ABIDE_fs-6.0.0/0050017/scripts/recon-all.log

Sat Oct  7 18:15:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050017 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050017/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050017
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-105 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:     264574092  244712940   19861152    1729820          0  239244412
-/+ buffers/cache:    5468528  259105564
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:24-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:15:25-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-105  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-6.0.0/0050017

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050017/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050017/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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/Pitt/0050017/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-6.0.0/0050017/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 18:15:29 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/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-6.0.0/0050017/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 18:15:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/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-105 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:15:40 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.2148
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2148/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2148/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.2148/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:15:42 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.2148/nu0.mnc ./tmp.mri_nu_correct.mni.2148/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2148/0/ -iterations 1000 -distance 50
[ntraut@tars-105:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/] [2017-10-07 18:15:42] 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.2148/0/ ./tmp.mri_nu_correct.mni.2148/nu0.mnc ./tmp.mri_nu_correct.mni.2148/nu1.imp

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Number of iterations: 70 
CV of field change: 0.000982429
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.2148/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.2148/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.2148/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 18:17:08 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 18:17:08 CEST 2017
Ended   at Sat Oct  7 18:17:40 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 18:17:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5031, pval=0.1531 >= 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-6.0.0/0050017/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/transforms/talairach_avi.log 

TalAviQA: 0.97597
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 18:17:42 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-6.0.0/0050017/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-105 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:17:42 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.3275
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3275/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3275/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.3275/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:17:44 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.3275/nu0.mnc ./tmp.mri_nu_correct.mni.3275/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3275/0/
[ntraut@tars-105:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/] [2017-10-07 18:17:44] 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.3275/0/ ./tmp.mri_nu_correct.mni.3275/nu0.mnc ./tmp.mri_nu_correct.mni.3275/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00195688
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 18:18:36 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.3275/nu1.mnc ./tmp.mri_nu_correct.mni.3275/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.3275/1/
[ntraut@tars-105:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/] [2017-10-07 18:18:36] 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.3275/1/ ./tmp.mri_nu_correct.mni.3275/nu1.mnc ./tmp.mri_nu_correct.mni.3275/nu2.imp

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Number of iterations: 49 
CV of field change: 0.00097353
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.3275/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3275/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-6.0.0/0050017/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.3275/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3275/ones.mgz 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.3275/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.3275/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.3275/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3275/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3275/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.3275/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3275/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3275/input.mean.dat 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.3275/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.3275/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3275/ones.mgz --i ./tmp.mri_nu_correct.mni.3275/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3275/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3275/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.3275/ones.mgz --i ./tmp.mri_nu_correct.mni.3275/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3275/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3275/output.mean.dat 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.3275/ones.mgz
Loading ./tmp.mri_nu_correct.mni.3275/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.3275/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.3275/nu2.mnc ./tmp.mri_nu_correct.mni.3275/nu2.mnc mul .92440135919968376562
Saving result to './tmp.mri_nu_correct.mni.3275/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.3275/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.3275/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.3275/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 (16, 137) to ( 3, 110)
 
 
Sat Oct  7 18:20:05 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 18:20:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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
 1.06109   0.04608  -0.06446  -1.61937;
-0.01812   0.87600   0.37962  -4.53343;
 0.06947  -0.37082   0.95736   2.39229;
 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 = 8
Starting OpenSpline(): npoints = 8
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 64 (64), valley at 48 (48)
csf peak at 33, setting threshold to 53
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 62 (62), valley at 46 (46)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 7 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 18:22:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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=12.0
skull bounding box = (49, 42, 0) --> (214, 255, 206)
using (104, 113, 103) as brain centroid...
mean wm in atlas = 108, using box (84,87,78) --> (124, 139,128) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 101 +- 7.2
after smoothing, mri peak at 101, scaling input intensities by 1.069
scaling channel 0 by 1.06931
initial log_p = -4.330
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.371417 @ (-9.091, -9.091, -9.091)
max log p =    -4.351991 @ (4.545, 4.545, 4.545)
max log p =    -4.312114 @ (-2.273, -6.818, -6.818)
max log p =    -4.309133 @ (1.136, -1.136, 1.136)
max log p =    -4.299651 @ (-0.568, 0.568, -1.705)
max log p =    -4.299651 @ (0.000, 0.000, 0.000)
Found translation: (-6.3, -11.9, -11.9): log p = -4.300
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.111, old_max_log_p =-4.300 (thresh=-4.3)
 1.06580  -0.14771  -0.06413   13.67594;
 0.13053   1.04367   0.45313  -76.70140;
 0.00000  -0.33830   0.86364   58.76502;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.111, old_max_log_p =-4.111 (thresh=-4.1)
 1.06580  -0.14771  -0.06413   13.67594;
 0.13053   1.04367   0.45313  -76.70140;
 0.00000  -0.33830   0.86364   58.76502;
 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=-4.038, old_max_log_p =-4.111 (thresh=-4.1)
 1.09385  -0.01041  -0.00452  -12.72425;
-0.00988   1.07304   0.46588  -63.96874;
 0.00000  -0.34464   0.87984   57.78706;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.038, old_max_log_p =-4.038 (thresh=-4.0)
 1.07334  -0.01021  -0.00443  -10.14425;
-0.00988   1.07304   0.46588  -63.96874;
 0.00000  -0.34464   0.87984   57.78706;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.029, old_max_log_p =-4.038 (thresh=-4.0)
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01005   1.07269   0.47418  -64.39378;
 0.00008  -0.35382   0.87702   59.41486;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.025, old_max_log_p =-4.029 (thresh=-4.0)
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 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
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.025 (old=-4.330)
transform before final EM align:
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 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
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.4  tol 0.000000
final transform:
 1.07712  -0.01011  -0.00439  -10.64701;
-0.01007   1.07521   0.47529  -64.87793;
 0.00008  -0.35299   0.87497   59.53558;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1405.150384
mri_em_register stimesec    1.789727
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   157058
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    84575
mri_em_register ru_nivcsw   2717
registration took 13 minutes and 48 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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=128 y=113 z=112 r=85
      first estimation of the main basin volume: 2607119 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=149, y=107, z=74, Imax=255
      CSF=14, 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=9821642947 voxels, voxel volume =1.000 
                     = 9821642947 mmm3 = 9821642.752 cm3
done.
