010,436615,290556) : difference with theory (-46) = 3 

CORRECTING DEFECT 37 (vertices=84, convex hull=106, v0=65619)
After retessellation of defect 37 (v0=65619), euler #=-48 (146052,436788,290688) : difference with theory (-45) = 3 

CORRECTING DEFECT 38 (vertices=117, convex hull=125, v0=66700)
After retessellation of defect 38 (v0=66700), euler #=-47 (146088,436955,290820) : difference with theory (-44) = 3 

CORRECTING DEFECT 39 (vertices=24, convex hull=46, v0=69901)
After retessellation of defect 39 (v0=69901), euler #=-46 (146098,436999,290855) : difference with theory (-43) = 3 

CORRECTING DEFECT 40 (vertices=66, convex hull=107, v0=77217)
After retessellation of defect 40 (v0=77217), euler #=-45 (146136,437160,290979) : difference with theory (-42) = 3 

CORRECTING DEFECT 41 (vertices=10, convex hull=30, v0=85890)
After retessellation of defect 41 (v0=85890), euler #=-44 (146137,437171,290990) : difference with theory (-41) = 3 

CORRECTING DEFECT 42 (vertices=41, convex hull=25, v0=89333)
After retessellation of defect 42 (v0=89333), euler #=-43 (146142,437192,291007) : difference with theory (-40) = 3 

CORRECTING DEFECT 43 (vertices=43, convex hull=50, v0=89414)
After retessellation of defect 43 (v0=89414), euler #=-42 (146166,437286,291078) : difference with theory (-39) = 3 

CORRECTING DEFECT 44 (vertices=25, convex hull=39, v0=94629)
After retessellation of defect 44 (v0=94629), euler #=-41 (146182,437347,291124) : difference with theory (-38) = 3 

CORRECTING DEFECT 45 (vertices=23, convex hull=43, v0=95920)
After retessellation of defect 45 (v0=95920), euler #=-40 (146191,437391,291160) : difference with theory (-37) = 3 

CORRECTING DEFECT 46 (vertices=12, convex hull=23, v0=98181)
After retessellation of defect 46 (v0=98181), euler #=-39 (146193,437402,291170) : difference with theory (-36) = 3 

CORRECTING DEFECT 47 (vertices=8, convex hull=25, v0=103738)
After retessellation of defect 47 (v0=103738), euler #=-38 (146194,437412,291180) : difference with theory (-35) = 3 

CORRECTING DEFECT 48 (vertices=391, convex hull=179, v0=103766)
After retessellation of defect 48 (v0=103766), euler #=-37 (146209,437536,291290) : difference with theory (-34) = 3 

CORRECTING DEFECT 49 (vertices=41, convex hull=73, v0=106728)
After retessellation of defect 49 (v0=106728), euler #=-35 (146228,437631,291368) : difference with theory (-33) = 2 

CORRECTING DEFECT 50 (vertices=30, convex hull=72, v0=107684)
After retessellation of defect 50 (v0=107684), euler #=-34 (146248,437714,291432) : difference with theory (-32) = 2 

CORRECTING DEFECT 51 (vertices=153, convex hull=153, v0=107853)
After retessellation of defect 51 (v0=107853), euler #=-33 (146321,438005,291651) : difference with theory (-31) = 2 

CORRECTING DEFECT 52 (vertices=63, convex hull=115, v0=110179)
After retessellation of defect 52 (v0=110179), euler #=-32 (146365,438188,291791) : difference with theory (-30) = 2 

CORRECTING DEFECT 53 (vertices=15, convex hull=47, v0=111540)
After retessellation of defect 53 (v0=111540), euler #=-31 (146367,438211,291813) : difference with theory (-29) = 2 

CORRECTING DEFECT 54 (vertices=10, convex hull=29, v0=112672)
After retessellation of defect 54 (v0=112672), euler #=-30 (146369,438225,291826) : difference with theory (-28) = 2 

CORRECTING DEFECT 55 (vertices=251, convex hull=110, v0=113731)
After retessellation of defect 55 (v0=113731), euler #=-29 (146415,438413,291969) : difference with theory (-27) = 2 

CORRECTING DEFECT 56 (vertices=113, convex hull=128, v0=115558)
After retessellation of defect 56 (v0=115558), euler #=-28 (146462,438612,292122) : difference with theory (-26) = 2 

CORRECTING DEFECT 57 (vertices=7, convex hull=19, v0=117787)
After retessellation of defect 57 (v0=117787), euler #=-27 (146463,438620,292130) : difference with theory (-25) = 2 

CORRECTING DEFECT 58 (vertices=345, convex hull=189, v0=117988)
After retessellation of defect 58 (v0=117988), euler #=-26 (146560,439009,292423) : difference with theory (-24) = 2 

CORRECTING DEFECT 59 (vertices=58, convex hull=61, v0=118025)
After retessellation of defect 59 (v0=118025), euler #=-25 (146564,439050,292461) : difference with theory (-23) = 2 

CORRECTING DEFECT 60 (vertices=24, convex hull=21, v0=119033)
After retessellation of defect 60 (v0=119033), euler #=-24 (146570,439073,292479) : difference with theory (-22) = 2 

CORRECTING DEFECT 61 (vertices=194, convex hull=80, v0=122234)
After retessellation of defect 61 (v0=122234), euler #=-23 (146593,439172,292556) : difference with theory (-21) = 2 

CORRECTING DEFECT 62 (vertices=83, convex hull=71, v0=122300)
After retessellation of defect 62 (v0=122300), euler #=-22 (146607,439248,292619) : difference with theory (-20) = 2 

CORRECTING DEFECT 63 (vertices=20, convex hull=36, v0=122393)
After retessellation of defect 63 (v0=122393), euler #=-21 (146608,439264,292635) : difference with theory (-19) = 2 

CORRECTING DEFECT 64 (vertices=65, convex hull=40, v0=122463)
After retessellation of defect 64 (v0=122463), euler #=-20 (146625,439332,292687) : difference with theory (-18) = 2 

CORRECTING DEFECT 65 (vertices=8, convex hull=32, v0=123159)
After retessellation of defect 65 (v0=123159), euler #=-19 (146628,439347,292700) : difference with theory (-17) = 2 

CORRECTING DEFECT 66 (vertices=37, convex hull=21, v0=123219)
After retessellation of defect 66 (v0=123219), euler #=-18 (146635,439375,292722) : difference with theory (-16) = 2 

CORRECTING DEFECT 67 (vertices=13, convex hull=26, v0=124905)
After retessellation of defect 67 (v0=124905), euler #=-17 (146637,439390,292736) : difference with theory (-15) = 2 

CORRECTING DEFECT 68 (vertices=96, convex hull=100, v0=127378)
After retessellation of defect 68 (v0=127378), euler #=-15 (146648,439474,292811) : difference with theory (-14) = 1 

CORRECTING DEFECT 69 (vertices=23, convex hull=41, v0=128051)
After retessellation of defect 69 (v0=128051), euler #=-14 (146653,439503,292836) : difference with theory (-13) = 1 

CORRECTING DEFECT 70 (vertices=38, convex hull=71, v0=128172)
After retessellation of defect 70 (v0=128172), euler #=-13 (146680,439612,292919) : difference with theory (-12) = 1 

CORRECTING DEFECT 71 (vertices=5, convex hull=12, v0=131382)
After retessellation of defect 71 (v0=131382), euler #=-12 (146680,439614,292922) : difference with theory (-11) = 1 

CORRECTING DEFECT 72 (vertices=91, convex hull=67, v0=132242)
After retessellation of defect 72 (v0=132242), euler #=-11 (146692,439681,292978) : difference with theory (-10) = 1 

CORRECTING DEFECT 73 (vertices=152, convex hull=110, v0=136371)
After retessellation of defect 73 (v0=136371), euler #=-9 (146728,439838,293101) : difference with theory (-9) = 0 

CORRECTING DEFECT 74 (vertices=163, convex hull=111, v0=138061)
After retessellation of defect 74 (v0=138061), euler #=-7 (146758,439981,293216) : difference with theory (-8) = -1 

CORRECTING DEFECT 75 (vertices=58, convex hull=76, v0=139561)
After retessellation of defect 75 (v0=139561), euler #=-6 (146772,440056,293278) : difference with theory (-7) = -1 

CORRECTING DEFECT 76 (vertices=26, convex hull=50, v0=146952)
After retessellation of defect 76 (v0=146952), euler #=-5 (146785,440114,293324) : difference with theory (-6) = -1 

CORRECTING DEFECT 77 (vertices=26, convex hull=29, v0=147079)
After retessellation of defect 77 (v0=147079), euler #=-4 (146787,440129,293338) : difference with theory (-5) = -1 

CORRECTING DEFECT 78 (vertices=19, convex hull=21, v0=148463)
After retessellation of defect 78 (v0=148463), euler #=-3 (146789,440142,293350) : difference with theory (-4) = -1 

CORRECTING DEFECT 79 (vertices=32, convex hull=65, v0=148775)
After retessellation of defect 79 (v0=148775), euler #=-2 (146807,440222,293413) : difference with theory (-3) = -1 

CORRECTING DEFECT 80 (vertices=34, convex hull=64, v0=150488)
After retessellation of defect 80 (v0=150488), euler #=-1 (146822,440291,293468) : difference with theory (-2) = -1 

CORRECTING DEFECT 81 (vertices=85, convex hull=70, v0=151259)
After retessellation of defect 81 (v0=151259), euler #=0 (146847,440397,293550) : difference with theory (-1) = -1 

CORRECTING DEFECT 82 (vertices=470, convex hull=205, v0=151876)
After retessellation of defect 82 (v0=151876), euler #=1 (146943,440791,293849) : difference with theory (0) = -1 

CORRECTING DEFECT 83 (vertices=23, convex hull=24, v0=152409)
After retessellation of defect 83 (v0=152409), euler #=2 (146945,440801,293858) : difference with theory (1) = -1 

CORRECTING DEFECT 84 (vertices=50, convex hull=53, v0=152755)
After retessellation of defect 84 (v0=152755), euler #=2 (146952,440850,293900) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.25 (0.02-->11.82) (max @ vno 21270 --> 36330)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.25 (0.02-->11.82) (max @ vno 21270 --> 36330)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
266 mutations (35.1%), 491 crossovers (64.9%), 365 vertices were eliminated
building final representation...
6856 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=146952, nf=293900, ne=440850, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 56.7 minutes
0 defective edges
removing intersecting faces
000: 637 intersecting
001: 18 intersecting
mris_fix_topology utimesec    3406.084196
mris_fix_topology stimesec    0.197969
mris_fix_topology ru_maxrss   497200
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   58560
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  21664
mris_fix_topology ru_oublock  14392
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    691
mris_fix_topology ru_nivcsw   11043
FSRUNTIME@ mris_fix_topology lh  0.9458 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050345 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=-210 (nv=156632, nf=313684, ne=470526, g=106)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 8 iterations
marking ambiguous vertices...
22769 ambiguous faces found in tessellation
segmenting defects...
114 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 22 into 28
      -merging segment 35 into 33
      -merging segment 54 into 52
      -merging segment 73 into 70
      -merging segment 69 into 75
      -merging segment 91 into 80
      -merging segment 86 into 80
      -merging segment 102 into 99
106 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3965  (-4.6983)
      -vertex     loglikelihood: -6.3728  (-3.1864)
      -normal dot loglikelihood: -3.4959  (-3.4959)
      -quad curv  loglikelihood: -6.2139  (-3.1069)
      Total Loglikelihood : -25.4792

CORRECTING DEFECT 0 (vertices=454, convex hull=94, v0=0)
After retessellation of defect 0 (v0=0), euler #=-106 (143479,426709,283124) : difference with theory (-103) = 3 

CORRECTING DEFECT 1 (vertices=191, convex hull=54, v0=193)
After retessellation of defect 1 (v0=193), euler #=-105 (143488,426756,283163) : difference with theory (-102) = 3 

CORRECTING DEFECT 2 (vertices=2299, convex hull=401, v0=263)
L defect detected...
After retessellation of defect 2 (v0=263), euler #=-104 (143604,427306,283598) : difference with theory (-101) = 3 

CORRECTING DEFECT 3 (vertices=294, convex hull=203, v0=930)
After retessellation of defect 3 (v0=930), euler #=-103 (143690,427668,283875) : difference with theory (-100) = 3 

CORRECTING DEFECT 4 (vertices=43, convex hull=99, v0=3011)
After retessellation of defect 4 (v0=3011), euler #=-102 (143717,427790,283971) : difference with theory (-99) = 3 

CORRECTING DEFECT 5 (vertices=424, convex hull=254, v0=3036)
After retessellation of defect 5 (v0=3036), euler #=-101 (143805,428181,284275) : difference with theory (-98) = 3 

CORRECTING DEFECT 6 (vertices=83, convex hull=36, v0=6709)
After retessellation of defect 6 (v0=6709), euler #=-100 (143812,428215,284303) : difference with theory (-97) = 3 

CORRECTING DEFECT 7 (vertices=84, convex hull=146, v0=8282)
After retessellation of defect 7 (v0=8282), euler #=-99 (143867,428445,284479) : difference with theory (-96) = 3 

CORRECTING DEFECT 8 (vertices=110, convex hull=98, v0=8559)
After retessellation of defect 8 (v0=8559), euler #=-98 (143894,428573,284581) : difference with theory (-95) = 3 

CORRECTING DEFECT 9 (vertices=121, convex hull=50, v0=8829)
After retessellation of defect 9 (v0=8829), euler #=-97 (143903,428622,284622) : difference with theory (-94) = 3 

CORRECTING DEFECT 10 (vertices=67, convex hull=124, v0=10505)
After retessellation of defect 10 (v0=10505), euler #=-96 (143937,428777,284744) : difference with theory (-93) = 3 

CORRECTING DEFECT 11 (vertices=13, convex hull=32, v0=10631)
After retessellation of defect 11 (v0=10631), euler #=-95 (143939,428792,284758) : difference with theory (-92) = 3 

CORRECTING DEFECT 12 (vertices=28, convex hull=54, v0=10715)
After retessellation of defect 12 (v0=10715), euler #=-94 (143955,428864,284815) : difference with theory (-91) = 3 

CORRECTING DEFECT 13 (vertices=41, convex hull=58, v0=11327)
After retessellation of defect 13 (v0=11327), euler #=-93 (143966,428921,284862) : difference with theory (-90) = 3 

CORRECTING DEFECT 14 (vertices=28, convex hull=60, v0=11781)
After retessellation of defect 14 (v0=11781), euler #=-92 (143982,428994,284920) : difference with theory (-89) = 3 

CORRECTING DEFECT 15 (vertices=5, convex hull=24, v0=13508)
After retessellation of defect 15 (v0=13508), euler #=-91 (143982,429000,284927) : difference with theory (-88) = 3 

CORRECTING DEFECT 16 (vertices=7, convex hull=19, v0=13681)
After retessellation of defect 16 (v0=13681), euler #=-90 (143983,429008,284935) : difference with theory (-87) = 3 

CORRECTING DEFECT 17 (vertices=36, convex hull=73, v0=13683)
After retessellation of defect 17 (v0=13683), euler #=-89 (144003,429102,285010) : difference with theory (-86) = 3 

CORRECTING DEFECT 18 (vertices=6, convex hull=28, v0=13878)
After retessellation of defect 18 (v0=13878), euler #=-88 (144004,429115,285023) : difference with theory (-85) = 3 

CORRECTING DEFECT 19 (vertices=65, convex hull=79, v0=14563)
After retessellation of defect 19 (v0=14563), euler #=-87 (144031,429225,285107) : difference with theory (-84) = 3 

CORRECTING DEFECT 20 (vertices=48, convex hull=91, v0=15377)
After retessellation of defect 20 (v0=15377), euler #=-86 (144049,429315,285180) : difference with theory (-83) = 3 

CORRECTING DEFECT 21 (vertices=32, convex hull=72, v0=15976)
After retessellation of defect 21 (v0=15976), euler #=-85 (144059,429373,285229) : difference with theory (-82) = 3 

CORRECTING DEFECT 22 (vertices=47, convex hull=61, v0=17042)
After retessellation of defect 22 (v0=17042), euler #=-84 (144071,429432,285277) : difference with theory (-81) = 3 

CORRECTING DEFECT 23 (vertices=15, convex hull=19, v0=17275)
After retessellation of defect 23 (v0=17275), euler #=-83 (144073,429444,285288) : difference with theory (-80) = 3 

CORRECTING DEFECT 24 (vertices=39, convex hull=63, v0=17515)
After retessellation of defect 24 (v0=17515), euler #=-82 (144088,429514,285344) : difference with theory (-79) = 3 

CORRECTING DEFECT 25 (vertices=54, convex hull=57, v0=18064)
After retessellation of defect 25 (v0=18064), euler #=-81 (144096,429562,285385) : difference with theory (-78) = 3 

CORRECTING DEFECT 26 (vertices=68, convex hull=107, v0=18157)
After retessellation of defect 26 (v0=18157), euler #=-80 (144115,429667,285472) : difference with theory (-77) = 3 

CORRECTING DEFECT 27 (vertices=80, convex hull=115, v0=18222)
After retessellation of defect 27 (v0=18222), euler #=-78 (144136,429783,285569) : difference with theory (-76) = 2 

CORRECTING DEFECT 28 (vertices=53, convex hull=83, v0=18424)
After retessellation of defect 28 (v0=18424), euler #=-77 (144149,429859,285633) : difference with theory (-75) = 2 

CORRECTING DEFECT 29 (vertices=23, convex hull=50, v0=19825)
After retessellation of defect 29 (v0=19825), euler #=-76 (144160,429912,285676) : difference with theory (-74) = 2 

CORRECTING DEFECT 30 (vertices=5, convex hull=21, v0=20701)
After retessellation of defect 30 (v0=20701), euler #=-75 (144160,429916,285681) : difference with theory (-73) = 2 

CORRECTING DEFECT 31 (vertices=58, convex hull=37, v0=26918)
After retessellation of defect 31 (v0=26918), euler #=-74 (144169,429961,285718) : difference with theory (-72) = 2 

CORRECTING DEFECT 32 (vertices=96, convex hull=94, v0=27829)
After retessellation of defect 32 (v0=27829), euler #=-72 (144199,430095,285824) : difference with theory (-71) = 1 

CORRECTING DEFECT 33 (vertices=65, convex hull=115, v0=28962)
After retessellation of defect 33 (v0=28962), euler #=-71 (144222,430215,285922) : difference with theory (-70) = 1 

CORRECTING DEFECT 34 (vertices=31, convex hull=63, v0=33390)
After retessellation of defect 34 (v0=33390), euler #=-70 (144232,430272,285970) : difference with theory (-69) = 1 

CORRECTING DEFECT 35 (vertices=21, convex hull=22, v0=35740)
After retessellation of defect 35 (v0=35740), euler #=-69 (144238,430296,285989) : difference with theory (-68) = 1 

CORRECTING DEFECT 36 (vertices=5, convex hull=28, v0=36219)
After retessellation of defect 36 (v0=36219), euler #=-68 (144240,430309,286001) : difference with theory (-67) = 1 