PostAnalyze...Basin Prior
 74 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
      ambiguous basin, non merged: 24 ambiguous voxels; size: 20858 voxels
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=128,y=126, z=106, r=10259 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=30 , nb = 42039
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=27 , nb = -1031416251
  LEFT_CER     CSF_MIN=0, CSF_intensity=11, CSF_MAX=32 , nb = -1044169851
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = 1071244737
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 1065671118
    OTHER      CSF_MIN=1, CSF_intensity=12, CSF_MAX=52 , nb = 1079243056
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    30,      30,        32,   68
  after  analyzing :    30,      31,        32,   40
   RIGHT_CER   
  before analyzing :    27,      66,        77,   84
  after  analyzing :    27,      73,        77,   75
   LEFT_CER    
  before analyzing :    32,      35,        41,   79
  after  analyzing :    32,      39,        41,   49
  RIGHT_BRAIN  
  before analyzing :    26,      28,        33,   68
  after  analyzing :    26,      31,        33,   40
  LEFT_BRAIN   
  before analyzing :    32,      32,        32,   67
  after  analyzing :    23,      32,        32,   40
     OTHER     
  before analyzing :    52,      60,        64,   80
  after  analyzing :    52,      62,        64,   66
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...74 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.012
curvature mean = 71.576, std = 9.153

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.54, sigma = 5.96
      after  rotation: sse = 3.54, sigma = 5.96
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.26, its var is  7.01   
      before Erosion-Dilatation  2.17% of inacurate vertices
      after  Erosion-Dilatation  1.87% 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...46 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1876619 voxels, voxel volume = 1.000 mm3
           = 1876619 mmm3 = 1876.619 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    29.539509
mri_watershed stimesec    0.413937
mri_watershed ru_maxrss   836772
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   216519
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  3080
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    2229
mri_watershed ru_nivcsw   597
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:36:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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=27.0
skull bounding box = (63, 61, 28) --> (197, 196, 198)
using (108, 106, 113) as brain centroid...
mean wm in atlas = 107, using box (92,89,92) --> (124, 122,133) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 101 +- 5.8
after smoothing, mri peak at 101, scaling input intensities by 1.059
scaling channel 0 by 1.05941
initial log_p = -4.105
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.159790 @ (0.000, 0.000, 0.000)
max log p =    -4.101326 @ (-4.545, -4.545, -4.545)
max log p =    -4.064001 @ (2.273, -2.273, 2.273)
max log p =    -4.054326 @ (1.136, 3.409, -1.136)
max log p =    -4.043056 @ (-0.568, -2.841, -2.841)
max log p =    -4.043056 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -6.3, -6.3): log p = -4.043
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.737, old_max_log_p =-4.043 (thresh=-4.0)
 1.05465  -0.11216  -0.04392   10.26218;
 0.15011   0.92100   0.36066  -55.89568;
 0.00000  -0.37001   0.83875   65.71170;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.735, old_max_log_p =-3.737 (thresh=-3.7)
 1.06522   0.00902   0.00353  -11.60768;
 0.01116   0.92776   0.36331  -39.19392;
 0.00000  -0.37001   0.83875   65.71170;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.634, old_max_log_p =-3.735 (thresh=-3.7)
 1.04341  -0.00618  -0.03265  -3.20790;
 0.04689   0.95717   0.33878  -43.01159;
 0.04156  -0.34969   0.88219   51.36957;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.634, old_max_log_p =-3.634 (thresh=-3.6)
 1.04341  -0.00618  -0.03265  -3.20790;
 0.04689   0.95717   0.33878  -43.01159;
 0.04156  -0.34969   0.88219   51.36957;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.596, old_max_log_p =-3.634 (thresh=-3.6)
 1.04580   0.00346  -0.01256  -7.31296;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.590, old_max_log_p =-3.596 (thresh=-3.6)
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.590, old_max_log_p =-3.590 (thresh=-3.6)
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 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
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.590 (old=-4.105)
transform before final EM align:
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 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
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.0  tol 0.000000
final transform:
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1203.406054
mri_em_register stimesec    1.565761
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   158957
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    22934
mri_em_register ru_nivcsw   2745
registration took 10 minutes and 44 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:47:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

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

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=27.0
skull bounding box = (63, 61, 28) --> (197, 196, 198)
using (108, 106, 113) as brain centroid...
mean wm in atlas = 107, using box (92,89,92) --> (124, 122,133) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 101 +- 5.8
after smoothing, mri peak at 101, scaling input intensities by 1.059
scaling channel 0 by 1.05941
using 246344 sample points...
INFO: compute sample coordinates transform
 1.04825   0.00347  -0.01259  -7.62714;
 0.03062   0.95477   0.35460  -42.74929;
 0.02358  -0.36394   0.87384   55.88712;
 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 (127, 61, 27) --> (191, 182, 200)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 329 (0.6%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 60, 28) --> (131, 175, 200)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 344 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 155, 64) --> (176, 196, 121)
Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0
0 of 9 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 155, 61) --> (128, 196, 122)
Right_Cerebellum_White_Matter: limiting intensities to 124.0 --> 132.0
5 of 7 (71.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 137, 97) --> (146, 205, 132)
Brain_Stem: limiting intensities to 94.0 --> 132.0
3 of 8 (37.5%) samples deleted
using 697 total control points for intensity normalization...
bias field = 0.947 +- 0.055
4 of 687 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (127, 61, 27) --> (191, 182, 200)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 557 (0.2%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 60, 28) --> (131, 175, 200)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
0 of 572 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 155, 64) --> (176, 196, 121)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
10 of 36 (27.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 155, 61) --> (128, 196, 122)
Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0
7 of 26 (26.9%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 137, 97) --> (146, 205, 132)
Brain_Stem: limiting intensities to 98.0 --> 132.0
42 of 60 (70.0%) samples deleted
using 1251 total control points for intensity normalization...
bias field = 1.018 +- 0.066
8 of 1169 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (127, 61, 27) --> (191, 182, 200)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
5 of 716 (0.7%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 60, 28) --> (131, 175, 200)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 690 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 155, 64) --> (176, 196, 121)
Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0
49 of 62 (79.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 155, 61) --> (128, 196, 122)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
8 of 45 (17.8%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 137, 97) --> (146, 205, 132)
Brain_Stem: limiting intensities to 88.0 --> 132.0
49 of 86 (57.0%) samples deleted
using 1599 total control points for intensity normalization...
bias field = 1.024 +- 0.062
3 of 1453 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 46 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:49:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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) = 1.01 (predicted orig area = 7.9)
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=0.832, neg=0, invalid=762
0001: dt=221.952000, rms=0.762 (8.410%), neg=0, invalid=762
0002: dt=195.747748, rms=0.746 (2.145%), neg=0, invalid=762
0003: dt=180.313043, rms=0.738 (1.047%), neg=0, invalid=762
0004: dt=295.936000, rms=0.732 (0.832%), neg=0, invalid=762
0005: dt=130.831858, rms=0.728 (0.573%), neg=0, invalid=762
0006: dt=517.888000, rms=0.722 (0.763%), neg=0, invalid=762
0007: dt=129.472000, rms=0.720 (0.333%), neg=0, invalid=762
0008: dt=517.888000, rms=0.717 (0.424%), neg=0, invalid=762
0009: dt=129.472000, rms=0.715 (0.231%), neg=0, invalid=762
0010: dt=129.472000, rms=0.714 (0.095%), neg=0, invalid=762
0011: dt=129.472000, rms=0.713 (0.156%), neg=0, invalid=762
0012: dt=129.472000, rms=0.712 (0.220%), neg=0, invalid=762
0013: dt=129.472000, rms=0.710 (0.245%), neg=0, invalid=762
0014: dt=129.472000, rms=0.708 (0.258%), neg=0, invalid=762
0015: dt=129.472000, rms=0.706 (0.251%), neg=0, invalid=762
0016: dt=129.472000, rms=0.705 (0.226%), neg=0, invalid=762
0017: dt=129.472000, rms=0.703 (0.228%), neg=0, invalid=762
0018: dt=129.472000, rms=0.702 (0.206%), neg=0, invalid=762
0019: dt=129.472000, rms=0.700 (0.176%), neg=0, invalid=762
0020: dt=129.472000, rms=0.699 (0.159%), neg=0, invalid=762
0021: dt=129.472000, rms=0.698 (0.153%), neg=0, invalid=762
0022: dt=129.472000, rms=0.697 (0.151%), neg=0, invalid=762
0023: dt=129.472000, rms=0.696 (0.138%), neg=0, invalid=762
0024: dt=129.472000, rms=0.695 (0.124%), neg=0, invalid=762
0025: dt=129.472000, rms=0.695 (0.120%), neg=0, invalid=762
0026: dt=2071.552000, rms=0.693 (0.211%), neg=0, invalid=762
0027: dt=129.472000, rms=0.693 (0.069%), neg=0, invalid=762
0028: dt=129.472000, rms=0.693 (0.013%), neg=0, invalid=762
0029: dt=129.472000, rms=0.692 (0.015%), neg=0, invalid=762