CORRECTING DEFECT 37 (vertices=45, convex hull=91, v0=37409)
After retessellation of defect 37 (v0=37409), euler #=-67 (144261,430412,286084) : difference with theory (-66) = 1 

CORRECTING DEFECT 38 (vertices=35, convex hull=64, v0=37486)
After retessellation of defect 38 (v0=37486), euler #=-66 (144273,430472,286133) : difference with theory (-65) = 1 

CORRECTING DEFECT 39 (vertices=41, convex hull=54, v0=40857)
After retessellation of defect 39 (v0=40857), euler #=-65 (144279,430510,286166) : difference with theory (-64) = 1 

CORRECTING DEFECT 40 (vertices=46, convex hull=87, v0=40911)
After retessellation of defect 40 (v0=40911), euler #=-64 (144298,430606,286244) : difference with theory (-63) = 1 

CORRECTING DEFECT 41 (vertices=62, convex hull=54, v0=41087)
After retessellation of defect 41 (v0=41087), euler #=-63 (144310,430663,286290) : difference with theory (-62) = 1 

CORRECTING DEFECT 42 (vertices=77, convex hull=126, v0=48132)
After retessellation of defect 42 (v0=48132), euler #=-62 (144343,430821,286416) : difference with theory (-61) = 1 

CORRECTING DEFECT 43 (vertices=44, convex hull=22, v0=48558)
After retessellation of defect 43 (v0=48558), euler #=-61 (144345,430830,286424) : difference with theory (-60) = 1 

CORRECTING DEFECT 44 (vertices=164, convex hull=91, v0=49860)
After retessellation of defect 44 (v0=49860), euler #=-60 (144382,430981,286539) : difference with theory (-59) = 1 

CORRECTING DEFECT 45 (vertices=20, convex hull=50, v0=53005)
After retessellation of defect 45 (v0=53005), euler #=-59 (144390,431023,286574) : difference with theory (-58) = 1 

CORRECTING DEFECT 46 (vertices=23, convex hull=40, v0=60142)
After retessellation of defect 46 (v0=60142), euler #=-58 (144393,431046,286595) : difference with theory (-57) = 1 

CORRECTING DEFECT 47 (vertices=54, convex hull=30, v0=63477)
After retessellation of defect 47 (v0=63477), euler #=-57 (144396,431064,286611) : difference with theory (-56) = 1 

CORRECTING DEFECT 48 (vertices=59, convex hull=49, v0=63573)
After retessellation of defect 48 (v0=63573), euler #=-56 (144405,431112,286651) : difference with theory (-55) = 1 

CORRECTING DEFECT 49 (vertices=41, convex hull=61, v0=70181)
After retessellation of defect 49 (v0=70181), euler #=-55 (144427,431202,286720) : difference with theory (-54) = 1 

CORRECTING DEFECT 50 (vertices=100, convex hull=188, v0=71247)
After retessellation of defect 50 (v0=71247), euler #=-53 (144445,431340,286842) : difference with theory (-53) = 0 

CORRECTING DEFECT 51 (vertices=190, convex hull=196, v0=74002)
After retessellation of defect 51 (v0=74002), euler #=-52 (144511,431644,287081) : difference with theory (-52) = 0 

CORRECTING DEFECT 52 (vertices=57, convex hull=39, v0=78918)
After retessellation of defect 52 (v0=78918), euler #=-51 (144517,431676,287108) : difference with theory (-51) = 0 

CORRECTING DEFECT 53 (vertices=169, convex hull=157, v0=82553)
After retessellation of defect 53 (v0=82553), euler #=-50 (144572,431913,287291) : difference with theory (-50) = 0 

CORRECTING DEFECT 54 (vertices=18, convex hull=26, v0=85711)
After retessellation of defect 54 (v0=85711), euler #=-49 (144575,431928,287304) : difference with theory (-49) = 0 

CORRECTING DEFECT 55 (vertices=40, convex hull=26, v0=86305)
After retessellation of defect 55 (v0=86305), euler #=-48 (144577,431943,287318) : difference with theory (-48) = 0 

CORRECTING DEFECT 56 (vertices=826, convex hull=316, v0=88817)
After retessellation of defect 56 (v0=88817), euler #=-49 (144770,432704,287885) : difference with theory (-47) = 2 

CORRECTING DEFECT 57 (vertices=5, convex hull=17, v0=90129)
After retessellation of defect 57 (v0=90129), euler #=-48 (144770,432708,287890) : difference with theory (-46) = 2 

CORRECTING DEFECT 58 (vertices=29, convex hull=20, v0=93790)
After retessellation of defect 58 (v0=93790), euler #=-47 (144771,432718,287900) : difference with theory (-45) = 2 

CORRECTING DEFECT 59 (vertices=44, convex hull=58, v0=96192)
After retessellation of defect 59 (v0=96192), euler #=-47 (144780,432772,287945) : difference with theory (-44) = 3 

CORRECTING DEFECT 60 (vertices=10, convex hull=31, v0=96200)
After retessellation of defect 60 (v0=96200), euler #=-46 (144782,432788,287960) : difference with theory (-43) = 3 

CORRECTING DEFECT 61 (vertices=98, convex hull=61, v0=96948)
After retessellation of defect 61 (v0=96948), euler #=-45 (144798,432860,288017) : difference with theory (-42) = 3 

CORRECTING DEFECT 62 (vertices=145, convex hull=63, v0=104194)
After retessellation of defect 62 (v0=104194), euler #=-44 (144821,432958,288093) : difference with theory (-41) = 3 

CORRECTING DEFECT 63 (vertices=14, convex hull=13, v0=105116)
After retessellation of defect 63 (v0=105116), euler #=-43 (144823,432967,288101) : difference with theory (-40) = 3 

CORRECTING DEFECT 64 (vertices=10, convex hull=16, v0=106317)
After retessellation of defect 64 (v0=106317), euler #=-42 (144824,432972,288106) : difference with theory (-39) = 3 

CORRECTING DEFECT 65 (vertices=75, convex hull=74, v0=108429)
After retessellation of defect 65 (v0=108429), euler #=-41 (144833,433032,288158) : difference with theory (-38) = 3 

CORRECTING DEFECT 66 (vertices=81, convex hull=109, v0=108776)
After retessellation of defect 66 (v0=108776), euler #=-39 (144854,433143,288250) : difference with theory (-37) = 2 

CORRECTING DEFECT 67 (vertices=48, convex hull=39, v0=109522)
After retessellation of defect 67 (v0=109522), euler #=-38 (144867,433198,288293) : difference with theory (-36) = 2 

CORRECTING DEFECT 68 (vertices=960, convex hull=309, v0=109741)
After retessellation of defect 68 (v0=109741), euler #=-37 (145081,434005,288887) : difference with theory (-35) = 2 

CORRECTING DEFECT 69 (vertices=43, convex hull=37, v0=110825)
After retessellation of defect 69 (v0=110825), euler #=-36 (145088,434040,288916) : difference with theory (-34) = 2 

CORRECTING DEFECT 70 (vertices=410, convex hull=273, v0=113424)
After retessellation of defect 70 (v0=113424), euler #=-34 (145224,434585,289327) : difference with theory (-33) = 1 

CORRECTING DEFECT 71 (vertices=369, convex hull=63, v0=116178)
After retessellation of defect 71 (v0=116178), euler #=-33 (145252,434695,289410) : difference with theory (-32) = 1 

CORRECTING DEFECT 72 (vertices=86, convex hull=57, v0=116819)
After retessellation of defect 72 (v0=116819), euler #=-32 (145265,434757,289460) : difference with theory (-31) = 1 

CORRECTING DEFECT 73 (vertices=54, convex hull=38, v0=116924)
After retessellation of defect 73 (v0=116924), euler #=-31 (145271,434789,289487) : difference with theory (-30) = 1 

CORRECTING DEFECT 74 (vertices=38, convex hull=53, v0=117013)
After retessellation of defect 74 (v0=117013), euler #=-30 (145284,434854,289540) : difference with theory (-29) = 1 

CORRECTING DEFECT 75 (vertices=1304, convex hull=489, v0=117165)
L defect detected...
After retessellation of defect 75 (v0=117165), euler #=-29 (145559,435956,290368) : difference with theory (-28) = 1 

CORRECTING DEFECT 76 (vertices=21, convex hull=22, v0=118194)
After retessellation of defect 76 (v0=118194), euler #=-28 (145560,435964,290376) : difference with theory (-27) = 1 

CORRECTING DEFECT 77 (vertices=173, convex hull=90, v0=118729)
After retessellation of defect 77 (v0=118729), euler #=-27 (145624,436198,290547) : difference with theory (-26) = 1 

CORRECTING DEFECT 78 (vertices=189, convex hull=185, v0=119160)
After retessellation of defect 78 (v0=119160), euler #=-26 (145724,436588,290838) : difference with theory (-25) = 1 

CORRECTING DEFECT 79 (vertices=39, convex hull=78, v0=121444)
After retessellation of defect 79 (v0=121444), euler #=-25 (145742,436675,290908) : difference with theory (-24) = 1 

CORRECTING DEFECT 80 (vertices=11, convex hull=23, v0=122201)
After retessellation of defect 80 (v0=122201), euler #=-24 (145746,436693,290923) : difference with theory (-23) = 1 

CORRECTING DEFECT 81 (vertices=6, convex hull=29, v0=123484)
After retessellation of defect 81 (v0=123484), euler #=-23 (145747,436706,290936) : difference with theory (-22) = 1 

CORRECTING DEFECT 82 (vertices=37, convex hull=83, v0=124537)
After retessellation of defect 82 (v0=124537), euler #=-22 (145764,436794,291008) : difference with theory (-21) = 1 

CORRECTING DEFECT 83 (vertices=126, convex hull=34, v0=124645)
After retessellation of defect 83 (v0=124645), euler #=-21 (145771,436827,291035) : difference with theory (-20) = 1 

CORRECTING DEFECT 84 (vertices=221, convex hull=96, v0=124704)
After retessellation of defect 84 (v0=124704), euler #=-20 (145818,437010,291172) : difference with theory (-19) = 1 

CORRECTING DEFECT 85 (vertices=6, convex hull=20, v0=128887)
After retessellation of defect 85 (v0=128887), euler #=-19 (145820,437020,291181) : difference with theory (-18) = 1 

CORRECTING DEFECT 86 (vertices=52, convex hull=35, v0=129634)
After retessellation of defect 86 (v0=129634), euler #=-18 (145825,437048,291205) : difference with theory (-17) = 1 

CORRECTING DEFECT 87 (vertices=39, convex hull=51, v0=129683)
After retessellation of defect 87 (v0=129683), euler #=-17 (145833,437093,291243) : difference with theory (-16) = 1 

CORRECTING DEFECT 88 (vertices=5, convex hull=23, v0=134320)
After retessellation of defect 88 (v0=134320), euler #=-16 (145835,437104,291253) : difference with theory (-15) = 1 

CORRECTING DEFECT 89 (vertices=222, convex hull=97, v0=135039)
After retessellation of defect 89 (v0=135039), euler #=-15 (145870,437248,291363) : difference with theory (-14) = 1 

CORRECTING DEFECT 90 (vertices=73, convex hull=29, v0=135594)
After retessellation of defect 90 (v0=135594), euler #=-14 (145871,437259,291374) : difference with theory (-13) = 1 

CORRECTING DEFECT 91 (vertices=34, convex hull=70, v0=140104)
After retessellation of defect 91 (v0=140104), euler #=-13 (145881,437317,291423) : difference with theory (-12) = 1 

CORRECTING DEFECT 92 (vertices=92, convex hull=101, v0=141361)
After retessellation of defect 92 (v0=141361), euler #=-11 (145914,437465,291540) : difference with theory (-11) = 0 

CORRECTING DEFECT 93 (vertices=21, convex hull=47, v0=141601)
After retessellation of defect 93 (v0=141601), euler #=-10 (145922,437505,291573) : difference with theory (-10) = 0 

CORRECTING DEFECT 94 (vertices=24, convex hull=34, v0=143942)
After retessellation of defect 94 (v0=143942), euler #=-9 (145927,437532,291596) : difference with theory (-9) = 0 

CORRECTING DEFECT 95 (vertices=138, convex hull=81, v0=146756)
After retessellation of defect 95 (v0=146756), euler #=-8 (145954,437651,291689) : difference with theory (-8) = 0 

CORRECTING DEFECT 96 (vertices=6, convex hull=18, v0=147221)
After retessellation of defect 96 (v0=147221), euler #=-7 (145956,437663,291700) : difference with theory (-7) = 0 

CORRECTING DEFECT 97 (vertices=32, convex hull=71, v0=148995)
After retessellation of defect 97 (v0=148995), euler #=-6 (145965,437717,291746) : difference with theory (-6) = 0 

CORRECTING DEFECT 98 (vertices=56, convex hull=80, v0=152791)
After retessellation of defect 98 (v0=152791), euler #=-5 (145986,437814,291823) : difference with theory (-5) = 0 

CORRECTING DEFECT 99 (vertices=21, convex hull=52, v0=153663)
After retessellation of defect 99 (v0=153663), euler #=-4 (145997,437868,291867) : difference with theory (-4) = 0 

CORRECTING DEFECT 100 (vertices=15, convex hull=29, v0=153767)
After retessellation of defect 100 (v0=153767), euler #=-3 (145998,437879,291878) : difference with theory (-3) = 0 

CORRECTING DEFECT 101 (vertices=60, convex hull=67, v0=154159)
After retessellation of defect 101 (v0=154159), euler #=-2 (146021,437974,291951) : difference with theory (-2) = 0 

CORRECTING DEFECT 102 (vertices=125, convex hull=49, v0=155094)
After retessellation of defect 102 (v0=155094), euler #=-1 (146027,438013,291985) : difference with theory (-1) = 0 

CORRECTING DEFECT 103 (vertices=83, convex hull=83, v0=155516)
After retessellation of defect 103 (v0=155516), euler #=0 (146043,438100,292057) : difference with theory (0) = 0 

CORRECTING DEFECT 104 (vertices=15, convex hull=25, v0=155775)
After retessellation of defect 104 (v0=155775), euler #=1 (146044,438111,292068) : difference with theory (1) = 0 

CORRECTING DEFECT 105 (vertices=174, convex hull=55, v0=155942)
After retessellation of defect 105 (v0=155942), euler #=2 (146055,438159,292106) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.26 (0.04-->9.03) (max @ vno 113945 --> 151574)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.26 (0.04-->9.03) (max @ vno 113945 --> 151574)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
320 mutations (35.2%), 590 crossovers (64.8%), 654 vertices were eliminated
building final representation...
10577 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=146055, nf=292106, ne=438159, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 76.5 minutes
0 defective edges
removing intersecting faces
000: 837 intersecting
001: 37 intersecting
002: 4 intersecting
mris_fix_topology utimesec    4590.306167
mris_fix_topology stimesec    0.227965
mris_fix_topology ru_maxrss   511448
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   63752
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  14504
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    646
mris_fix_topology ru_nivcsw   8391
FSRUNTIME@ mris_fix_topology rh  1.2748 hours 1 threads
PIDs (27782 27785) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 146952 - 440850 + 293900 = 2 --> 0 holes
      F =2V-4:          293900 = 293904-4 (0)
      2E=3F:            881700 = 881700 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 146055 - 438159 + 292106 = 2 --> 0 holes
      F =2V-4:          292106 = 292110-4 (0)
      2E=3F:            876318 = 876318 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 84 intersecting
001: 5 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 154 intersecting
001: 18 intersecting
002: 4 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 04:52:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050345 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 04:52:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050345 rh 