0030: dt=129.472000, rms=0.692 (0.020%), neg=0, invalid=762
0031: dt=129.472000, rms=0.692 (0.027%), neg=0, invalid=762
0032: dt=129.472000, rms=0.692 (0.033%), neg=0, invalid=762
0033: dt=129.472000, rms=0.691 (0.053%), neg=0, invalid=762
0034: dt=129.472000, rms=0.691 (0.065%), neg=0, invalid=762
0035: dt=129.472000, rms=0.691 (0.070%), neg=0, invalid=762
0036: dt=129.472000, rms=0.690 (0.061%), neg=0, invalid=762
0037: dt=129.472000, rms=0.690 (0.063%), neg=0, invalid=762
0038: dt=129.472000, rms=0.689 (0.065%), neg=0, invalid=762
0039: dt=129.472000, rms=0.689 (0.061%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.689, neg=0, invalid=762
0040: dt=129.472000, rms=0.688 (0.157%), neg=0, invalid=762
0041: dt=129.472000, rms=0.688 (0.019%), neg=0, invalid=762
0042: dt=129.472000, rms=0.688 (0.020%), neg=0, invalid=762
0043: dt=129.472000, rms=0.688 (0.030%), neg=0, invalid=762
0044: dt=129.472000, rms=0.688 (0.041%), neg=0, invalid=762
0045: dt=129.472000, rms=0.687 (0.045%), neg=0, invalid=762
0046: dt=129.472000, rms=0.687 (0.042%), neg=0, invalid=762
0047: dt=129.472000, rms=0.687 (0.041%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.693, neg=0, invalid=762
0048: dt=112.038369, rms=0.687 (0.849%), neg=0, invalid=762
0049: dt=234.666667, rms=0.679 (1.144%), neg=0, invalid=762
0050: dt=58.553191, rms=0.675 (0.664%), neg=0, invalid=762
0051: dt=331.776000, rms=0.669 (0.866%), neg=0, invalid=762
0052: dt=54.400000, rms=0.665 (0.552%), neg=0, invalid=762
0053: dt=248.832000, rms=0.661 (0.553%), neg=0, invalid=762
0054: dt=36.288000, rms=0.660 (0.216%), neg=0, invalid=762
0055: dt=36.288000, rms=0.660 (0.050%), neg=0, invalid=762
0056: dt=36.288000, rms=0.659 (0.087%), neg=0, invalid=762
0057: dt=36.288000, rms=0.658 (0.162%), neg=0, invalid=762
0058: dt=36.288000, rms=0.656 (0.247%), neg=0, invalid=762
0059: dt=36.288000, rms=0.654 (0.300%), neg=0, invalid=762
0060: dt=36.288000, rms=0.652 (0.309%), neg=0, invalid=762
0061: dt=36.288000, rms=0.650 (0.288%), neg=0, invalid=762
0062: dt=36.288000, rms=0.649 (0.273%), neg=0, invalid=762
0063: dt=36.288000, rms=0.647 (0.283%), neg=0, invalid=762
0064: dt=36.288000, rms=0.645 (0.292%), neg=0, invalid=762
0065: dt=36.288000, rms=0.643 (0.277%), neg=0, invalid=762
0066: dt=36.288000, rms=0.642 (0.257%), neg=0, invalid=762
0067: dt=36.288000, rms=0.640 (0.235%), neg=0, invalid=762
0068: dt=36.288000, rms=0.639 (0.211%), neg=0, invalid=762
0069: dt=36.288000, rms=0.637 (0.206%), neg=0, invalid=762
0070: dt=36.288000, rms=0.636 (0.192%), neg=0, invalid=762
0071: dt=36.288000, rms=0.635 (0.154%), neg=0, invalid=762
0072: dt=36.288000, rms=0.634 (0.127%), neg=0, invalid=762
0073: dt=36.288000, rms=0.634 (0.108%), neg=0, invalid=762
0074: dt=36.288000, rms=0.633 (0.103%), neg=0, invalid=762
0075: dt=145.152000, rms=0.633 (0.052%), neg=0, invalid=762
0076: dt=145.152000, rms=0.633 (-0.301%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.633, neg=0, invalid=762
0077: dt=36.288000, rms=0.632 (0.200%), neg=0, invalid=762
0078: dt=82.944000, rms=0.632 (0.058%), neg=0, invalid=762
0079: dt=82.944000, rms=0.631 (0.044%), neg=0, invalid=762
0080: dt=82.944000, rms=0.631 (0.017%), neg=0, invalid=762
0081: dt=82.944000, rms=0.631 (-0.022%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.656, neg=0, invalid=762
0082: dt=6.400000, rms=0.655 (0.138%), neg=0, invalid=762
0083: dt=1.600000, rms=0.655 (0.003%), neg=0, invalid=762
0084: dt=1.600000, rms=0.655 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.656, neg=0, invalid=762
0085: dt=0.000000, rms=0.655 (0.095%), neg=0, invalid=762
0086: dt=0.000000, rms=0.655 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.721, neg=0, invalid=762
0087: dt=6.753968, rms=0.698 (3.111%), neg=0, invalid=762
0088: dt=4.352941, rms=0.697 (0.173%), neg=0, invalid=762
0089: dt=4.352941, rms=0.697 (-0.012%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.698, neg=0, invalid=762
0090: dt=0.000000, rms=0.697 (0.078%), neg=0, invalid=762
0091: dt=0.000000, rms=0.697 (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=0.752, neg=0, invalid=762
0092: dt=0.448000, rms=0.751 (0.173%), neg=0, invalid=762
0093: dt=1.024000, rms=0.750 (0.132%), neg=0, invalid=762
0094: dt=1.024000, rms=0.747 (0.323%), neg=0, invalid=762
0095: dt=1.024000, rms=0.746 (0.253%), neg=0, invalid=762
0096: dt=1.024000, rms=0.746 (-0.108%), neg=0, invalid=762
0097: dt=1.792000, rms=0.745 (0.123%), neg=0, invalid=762
0098: dt=4.096000, rms=0.742 (0.359%), neg=0, invalid=762
0099: dt=0.000000, rms=0.742 (0.001%), neg=0, invalid=762
0100: dt=0.100000, rms=0.742 (-0.008%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.742, neg=0, invalid=762
0101: dt=0.112000, rms=0.742 (0.079%), neg=0, invalid=762
0102: dt=0.080000, rms=0.742 (0.001%), neg=0, invalid=762