Waiting for PID 32511 of (32511 32514) to complete...
Waiting for PID 32514 of (32511 32514) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050345 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-6.0.0/0050345/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
16412 bright wm thresholded.
1844 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.orig...
computing class statistics...
border white:    279082 voxels (1.66%)
border gray      336333 voxels (2.00%)
WM (95.0): 95.9 +- 8.5 [70.0 --> 110.0]
GM (71.0) : 70.0 +- 11.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 56.0 (was 70)
setting MAX_BORDER_WHITE to 108.5 (was 105)
setting MIN_BORDER_WHITE to 67.0 (was 85)
setting MAX_CSF to 45.0 (was 40)
setting MAX_GRAY to 91.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 56.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.02-->4.85) (max @ vno 13670 --> 145404)
face area 0.28 +- 0.13 (0.00-->2.75)
mean absolute distance = 0.73 +- 0.91
4637 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=67+-8.7
mean inside = 91.7, mean outside = 74.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.1, 177 (177) missing vertices, mean dist 0.3 [0.6 (%35.6)->0.8 (%64.4))]
%67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.10-->5.08) (max @ vno 13670 --> 145404)
face area 0.28 +- 0.13 (0.00-->3.32)
mean absolute distance = 0.41 +- 0.71
5999 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3379890.8, rms=9.909
001: dt: 0.5000, sse=1975561.5, rms=7.041 (28.944%)
002: dt: 0.5000, sse=1368478.9, rms=5.297 (24.768%)
003: dt: 0.5000, sse=1103437.6, rms=4.326 (18.338%)
004: dt: 0.5000, sse=992012.6, rms=3.812 (11.881%)
005: dt: 0.5000, sse=948633.8, rms=3.596 (5.652%)
006: dt: 0.5000, sse=932556.2, rms=3.470 (3.504%)
rms = 3.43, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=925975.7, rms=3.433 (1.069%)
008: dt: 0.2500, sse=756778.0, rms=2.386 (30.490%)
009: dt: 0.2500, sse=720660.6, rms=2.120 (11.162%)
010: dt: 0.2500, sse=714715.6, rms=2.048 (3.416%)
011: dt: 0.2500, sse=724681.2, rms=1.991 (2.747%)
rms = 1.96, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=707891.2, rms=1.962 (1.486%)
rms = 1.93, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=699578.6, rms=1.927 (1.788%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 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
mean border=81.8, 173 (63) missing vertices, mean dist -0.2 [0.5 (%68.2)->0.3 (%31.8))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.07-->4.72) (max @ vno 13670 --> 145404)
face area 0.35 +- 0.17 (0.00-->4.36)
mean absolute distance = 0.32 +- 0.51
5132 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1294371.2, rms=4.392
014: dt: 0.5000, sse=1018239.2, rms=3.013 (31.400%)
015: dt: 0.5000, sse=988868.1, rms=2.928 (2.815%)
rms = 2.93, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=892961.2, rms=2.255 (22.992%)
017: dt: 0.2500, sse=858806.1, rms=1.865 (17.305%)
018: dt: 0.2500, sse=841602.9, rms=1.758 (5.740%)
019: dt: 0.2500, sse=834451.8, rms=1.693 (3.680%)
rms = 1.64, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=828503.1, rms=1.644 (2.907%)
rms = 1.59, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=823735.7, rms=1.594 (3.009%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 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
mean border=83.5, 203 (42) missing vertices, mean dist -0.1 [0.4 (%62.3)->0.2 (%37.7))]
%80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.06-->4.51) (max @ vno 13670 --> 145404)
face area 0.34 +- 0.17 (0.00-->4.36)
mean absolute distance = 0.29 +- 0.43
4471 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=968915.1, rms=2.909
022: dt: 0.5000, sse=906716.3, rms=2.364 (18.744%)
rms = 2.53, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=828298.0, rms=1.821 (22.955%)
024: dt: 0.2500, sse=809358.5, rms=1.547 (15.051%)
025: dt: 0.2500, sse=795942.3, rms=1.469 (5.018%)
rms = 1.44, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=799739.5, rms=1.444 (1.717%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=786684.1, rms=1.404 (2.750%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=84.3, 281 (30) missing vertices, mean dist -0.1 [0.3 (%54.4)->0.3 (%45.6))]
%83 local maxima, %12 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-6.0.0/0050345/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=814822.0, rms=1.825
028: dt: 0.5000, sse=823581.9, rms=1.689 (7.466%)
rms = 2.14, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=766951.8, rms=1.263 (25.217%)
030: dt: 0.2500, sse=765187.3, rms=1.176 (6.914%)
031: dt: 0.2500, sse=754516.8, rms=1.111 (5.537%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
rms = 1.09, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=751732.1, rms=1.093 (1.563%)
positioning took 0.7 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7659 vertices
erasing segment 0 (vno[0] = 38838)
erasing segment 2 (vno[0] = 56832)
erasing segment 3 (vno[0] = 57974)
erasing segment 4 (vno[0] = 61344)
erasing segment 5 (vno[0] = 86008)
erasing segment 6 (vno[0] = 103149)
erasing segment 7 (vno[0] = 104238)
erasing segment 8 (vno[0] = 105281)
erasing segment 9 (vno[0] = 109375)
erasing segment 10 (vno[0] = 111586)
erasing segment 11 (vno[0] = 115366)
erasing segment 12 (vno[0] = 117802)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.area
vertex spacing 0.90 +- 0.26 (0.02-->4.42) (max @ vno 21270 --> 145576)
face area 0.34 +- 0.16 (0.00-->4.58)
refinement took 5.6 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050345 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-6.0.0/0050345/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
16412 bright wm thresholded.
1844 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.orig...
computing class statistics...
border white:    279082 voxels (1.66%)
border gray      336333 voxels (2.00%)
WM (95.0): 95.9 +- 8.5 [70.0 --> 110.0]
GM (71.0) : 70.0 +- 11.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 54.0 (was 70)
setting MAX_BORDER_WHITE to 108.5 (was 105)
setting MIN_BORDER_WHITE to 65.0 (was 85)
setting MAX_CSF to 43.0 (was 40)
setting MAX_GRAY to 91.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 54.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.9 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.03-->6.58) (max @ vno 144909 --> 145002)
face area 0.28 +- 0.13 (0.00-->8.53)
mean absolute distance = 0.72 +- 0.87
4732 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=65+-9.6
mean inside = 91.7, mean outside = 74.2
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=78.3, 236 (236) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))]
%71 local maxima, %24 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 +- 0.27 (0.10-->6.22) (max @ vno 144909 --> 145002)
face area 0.28 +- 0.14 (0.00-->6.40)
mean absolute distance = 0.38 +- 0.67
4984 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3671441.0, rms=10.442
001: dt: 0.5000, sse=2253549.8, rms=7.751 (25.769%)
002: dt: 0.5000, sse=1595388.5, rms=6.048 (21.976%)
003: dt: 0.5000, sse=1253238.6, rms=4.932 (18.455%)
004: dt: 0.5000, sse=1079752.8, rms=4.251 (13.797%)
005: dt: 0.5000, sse=998955.6, rms=3.881 (8.722%)
006: dt: 0.5000, sse=955781.9, rms=3.686 (5.022%)
007: dt: 0.5000, sse=936540.7, rms=3.589 (2.625%)
008: dt: 0.5000, sse=923599.4, rms=3.511 (2.177%)
rms = 3.47, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=915930.6, rms=3.470 (1.175%)
010: dt: 0.2500, sse=756942.4, rms=2.385 (31.268%)
011: dt: 0.2500, sse=720198.6, rms=2.126 (10.856%)
012: dt: 0.2500, sse=710207.6, rms=2.044 (3.842%)
013: dt: 0.2500, sse=703212.2, rms=1.979 (3.204%)
rms = 1.95, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=702958.8, rms=1.948 (1.540%)
015: dt: 0.1250, sse=697201.6, rms=1.886 (3.197%)
rms = 1.86, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=690405.8, rms=1.858 (1.464%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
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=80.7, 209 (80) missing vertices, mean dist -0.2 [0.4 (%66.2)->0.3 (%33.8))]
%76 local maxima, %19 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 +- 0.27 (0.07-->6.21) (max @ vno 144909 --> 145002)
face area 0.36 +- 0.18 (0.00-->8.88)
mean absolute distance = 0.31 +- 0.49
4722 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1261247.6, rms=4.238
017: dt: 0.5000, sse=1012614.2, rms=2.941 (30.585%)
rms = 2.94, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=1010403.8, rms=2.938 (0.103%)
019: dt: 0.2500, sse=867504.4, rms=1.932 (34.252%)
020: dt: 0.2500, sse=878319.6, rms=1.724 (10.783%)
021: dt: 0.2500, sse=843222.9, rms=1.670 (3.092%)
rms = 1.62, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=832575.7, rms=1.622 (2.900%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=828349.5, rms=1.572 (3.071%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
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 1 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=82.3, 209 (41) missing vertices, mean dist -0.1 [0.4 (%60.6)->0.3 (%39.4))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.91 +- 0.26 (0.08-->6.09) (max @ vno 144909 --> 145002)
face area 0.35 +- 0.18 (0.00-->8.64)
mean absolute distance = 0.29 +- 0.43
4604 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=958314.5, rms=2.789
024: dt: 0.5000, sse=903636.6, rms=2.393 (14.195%)
rms = 2.61, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=832415.7, rms=1.805 (24.577%)
026: dt: 0.2500, sse=810611.2, rms=1.538 (14.794%)
027: dt: 0.2500, sse=800596.9, rms=1.459 (5.160%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
rms = 1.43, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=797540.6, rms=1.431 (1.866%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.0, 243 (30) missing vertices, mean dist -0.1 [0.3 (%53.6)->0.3 (%46.4))]
%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-6.0.0/0050345/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=827601.6, rms=1.861
rms = 1.82, time step reduction 1 of 3 to 0.250...
029: dt: 0.5000, sse=826344.9, rms=1.823 (2.021%)
030: dt: 0.2500, sse=785634.1, rms=1.383 (24.169%)
031: dt: 0.2500, sse=772510.2, rms=1.266 (8.403%)
rms = 1.28, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=766201.7, rms=1.187 (6.277%)
033: dt: 0.1250, sse=761657.2, rms=1.077 (9.285%)
rms = 1.06, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=762785.3, rms=1.064 (1.168%)
positioning took 0.7 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 7982 vertices
erasing segment 0 (vno[0] = 40533)
erasing segment 1 (vno[0] = 45250)
erasing segment 2 (vno[0] = 45324)
erasing segment 4 (vno[0] = 62543)
erasing segment 5 (vno[0] = 72780)
erasing segment 6 (vno[0] = 107651)
erasing segment 7 (vno[0] = 107737)
erasing segment 8 (vno[0] = 110531)
erasing segment 9 (vno[0] = 113014)
erasing segment 10 (vno[0] = 114776)
erasing segment 11 (vno[0] = 126483)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.area
vertex spacing 0.91 +- 0.26 (0.03-->5.89) (max @ vno 144909 --> 145002)
face area 0.35 +- 0.17 (0.00-->8.16)
refinement took 5.7 minutes
PIDs (32511 32514) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 04:58:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 04:58:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

Waiting for PID 317 of (317 320) to complete...
Waiting for PID 320 of (317 320) 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 (317 320) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 04:58:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 04:58:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 363 of (363 366) to complete...
Waiting for PID 366 of (363 366) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 48.6 mm, total surface area = 89421 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.183 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.101 (target=0.015)   
step 015: RMS=0.082 (target=0.015)   
step 020: RMS=0.071 (target=0.015)   
step 025: RMS=0.060 (target=0.015)   
step 030: RMS=0.051 (target=0.015)   
step 035: RMS=0.043 (target=0.015)   
step 040: RMS=0.038 (target=0.015)   
step 045: RMS=0.034 (target=0.015)   
step 050: RMS=0.031 (target=0.015)   
step 055: RMS=0.029 (target=0.015)   
step 060: RMS=0.028 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    46.275964
mris_inflate stimesec    0.094985
mris_inflate ru_maxrss   215060
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30835
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11512
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2263
mris_inflate ru_nivcsw   3953

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 47.7 mm, total surface area = 90278 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.187 (target=0.015)   
step 005: RMS=0.132 (target=0.015)   
step 010: RMS=0.104 (target=0.015)   
step 015: RMS=0.087 (target=0.015)   
step 020: RMS=0.073 (target=0.015)   
step 025: RMS=0.062 (target=0.015)   
step 030: RMS=0.051 (target=0.015)   
step 035: RMS=0.044 (target=0.015)   
step 040: RMS=0.039 (target=0.015)   
step 045: RMS=0.034 (target=0.015)   
step 050: RMS=0.031 (target=0.015)   
step 055: RMS=0.030 (target=0.015)   
step 060: RMS=0.028 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    46.262966
mris_inflate stimesec    0.083987
mris_inflate ru_maxrss   214012
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31594
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11440
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2237
mris_inflate ru_nivcsw   3499
PIDs (363 366) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 04:59:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 04:59:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 463 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 466 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 469 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 472 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 475 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 478 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 481 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 484 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 487 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 490 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 494 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...
Waiting for PID 497 of (463 466 469 472 475 478 481 484 487 490 494 497) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 25.797*4pi (324.173) --> -25 handles
ICI = 240.0, FI = 1900.8, variation=31680.640
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
178 vertices thresholded to be in k1 ~ [-0.37 0.41], k2 ~ [-0.13 0.22]
total integrated curvature = 0.316*4pi (3.973) --> 1 handles
ICI = 1.3, FI = 9.6, variation=161.707
165 vertices thresholded to be in [-0.04 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
134 vertices thresholded to be in [-0.16 0.18]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 34.452*4pi (432.936) --> -33 handles
ICI = 255.6, FI = 1955.2, variation=32784.649
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
191 vertices thresholded to be in k1 ~ [-0.34 0.35], k2 ~ [-0.11 0.10]
total integrated curvature = 0.352*4pi (4.424) --> 1 handles
ICI = 1.4, FI = 9.4, variation=161.810
142 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
133 vertices thresholded to be in [-0.14 0.17]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023
done.
PIDs (463 466 469 472 475 478 481 484 487 490 494 497) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 05:00:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050345 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      [ 0050345/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                      [ 308 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.368580
WARN:    S explicit min:                          0.000000	vertex = 447

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 05:00:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050345 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      [ 0050345/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                      [ 297 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.651223
WARN:    S explicit min:                          0.000000	vertex = 22
#--------------------------------------------
#@# Sphere lh Sun Oct  8 05:00:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 05:00:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 656 of (656 660) to complete...
Waiting for PID 660 of (656 660) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere

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

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.287...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.12
pass 1: epoch 2 of 3 starting distance error %20.08
unfolding complete - removing small folds...
starting distance error %19.98
removing remaining folds...
final distance error %20.01
MRISunfold() return, current seed 1234
-01: dt=0.0000, 243 negative triangles
200: dt=0.9900, 243 negative triangles
201: dt=0.9900, 116 negative triangles
202: dt=0.9900, 69 negative triangles
203: dt=0.9900, 69 negative triangles
204: dt=0.9900, 65 negative triangles
205: dt=0.9900, 47 negative triangles
206: dt=0.9900, 39 negative triangles
207: dt=0.9900, 36 negative triangles
208: dt=0.9900, 39 negative triangles
209: dt=0.9900, 28 negative triangles
210: dt=0.9900, 28 negative triangles
211: dt=0.9900, 29 negative triangles
212: dt=0.9900, 19 negative triangles
213: dt=0.9900, 18 negative triangles
214: dt=0.9900, 18 negative triangles
215: dt=0.9900, 18 negative triangles
216: dt=0.9900, 12 negative triangles
217: dt=0.9900, 6 negative triangles
218: dt=0.9900, 7 negative triangles
219: dt=0.9900, 9 negative triangles
220: dt=0.9900, 4 negative triangles
221: dt=0.9900, 5 negative triangles
222: dt=0.9900, 4 negative triangles
223: dt=0.9900, 4 negative triangles
224: dt=0.9900, 3 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.09 hours
mris_sphere utimesec    3928.302807
mris_sphere stimesec    1.234812
mris_sphere ru_maxrss   302108
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   53259
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10384
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    171066
mris_sphere ru_nivcsw   315790
FSRUNTIME@ mris_sphere  1.0907 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere

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

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.286...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.48
pass 1: epoch 2 of 3 starting distance error %21.36
unfolding complete - removing small folds...
starting distance error %21.13
removing remaining folds...
final distance error %21.16
MRISunfold() return, current seed 1234
-01: dt=0.0000, 211 negative triangles
240: dt=0.9900, 211 negative triangles
241: dt=0.9900, 105 negative triangles
242: dt=0.9900, 78 negative triangles
243: dt=0.9900, 52 negative triangles
244: dt=0.9900, 45 negative triangles
245: dt=0.9900, 37 negative triangles
246: dt=0.9900, 32 negative triangles
247: dt=0.9900, 34 negative triangles
248: dt=0.9900, 26 negative triangles
249: dt=0.9900, 29 negative triangles
250: dt=0.9900, 25 negative triangles
251: dt=0.9900, 20 negative triangles
252: dt=0.9900, 15 negative triangles
253: dt=0.9900, 11 negative triangles
254: dt=0.9900, 4 negative triangles
255: dt=0.9900, 11 negative triangles
256: dt=0.9900, 9 negative triangles
257: dt=0.9900, 7 negative triangles
258: dt=0.9900, 8 negative triangles
259: dt=0.9900, 2 negative triangles
260: dt=0.9900, 6 negative triangles
261: dt=0.9900, 7 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.09 hours
mris_sphere utimesec    3937.961338
mris_sphere stimesec    1.079835
mris_sphere ru_maxrss   300080
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   52758
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10312
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    143984
mris_sphere ru_nivcsw   324798
FSRUNTIME@ mris_sphere  1.0925 hours 1 threads
PIDs (656 660) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 06:06:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 06:06:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 3851 of (3851 3854) to complete...
Waiting for PID 3854 of (3851 3854) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 5.691
curvature mean = 0.033, std = 0.817
curvature mean = 0.018, std = 0.855
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, -16.00) sse = 331564.4, tmin=1.1276
  d=32.00 min @ (0.00, 0.00, 8.00) sse = 265948.8, tmin=2.2837
  d=16.00 min @ (-4.00, 0.00, 0.00) sse = 251332.0, tmin=3.4492
  d=8.00 min @ (2.00, 2.00, 0.00) sse = 245163.3, tmin=4.6226
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 244720.6, tmin=5.8071
  d=2.00 min @ (0.50, -0.50, -0.50) sse = 243937.9, tmin=6.9949
  d=1.00 min @ (0.00, 0.25, 0.00) sse = 243921.4, tmin=8.1784
  d=0.50 min @ (0.00, -0.12, 0.12) sse = 243868.0, tmin=9.3652
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.37 min
curvature mean = 0.015, std = 0.835
curvature mean = 0.006, std = 0.946
curvature mean = 0.012, std = 0.846
curvature mean = 0.002, std = 0.978
curvature mean = 0.012, std = 0.849
curvature mean = 0.001, std = 0.991
2 Reading smoothwm
curvature mean = -0.034, std = 0.304
curvature mean = 0.042, std = 0.248
curvature mean = 0.068, std = 0.334
curvature mean = 0.035, std = 0.305
curvature mean = 0.048, std = 0.509
curvature mean = 0.034, std = 0.332
curvature mean = 0.029, std = 0.645
curvature mean = 0.034, std = 0.343
curvature mean = 0.011, std = 0.755
MRISregister() return, current seed 0
-01: dt=0.0000, 92 negative triangles
126: dt=0.9900, 92 negative triangles
expanding nbhd size to 1
127: dt=0.9900, 124 negative triangles
128: dt=0.9900, 92 negative triangles
129: dt=0.9900, 93 negative triangles
130: dt=0.9405, 97 negative triangles
131: dt=0.9405, 92 negative triangles
132: dt=0.9405, 88 negative triangles
133: dt=0.9405, 81 negative triangles
134: dt=0.9405, 76 negative triangles
135: dt=0.9405, 74 negative triangles
136: dt=0.9405, 63 negative triangles
137: dt=0.9405, 67 negative triangles
138: dt=0.9405, 64 negative triangles
139: dt=0.9405, 54 negative triangles
140: dt=0.9405, 49 negative triangles
141: dt=0.9405, 47 negative triangles
142: dt=0.9405, 45 negative triangles
143: dt=0.9405, 47 negative triangles
144: dt=0.9405, 43 negative triangles
145: dt=0.9405, 35 negative triangles
146: dt=0.9405, 34 negative triangles
147: dt=0.9405, 32 negative triangles
148: dt=0.9405, 32 negative triangles
149: dt=0.9405, 27 negative triangles
150: dt=0.9405, 29 negative triangles
151: dt=0.9405, 27 negative triangles
152: dt=0.9405, 26 negative triangles
153: dt=0.9405, 24 negative triangles
154: dt=0.9405, 22 negative triangles
155: dt=0.9405, 22 negative triangles
156: dt=0.9405, 22 negative triangles
157: dt=0.9405, 19 negative triangles
158: dt=0.9405, 17 negative triangles
159: dt=0.9405, 16 negative triangles
160: dt=0.9405, 15 negative triangles
161: dt=0.9405, 16 negative triangles
162: dt=0.9405, 16 negative triangles
163: dt=0.9405, 14 negative triangles
164: dt=0.9405, 14 negative triangles
165: dt=0.9405, 12 negative triangles
166: dt=0.9405, 12 negative triangles
167: dt=0.9405, 10 negative triangles
168: dt=0.9405, 10 negative triangles
169: dt=0.9405, 10 negative triangles
170: dt=0.9405, 11 negative triangles
171: dt=0.9405, 11 negative triangles
172: dt=0.9405, 12 negative triangles
173: dt=0.9405, 11 negative triangles
174: dt=0.9405, 12 negative triangles
175: dt=0.9405, 10 negative triangles
176: dt=0.9405, 10 negative triangles
177: dt=0.9405, 9 negative triangles
178: dt=0.9405, 9 negative triangles
179: dt=0.9405, 9 negative triangles
180: dt=0.9405, 9 negative triangles
181: dt=0.9405, 9 negative triangles
182: dt=0.9405, 10 negative triangles
183: dt=0.9405, 10 negative triangles
184: dt=0.9405, 11 negative triangles
185: dt=0.9405, 10 negative triangles
186: dt=0.9405, 11 negative triangles
187: dt=0.9405, 7 negative triangles
188: dt=0.9405, 7 negative triangles
189: dt=0.9405, 7 negative triangles
190: dt=0.9405, 7 negative triangles
191: dt=0.9405, 7 negative triangles
192: dt=0.9405, 7 negative triangles
193: dt=0.9405, 7 negative triangles
194: dt=0.9405, 7 negative triangles
195: dt=0.9405, 6 negative triangles
196: dt=0.9405, 6 negative triangles
197: dt=0.9405, 6 negative triangles
198: dt=0.9405, 7 negative triangles
199: dt=0.9405, 5 negative triangles
200: dt=0.9405, 5 negative triangles
201: dt=0.9405, 5 negative triangles
202: dt=0.9405, 3 negative triangles
203: dt=0.9405, 3 negative triangles
204: dt=0.9405, 3 negative triangles
205: dt=0.9405, 3 negative triangles
206: dt=0.9405, 3 negative triangles
207: dt=0.9405, 1 negative triangles
208: dt=0.9405, 2 negative triangles
209: dt=0.9405, 1 negative triangles
210: dt=0.9405, 2 negative triangles
211: dt=0.9405, 1 negative triangles
212: dt=0.9405, 2 negative triangles
213: dt=0.9405, 1 negative triangles
214: dt=0.9405, 1 negative triangles
215: dt=0.9405, 1 negative triangles
216: dt=0.9405, 1 negative triangles
217: dt=0.8935, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.32 hours
mris_register utimesec    4740.439343
mris_register stimesec    2.231660
mris_register ru_maxrss   269196
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38402
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10456
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    356366
mris_register ru_nivcsw   235255
FSRUNTIME@ mris_register  1.3169 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 5.717
curvature mean = 0.017, std = 0.806
curvature mean = 0.013, std = 0.856
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 334337.8, tmin=1.1230
  d=32.00 min @ (-8.00, -8.00, 8.00) sse = 286918.8, tmin=2.2669
  d=16.00 min @ (0.00, 4.00, 0.00) sse = 259769.7, tmin=3.4287
  d=8.00 min @ (2.00, 0.00, -2.00) sse = 249457.7, tmin=4.5939
  d=4.00 min @ (0.00, 0.00, 1.00) sse = 248595.9, tmin=5.7679
  d=2.00 min @ (-0.50, 0.00, -0.50) sse = 248199.9, tmin=6.9460
  d=1.00 min @ (0.25, 0.25, 0.25) sse = 248006.9, tmin=8.1249
  d=0.50 min @ (0.00, 0.00, -0.12) sse = 247994.5, tmin=9.3194
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.32 min
curvature mean = -0.008, std = 0.817
curvature mean = 0.005, std = 0.945
curvature mean = -0.014, std = 0.827
curvature mean = 0.002, std = 0.978
curvature mean = -0.015, std = 0.828
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.036, std = 0.299
curvature mean = 0.032, std = 0.240
curvature mean = 0.069, std = 0.345
curvature mean = 0.028, std = 0.298
curvature mean = 0.053, std = 0.514
curvature mean = 0.027, std = 0.324
curvature mean = 0.031, std = 0.653
curvature mean = 0.027, std = 0.335
curvature mean = 0.012, std = 0.766
MRISregister() return, current seed 0
-01: dt=0.0000, 112 negative triangles
124: dt=0.9900, 112 negative triangles
expanding nbhd size to 1
125: dt=0.9900, 148 negative triangles
126: dt=0.9900, 119 negative triangles
127: dt=0.9900, 107 negative triangles
128: dt=0.9900, 124 negative triangles
129: dt=0.9900, 111 negative triangles
130: dt=0.9900, 115 negative triangles
131: dt=0.9900, 107 negative triangles
132: dt=0.9900, 92 negative triangles
133: dt=0.9900, 85 negative triangles
134: dt=0.9900, 72 negative triangles
135: dt=0.9900, 70 negative triangles
136: dt=0.9900, 66 negative triangles
137: dt=0.9900, 50 negative triangles
138: dt=0.9900, 45 negative triangles
139: dt=0.9900, 41 negative triangles
140: dt=0.9900, 28 negative triangles
141: dt=0.9900, 26 negative triangles
142: dt=0.9900, 25 negative triangles
143: dt=0.9900, 21 negative triangles
144: dt=0.9900, 19 negative triangles
145: dt=0.9900, 14 negative triangles
146: dt=0.9900, 13 negative triangles
147: dt=0.9900, 10 negative triangles
148: dt=0.9900, 7 negative triangles
149: dt=0.9900, 9 negative triangles
150: dt=0.9900, 5 negative triangles
151: dt=0.9900, 6 negative triangles
152: dt=0.9900, 4 negative triangles
153: dt=0.9900, 2 negative triangles
154: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.42 hours
mris_register utimesec    5320.305190
mris_register stimesec    2.527615
mris_register ru_maxrss   268020
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39934
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10376
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    397938
mris_register ru_nivcsw   236859
FSRUNTIME@ mris_register  1.4172 hours 1 threads
PIDs (3851 3854) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 07:31:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 07:31:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