0103: dt=0.080000, rms=0.742 (-0.001%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.704, neg=0, invalid=762
0104: dt=0.805047, rms=0.687 (2.403%), neg=0, invalid=762
0105: dt=0.080000, rms=0.686 (0.126%), neg=0, invalid=762
0106: dt=0.080000, rms=0.686 (-0.077%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.687, neg=0, invalid=762
0107: dt=0.028000, rms=0.686 (0.102%), neg=0, invalid=762
0108: dt=0.007000, rms=0.686 (0.001%), neg=0, invalid=762
0109: dt=0.007000, rms=0.686 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.07013 (13)
Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (1926 voxels, overlap=0.492)
Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (1926 voxels, peak = 13), gca=13.3
gca peak = 0.15565 (16)
mri peak = 0.09406 (18)
Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1232 voxels, overlap=0.614)
Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1232 voxels, peak = 13), gca=12.7
gca peak = 0.26829 (96)
mri peak = 0.07230 (84)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (1228 voxels, overlap=0.947)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (1228 voxels, peak = 85), gca=85.0
gca peak = 0.20183 (93)
mri peak = 0.07255 (84)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (952 voxels, overlap=0.520)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (952 voxels, peak = 82), gca=82.3
gca peak = 0.21683 (55)
mri peak = 0.07847 (62)
Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (1072 voxels, overlap=0.999)
Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (1072 voxels, peak = 61), gca=61.3
gca peak = 0.30730 (58)
mri peak = 0.06545 (62)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (886 voxels, overlap=1.000)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (886 voxels, peak = 61), gca=60.6
gca peak = 0.11430 (101)
mri peak = 0.06817 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (77372 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (77372 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.06793 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (78525 voxels, overlap=0.828)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (78525 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.02853 (70)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (29727 voxels, overlap=0.305)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (29727 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.02917 (68)
Right_Cerebral_Cortex (42): linear fit = 1.17 x + 0.0 (31052 voxels, overlap=0.385)
Right_Cerebral_Cortex (42): linear fit = 1.17 x + 0.0 (31052 voxels, peak = 68), gca=68.1
gca peak = 0.14161 (67)
mri peak = 0.07237 (69)
Right_Caudate (50): linear fit = 1.03 x + 0.0 (921 voxels, overlap=0.984)
Right_Caudate (50): linear fit = 1.03 x + 0.0 (921 voxels, peak = 69), gca=69.3
gca peak = 0.15243 (71)
mri peak = 0.08540 (75)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1237 voxels, overlap=0.989)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1237 voxels, peak = 71), gca=71.0
gca peak = 0.13336 (57)
mri peak = 0.03267 (57)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27148 voxels, overlap=0.977)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27148 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.03830 (55)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (26781 voxels, overlap=0.995)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (26781 voxels, peak = 59), gca=58.5
gca peak = 0.18181 (84)
mri peak = 0.03884 (80)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (9122 voxels, overlap=0.976)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (9122 voxels, peak = 83), gca=82.7
gca peak = 0.20573 (83)
mri peak = 0.03782 (79)
Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (7342 voxels, overlap=0.881)
Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (7342 voxels, peak = 78), gca=77.6
gca peak = 0.21969 (57)
mri peak = 0.07087 (65)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (330 voxels, overlap=0.788)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (330 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.05485 (62)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (502 voxels, overlap=0.907)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (502 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.06141 (84)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (6705 voxels, overlap=0.969)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (6705 voxels, peak = 83), gca=82.9
gca peak = 0.11978 (83)
mri peak = 0.08874 (83)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5274 voxels, overlap=0.902)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5274 voxels, peak = 82), gca=81.8
gca peak = 0.13399 (79)
mri peak = 0.06081 (82)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2845 voxels, overlap=1.000)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2845 voxels, peak = 81), gca=81.0