Waiting for PID 7374 of (7374 7377) to complete...
Waiting for PID 7377 of (7374 7377) 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 (7374 7377) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 07:31:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

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

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 07:31:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 7418 of (7418 7421) to complete...
Waiting for PID 7421 of (7418 7421) 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 (7418 7421) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 07:31:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 07:31:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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 7462 of (7462 7465) to complete...
Waiting for PID 7465 of (7462 7465) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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...
1271 labels changed using aseg
relabeling using gibbs priors...
000:   3295 changed, 146952 examined...
001:    776 changed, 13741 examined...
002:    188 changed, 4349 examined...
003:     62 changed, 1154 examined...
004:     20 changed, 354 examined...
005:      8 changed, 126 examined...
006:      3 changed, 42 examined...
007:      2 changed, 24 examined...
008:      0 changed, 8 examined...
251 labels changed using aseg
000: 132 total segments, 83 labels (395 vertices) changed
001: 50 total segments, 1 labels (6 vertices) changed
002: 49 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1750 vertices marked for relabeling...
1750 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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...
1335 labels changed using aseg
relabeling using gibbs priors...
000:   2878 changed, 146055 examined...
001:    602 changed, 12515 examined...
002:    136 changed, 3478 examined...
003:     44 changed, 830 examined...
004:     25 changed, 292 examined...
005:      9 changed, 132 examined...
006:      5 changed, 56 examined...
007:      3 changed, 35 examined...
008:      1 changed, 18 examined...
009:      0 changed, 11 examined...
148 labels changed using aseg
000: 108 total segments, 70 labels (326 vertices) changed
001: 40 total segments, 2 labels (7 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1608 vertices marked for relabeling...
1608 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 15 seconds.
PIDs (7462 7465) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 07:31:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050345 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 07:31:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050345 rh 