gca peak = 0.14159 (79)
mri peak = 0.05949 (75)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (3015 voxels, overlap=1.000)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (3015 voxels, peak = 79), gca=78.6
gca peak = 0.10025 (80)
mri peak = 0.08238 (83)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (9847 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (9847 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.08798 (84)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (1472 voxels, overlap=0.720)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (1472 voxels, peak = 83), gca=83.0
gca peak = 0.12801 (89)
mri peak = 0.12086 (83)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1641 voxels, overlap=0.849)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1641 voxels, peak = 85), gca=85.0
gca peak = 0.20494 (23)
mri peak = 0.12509 (19)
gca peak = 0.15061 (21)
mri peak = 0.05442 (19)
Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (247 voxels, overlap=0.586)
Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (247 voxels, peak = 27), gca=26.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.12 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.91 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=0.687, neg=0, invalid=762
0110: dt=133.947955, rms=0.677 (1.523%), neg=0, invalid=762
0111: dt=295.936000, rms=0.672 (0.702%), neg=0, invalid=762
0112: dt=129.472000, rms=0.670 (0.263%), neg=0, invalid=762
0113: dt=295.936000, rms=0.668 (0.327%), neg=0, invalid=762
0114: dt=92.480000, rms=0.667 (0.169%), neg=0, invalid=762
0115: dt=1183.744000, rms=0.663 (0.535%), neg=0, invalid=762
0116: dt=92.480000, rms=0.662 (0.163%), neg=0, invalid=762
0117: dt=1183.744000, rms=0.660 (0.275%), neg=0, invalid=762
0118: dt=92.480000, rms=0.660 (0.114%), neg=0, invalid=762
0119: dt=517.888000, rms=0.659 (0.100%), neg=0, invalid=762
0120: dt=129.472000, rms=0.659 (0.035%), neg=0, invalid=762
0121: dt=129.472000, rms=0.659 (0.032%), neg=0, invalid=762
0122: dt=129.472000, rms=0.658 (0.042%), neg=0, invalid=762
0123: dt=129.472000, rms=0.658 (0.056%), neg=0, invalid=762
0124: dt=129.472000, rms=0.658 (0.064%), neg=0, invalid=762
0125: dt=129.472000, rms=0.657 (0.083%), neg=0, invalid=762
0126: dt=129.472000, rms=0.656 (0.084%), neg=0, invalid=762
0127: dt=129.472000, rms=0.656 (0.085%), neg=0, invalid=762
0128: dt=129.472000, rms=0.655 (0.082%), neg=0, invalid=762
0129: dt=129.472000, rms=0.655 (0.078%), neg=0, invalid=762
0130: dt=129.472000, rms=0.654 (0.082%), neg=0, invalid=762
0131: dt=129.472000, rms=0.654 (0.081%), neg=0, invalid=762
0132: dt=129.472000, rms=0.653 (0.075%), neg=0, invalid=762
0133: dt=129.472000, rms=0.653 (0.073%), neg=0, invalid=762
0134: dt=129.472000, rms=0.652 (0.073%), neg=0, invalid=762
0135: dt=129.472000, rms=0.652 (0.075%), neg=0, invalid=762
0136: dt=129.472000, rms=0.651 (0.071%), neg=0, invalid=762
0137: dt=129.472000, rms=0.651 (0.071%), neg=0, invalid=762
0138: dt=129.472000, rms=0.650 (0.071%), neg=0, invalid=762
0139: dt=129.472000, rms=0.650 (0.074%), neg=0, invalid=762
0140: dt=129.472000, rms=0.649 (0.075%), neg=0, invalid=762
0141: dt=129.472000, rms=0.649 (0.074%), neg=0, invalid=762
0142: dt=129.472000, rms=0.649 (0.073%), neg=0, invalid=762
0143: dt=129.472000, rms=0.648 (0.070%), neg=0, invalid=762
0144: dt=129.472000, rms=0.648 (0.071%), neg=0, invalid=762
0145: dt=129.472000, rms=0.647 (0.065%), neg=0, invalid=762
0146: dt=129.472000, rms=0.647 (0.062%), neg=0, invalid=762
0147: dt=129.472000, rms=0.646 (0.060%), neg=0, invalid=762
0148: dt=129.472000, rms=0.646 (0.060%), neg=0, invalid=762
0149: dt=129.472000, rms=0.646 (0.057%), neg=0, invalid=762
0150: dt=129.472000, rms=0.645 (0.049%), neg=0, invalid=762
0151: dt=129.472000, rms=0.645 (0.043%), neg=0, invalid=762
0152: dt=129.472000, rms=0.645 (0.040%), neg=0, invalid=762
0153: dt=129.472000, rms=0.645 (0.041%), neg=0, invalid=762
0154: dt=129.472000, rms=0.644 (0.041%), neg=0, invalid=762
0155: dt=129.472000, rms=0.644 (0.037%), neg=0, invalid=762
0156: dt=129.472000, rms=0.644 (0.035%), neg=0, invalid=762
0157: dt=129.472000, rms=0.644 (0.034%), neg=0, invalid=762
0158: dt=129.472000, rms=0.643 (0.031%), neg=0, invalid=762
0159: dt=129.472000, rms=0.643 (0.029%), neg=0, invalid=762
0160: dt=129.472000, rms=0.643 (0.027%), neg=0, invalid=762
0161: dt=129.472000, rms=0.643 (0.026%), neg=0, invalid=762
0162: dt=129.472000, rms=0.643 (0.026%), neg=0, invalid=762
0163: dt=129.472000, rms=0.643 (0.026%), neg=0, invalid=762
0164: dt=129.472000, rms=0.642 (0.024%), neg=0, invalid=762
0165: dt=129.472000, rms=0.642 (0.023%), neg=0, invalid=762
0166: dt=2071.552000, rms=0.642 (0.019%), neg=0, invalid=762
0167: dt=2071.552000, rms=0.642 (-2.335%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.643, neg=0, invalid=762