Waiting for PID 7510 of (7510 7513) to complete...
Waiting for PID 7513 of (7510 7513) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050345 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-6.0.0/0050345/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
16412 bright wm thresholded.
1844 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.orig...
computing class statistics...
border white:    279082 voxels (1.66%)
border gray      336333 voxels (2.00%)
WM (95.0): 95.9 +- 8.5 [70.0 --> 110.0]
GM (71.0) : 70.0 +- 11.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 56.0 (was 70)
setting MAX_BORDER_WHITE to 108.5 (was 105)
setting MIN_BORDER_WHITE to 67.0 (was 85)
setting MAX_CSF to 45.0 (was 40)
setting MAX_GRAY to 91.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 56.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=67+-8.7
mean inside = 91.7, mean outside = 74.5
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 0.90 +- 0.26 (0.02-->4.42) (max @ vno 21270 --> 145576)
face area 0.34 +- 0.16 (0.00-->4.55)
mean absolute distance = 0.62 +- 0.92
3873 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
deleting segment 1 with 8 points - only 0.00% unknown
deleting segment 2 with 80 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 5 with 20 points - only 0.00% unknown
deleting segment 6 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 17 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
deleting segment 14 with 6 points - only 0.00% unknown
deleting segment 15 with 274 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 6 points - only 0.00% unknown
deleting segment 18 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 19 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
mean border=79.0, 220 (215) missing vertices, mean dist 0.3 [0.8 (%18.6)->0.6 (%81.4))]
%64 local maxima, %31 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 +- 0.27 (0.06-->4.34) (max @ vno 13670 --> 145404)
face area 0.34 +- 0.17 (0.00-->4.45)
mean absolute distance = 0.40 +- 0.69
5131 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2167011.2, rms=7.186
001: dt: 0.5000, sse=1349139.0, rms=4.671 (35.002%)
002: dt: 0.5000, sse=1086381.4, rms=3.627 (22.343%)
003: dt: 0.5000, sse=1050376.4, rms=3.387 (6.624%)
004: dt: 0.5000, sse=998381.8, rms=3.199 (5.564%)
rms = 3.26, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=888284.0, rms=2.483 (22.362%)
006: dt: 0.2500, sse=846744.3, rms=2.128 (14.303%)
007: dt: 0.2500, sse=834573.6, rms=2.022 (4.995%)
rms = 1.97, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=839692.9, rms=1.974 (2.382%)
rms = 1.93, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=823901.0, rms=1.928 (2.318%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 11 points - only 0.00% unknown
deleting segment 2 with 86 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 12 points - only 0.00% unknown
deleting segment 6 with 22 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 13 points - only 0.00% unknown
deleting segment 10 with 24 points - only 0.00% unknown
deleting segment 11 with 155 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
mean border=81.8, 194 (72) missing vertices, mean dist -0.2 [0.5 (%68.1)->0.2 (%31.9))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.09-->4.86) (max @ vno 72933 --> 74173)
face area 0.36 +- 0.18 (0.00-->4.71)
mean absolute distance = 0.32 +- 0.50
4758 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1275856.6, rms=4.267
010: dt: 0.5000, sse=1018497.8, rms=2.935 (31.226%)
011: dt: 0.5000, sse=990532.6, rms=2.841 (3.189%)
rms = 2.86, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=896036.2, rms=2.182 (23.197%)
013: dt: 0.2500, sse=854582.1, rms=1.779 (18.484%)
014: dt: 0.2500, sse=853561.2, rms=1.650 (7.251%)
015: dt: 0.2500, sse=837612.1, rms=1.576 (4.480%)
rms = 1.53, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=835026.8, rms=1.532 (2.798%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=829918.9, rms=1.493 (2.556%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 10 points - only 0.00% unknown
deleting segment 2 with 88 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 19 points - only 0.00% unknown
deleting segment 6 with 10 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 14 points - only 0.00% unknown
deleting segment 10 with 23 points - only 0.00% unknown
deleting segment 11 with 180 points - only 0.00% unknown
deleting segment 12 with 9 points - only 33.33% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
mean border=83.5, 217 (55) missing vertices, mean dist -0.1 [0.4 (%62.4)->0.2 (%37.6))]
%80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.26 (0.09-->5.05) (max @ vno 72933 --> 74173)
face area 0.35 +- 0.17 (0.00-->4.50)
mean absolute distance = 0.29 +- 0.43
3719 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=969844.6, rms=2.849
018: dt: 0.5000, sse=907587.6, rms=2.310 (18.918%)
rms = 2.47, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=833762.9, rms=1.749 (24.289%)
020: dt: 0.2500, sse=805280.9, rms=1.472 (15.824%)
021: dt: 0.2500, sse=797395.3, rms=1.394 (5.319%)
rms = 1.38, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=800628.5, rms=1.383 (0.785%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=792546.8, rms=1.340 (3.105%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 10 points - only 0.00% unknown
deleting segment 2 with 79 points - only 0.00% unknown
deleting segment 3 with 11 points - only 0.00% unknown
deleting segment 4 with 44 points - only 0.00% unknown
deleting segment 5 with 11 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 23 points - only 0.00% unknown
deleting segment 9 with 178 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
deleting segment 12 with 9 points - only 33.33% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
mean border=84.2, 263 (45) missing vertices, mean dist -0.1 [0.3 (%54.2)->0.3 (%45.8))]
%83 local maxima, %12 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-6.0.0/0050345/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=819792.9, rms=1.771
024: dt: 0.5000, sse=827223.2, rms=1.649 (6.886%)
rms = 2.13, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=773653.7, rms=1.228 (25.569%)
026: dt: 0.2500, sse=773057.5, rms=1.154 (6.038%)
027: dt: 0.2500, sse=763069.1, rms=1.094 (5.149%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
rms = 1.08, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=759382.1, rms=1.077 (1.575%)
positioning took 0.7 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7666 vertices
erasing segment 0 (vno[0] = 38858)
erasing segment 2 (vno[0] = 57960)
erasing segment 3 (vno[0] = 80578)
erasing segment 4 (vno[0] = 92247)
erasing segment 5 (vno[0] = 94751)
erasing segment 6 (vno[0] = 96642)
erasing segment 7 (vno[0] = 104238)
erasing segment 8 (vno[0] = 105281)
erasing segment 9 (vno[0] = 109375)
erasing segment 10 (vno[0] = 111586)
erasing segment 11 (vno[0] = 115366)
erasing segment 12 (vno[0] = 117802)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.area
vertex spacing 0.90 +- 0.27 (0.02-->5.07) (max @ vno 72933 --> 74173)
face area 0.34 +- 0.17 (0.00-->4.69)
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 32 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
deleting segment 2 with 16 points - only 0.00% unknown
deleting segment 4 with 71 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=54.4, 188 (188) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.9 (%100.0))]
%12 local maxima, %43 large gradients and %41 min vals, 710 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=26994096.0, rms=30.560
001: dt: 0.0500, sse=24142262.0, rms=28.854 (5.582%)
002: dt: 0.0500, sse=22077904.0, rms=27.553 (4.509%)
003: dt: 0.0500, sse=20478356.0, rms=26.501 (3.818%)
004: dt: 0.0500, sse=19170066.0, rms=25.609 (3.368%)
005: dt: 0.0500, sse=18056504.0, rms=24.823 (3.066%)
006: dt: 0.0500, sse=17082290.0, rms=24.115 (2.852%)
007: dt: 0.0500, sse=16213970.0, rms=23.466 (2.691%)
008: dt: 0.0500, sse=15428657.0, rms=22.863 (2.569%)
009: dt: 0.0500, sse=14710040.0, rms=22.297 (2.476%)
010: dt: 0.0500, sse=14047347.0, rms=21.762 (2.400%)
positioning took 1.0 minutes
mean border=54.2, 150 (86) missing vertices, mean dist 1.4 [0.2 (%0.0)->2.4 (%100.0))]
%13 local maxima, %43 large gradients and %40 min vals, 660 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=15011012.0, rms=22.534
011: dt: 0.0500, sse=14389823.0, rms=22.038 (2.199%)
012: dt: 0.0500, sse=13810942.0, rms=21.566 (2.142%)
013: dt: 0.0500, sse=13270286.0, rms=21.116 (2.089%)
014: dt: 0.0500, sse=12764846.0, rms=20.685 (2.037%)
015: dt: 0.0500, sse=12291767.0, rms=20.274 (1.987%)
016: dt: 0.0500, sse=11848999.0, rms=19.882 (1.935%)
017: dt: 0.0500, sse=11433786.0, rms=19.507 (1.887%)
018: dt: 0.0500, sse=11044904.0, rms=19.149 (1.836%)
019: dt: 0.0500, sse=10679237.0, rms=18.806 (1.792%)
020: dt: 0.0500, sse=10336946.0, rms=18.478 (1.739%)
positioning took 1.0 minutes
mean border=54.0, 162 (67) missing vertices, mean dist 1.2 [0.1 (%1.5)->2.1 (%98.5))]
%13 local maxima, %43 large gradients and %40 min vals, 664 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=10474562.0, rms=18.616
021: dt: 0.0500, sse=10143332.0, rms=18.296 (1.717%)
022: dt: 0.0500, sse=9833296.0, rms=17.992 (1.664%)
023: dt: 0.0500, sse=9540048.0, rms=17.699 (1.628%)
024: dt: 0.0500, sse=9265248.0, rms=17.420 (1.576%)
025: dt: 0.0500, sse=9007141.0, rms=17.153 (1.528%)
026: dt: 0.0500, sse=8765035.0, rms=16.900 (1.479%)
027: dt: 0.0500, sse=8536002.0, rms=16.656 (1.441%)
028: dt: 0.0500, sse=8317416.5, rms=16.420 (1.417%)
029: dt: 0.0500, sse=8108597.0, rms=16.192 (1.393%)
030: dt: 0.0500, sse=7909192.5, rms=15.970 (1.368%)
positioning took 1.0 minutes
mean border=54.0, 199 (59) missing vertices, mean dist 1.0 [0.1 (%11.7)->2.0 (%88.3))]
%13 local maxima, %43 large gradients and %39 min vals, 632 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=8015507.0, rms=16.087
031: dt: 0.5000, sse=6585916.5, rms=14.414 (10.396%)
032: dt: 0.5000, sse=5582234.5, rms=13.105 (9.083%)
033: dt: 0.5000, sse=4803321.5, rms=11.992 (8.490%)
034: dt: 0.5000, sse=4213268.5, rms=11.069 (7.697%)
035: dt: 0.5000, sse=3723564.5, rms=10.242 (7.477%)
036: dt: 0.5000, sse=3323514.0, rms=9.510 (7.150%)
037: dt: 0.5000, sse=2958785.8, rms=8.794 (7.528%)
038: dt: 0.5000, sse=2664381.2, rms=8.168 (7.118%)
039: dt: 0.5000, sse=2410856.0, rms=7.591 (7.065%)
040: dt: 0.5000, sse=2220415.8, rms=7.123 (6.156%)
041: dt: 0.5000, sse=2064666.4, rms=6.721 (5.654%)
042: dt: 0.5000, sse=1971201.1, rms=6.463 (3.833%)
043: dt: 0.5000, sse=1893720.4, rms=6.245 (3.373%)
044: dt: 0.5000, sse=1853931.8, rms=6.127 (1.885%)
045: dt: 0.5000, sse=1812148.9, rms=6.004 (2.007%)
rms = 5.96, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1797934.2, rms=5.958 (0.767%)
047: dt: 0.2500, sse=1690313.8, rms=5.590 (6.171%)
048: dt: 0.2500, sse=1656759.4, rms=5.481 (1.965%)
rms = 5.47, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1654462.1, rms=5.471 (0.167%)
050: dt: 0.1250, sse=1627575.9, rms=5.378 (1.716%)
rms = 5.35, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1620146.8, rms=5.353 (0.464%)
positioning took 2.9 minutes
mean border=53.0, 2516 (29) missing vertices, mean dist 0.2 [0.2 (%49.1)->0.8 (%50.9))]
%22 local maxima, %37 large gradients and %36 min vals, 291 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=1868831.4, rms=5.444
052: dt: 0.5000, sse=1793125.9, rms=5.204 (4.410%)
053: dt: 0.5000, sse=1708531.4, rms=4.932 (5.216%)
rms = 5.06, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1604349.5, rms=4.502 (8.726%)
055: dt: 0.2500, sse=1579995.1, rms=4.389 (2.516%)
rms = 4.39, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1579433.5, rms=4.387 (0.032%)
057: dt: 0.1250, sse=1542373.9, rms=4.224 (3.716%)
rms = 4.19, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1534193.5, rms=4.190 (0.806%)
positioning took 1.3 minutes
mean border=52.4, 2782 (23) missing vertices, mean dist 0.1 [0.2 (%51.1)->0.6 (%48.9))]
%29 local maxima, %30 large gradients and %35 min vals, 378 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=1587900.1, rms=4.380
rms = 4.73, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1556428.2, rms=4.247 (3.041%)
rms = 4.22, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1548704.8, rms=4.221 (0.611%)
061: dt: 0.1250, sse=1533000.2, rms=4.151 (1.669%)
rms = 4.12, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1526066.2, rms=4.124 (0.648%)
positioning took 0.8 minutes
mean border=51.9, 5558 (20) missing vertices, mean dist 0.1 [0.2 (%49.8)->0.4 (%50.2))]
%33 local maxima, %25 large gradients and %34 min vals, 373 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-6.0.0/0050345/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1549063.6, rms=4.202
rms = 4.41, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1525002.8, rms=4.100 (2.438%)
064: dt: 0.2500, sse=1502785.9, rms=4.021 (1.928%)
rms = 4.01, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1497859.9, rms=4.010 (0.261%)
066: dt: 0.1250, sse=1466795.5, rms=3.867 (3.584%)
rms = 3.82, time step reduction 3 of 3 to 0.062...
067: dt: 0.1250, sse=1456561.0, rms=3.824 (1.113%)
positioning took 1.0 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.area.pial
vertex spacing 1.04 +- 0.47 (0.07-->6.99) (max @ vno 101301 --> 102350)
face area 0.43 +- 0.35 (0.00-->9.06)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 146952 vertices processed
25000 of 146952 vertices processed
50000 of 146952 vertices processed
75000 of 146952 vertices processed
100000 of 146952 vertices processed
125000 of 146952 vertices processed
0 of 146952 vertices processed
25000 of 146952 vertices processed
50000 of 146952 vertices processed
75000 of 146952 vertices processed
100000 of 146952 vertices processed
125000 of 146952 vertices processed
thickness calculation complete, 358:1182 truncations.
31675 vertices at 0 distance
98072 vertices at 1 distance
88927 vertices at 2 distance
40898 vertices at 3 distance
14396 vertices at 4 distance
4755 vertices at 5 distance
1629 vertices at 6 distance
680 vertices at 7 distance
272 vertices at 8 distance
113 vertices at 9 distance
65 vertices at 10 distance
51 vertices at 11 distance
30 vertices at 12 distance
31 vertices at 13 distance
41 vertices at 14 distance
18 vertices at 15 distance
15 vertices at 16 distance
23 vertices at 17 distance
16 vertices at 18 distance
11 vertices at 19 distance
12 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.thickness
positioning took 16.9 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050345 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-6.0.0/0050345/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
16412 bright wm thresholded.
1844 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.orig...
computing class statistics...
border white:    279082 voxels (1.66%)
border gray      336333 voxels (2.00%)
WM (95.0): 95.9 +- 8.5 [70.0 --> 110.0]
GM (71.0) : 70.0 +- 11.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 54.0 (was 70)
setting MAX_BORDER_WHITE to 108.5 (was 105)
setting MIN_BORDER_WHITE to 65.0 (was 85)
setting MAX_CSF to 43.0 (was 40)
setting MAX_GRAY to 91.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 54.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.9 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=65+-9.6
mean inside = 91.7, mean outside = 74.2
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.91 +- 0.26 (0.03-->5.89) (max @ vno 144909 --> 145002)
face area 0.34 +- 0.17 (0.00-->8.09)
mean absolute distance = 0.57 +- 0.87
4099 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 92 points - only 0.00% unknown
deleting segment 1 with 17 points - only 0.00% unknown
deleting segment 2 with 52 points - only 0.00% unknown
deleting segment 5 with 271 points - only 0.00% unknown
deleting segment 6 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 25 points - only 0.00% unknown
deleting segment 9 with 41 points - only 0.00% unknown
deleting segment 10 with 43 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
deleting segment 13 with 9 points - only 0.00% unknown
mean border=78.0, 230 (225) missing vertices, mean dist 0.3 [0.6 (%20.4)->0.6 (%79.6))]
%68 local maxima, %27 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 +- 0.28 (0.04-->5.64) (max @ vno 144909 --> 145002)
face area 0.34 +- 0.18 (0.00-->7.11)
mean absolute distance = 0.38 +- 0.66
4635 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2083305.6, rms=6.970
001: dt: 0.5000, sse=1305206.1, rms=4.547 (34.762%)
002: dt: 0.5000, sse=1091256.5, rms=3.618 (20.427%)
003: dt: 0.5000, sse=1057756.6, rms=3.441 (4.903%)
004: dt: 0.5000, sse=1014940.3, rms=3.262 (5.208%)
rms = 3.33, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=898663.8, rms=2.479 (24.006%)
006: dt: 0.2500, sse=858006.4, rms=2.105 (15.077%)
007: dt: 0.2500, sse=844016.7, rms=2.007 (4.673%)
rms = 1.97, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=840305.1, rms=1.966 (2.002%)
rms = 1.92, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=833970.7, rms=1.920 (2.381%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 86 points - only 0.00% unknown
deleting segment 1 with 19 points - only 0.00% unknown
deleting segment 2 with 43 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 178 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 19 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
deleting segment 10 with 44 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
deleting segment 12 with 6 points - only 16.67% unknown
deleting segment 13 with 6 points - only 0.00% unknown
deleting segment 14 with 12 points - only 0.00% unknown
mean border=80.6, 180 (83) missing vertices, mean dist -0.2 [0.4 (%66.5)->0.3 (%33.5))]
%76 local maxima, %20 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 +- 0.27 (0.07-->5.56) (max @ vno 144909 --> 145002)
face area 0.36 +- 0.19 (0.00-->8.56)
mean absolute distance = 0.31 +- 0.50
4522 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1246020.9, rms=4.108
010: dt: 0.5000, sse=1015074.0, rms=2.894 (29.540%)
rms = 2.86, time step reduction 1 of 3 to 0.250...
011: dt: 0.5000, sse=1002323.9, rms=2.862 (1.115%)
012: dt: 0.2500, sse=873015.0, rms=1.874 (34.532%)
013: dt: 0.2500, sse=859485.4, rms=1.668 (10.995%)
014: dt: 0.2500, sse=849267.2, rms=1.612 (3.347%)
rms = 1.59, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=846984.8, rms=1.585 (1.647%)
rms = 1.54, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=841690.5, rms=1.537 (3.029%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 83 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 44 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 4 with 212 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
deleting segment 6 with 15 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
deleting segment 9 with 46 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 6 points - only 16.67% unknown
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 12 points - only 0.00% unknown
mean border=82.2, 190 (61) missing vertices, mean dist -0.1 [0.4 (%61.0)->0.2 (%39.0))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.91 +- 0.27 (0.08-->5.53) (max @ vno 144909 --> 145002)
face area 0.35 +- 0.18 (0.00-->7.64)
mean absolute distance = 0.30 +- 0.43
3793 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=967132.2, rms=2.771
017: dt: 0.5000, sse=922948.7, rms=2.373 (14.351%)
rms = 2.60, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=842221.9, rms=1.783 (24.872%)
019: dt: 0.2500, sse=824162.4, rms=1.533 (14.015%)
020: dt: 0.2500, sse=816535.8, rms=1.466 (4.349%)
rms = 1.47, time step reduction 2 of 3 to 0.125...
rms = 1.44, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=810031.5, rms=1.439 (1.865%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 89 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 47 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 199 points - only 0.00% unknown
deleting segment 6 with 9 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
deleting segment 11 with 46 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
deleting segment 13 with 6 points - only 16.67% unknown
deleting segment 14 with 6 points - only 0.00% unknown
deleting segment 15 with 13 points - only 0.00% unknown
mean border=82.9, 265 (55) missing vertices, mean dist -0.1 [0.3 (%53.6)->0.3 (%46.4))]
%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-6.0.0/0050345/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=837905.7, rms=1.856
rms = 1.84, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=847666.8, rms=1.840 (0.818%)
023: dt: 0.2500, sse=804854.6, rms=1.407 (23.542%)
024: dt: 0.2500, sse=785492.5, rms=1.280 (8.998%)
rms = 1.31, time step reduction 2 of 3 to 0.125...
025: dt: 0.1250, sse=780301.9, rms=1.199 (6.355%)
026: dt: 0.1250, sse=770257.0, rms=1.090 (9.117%)
rms = 1.08, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=768303.4, rms=1.080 (0.859%)
positioning took 0.7 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7960 vertices
erasing segment 0 (vno[0] = 40533)
erasing segment 1 (vno[0] = 44177)
erasing segment 3 (vno[0] = 48674)
erasing segment 4 (vno[0] = 61360)
erasing segment 5 (vno[0] = 62543)
erasing segment 6 (vno[0] = 71670)
erasing segment 7 (vno[0] = 93455)
erasing segment 8 (vno[0] = 107651)
erasing segment 9 (vno[0] = 107737)
erasing segment 10 (vno[0] = 113014)
erasing segment 11 (vno[0] = 114776)
erasing segment 12 (vno[0] = 126484)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.area
vertex spacing 0.91 +- 0.27 (0.05-->5.44) (max @ vno 144909 --> 145002)
face area 0.35 +- 0.18 (0.00-->7.57)
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 52 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 49 points - only 0.00% unknown
removing 4 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=53.0, 206 (206) missing vertices, mean dist 1.5 [2.0 (%0.0)->2.9 (%100.0))]
%10 local maxima, %40 large gradients and %45 min vals, 645 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=26899346.0, rms=30.633
001: dt: 0.0500, sse=24041238.0, rms=28.912 (5.618%)
002: dt: 0.0500, sse=21958062.0, rms=27.589 (4.573%)
003: dt: 0.0500, sse=20339530.0, rms=26.516 (3.889%)
004: dt: 0.0500, sse=19014266.0, rms=25.604 (3.440%)
005: dt: 0.0500, sse=17887356.0, rms=24.802 (3.133%)
006: dt: 0.0500, sse=16902528.0, rms=24.079 (2.915%)
007: dt: 0.0500, sse=16025178.0, rms=23.416 (2.753%)
008: dt: 0.0500, sse=15232558.0, rms=22.801 (2.629%)
009: dt: 0.0500, sse=14508930.0, rms=22.224 (2.530%)
010: dt: 0.0500, sse=13842950.0, rms=21.679 (2.450%)
positioning took 1.0 minutes
mean border=52.9, 169 (117) missing vertices, mean dist 1.3 [0.6 (%0.0)->2.4 (%100.0))]
%11 local maxima, %40 large gradients and %44 min vals, 617 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=14767660.0, rms=22.431
011: dt: 0.0500, sse=14144385.0, rms=21.927 (2.248%)
012: dt: 0.0500, sse=13565463.0, rms=21.448 (2.185%)
013: dt: 0.0500, sse=13025999.0, rms=20.991 (2.127%)
014: dt: 0.0500, sse=12522374.0, rms=20.556 (2.073%)
015: dt: 0.0500, sse=12051623.0, rms=20.141 (2.021%)
016: dt: 0.0500, sse=11611374.0, rms=19.744 (1.968%)
017: dt: 0.0500, sse=11199693.0, rms=19.366 (1.915%)
018: dt: 0.0500, sse=10814078.0, rms=19.005 (1.865%)
019: dt: 0.0500, sse=10452839.0, rms=18.660 (1.814%)
020: dt: 0.0500, sse=10114803.0, rms=18.332 (1.761%)
positioning took 1.0 minutes
mean border=52.7, 183 (96) missing vertices, mean dist 1.1 [0.1 (%1.4)->2.1 (%98.6))]
%11 local maxima, %40 large gradients and %44 min vals, 593 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=10230146.0, rms=18.450
021: dt: 0.0500, sse=9905711.0, rms=18.131 (1.729%)
022: dt: 0.0500, sse=9602720.0, rms=17.828 (1.672%)
023: dt: 0.0500, sse=9317429.0, rms=17.537 (1.628%)
024: dt: 0.0500, sse=9050923.0, rms=17.262 (1.572%)
025: dt: 0.0500, sse=8801631.0, rms=17.000 (1.518%)
026: dt: 0.0500, sse=8567910.0, rms=16.750 (1.468%)
027: dt: 0.0500, sse=8347914.5, rms=16.512 (1.423%)
028: dt: 0.0500, sse=8139080.0, rms=16.282 (1.391%)
029: dt: 0.0500, sse=7940285.5, rms=16.060 (1.362%)
030: dt: 0.0500, sse=7750781.5, rms=15.846 (1.335%)
positioning took 1.0 minutes
mean border=52.7, 246 (88) missing vertices, mean dist 1.0 [0.1 (%10.7)->2.0 (%89.3))]
%11 local maxima, %40 large gradients and %44 min vals, 521 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=7857375.5, rms=15.966
031: dt: 0.5000, sse=6490702.5, rms=14.340 (10.180%)
032: dt: 0.5000, sse=5539477.5, rms=13.083 (8.769%)
033: dt: 0.5000, sse=4797562.0, rms=12.013 (8.177%)
034: dt: 0.5000, sse=4216507.0, rms=11.097 (7.622%)
035: dt: 0.5000, sse=3730529.0, rms=10.272 (7.439%)
036: dt: 0.5000, sse=3325936.0, rms=9.528 (7.246%)
037: dt: 0.5000, sse=2973717.5, rms=8.833 (7.291%)
038: dt: 0.5000, sse=2694104.0, rms=8.238 (6.738%)
039: dt: 0.5000, sse=2461560.5, rms=7.711 (6.398%)
040: dt: 0.5000, sse=2283015.8, rms=7.277 (5.622%)
041: dt: 0.5000, sse=2145658.0, rms=6.929 (4.785%)
042: dt: 0.5000, sse=2052022.5, rms=6.678 (3.630%)
043: dt: 0.5000, sse=1982435.9, rms=6.487 (2.849%)
044: dt: 0.5000, sse=1936848.9, rms=6.356 (2.024%)
045: dt: 0.5000, sse=1901465.8, rms=6.255 (1.587%)
046: dt: 0.5000, sse=1883707.4, rms=6.200 (0.882%)
047: dt: 0.5000, sse=1860625.2, rms=6.135 (1.046%)
rms = 6.11, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1852422.1, rms=6.108 (0.449%)
049: dt: 0.2500, sse=1763228.5, rms=5.804 (4.974%)
050: dt: 0.2500, sse=1731012.0, rms=5.702 (1.752%)
rms = 5.70, time step reduction 2 of 3 to 0.125...
rms = 5.67, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1721806.4, rms=5.671 (0.550%)
positioning took 3.1 minutes
mean border=51.7, 2953 (35) missing vertices, mean dist 0.2 [0.2 (%48.7)->0.8 (%51.3))]
%19 local maxima, %35 large gradients and %40 min vals, 259 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=1993413.9, rms=5.803
052: dt: 0.5000, sse=1879435.2, rms=5.450 (6.072%)
053: dt: 0.5000, sse=1811155.0, rms=5.248 (3.712%)
rms = 5.29, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1709238.6, rms=4.849 (7.596%)
055: dt: 0.2500, sse=1684420.8, rms=4.741 (2.232%)
rms = 4.73, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1681565.4, rms=4.731 (0.206%)
057: dt: 0.1250, sse=1646255.8, rms=4.586 (3.081%)
rms = 4.55, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1637530.4, rms=4.552 (0.733%)
positioning took 1.3 minutes
mean border=51.2, 3440 (29) missing vertices, mean dist 0.1 [0.2 (%51.4)->0.6 (%48.6))]
%26 local maxima, %28 large gradients and %40 min vals, 274 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=1685911.9, rms=4.704
rms = 5.03, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1655634.2, rms=4.584 (2.548%)
rms = 4.56, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1647643.6, rms=4.560 (0.521%)
061: dt: 0.1250, sse=1631560.2, rms=4.492 (1.495%)
rms = 4.46, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1622402.6, rms=4.458 (0.752%)
positioning took 0.9 minutes
mean border=50.7, 6577 (27) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.5 (%50.5))]
%30 local maxima, %23 large gradients and %38 min vals, 312 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-6.0.0/0050345/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1645728.1, rms=4.531
rms = 4.73, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1620318.9, rms=4.430 (2.232%)
064: dt: 0.2500, sse=1597464.6, rms=4.355 (1.686%)
rms = 4.35, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1593924.8, rms=4.353 (0.059%)
066: dt: 0.1250, sse=1559386.1, rms=4.203 (3.432%)
rms = 4.15, time step reduction 3 of 3 to 0.062...
067: dt: 0.1250, sse=1547103.9, rms=4.155 (1.150%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.area.pial
vertex spacing 1.05 +- 0.48 (0.05-->7.23) (max @ vno 100959 --> 99842)
face area 0.44 +- 0.37 (0.00-->7.05)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 146055 vertices processed
25000 of 146055 vertices processed
50000 of 146055 vertices processed
75000 of 146055 vertices processed
100000 of 146055 vertices processed
125000 of 146055 vertices processed
0 of 146055 vertices processed
25000 of 146055 vertices processed
50000 of 146055 vertices processed
75000 of 146055 vertices processed
100000 of 146055 vertices processed
125000 of 146055 vertices processed
thickness calculation complete, 510:1240 truncations.
30180 vertices at 0 distance
95713 vertices at 1 distance
88422 vertices at 2 distance
41850 vertices at 3 distance
14875 vertices at 4 distance
4980 vertices at 5 distance
1720 vertices at 6 distance
689 vertices at 7 distance
311 vertices at 8 distance
146 vertices at 9 distance
116 vertices at 10 distance
87 vertices at 11 distance
69 vertices at 12 distance
52 vertices at 13 distance
36 vertices at 14 distance
34 vertices at 15 distance
10 vertices at 16 distance
9 vertices at 17 distance
13 vertices at 18 distance
14 vertices at 19 distance
12 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.thickness
positioning took 16.9 minutes
PIDs (7510 7513) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 07:48:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label
Total face volume 277491
Total vertex volume 273465 (mask=0)
#@# 0050345 lh 273465
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 07:48:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label
Total face volume 277731
Total vertex volume 274478 (mask=0)
#@# 0050345 rh 274478
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 07:48:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 

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 = 313
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/ribbon.mgz
mris_volmask took 15.11 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 08:03:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 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 0050345 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 08:03:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 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 0050345 rh pial 