0168: dt=129.472000, rms=0.641 (0.188%), neg=0, invalid=762
0169: dt=517.888000, rms=0.641 (0.126%), neg=0, invalid=762
0170: dt=129.472000, rms=0.640 (0.029%), neg=0, invalid=762
0171: dt=129.472000, rms=0.640 (0.018%), neg=0, invalid=762
0172: dt=129.472000, rms=0.640 (0.021%), neg=0, invalid=762
0173: dt=129.472000, rms=0.640 (0.026%), neg=0, invalid=762
0174: dt=129.472000, rms=0.640 (0.028%), neg=0, invalid=762
0175: dt=129.472000, rms=0.640 (0.029%), neg=0, invalid=762
0176: dt=129.472000, rms=0.640 (0.029%), neg=0, invalid=762
0177: dt=129.472000, rms=0.639 (0.027%), neg=0, invalid=762
0178: dt=129.472000, rms=0.639 (0.031%), neg=0, invalid=762
0179: dt=129.472000, rms=0.639 (0.034%), neg=0, invalid=762
0180: dt=129.472000, rms=0.639 (0.034%), neg=0, invalid=762
0181: dt=129.472000, rms=0.639 (0.029%), neg=0, invalid=762
0182: dt=129.472000, rms=0.638 (0.023%), neg=0, invalid=762
0183: dt=129.472000, rms=0.638 (0.021%), neg=0, invalid=762
0184: dt=517.888000, rms=0.638 (0.024%), neg=0, invalid=762
0185: dt=32.368000, rms=0.638 (-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=0.640, neg=0, invalid=762
0186: dt=108.705882, rms=0.636 (0.566%), neg=0, invalid=762
0187: dt=210.000000, rms=0.631 (0.797%), neg=0, invalid=762
0188: dt=61.935484, rms=0.628 (0.516%), neg=0, invalid=762
0189: dt=145.152000, rms=0.625 (0.528%), neg=0, invalid=762
0190: dt=69.387205, rms=0.623 (0.227%), neg=0, invalid=762
0191: dt=145.152000, rms=0.620 (0.444%), neg=0, invalid=762
0192: dt=65.350211, rms=0.619 (0.173%), neg=0, invalid=762
0193: dt=331.776000, rms=0.616 (0.511%), neg=0, invalid=762
0194: dt=36.288000, rms=0.614 (0.372%), neg=0, invalid=762
0195: dt=103.680000, rms=0.613 (0.117%), neg=0, invalid=762
0196: dt=124.416000, rms=0.612 (0.239%), neg=0, invalid=762
0197: dt=36.288000, rms=0.611 (0.128%), neg=0, invalid=762
0198: dt=248.832000, rms=0.610 (0.216%), neg=0, invalid=762
0199: dt=71.731544, rms=0.608 (0.277%), neg=0, invalid=762
0200: dt=62.208000, rms=0.607 (0.084%), neg=0, invalid=762
0201: dt=414.720000, rms=0.605 (0.356%), neg=0, invalid=762
0202: dt=36.288000, rms=0.604 (0.257%), neg=0, invalid=762
0203: dt=82.944000, rms=0.603 (0.061%), neg=0, invalid=762
0204: dt=145.152000, rms=0.602 (0.166%), neg=0, invalid=762
0205: dt=36.288000, rms=0.602 (0.060%), neg=0, invalid=762
0206: dt=414.720000, rms=0.601 (0.190%), neg=0, invalid=762
0207: dt=36.288000, rms=0.599 (0.217%), neg=0, invalid=762
0208: dt=331.776000, rms=0.598 (0.221%), neg=0, invalid=762
0209: dt=36.288000, rms=0.597 (0.115%), neg=0, invalid=762
0210: dt=82.944000, rms=0.597 (0.026%), neg=0, invalid=762
0211: dt=82.944000, rms=0.597 (0.092%), neg=0, invalid=762
0212: dt=82.944000, rms=0.596 (0.116%), neg=0, invalid=762
0213: dt=82.944000, rms=0.595 (0.128%), neg=0, invalid=762
0214: dt=82.944000, rms=0.594 (0.169%), neg=0, invalid=762
0215: dt=82.944000, rms=0.593 (0.226%), neg=0, invalid=762
0216: dt=20.736000, rms=0.593 (0.012%), neg=0, invalid=762
0217: dt=5.184000, rms=0.593 (0.002%), neg=0, invalid=762
0218: dt=2.268000, rms=0.593 (0.001%), neg=0, invalid=762
0219: dt=2.268000, rms=0.593 (0.001%), neg=0, invalid=762
0220: dt=0.283500, rms=0.593 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.594, neg=0, invalid=762
0221: dt=122.666667, rms=0.590 (0.535%), neg=0, invalid=762
0222: dt=82.944000, rms=0.589 (0.228%), neg=0, invalid=762
0223: dt=82.944000, rms=0.589 (0.095%), neg=0, invalid=762
0224: dt=145.152000, rms=0.588 (0.147%), neg=0, invalid=762
0225: dt=36.288000, rms=0.587 (0.070%), neg=0, invalid=762
0226: dt=145.152000, rms=0.587 (0.093%), neg=0, invalid=762
0227: dt=103.680000, rms=0.586 (0.089%), neg=0, invalid=762
0228: dt=36.288000, rms=0.586 (0.040%), neg=0, invalid=762
0229: dt=36.288000, rms=0.586 (0.023%), neg=0, invalid=762
0230: dt=36.288000, rms=0.586 (0.042%), neg=0, invalid=762
0231: dt=36.288000, rms=0.585 (0.061%), neg=0, invalid=762
0232: dt=36.288000, rms=0.585 (0.077%), neg=0, invalid=762
0233: dt=36.288000, rms=0.584 (0.083%), neg=0, invalid=762
0234: dt=36.288000, rms=0.584 (0.085%), neg=0, invalid=762
0235: dt=36.288000, rms=0.583 (0.083%), neg=0, invalid=762
0236: dt=36.288000, rms=0.583 (0.090%), neg=0, invalid=762
0237: dt=36.288000, rms=0.582 (0.090%), neg=0, invalid=762
0238: dt=36.288000, rms=0.582 (0.094%), neg=0, invalid=762
0239: dt=36.288000, rms=0.581 (0.093%), neg=0, invalid=762
0240: dt=36.288000, rms=0.581 (0.011%), neg=0, invalid=762
0241: dt=36.288000, rms=0.581 (0.027%), neg=0, invalid=762
0242: dt=36.288000, rms=0.581 (0.035%), neg=0, invalid=762
0243: dt=36.288000, rms=0.580 (0.039%), neg=0, invalid=762
0244: dt=36.288000, rms=0.580 (0.050%), neg=0, invalid=762
0245: dt=36.288000, rms=0.580 (0.055%), neg=0, invalid=762
0246: dt=36.288000, rms=0.580 (0.061%), neg=0, invalid=762