Waiting for PID 9243 of (9243 9246 9249 9252) to complete...
Waiting for PID 9246 of (9243 9246 9249 9252) to complete...
Waiting for PID 9249 of (9243 9246 9249 9252) to complete...
Waiting for PID 9252 of (9243 9246 9249 9252) 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 0050345 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277491
Total vertex volume 273465 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1257    916   2593  2.370 0.611     0.119     0.026       11     1.4  bankssts
  903    603   1729  2.868 0.592     0.133     0.030       15     1.0  caudalanteriorcingulate
 4212   2804   8650  2.808 0.663     0.122     0.043       48     7.1  caudalmiddlefrontal
 2192   1491   3182  1.883 0.526     0.165     0.048       38     4.7  cuneus
  933    659   2401  2.588 0.873     0.171     0.078       23     3.6  entorhinal
 4521   3496  10595  2.561 0.752     0.159     0.043       69     8.6  fusiform
 6813   4693  12395  2.345 0.588     0.132     0.034       80     9.5  inferiorparietal
 5294   3410   9880  2.329 0.746     0.129     0.046       91    10.8  inferiortemporal
 1592   1057   2895  2.384 0.839     0.143     0.036       27     2.0  isthmuscingulate
 7592   5382  14451  2.235 0.672     0.160     0.045      123    14.7  lateraloccipital
 3912   2709   8758  2.765 0.759     0.139     0.040       50     6.5  lateralorbitofrontal
 3753   2773   6896  2.109 0.688     0.163     0.052       58     8.4  lingual
 2764   1845   5712  2.533 0.854     0.128     0.049       74     5.9  medialorbitofrontal
 4979   3459  12614  2.613 0.791     0.147     0.046       90     9.8  middletemporal
 1194    922   2770  2.623 0.715     0.129     0.035       11     2.0  parahippocampal
 2358   1533   4454  2.574 0.721     0.122     0.030       24     3.0  paracentral
 2809   1906   6537  2.792 0.665     0.117     0.027       28     3.0  parsopercularis
 1094    764   3205  2.960 0.787     0.151     0.050       19     2.0  parsorbitalis
 2350   1616   5106  2.651 0.627     0.129     0.034       27     3.3  parstriangularis
 1842   1340   2423  1.860 0.555     0.147     0.042       20     3.4  pericalcarine
 7612   4986  12110  2.190 0.681     0.132     0.036       86    11.4  postcentral
 1578   1118   3032  2.594 0.667     0.148     0.034       26     2.0  posteriorcingulate
 9260   6012  17852  2.716 0.673     0.116     0.029       85    10.8  precentral
 5181   3558  10234  2.525 0.666     0.144     0.040       69     8.4  precuneus
 1457    975   2687  2.460 1.006     0.122     0.038       25     2.2  rostralanteriorcingulate
10008   6892  20317  2.563 0.714     0.140     0.040      131    17.0  rostralmiddlefrontal
13912   9225  30361  2.879 0.765     0.129     0.039      174    22.7  superiorfrontal
 8341   5513  13587  2.214 0.587     0.135     0.036      100    12.0  superiorparietal
 6996   4589  12058  2.410 0.634     0.110     0.030       67     8.8  superiortemporal
 6149   4140  11769  2.592 0.592     0.134     0.034       78     8.2  supramarginal
  477    316   1384  2.974 0.626     0.182     0.080       10     1.4  frontalpole
  638    453   1591  2.295 0.794     0.161     0.075       13     1.9  temporalpole
  877    528   1284  2.123 0.447     0.106     0.026        7     0.8  transversetemporal
 3739   2526   7929  3.083 0.796     0.122     0.036       39     5.5  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 0050345 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277491
Total vertex volume 273465 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1257   1187   2593  2.370 0.611     0.160     0.035       15     2.2  bankssts
  903    715   1729  2.868 0.592     0.158     0.038       18     1.5  caudalanteriorcingulate
 4212   3274   8650  2.808 0.663     0.126     0.032       62     5.9  caudalmiddlefrontal
 2192   1925   3182  1.883 0.526     0.181     0.050       32     5.1  cuneus
  933   1141   2401  2.588 0.873     0.236     0.071       28     3.2  entorhinal
 4521   4650  10595  2.561 0.752     0.193     0.048       72    10.2  fusiform
 6813   5929  12395  2.345 0.588     0.160     0.039       92    12.8  inferiorparietal
 5294   4732   9880  2.329 0.746     0.175     0.050       90    13.1  inferiortemporal
 1592   1367   2895  2.384 0.839     0.167     0.049       36     3.6  isthmuscingulate
 7592   7406  14451  2.235 0.672     0.182     0.047      117    17.4  lateraloccipital
 3912   3546   8758  2.765 0.759     0.182     0.052       68     9.3  lateralorbitofrontal
 3753   3591   6896  2.109 0.688     0.194     0.076      168    16.6  lingual
 2764   2654   5712  2.533 0.854     0.172     0.047       38     5.7  medialorbitofrontal
 4979   5730  12614  2.613 0.791     0.197     0.049       72    11.9  middletemporal
 1194   1165   2770  2.623 0.715     0.164     0.041       13     2.4  parahippocampal
 2358   2004   4454  2.574 0.721     0.148     0.033       25     4.0  paracentral
 2809   2690   6537  2.792 0.665     0.170     0.038       36     5.3  parsopercularis
 1094   1300   3205  2.960 0.787     0.199     0.043       16     2.3  parsorbitalis
 2350   2165   5106  2.651 0.627     0.178     0.043       37     5.0  parstriangularis
 1842   1331   2423  1.860 0.555     0.172     0.052       34     4.4  pericalcarine
 7612   5986  12110  2.190 0.681     0.134     0.030       99    10.3  postcentral
 1578   1286   3032  2.594 0.667     0.169     0.047       50     3.0  posteriorcingulate
 9260   6844  17852  2.716 0.673     0.118     0.028      120    11.3  precentral
 5181   4415  10234  2.525 0.666     0.171     0.047       75    11.9  precuneus
 1457   1221   2687  2.460 1.006     0.167     0.046       22     3.2  rostralanteriorcingulate
10008   8594  20317  2.563 0.714     0.155     0.037      145    18.3  rostralmiddlefrontal
13912  11476  30361  2.879 0.765     0.144     0.036      238    22.8  superiorfrontal
 8341   6672  13587  2.214 0.587     0.146     0.037      114    13.9  superiorparietal
 6996   5390  12058  2.410 0.634     0.140     0.038       95    12.4  superiortemporal
 6149   4975  11769  2.592 0.592     0.150     0.036       86    10.3  supramarginal
  477    580   1384  2.974 0.626     0.208     0.051        6     1.2  frontalpole
  638    881   1591  2.295 0.794     0.253     0.067       20     1.8  temporalpole
  877    709   1284  2.123 0.447     0.122     0.030        5     1.1  transversetemporal
 3739   2525   7929  3.083 0.796     0.150     0.046       72     8.1  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050345 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277731
Total vertex volume 274478 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1165    824   1892  2.268 0.552     0.107     0.022        7     1.1  bankssts
 1235    824   2614  2.749 0.762     0.135     0.026       18     1.3  caudalanteriorcingulate
 4354   2999   9157  2.748 0.616     0.121     0.034       48     6.0  caudalmiddlefrontal
 2689   1893   4388  1.999 0.552     0.173     0.056       46     6.7  cuneus
  510    391   1359  2.495 0.997     0.137     0.035        5     0.8  entorhinal
 4959   3555   9500  2.288 0.699     0.146     0.040       71     8.9  fusiform
 7619   5216  14320  2.380 0.633     0.138     0.040       92    12.7  inferiorparietal
 5945   4084  13214  2.520 0.821     0.156     0.064      113    17.5  inferiortemporal
 1578   1040   2922  2.466 0.917     0.136     0.044       25     2.5  isthmuscingulate
 7412   5408  14831  2.286 0.742     0.164     0.049      120    15.8  lateraloccipital
 3864   2569   8032  2.814 0.743     0.140     0.047       55     7.1  lateralorbitofrontal
 4537   3440   7816  1.992 0.665     0.173     0.057       79    12.0  lingual
 3062   2090   6162  2.539 0.836     0.127     0.041       47     5.3  medialorbitofrontal
 5607   3914  12550  2.525 0.723     0.148     0.052      101    13.1  middletemporal
  960    650   1731  2.214 0.723     0.111     0.027        7     1.0  parahippocampal
 2416   1576   4813  2.729 0.716     0.118     0.027       19     2.8  paracentral
 2255   1597   4810  2.691 0.599     0.139     0.040       31     3.4  parsopercularis
 1318    923   3252  2.740 0.879     0.175     0.067       28     3.6  parsorbitalis
 2464   1740   5461  2.611 0.638     0.145     0.042       36     4.3  parstriangularis
 2511   1786   2886  1.661 0.432     0.150     0.046       35     4.7  pericalcarine
 7263   4943  12387  2.207 0.721     0.130     0.033       88    10.2  postcentral
 1802   1261   3692  2.614 0.898     0.157     0.039       32     2.8  posteriorcingulate
 8918   5931  17137  2.623 0.687     0.119     0.033       90    12.7  precentral
 5519   3826  10270  2.410 0.644     0.137     0.037       68     9.1  precuneus
 1001    690   2363  2.762 0.666     0.152     0.057       22     2.6  rostralanteriorcingulate
 9221   6648  21260  2.628 0.705     0.149     0.042      137    16.5  rostralmiddlefrontal
12461   8585  30381  3.021 0.742     0.133     0.041      161    22.0  superiorfrontal
 9276   6339  14002  2.062 0.531     0.131     0.034      103    13.2  superiorparietal
 5121   3578   9287  2.279 0.637     0.119     0.032       53     6.6  superiortemporal
 5228   3512  10163  2.616 0.628     0.132     0.032       63     6.6  supramarginal
  438    328   1673  3.291 0.895     0.200     0.106       13     2.0  frontalpole
  666    527   1904  2.559 0.937     0.193     0.073       14     2.3  temporalpole
  547    338    836  2.199 0.547     0.105     0.032        5     0.5  transversetemporal
 3655   2525   7364  2.806 0.785     0.132     0.046       50     6.7  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 0050345 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277731
Total vertex volume 274478 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1165    838   1892  2.268 0.552     0.138     0.036       15     1.9  bankssts
 1235   1032   2614  2.749 0.762     0.160     0.040       34     1.9  caudalanteriorcingulate
 4354   3478   9157  2.748 0.616     0.124     0.028       67     5.6  caudalmiddlefrontal
 2689   2517   4388  1.999 0.552     0.183     0.050       71     6.1  cuneus
  510    660   1359  2.495 0.997     0.226     0.060        8     1.4  entorhinal
 4959   4671   9500  2.288 0.699     0.180     0.047       73    10.8  fusiform
 7619   6680  14320  2.380 0.633     0.165     0.043      104    15.4  inferiorparietal
 5945   5874  13214  2.520 0.821     0.179     0.047       94    13.0  inferiortemporal
 1578   1353   2922  2.466 0.917     0.167     0.051       45     3.4  isthmuscingulate
 7412   7180  14831  2.286 0.742     0.175     0.042      122    15.0  lateraloccipital
 3864   3120   8032  2.814 0.743     0.172     0.054       72     9.6  lateralorbitofrontal
 4537   4429   7816  1.992 0.665     0.181     0.047       76    10.1  lingual
 3062   2813   6162  2.539 0.836     0.169     0.050       43     7.2  medialorbitofrontal
 5607   5863  12550  2.525 0.723     0.204     0.055       89    15.4  middletemporal
  960    875   1731  2.214 0.723     0.169     0.043       15     2.0  parahippocampal
 2416   1980   4813  2.729 0.716     0.138     0.033       34     3.8  paracentral
 2255   1955   4810  2.691 0.599     0.160     0.040       31     4.0  parsopercularis
 1318   1436   3252  2.740 0.879     0.219     0.053       29     3.4  parsorbitalis
 2464   2579   5461  2.611 0.638     0.199     0.051       41     6.2  parstriangularis
 2511   1765   2886  1.661 0.432     0.145     0.047       43     5.2  pericalcarine
 7263   6285  12387  2.207 0.721     0.145     0.032       83    11.0  postcentral
 1802   1531   3692  2.614 0.898     0.159     0.045       40     3.1  posteriorcingulate
 8918   6888  17137  2.623 0.687     0.123     0.028      123    11.4  precentral
 5519   4589  10270  2.410 0.644     0.159     0.040       83    10.6  precuneus
 1001   1018   2363  2.762 0.666     0.191     0.051       19     2.3  rostralanteriorcingulate
 9221   9226  21260  2.628 0.705     0.183     0.044      160    19.7  rostralmiddlefrontal
12461  10966  30381  3.021 0.742     0.150     0.037      227    20.1  superiorfrontal
 9276   7274  14002  2.062 0.531     0.135     0.034      135    13.9  superiorparietal
 5121   4603   9287  2.279 0.637     0.162     0.042       68     9.5  superiortemporal
 5228   4212  10163  2.616 0.628     0.150     0.039       75     9.1  supramarginal
  438    621   1673  3.291 0.895     0.228     0.040        6     0.9  frontalpole
  666    971   1904  2.559 0.937     0.256     0.062       15     1.8  temporalpole
  547    436    836  2.199 0.547     0.149     0.043        5     1.0  transversetemporal
 3655   2571   7364  2.806 0.785     0.157     0.054       84     8.0  insula
PIDs (9243 9246 9249 9252) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 08:05:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 08:05:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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 9352 of (9352 9355) to complete...
Waiting for PID 9355 of (9352 9355) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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...
55 labels changed using aseg
relabeling using gibbs priors...
000:   9376 changed, 146952 examined...
001:   2187 changed, 36785 examined...
002:    628 changed, 11540 examined...
003:    276 changed, 3578 examined...
004:    137 changed, 1588 examined...
005:     69 changed, 803 examined...
006:     45 changed, 377 examined...
007:     18 changed, 236 examined...
008:     12 changed, 111 examined...
009:      1 changed, 64 examined...
010:      1 changed, 11 examined...
011:      0 changed, 5 examined...
18 labels changed using aseg
000: 302 total segments, 219 labels (3302 vertices) changed
001: 98 total segments, 15 labels (100 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 14 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1062 vertices marked for relabeling...
1062 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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...
40 labels changed using aseg
relabeling using gibbs priors...
000:   9332 changed, 146055 examined...
001:   2117 changed, 36607 examined...
002:    588 changed, 11206 examined...
003:    255 changed, 3394 examined...
004:     90 changed, 1470 examined...
005:     38 changed, 539 examined...
006:     11 changed, 230 examined...
007:      5 changed, 70 examined...
008:      7 changed, 35 examined...
009:      2 changed, 30 examined...
010:      1 changed, 17 examined...
011:      3 changed, 9 examined...
012:      0 changed, 13 examined...
0 labels changed using aseg
000: 278 total segments, 199 labels (3457 vertices) changed
001: 98 total segments, 19 labels (252 vertices) changed
002: 79 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 39 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1111 vertices marked for relabeling...
1111 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (9352 9355) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 08:05:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 08:05:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 rh white 

Waiting for PID 9399 of (9399 9402) to complete...
Waiting for PID 9402 of (9399 9402) 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 0050345 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277491
Total vertex volume 273465 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1287    932   2647  2.510 0.647     0.154     0.045       18     2.3  G&S_frontomargin
 1918   1414   3786  2.257 0.675     0.168     0.048       35     4.1  G&S_occipital_inf
 1956   1212   3665  2.392 0.741     0.129     0.038       22     3.4  G&S_paracentral
 1566   1001   3388  2.720 0.681     0.124     0.033       17     2.1  G&S_subcentral
 1122    730   2520  2.595 0.651     0.159     0.071       21     2.9  G&S_transv_frontopol
 2382   1698   5132  2.712 0.769     0.125     0.032       27     3.1  G&S_cingul-Ant
 1208    834   2224  2.726 0.583     0.120     0.028       13     1.3  G&S_cingul-Mid-Ant
 1444   1020   2604  2.472 0.657     0.129     0.026       15     1.6  G&S_cingul-Mid-Post
  469    350   1483  3.012 0.615     0.179     0.044       12     0.7  G_cingul-Post-dorsal
  402    258    922  2.790 0.761     0.142     0.055        7     0.7  G_cingul-Post-ventral
 1984   1335   3276  1.980 0.565     0.169     0.055       37     4.7  G_cuneus
 1484    978   4227  2.948 0.628     0.134     0.035       21     2.0  G_front_inf-Opercular
  545    366   1578  2.867 0.602     0.154     0.049        9     1.1  G_front_inf-Orbital
 1512   1019   4222  2.911 0.668     0.145     0.041       24     2.6  G_front_inf-Triangul
 5906   3877  14349  2.801 0.812     0.151     0.054      100    13.3  G_front_middle
 9875   6321  23914  3.026 0.785     0.141     0.047      154    19.5  G_front_sup
  784    531   1878  3.241 0.803     0.135     0.046       10     1.4  G_Ins_lg&S_cent_ins
  787    526   2456  3.380 0.682     0.135     0.050       13     1.6  G_insular_short
 2262   1561   5138  2.441 0.742     0.163     0.047       42     4.6  G_occipital_middle
 1280    863   2242  2.078 0.589     0.144     0.039       18     2.0  G_occipital_sup
 1895   1461   5533  2.896 0.697     0.186     0.054       42     4.5  G_oc-temp_lat-fusifor
 2385   1777   5370  2.294 0.708     0.191     0.067       49     6.8  G_oc-temp_med-Lingual
 1867   1272   4753  2.737 0.717     0.131     0.050       28     4.1  G_oc-temp_med-Parahip
 2452   1727   7442  2.969 0.680     0.164     0.060       53     6.1  G_orbital
 3170   2071   6180  2.403 0.553     0.147     0.042       50     5.3  G_pariet_inf-Angular
 2899   1937   6321  2.651 0.638     0.139     0.041       43     4.5  G_pariet_inf-Supramar
 3294   2142   5939  2.240 0.579     0.138     0.040       45     5.2  G_parietal_sup
 3219   2043   5687  2.327 0.703     0.145     0.045       44     6.0  G_postcentral
 3529   2145   8297  2.894 0.765     0.123     0.039       41     5.6  G_precentral
 2690   1794   7073  2.907 0.622     0.165     0.054       50     6.0  G_precuneus
 1118    713   2994  2.754 0.734     0.159     0.079       59     4.1  G_rectus
  581    351    675  1.958 0.935     0.105     0.050       11     1.0  G_subcallosal
  778    452   1097  2.017 0.458     0.106     0.026        6     0.8  G_temp_sup-G_T_transv
 2558   1639   6210  2.670 0.731     0.144     0.051       45     5.6  G_temp_sup-Lateral
  832    579   1464  2.244 0.582     0.088     0.023        4     0.8  G_temp_sup-Plan_polar
 1454    963   2529  2.459 0.485     0.114     0.028       16     1.6  G_temp_sup-Plan_tempo
 2715   1713   6150  2.555 0.765     0.147     0.062       71     7.6  G_temporal_inf
 2884   1969   8751  2.882 0.766     0.160     0.057       67     6.6  G_temporal_middle
  365    246    475  2.296 0.446     0.111     0.022        2     0.3  Lat_Fis-ant-Horizont
  368    268    535  2.183 0.621     0.095     0.011        2     0.2  Lat_Fis-ant-Vertical
 1317    902   1797  2.434 0.487     0.121     0.025       11     1.2  Lat_Fis-post
 2113   1531   4824  2.322 0.778     0.175     0.054       40     5.2  Pole_occipital
 1734   1250   4594  2.385 0.840     0.170     0.071       37     5.6  Pole_temporal
 2499   1778   3191  1.973 0.643     0.137     0.039       25     4.1  S_calcarine
 3741   2588   4779  2.116 0.678     0.116     0.022       29     3.4  S_central
 1136    816   1875  2.371 0.494     0.132     0.033       12     1.4  S_cingul-Marginalis
  654    441   1166  2.986 0.650     0.109     0.023        3     0.7  S_circular_insula_ant
 1570   1066   2300  2.512 0.916     0.086     0.017        6     1.2  S_circular_insula_inf
 1838   1252   2699  2.683 0.597     0.104     0.021       10     1.6  S_circular_insula_sup
 1101    759   1434  2.013 0.635     0.106     0.026        7     1.0  S_collat_transv_ant
  288    221    438  2.049 0.544     0.145     0.035        2     0.5  S_collat_transv_post
 2500   1758   4320  2.605 0.496     0.107     0.020       16     2.1  S_front_inf
 2062   1429   3162  2.429 0.618     0.118     0.023       15     2.1  S_front_middle
 3448   2468   5367  2.445 0.612     0.096     0.020       17     2.5  S_front_sup
  194    146    374  2.876 0.564     0.154     0.032        2     0.3  S_interm_prim-Jensen
 2836   1934   3778  2.242 0.471     0.131     0.029       28     3.5  S_intrapariet&P_trans
 1186    847   1746  2.145 0.585     0.137     0.033       13     1.6  S_oc_middle&Lunatus
 1148    800   1312  1.762 0.371     0.108     0.021        7     1.0  S_oc_sup&transversal
  640    434    797  2.148 0.477     0.117     0.027        4     0.7  S_occipital_ant
  979    663   1416  2.291 0.600     0.112     0.023        7     0.9  S_oc-temp_lat
 1964   1663   3251  2.072 0.692     0.147     0.033       17     3.2  S_oc-temp_med&Lingual
  544    371    809  2.387 0.518     0.109     0.024        3     0.6  S_orbital_lateral
  658    477    984  2.349 0.854     0.123     0.025        6     0.7  S_orbital_med-olfact
 1359    940   2710  2.723 0.899     0.130     0.035       13     2.0  S_orbital-H_Shaped
 2021   1397   2780  2.078 0.633     0.126     0.028       19     2.3  S_parieto_occipital
 1350    801   1320  2.203 0.922     0.128     0.022       24     1.1  S_pericallosal
 3438   2338   4881  2.314 0.491     0.127     0.028       33     3.7  S_postcentral
 1776   1220   3014  2.708 0.429     0.104     0.020       12     1.4  S_precentral-inf-part
 2109   1451   3362  2.650 0.501     0.102     0.017       12     1.6  S_precentral-sup-part
  738    509   1117  2.308 0.959     0.096     0.016        3     0.5  S_suborbital
  785    560   1192  2.256 0.458     0.128     0.029        7     0.9  S_subparietal
 1497   1026   1845  1.914 0.476     0.108     0.021        9     1.3  S_temporal_inf
 5773   4043   9251  2.330 0.556     0.112     0.023       42     5.7  S_temporal_sup
  379    246    446  2.282 0.394     0.112     0.020        2     0.3  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 0050345 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277731
Total vertex volume 274478 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
  776    567   1894  2.456 0.906     0.152     0.055       12     1.7  G&S_frontomargin
 1495   1150   3371  2.421 0.738     0.175     0.057       26     4.0  G&S_occipital_inf
 1640   1056   3052  2.382 0.732     0.133     0.045       19     3.2  G&S_paracentral
 1879   1263   3880  2.605 0.670     0.140     0.037       26     3.0  G&S_subcentral
 1074    755   3867  3.276 0.782     0.178     0.062       24     2.8  G&S_transv_frontopol
 2943   2064   6367  2.885 0.651     0.128     0.037       41     4.6  G&S_cingul-Ant
 1318    937   3052  2.970 0.590     0.125     0.026       14     1.4  G&S_cingul-Mid-Ant
 1560   1089   3160  2.784 0.680     0.136     0.033       16     2.1  G&S_cingul-Mid-Post
  598    418   1772  3.268 0.872     0.176     0.058       11     1.3  G_cingul-Post-dorsal
  370    242    924  2.836 0.719     0.149     0.054        8     0.7  G_cingul-Post-ventral
 2573   1813   4168  1.937 0.579     0.176     0.058       46     6.4  G_cuneus
 1611   1123   4119  2.801 0.635     0.152     0.050       29     3.1  G_front_inf-Opercular
  537    362   1318  2.687 0.804     0.184     0.092       14     2.0  G_front_inf-Orbital
 1203    824   3054  2.660 0.637     0.156     0.048       22     2.4  G_front_inf-Triangul
 4956   3504  14358  2.914 0.743     0.165     0.054       98    11.5  G_front_middle
 8611   5781  23686  3.151 0.769     0.146     0.051      138    19.2  G_front_sup
  637    477   1505  2.917 0.646     0.148     0.047       10     1.2  G_Ins_lg&S_cent_ins
  829    570   2247  2.918 1.073     0.180     0.084       25     2.7  G_insular_short
 2413   1768   5497  2.404 0.609     0.176     0.055       45     5.8  G_occipital_middle
 1764   1225   2810  1.938 0.612     0.158     0.043       27     3.4  G_occipital_sup
 2269   1674   5227  2.525 0.720     0.182     0.056       47     5.9  G_oc-temp_lat-fusifor
 2848   2069   5485  2.114 0.716     0.173     0.062       57     7.6  G_oc-temp_med-Lingual
 1321    922   3409  2.563 0.871     0.136     0.040       15     2.3  G_oc-temp_med-Parahip
 2910   1992   7760  2.812 0.820     0.162     0.063       60     7.4  G_orbital
 2957   1938   6246  2.481 0.686     0.149     0.053       48     6.4  G_pariet_inf-Angular
 2510   1706   6166  2.788 0.628     0.147     0.039       41     3.8  G_pariet_inf-Supramar
 3138   2100   5528  2.171 0.568     0.132     0.039       37     5.3  G_parietal_sup
 2777   1819   5786  2.425 0.771     0.147     0.048       45     5.6  G_postcentral
 3383   2162   7982  2.831 0.718     0.125     0.042       44     6.2  G_precentral
 2244   1553   5117  2.530 0.692     0.142     0.039       31     3.4  G_precuneus
  915    605   2074  2.335 0.707     0.161     0.069       27     2.9  G_rectus
  647    400    999  2.499 1.008     0.083     0.034        4     0.6  G_subcallosal
  511    307    825  2.209 0.555     0.109     0.027        4     0.6  G_temp_sup-G_T_transv
 1595   1172   4029  2.478 0.702     0.151     0.047       27     3.0  G_temp_sup-Lateral
  971    681   1776  2.301 0.812     0.126     0.048       12     1.9  G_temp_sup-Plan_polar
  806    562   1350  2.139 0.554     0.103     0.023        6     0.8  G_temp_sup-Plan_tempo
 3634   2491   9909  2.715 0.889     0.182     0.087       94    14.6  G_temporal_inf
 3223   2270   9104  2.732 0.730     0.170     0.066       79     9.6  G_temporal_middle
  404    277    656  2.541 0.607     0.112     0.030        3     0.4  Lat_Fis-ant-Horizont
  167    126    270  2.588 0.657     0.136     0.025        1     0.2  Lat_Fis-ant-Vertical
 1429    953   1929  2.538 0.620     0.108     0.023        9     1.2  Lat_Fis-post
 3355   2446   6549  2.182 0.840     0.174     0.059       64     8.5  Pole_occipital
 1503   1222   3995  2.386 0.831     0.191     0.067       34     4.7  Pole_temporal
 2703   2007   3445  1.889 0.548     0.150     0.044       29     5.5  S_calcarine
 3503   2434   3964  1.853 0.554     0.116     0.022       27     3.3  S_central
 1282    876   2001  2.394 0.455     0.121     0.031       13     1.8  S_cingul-Marginalis
  765    505   1286  3.190 0.716     0.115     0.025        5     0.9  S_circular_insula_ant
 1133    768   1727  2.476 0.737     0.087     0.016        4     0.8  S_circular_insula_inf
 1704   1179   2690  2.718 0.583     0.094     0.017        7     1.3  S_circular_insula_sup
 1247    863   1744  2.148 0.584     0.096     0.016        6     0.8  S_collat_transv_ant
  371    264    452  1.890 0.300     0.130     0.029        3     0.4  S_collat_transv_post
 2141   1517   3377  2.331 0.517     0.112     0.022       15     2.1  S_front_inf
 2476   1751   4151  2.478 0.526     0.128     0.032       25     3.0  S_front_middle
 3617   2643   6783  2.648 0.532     0.108     0.022       24     3.5  S_front_sup
  214    141    305  1.993 0.596     0.107     0.020        1     0.2  S_interm_prim-Jensen
 3555   2425   4920  2.189 0.532     0.114     0.024       28     3.4  S_intrapariet&P_trans
  566    404    719  1.893 0.411     0.124     0.027        4     0.6  S_oc_middle&Lunatus
 1696   1187   2097  1.889 0.461     0.134     0.029       16     2.0  S_oc_sup&transversal
  929    666   1360  2.077 0.482     0.133     0.034        9     1.2  S_occipital_ant
 1377    898   1802  2.159 0.549     0.103     0.021       11     1.1  S_oc-temp_lat
 1803   1278   2086  1.746 0.438     0.111     0.023       13     1.6  S_oc-temp_med&Lingual
  352    276    599  2.226 0.638     0.128     0.027        3     0.4  S_orbital_lateral
  603    428    833  2.227 0.596     0.113     0.021        4     0.5  S_orbital_med-olfact
 1279    889   2388  2.668 0.629     0.143     0.043       14     2.3  S_orbital-H_Shaped
 2473   1694   3280  2.092 0.549     0.122     0.030       23     3.3  S_parieto_occipital
 1768   1097   1757  2.042 0.711     0.127     0.030       30     2.0  S_pericallosal
 2812   1940   3738  2.258 0.518     0.125     0.025       26     2.8  S_postcentral
 2155   1488   3662  2.673 0.465     0.109     0.024       16     1.9  S_precentral-inf-part
 1958   1364   2956  2.531 0.453     0.105     0.017       13     1.4  S_precentral-sup-part
  309    236    676  2.884 0.824     0.126     0.021        2     0.2  S_suborbital
 1104    798   2029  2.545 0.660     0.150     0.043       16     2.3  S_subparietal
 1637   1101   2285  2.294 0.623     0.119     0.034       13     2.3  S_temporal_inf
 5501   3840   8766  2.311 0.570     0.113     0.025       40     6.0  S_temporal_sup
  265    181    325  2.106 0.375     0.127     0.027        3     0.2  S_temporal_transverse
PIDs (9399 9402) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 08:06:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 08:06:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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 9472 of (9472 9475) to complete...
Waiting for PID 9475 of (9472 9475) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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...
1480 labels changed using aseg
relabeling using gibbs priors...
000:   2226 changed, 146952 examined...
001:    520 changed, 10246 examined...
002:    148 changed, 2920 examined...
003:     68 changed, 874 examined...
004:     49 changed, 414 examined...
005:     26 changed, 268 examined...
006:     16 changed, 143 examined...
007:      7 changed, 94 examined...
008:      4 changed, 45 examined...
009:      3 changed, 28 examined...
010:      2 changed, 17 examined...
011:      2 changed, 12 examined...
012:      3 changed, 14 examined...
013:      3 changed, 21 examined...
014:      0 changed, 16 examined...
246 labels changed using aseg
000: 77 total segments, 44 labels (510 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
707 vertices marked for relabeling...
707 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050345 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...
1472 labels changed using aseg
relabeling using gibbs priors...
000:   2054 changed, 146055 examined...
001:    473 changed, 9637 examined...
002:    112 changed, 2675 examined...
003:     49 changed, 679 examined...
004:     25 changed, 280 examined...
005:     16 changed, 146 examined...
006:     17 changed, 86 examined...
007:     10 changed, 76 examined...
008:      3 changed, 55 examined...
009:      2 changed, 15 examined...
010:      2 changed, 17 examined...
011:      0 changed, 14 examined...
194 labels changed using aseg
000: 57 total segments, 24 labels (176 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
994 vertices marked for relabeling...
994 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.
PIDs (9472 9475) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 08:06:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 08:06:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 rh white 

Waiting for PID 9520 of (9520 9523) to complete...
Waiting for PID 9523 of (9520 9523) 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 0050345 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277491
Total vertex volume 273465 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1704   1157   3430  2.905 0.659     0.131     0.029       23     1.8  caudalanteriorcingulate
 4556   3044   9455  2.799 0.663     0.123     0.043       53     7.7  caudalmiddlefrontal
 2880   1963   4158  1.876 0.524     0.151     0.043       43     5.5  cuneus
  861    610   2367  2.691 0.845     0.164     0.075       19     3.2  entorhinal
 3996   3140   9428  2.612 0.741     0.160     0.043       61     7.5  fusiform
 7028   4793  12723  2.335 0.596     0.135     0.035       87    10.2  inferiorparietal
 5372   3498  10333  2.328 0.749     0.134     0.049       97    11.8  inferiortemporal
 1571   1038   2830  2.388 0.838     0.143     0.037       27     2.0  isthmuscingulate
 7528   5310  14171  2.220 0.675     0.158     0.044      121    14.2  lateraloccipital
 4109   2895   9718  2.796 0.794     0.148     0.049       60     8.6  lateralorbitofrontal
 3847   2821   7058  2.105 0.686     0.163     0.052       60     8.6  lingual
 2503   1630   5116  2.489 0.854     0.131     0.054       72     5.9  medialorbitofrontal
 6352   4400  14829  2.527 0.766     0.138     0.041       99    11.0  middletemporal
 1275    994   2937  2.593 0.730     0.136     0.037       14     2.3  parahippocampal
 2832   1861   5396  2.599 0.697     0.121     0.032       30     3.7  paracentral
 2541   1722   5782  2.768 0.649     0.121     0.028       26     2.9  parsopercularis
 1162    782   2789  2.737 0.638     0.137     0.039       15     1.8  parsorbitalis
 2895   2012   6442  2.705 0.642     0.126     0.031       32     3.9  parstriangularis
 1863   1351   2465  1.872 0.556     0.148     0.043       22     3.5  pericalcarine
 8826   5785  14084  2.217 0.688     0.133     0.037      100    13.6  postcentral
 1818   1283   3462  2.604 0.646     0.146     0.033       29     2.3  posteriorcingulate
 8981   5825  17275  2.729 0.663     0.116     0.029       81    10.3  precentral
 5064   3461  10427  2.588 0.640     0.146     0.041       69     8.3  precuneus
 2067   1394   4278  2.638 0.946     0.127     0.037       34     3.1  rostralanteriorcingulate
 7380   5015  15471  2.615 0.749     0.138     0.036       96    11.3  rostralmiddlefrontal
14704   9796  31645  2.809 0.785     0.132     0.042      187    25.1  superiorfrontal
 6625   4392  10643  2.220 0.571     0.133     0.034       79     9.1  superiorparietal
 8607   5783  15838  2.414 0.642     0.119     0.035       93    12.7  superiortemporal
 5576   3756  10594  2.602 0.588     0.133     0.033       70     7.4  supramarginal
  857    518   1262  2.132 0.449     0.107     0.026        7     0.8  transversetemporal
 3221   2186   7060  3.111 0.792     0.117     0.032       31     4.1  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 0050345 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 277731
Total vertex volume 274478 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1297    872   2739  2.734 0.781     0.136     0.026       19     1.3  caudalanteriorcingulate
 4536   3119   9441  2.745 0.606     0.122     0.034       50     6.2  caudalmiddlefrontal
 3241   2276   5080  1.939 0.532     0.164     0.053       52     7.4  cuneus
  503    379   1331  2.446 0.972     0.141     0.035        5     0.8  entorhinal
 4545   3198   8311  2.282 0.680     0.143     0.039       63     7.6  fusiform
 7441   5096  13971  2.381 0.628     0.140     0.041       92    12.6  inferiorparietal
 6451   4523  14864  2.530 0.822     0.156     0.061      121    18.3  inferiortemporal
 1584   1038   2896  2.450 0.899     0.136     0.044       25     2.5  isthmuscingulate
 7503   5429  14530  2.246 0.743     0.164     0.048      122    16.0  lateraloccipital
 4034   2734   8967  2.725 0.707     0.149     0.052       64     8.4  lateralorbitofrontal
 4415   3341   7626  1.995 0.669     0.171     0.057       75    11.6  lingual
 2302   1567   4972  2.519 0.810     0.137     0.050       45     4.9  medialorbitofrontal
 6628   4632  14164  2.479 0.703     0.144     0.050      110    14.8  middletemporal
 1032    708   1855  2.204 0.753     0.112     0.027        8     1.2  parahippocampal
 2509   1645   5028  2.727 0.727     0.118     0.028       19     3.1  paracentral
 2581   1831   5339  2.631 0.621     0.140     0.041       35     4.0  parsopercularis
 1295    866   2883  2.807 0.952     0.162     0.064       24     3.2  parsorbitalis
 2379   1686   5336  2.634 0.639     0.149     0.044       37     4.8  parstriangularis
 2408   1729   2829  1.675 0.436     0.152     0.047       34     4.7  pericalcarine
 7937   5404  13239  2.194 0.699     0.129     0.033       93    11.2  postcentral
 1867   1309   3837  2.650 0.875     0.159     0.040       33     3.0  posteriorcingulate
 8498   5653  16638  2.638 0.695     0.120     0.034       87    12.3  precentral
 5704   3944  10546  2.395 0.646     0.137     0.037       70     9.2  precuneus
 1322    899   2821  2.707 0.800     0.133     0.048       23     2.8  rostralanteriorcingulate
 6864   4990  15645  2.595 0.706     0.148     0.041      104    12.1  rostralmiddlefrontal
15383  10649  37285  2.974 0.746     0.134     0.042      199    27.0  superiorfrontal
 7829   5387  12184  2.094 0.544     0.132     0.034       87    11.3  superiorparietal
 6478   4572  12244  2.309 0.672     0.126     0.036       73     9.8  superiortemporal
 4999   3350   9854  2.639 0.632     0.132     0.032       62     6.3  supramarginal
  513    317    801  2.213 0.573     0.102     0.031        4     0.4  transversetemporal
 3524   2430   7222  2.898 0.797     0.127     0.042       45     5.8  insula
PIDs (9520 9523) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 08:07:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 pctsurfcon --s 0050345 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 08:07:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts

 pctsurfcon --s 0050345 --rh-only 

Waiting for PID 9590 of (9590 9602) to complete...
Waiting for PID 9602 of (9590 9602) to complete...

 pctsurfcon --s 0050345 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts/pctsurfcon.log
Sun Oct  8 08:07:19 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-610 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-6.0.0/0050345/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9590/lh.wm.mgh --regheader 0050345 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 69602
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9590/lh.wm.mgh
Dim: 146952 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9590/lh.gm.mgh --projfrac 0.3 --regheader 0050345 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 83251
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9590/lh.gm.mgh
Dim: 146952 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9590/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9590/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.w-g.pct.mgh --annot 0050345 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/lh.w-g.pct.mgh --annot 0050345 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/lh.w-g.pct.mgh
Vertex Area is 0.678652 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 0050345 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/scripts/pctsurfcon.log
Sun Oct  8 08:07:19 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-610 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-6.0.0/0050345/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9602/rh.wm.mgh --regheader 0050345 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 70400
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9602/rh.wm.mgh
Dim: 146055 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9602/rh.gm.mgh --projfrac 0.3 --regheader 0050345 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 83377
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9602/rh.gm.mgh
Dim: 146055 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9602/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/tmp.pctsurfcon.9602/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.w-g.pct.mgh --annot 0050345 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.w-g.pct.mgh --annot 0050345 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.w-g.pct.mgh
Vertex Area is 0.692114 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 (9590 9602) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 08:07:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2797 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
3057 voxels changed to hypointensity...
5934 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 08:07:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345

 mri_aparc2aseg --s 0050345 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 08:07:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345

 mri_aparc2aseg --s 0050345 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 08:07:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345

 mri_aparc2aseg --s 0050345 --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 9801 of (9801 9804 9807) to complete...
Waiting for PID 9804 of (9801 9804 9807) to complete...
Waiting for PID 9807 of (9801 9804 9807) to complete...

 mri_aparc2aseg --s 0050345 --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 0050345
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/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-6.0.0/0050345/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 6.76
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 103
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 13
rescaling Left_Inf_Lat_Vent from 34 --> 27
rescaling Left_Cerebellum_White_Matter from 86 --> 69
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 99
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 77
rescaling Left_Pallidum from 98 --> 92
rescaling Third_Ventricle from 25 --> 19
rescaling Fourth_Ventricle from 22 --> 12
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 57
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 26
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 63
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 79
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 71
rescaling Right_Pallidum from 97 --> 90
rescaling Right_Hippocampus from 53 --> 56
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 97
rescaling Fifth_Ventricle from 40 --> 23
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 542446
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 12 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050345 --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 0050345
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/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-6.0.0/0050345/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 6.76
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 103
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 13
rescaling Left_Inf_Lat_Vent from 34 --> 27
rescaling Left_Cerebellum_White_Matter from 86 --> 69
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 99
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 77
rescaling Left_Pallidum from 98 --> 92
rescaling Third_Ventricle from 25 --> 19
rescaling Fourth_Ventricle from 22 --> 12
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 57
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 26
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 63
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 79
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 71
rescaling Right_Pallidum from 97 --> 90
rescaling Right_Hippocampus from 53 --> 56
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 97
rescaling Fifth_Ventricle from 40 --> 23
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 542502
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 12 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050345 --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 0050345
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/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-6.0.0/0050345/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 6.76
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 103
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 13
rescaling Left_Inf_Lat_Vent from 34 --> 27
rescaling Left_Cerebellum_White_Matter from 86 --> 69
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 99
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 77
rescaling Left_Pallidum from 98 --> 92
rescaling Third_Ventricle from 25 --> 19
rescaling Fourth_Ventricle from 22 --> 12
rescaling Brain_Stem from 81 --> 87
rescaling Left_Hippocampus from 57 --> 57
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 26
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 63
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 79
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 71
rescaling Right_Pallidum from 97 --> 90
rescaling Right_Hippocampus from 53 --> 56
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 97
rescaling Fifth_Ventricle from 40 --> 23
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 542502
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 12 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (9801 9804 9807) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 08:15:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri

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

Sun Oct  8 08:15:41 CEST 2017

setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-610 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-6.0.0/0050345/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-610
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 08:15:41 CEST 2017 
Ended   at Sun Oct  8 08:15:47 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 08:15:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345

 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 0050345 


$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 0050345 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1145888 mm^3    (det: 1.700084 )
Computing euler number
orig.nofix lheno = -178, rheno = -210
orig.nofix lhholes =   90, rhholes = 106
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 08:17:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345

 mri_aparc2aseg --s 0050345 --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 0050345
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-6.0.0/0050345/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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-6.0.0/0050345/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8363 vertices from left hemi
Ripped 8479 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-6.0.0/0050345/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 = 1024799
Used brute-force search on 240 voxels
Fixing Parahip LH WM
  Found 16 clusters
     0 k 2.000000
     1 k 634.000000
     2 k 1.000000
     3 k 32.000000
     4 k 2.000000
     5 k 1.000000
     6 k 2.000000
     7 k 4.000000
     8 k 1.000000
     9 k 1.000000
     10 k 1.000000
     11 k 2.000000
     12 k 1.000000
     13 k 1379.000000
     14 k 9.000000
     15 k 1.000000
Fixing Parahip RH WM
  Found 12 clusters
     0 k 1.000000
     1 k 1331.000000
     2 k 1.000000
     3 k 1.000000
     4 k 5.000000
     5 k 16.000000
     6 k 2.000000
     7 k 3.000000
     8 k 1.000000
     9 k 26.000000
     10 k 1.000000
     11 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 0050345 --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 0050345 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-610
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1145888 mm^3    (det: 1.700084 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
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-6.0.0/0050345/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 08:26:55 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11140 of (11140 11146 11152 11158 11162) to complete...
Waiting for PID 11146 of (11140 11146 11152 11158 11162) to complete...
Waiting for PID 11152 of (11140 11146 11152 11158 11162) to complete...
Waiting for PID 11158 of (11140 11146 11152 11158 11162) to complete...
Waiting for PID 11162 of (11140 11146 11152 11158 11162) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 647
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4776
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 1066
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8975
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 241
Checking for and removing duplicates
Writing label file ./lh.BA3a_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.BA3b_exvivo.label --trgsubject 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 474
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6457
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 888
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6672
mri_label2label: Done

PIDs (11140 11146 11152 11158 11162) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11290 of (11290 11296 11302 11308) to complete...
Waiting for PID 11296 of (11290 11296 11302 11308) to complete...
Waiting for PID 11302 of (11290 11296 11302 11308) to complete...
Waiting for PID 11308 of (11290 11296 11302 11308) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 370
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4440
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 3187
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16776
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 506
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4687
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 989
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4411
mri_label2label: Done

PIDs (11290 11296 11302 11308) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11451 of (11451 11457 11463 11468 11473) to complete...
Waiting for PID 11457 of (11451 11457 11463 11468 11473) to complete...
Waiting for PID 11463 of (11451 11457 11463 11468 11473) to complete...
Waiting for PID 11468 of (11451 11457 11463 11468 11473) to complete...
Waiting for PID 11473 of (11451 11457 11463 11468 11473) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 1192
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5833
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 2076
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10190
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 525
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2543
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 384
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1674
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 284
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1483
mri_label2label: Done

PIDs (11451 11457 11463 11468 11473) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11540 of (11540 11546 11552 11556 11564) to complete...
Waiting for PID 11546 of (11540 11546 11552 11556 11564) to complete...
Waiting for PID 11552 of (11540 11546 11552 11556 11564) to complete...
Waiting for PID 11556 of (11540 11546 11552 11556 11564) to complete...
Waiting for PID 11564 of (11540 11546 11552 11556 11564) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 134
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1148
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 531
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2623
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 92
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1596
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 236
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2232
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 275
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2594
mri_label2label: Done

PIDs (11540 11546 11552 11556 11564) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11615 of (11615 11621 11627 11632) to complete...
Waiting for PID 11621 of (11615 11621 11627 11632) to complete...
Waiting for PID 11627 of (11615 11621 11627 11632) to complete...
Waiting for PID 11632 of (11615 11621 11627 11632) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 111
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1660
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 1731
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8766
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 211
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2123
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 436
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1587
mri_label2label: Done

PIDs (11615 11621 11627 11632) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11741 of (11741 11747 11753 11758 11763) to complete...
Waiting for PID 11747 of (11741 11747 11753 11758 11763) to complete...
Waiting for PID 11753 of (11741 11747 11753 11758 11763) to complete...
Waiting for PID 11758 of (11741 11747 11753 11758 11763) to complete...
Waiting for PID 11763 of (11741 11747 11753 11758 11763) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 823
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4228
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 991
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4325
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 114
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 627
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 219
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 689
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146952
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 583
mri_label2label: Done

PIDs (11741 11747 11753 11758 11763) completed and logs appended.

 mris_label2annot --s 0050345 --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-6.0.0/0050345/label
cmdline mris_label2annot --s 0050345 --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-610
machine  x86_64
user     ntraut

subject 0050345
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-6.0.0/0050345/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 99837 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050345 --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-6.0.0/0050345/label
cmdline mris_label2annot --s 0050345 --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-610
machine  x86_64
user     ntraut

subject 0050345
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-6.0.0/0050345/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 118445 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 277491
Total vertex volume 273465 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1416    886   2579  2.324 0.691     0.139     0.039       18     2.3  BA1_exvivo
 4830   3206   7835  2.380 0.611     0.136     0.034       56     6.5  BA2_exvivo
 1238    817   1203  1.869 0.514     0.130     0.028       12     1.3  BA3a_exvivo
 2555   1688   4230  2.147 0.804     0.128     0.035       27     3.8  BA3b_exvivo
 1983   1183   3804  2.871 0.643     0.104     0.030       18     2.6  BA4a_exvivo
 1489   1059   2506  2.518 0.583     0.114     0.023        9     1.4  BA4p_exvivo
12854   8276  27172  2.843 0.714     0.125     0.038      159    20.1  BA6_exvivo
 2534   1727   5674  2.780 0.563     0.124     0.029       27     3.1  BA44_exvivo
 3521   2408   8531  2.811 0.704     0.129     0.033       42     4.5  BA45_exvivo
 3263   2421   6007  2.043 0.733     0.161     0.050       49     7.0  V1_exvivo
 7442   5298  12980  2.078 0.641     0.167     0.051      125    16.6  V2_exvivo
 2244   1564   3890  2.253 0.599     0.142     0.033       30     3.2  MT_exvivo
  882    604   2093  2.654 0.789     0.126     0.056       12     2.5  perirhinal_exvivo
  864    646   2338  2.571 0.807     0.176     0.070       20     2.4  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 0050345 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 277491
Total vertex volume 273465 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
  861    538   1655  2.486 0.643     0.142     0.040       11     1.5  BA1_exvivo
 2255   1484   3781  2.340 0.650     0.137     0.037       27     3.6  BA2_exvivo
 1082    704    980  1.824 0.497     0.132     0.028       11     1.2  BA3a_exvivo
 1702   1133   2201  1.836 0.577     0.117     0.029       16     1.9  BA3b_exvivo
 1888   1180   3828  2.939 0.597     0.102     0.024       14     2.0  BA4a_exvivo
 1222    872   1991  2.462 0.590     0.118     0.024        9     1.3  BA4p_exvivo
 7545   4690  15175  2.794 0.675     0.119     0.035       89    10.5  BA6_exvivo
 1650   1137   3817  2.769 0.577     0.130     0.032       19     2.2  BA44_exvivo
 1488   1005   4045  2.952 0.705     0.134     0.031       19     1.8  BA45_exvivo
 3444   2584   6631  2.070 0.740     0.168     0.054       57     8.4  V1_exvivo
 3826   2657   6612  2.107 0.657     0.169     0.054       66     8.7  V2_exvivo
  564    397    886  2.141 0.512     0.130     0.028        6     0.7  MT_exvivo
  492    328    929  2.420 0.725     0.143     0.072       10     1.8  perirhinal_exvivo
  488    356   1442  2.946 0.669     0.182     0.078       13     1.6  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 08:30:09 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 12028 of (12028 12034 12040 12046 12052) to complete...
Waiting for PID 12034 of (12028 12034 12040 12046 12052) to complete...
Waiting for PID 12040 of (12028 12034 12040 12046 12052) to complete...
Waiting for PID 12046 of (12028 12034 12040 12046 12052) to complete...
Waiting for PID 12052 of (12028 12034 12040 12046 12052) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 596
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4558
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 660
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7347
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 201
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4181
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 460
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4982
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 660
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6407
mri_label2label: Done

PIDs (12028 12034 12040 12046 12052) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 12167 of (12167 12173 12179 12185) to complete...
Waiting for PID 12173 of (12167 12173 12179 12185) to complete...
Waiting for PID 12179 of (12167 12173 12179 12185) to complete...
Waiting for PID 12185 of (12167 12173 12179 12185) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 347
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4820
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1978
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14234
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1118
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8030
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1330
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6685
mri_label2label: Done

PIDs (12167 12173 12179 12185) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 12294 of (12294 12300 12306 12311 12316) to complete...
Waiting for PID 12300 of (12294 12300 12306 12311 12316) to complete...
Waiting for PID 12306 of (12294 12300 12306 12311 12316) to complete...
Waiting for PID 12311 of (12294 12300 12306 12311 12316) to complete...
Waiting for PID 12316 of (12294 12300 12306 12311 12316) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1772
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6499
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 2799
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10815
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 616
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2548
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 161
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1199
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 152
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 904
mri_label2label: Done

PIDs (12294 12300 12306 12311 12316) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12379 of (12379 12385 12393 12416 12438) to complete...
Waiting for PID 12385 of (12379 12385 12393 12416 12438) to complete...
Waiting for PID 12393 of (12379 12385 12393 12416 12438) to complete...
Waiting for PID 12416 of (12379 12385 12393 12416 12438) to complete...
Waiting for PID 12438 of (12379 12385 12393 12416 12438) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 186
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1062
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 245
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2933
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 76
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1774
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 215
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2398
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 120
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1508
mri_label2label: Done

PIDs (12379 12385 12393 12416 12438) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12511 of (12511 12517 12523 12527) to complete...
Waiting for PID 12517 of (12511 12517 12523 12527) to complete...
Waiting for PID 12523 of (12511 12517 12523 12527) to complete...
Waiting for PID 12527 of (12511 12517 12523 12527) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 117
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1606
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1081
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8040
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 203
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1215
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 276
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1454
mri_label2label: Done

PIDs (12511 12517 12523 12527) 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 0050345 --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 0050345 --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 0050345 --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 0050345 --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 0050345 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12616 of (12616 12622 12628 12633 12640) to complete...
Waiting for PID 12622 of (12616 12622 12628 12633 12640) to complete...
Waiting for PID 12628 of (12616 12622 12628 12633 12640) to complete...
Waiting for PID 12633 of (12616 12622 12628 12633 12640) to complete...
Waiting for PID 12640 of (12616 12622 12628 12633 12640) 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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1270
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4502
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 1365
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4802
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 99
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 367
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 779
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 0050345 --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 = 0050345
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-6.0.0/0050345/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 146055
Number of reverse mapping hits = 66
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 357
mri_label2label: Done

PIDs (12616 12622 12628 12633 12640) completed and logs appended.

 mris_label2annot --s 0050345 --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-6.0.0/0050345/label
cmdline mris_label2annot --s 0050345 --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-610
machine  x86_64
user     ntraut

subject 0050345
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-6.0.0/0050345/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 100527 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050345 --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-6.0.0/0050345/label
cmdline mris_label2annot --s 0050345 --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-610
machine  x86_64
user     ntraut

subject 0050345
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-6.0.0/0050345/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 120101 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/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 0050345 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 277731
Total vertex volume 274478 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
 1160    724   2464  2.567 0.750     0.158     0.055       20     2.7  BA1_exvivo
 3531   2427   5913  2.301 0.624     0.128     0.032       39     4.6  BA2_exvivo
 1169    778   1068  1.858 0.426     0.133     0.031       12     1.4  BA3a_exvivo
 2292   1598   3301  1.787 0.621     0.122     0.026       23     2.7  BA3b_exvivo
 1683   1089   3412  2.826 0.687     0.117     0.042       20     3.4  BA4a_exvivo
 1446    998   2066  2.183 0.595     0.114     0.024       11     1.4  BA4p_exvivo
10014   6756  22879  2.867 0.740     0.127     0.042      125    18.4  BA6_exvivo
 4093   2778   8659  2.802 0.586     0.128     0.035       46     5.3  BA44_exvivo
 4628   3285  10430  2.620 0.725     0.158     0.051       79    10.1  BA45_exvivo
 4102   3079   6793  1.910 0.692     0.168     0.058       74    10.6  V1_exvivo
 8090   5798  13906  2.093 0.687     0.170     0.053      133    18.9  V2_exvivo
 2261   1624   4072  2.272 0.524     0.140     0.038       26     3.6  MT_exvivo
  635    478   1776  2.591 0.964     0.138     0.037        7     0.9  perirhinal_exvivo
  424    320   1295  2.709 0.765     0.176     0.062        8     1.4  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 0050345 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050345/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 277731
Total vertex volume 274478 (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) = 1145888 mm^3    (det: 1.700084 )
lhCtxGM: 266775.335 266394.000  diff=  381.3  pctdiff= 0.143
rhCtxGM: 268796.383 268347.000  diff=  449.4  pctdiff= 0.167
lhCtxWM: 239174.991 240128.500  diff= -953.5  pctdiff=-0.399
rhCtxWM: 242698.300 242954.500  diff= -256.2  pctdiff=-0.106
SubCortGMVol  64760.000
SupraTentVol  1114288.009 (1101851.000) diff=12437.009 pctdiff=1.116
SupraTentVolNotVent  1095097.009 (1082660.000) diff=12437.009 pctdiff=1.136
BrainSegVol  1177355.000 (1175310.000) diff=2045.000 pctdiff=0.174
BrainSegVolNotVent  1155084.000 (1154548.009) diff=535.991 pctdiff=0.046
BrainSegVolNotVent  1155084.000
CerebellumVol 72267.000
VentChorVol   19191.000
3rd4th5thCSF   3080.000
CSFVol  1035.000, OptChiasmVol   157.000
MaskVol 1502113.000
  830    525   1808  2.661 0.742     0.156     0.051       15     1.8  BA1_exvivo
 2054   1412   3914  2.400 0.660     0.122     0.032       22     2.7  BA2_exvivo
 1078    707    937  1.866 0.400     0.137     0.033       11     1.5  BA3a_exvivo
 1795   1282   2163  1.591 0.462     0.106     0.018       12     1.5  BA3b_exvivo
 1013    634   2400  3.054 0.678     0.135     0.058       16     3.0  BA4a_exvivo
 1193    843   1613  2.120 0.646     0.118     0.024        9     1.2  BA4p_exvivo
 6401   4235  14349  2.837 0.718     0.119     0.035       70     9.5  BA6_exvivo
 1011    690   2239  2.719 0.613     0.152     0.050       17     1.8  BA44_exvivo
 1251    890   3157  2.625 0.626     0.154     0.046       21     2.2  BA45_exvivo
 3966   2960   6344  1.887 0.671     0.167     0.057       70    10.4  V1_exvivo
 4366   3177   7517  2.053 0.729     0.180     0.056       79    10.6  V2_exvivo
  338    255    740  2.316 0.572     0.161     0.039        6     0.6  MT_exvivo
  360    277   1021  2.603 0.949     0.129     0.028        3     0.5  perirhinal_exvivo
  298    214    712  2.437 0.855     0.143     0.038        3     0.6  entorhinal_exvivo

Started at Sat Oct 7 23:40:21 CEST 2017 
Ended   at Sun Oct 8 08:33:21 CEST 2017
#@#%# recon-all-run-time-hours 8.883
recon-all -s 0050345 finished without error at Sun Oct  8 08:33:21 CEST 2017