0247: dt=36.288000, rms=0.579 (0.010%), neg=0, invalid=762
0248: dt=36.288000, rms=0.579 (0.013%), neg=0, invalid=762
0249: dt=1.134000, rms=0.579 (0.000%), neg=0, invalid=762
0250: dt=0.567000, rms=0.579 (0.000%), neg=0, invalid=762
0251: dt=0.070875, rms=0.579 (0.000%), neg=0, invalid=762
0252: dt=0.017719, rms=0.579 (0.000%), neg=0, invalid=762
0253: dt=0.008859, rms=0.579 (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=0.586, neg=0, invalid=762
0254: dt=0.000000, rms=0.586 (0.135%), neg=0, invalid=762
0255: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762
0256: dt=0.000061, rms=0.586 (0.000%), neg=0, invalid=762
0257: dt=0.000031, rms=0.586 (0.000%), neg=0, invalid=762
0258: dt=0.000031, rms=0.586 (0.000%), neg=0, invalid=762
0259: dt=0.000008, rms=0.586 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.586, neg=0, invalid=762
0260: dt=150.950937, rms=0.574 (2.092%), neg=0, invalid=762
0261: dt=32.000000, rms=0.568 (1.009%), neg=0, invalid=762
0262: dt=2.800000, rms=0.568 (0.053%), neg=0, invalid=762
0263: dt=2.000000, rms=0.568 (0.032%), neg=0, invalid=762
0264: dt=0.250000, rms=0.568 (0.004%), neg=0, invalid=762
0265: dt=0.062500, rms=0.568 (0.001%), neg=0, invalid=762
0266: dt=0.031250, rms=0.568 (0.000%), neg=0, invalid=762
0267: dt=0.010937, rms=0.568 (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=0.584, neg=0, invalid=762
0268: dt=0.000984, rms=0.583 (0.124%), neg=0, invalid=762
0269: dt=0.000246, rms=0.583 (0.000%), neg=0, invalid=762
0270: dt=0.000062, rms=0.583 (0.000%), neg=0, invalid=762
0271: dt=0.000031, rms=0.583 (0.000%), neg=0, invalid=762
0272: dt=0.000008, rms=0.583 (0.000%), neg=0, invalid=762
0273: dt=0.000000, rms=0.583 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.584, neg=0, invalid=762
0274: dt=20.155844, rms=0.575 (1.386%), neg=0, invalid=762
0275: dt=16.128000, rms=0.570 (1.017%), neg=0, invalid=762
0276: dt=20.266667, rms=0.569 (0.186%), neg=0, invalid=762
0277: dt=16.128000, rms=0.566 (0.390%), neg=0, invalid=762
0278: dt=11.428571, rms=0.566 (0.081%), neg=0, invalid=762
0279: dt=16.128000, rms=0.565 (0.151%), neg=0, invalid=762
0280: dt=19.636364, rms=0.564 (0.098%), neg=0, invalid=762
0281: dt=11.520000, rms=0.564 (0.098%), neg=0, invalid=762
0282: dt=0.864000, rms=0.564 (0.030%), neg=0, invalid=762
0283: dt=0.027000, rms=0.564 (0.002%), neg=0, invalid=762
0284: dt=0.006750, rms=0.564 (0.000%), neg=0, invalid=762
0285: dt=0.003375, rms=0.564 (0.000%), neg=0, invalid=762
0286: dt=0.001688, rms=0.564 (0.000%), neg=0, invalid=762
0287: dt=0.000844, rms=0.564 (0.000%), neg=0, invalid=762
0288: dt=0.000984, rms=0.564 (0.000%), neg=0, invalid=762
0289: dt=0.000246, rms=0.564 (0.000%), neg=0, invalid=762
0290: dt=0.000000, rms=0.564 (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=0.581, neg=0, invalid=762
0291: dt=0.000000, rms=0.580 (0.117%), neg=0, invalid=762
0292: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0293: dt=0.100000, rms=0.580 (-0.085%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.581, neg=0, invalid=762
0294: dt=0.000000, rms=0.580 (0.117%), neg=0, invalid=762
0295: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0296: dt=0.100000, rms=0.580 (-0.070%), 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=0.553, neg=0, invalid=762
0297: dt=0.448000, rms=0.539 (2.513%), neg=0, invalid=762
0298: dt=0.384000, rms=0.537 (0.526%), neg=0, invalid=762
0299: dt=0.448000, rms=0.535 (0.382%), neg=0, invalid=762
0300: dt=0.448000, rms=0.533 (0.231%), neg=0, invalid=762
0301: dt=0.448000, rms=0.532 (0.171%), neg=0, invalid=762
0302: dt=0.448000, rms=0.532 (0.121%), neg=0, invalid=762
0303: dt=0.448000, rms=0.531 (0.107%), neg=0, invalid=762
0304: dt=0.448000, rms=0.531 (0.078%), neg=0, invalid=762
0305: dt=0.448000, rms=0.530 (0.075%), neg=0, invalid=762
0306: dt=0.448000, rms=0.530 (0.055%), neg=0, invalid=762
0307: dt=0.448000, rms=0.530 (0.053%), neg=0, invalid=762
0308: dt=0.448000, rms=0.530 (0.042%), neg=0, invalid=762
0309: dt=0.448000, rms=0.529 (0.040%), neg=0, invalid=762
0310: dt=0.448000, rms=0.529 (0.069%), neg=0, invalid=762
0311: dt=0.224000, rms=0.529 (0.014%), neg=0, invalid=762
0312: dt=0.224000, rms=0.529 (0.026%), neg=0, invalid=762
0313: dt=0.224000, rms=0.529 (0.039%), neg=0, invalid=762
0314: dt=0.224000, rms=0.528 (0.041%), neg=0, invalid=762
0315: dt=0.224000, rms=0.528 (0.041%), neg=0, invalid=762
0316: dt=0.224000, rms=0.528 (0.040%), neg=0, invalid=762
0317: dt=0.224000, rms=0.528 (0.006%), neg=0, invalid=762
0318: dt=0.224000, rms=0.528 (0.010%), neg=0, invalid=762
0319: dt=0.224000, rms=0.528 (0.009%), neg=0, invalid=762
0320: dt=0.448000, rms=0.528 (0.006%), neg=0, invalid=762
0321: dt=0.224000, rms=0.528 (0.004%), neg=0, invalid=762
0322: dt=0.224000, rms=0.528 (0.005%), neg=0, invalid=762
0323: dt=0.224000, rms=0.528 (0.010%), neg=0, invalid=762
0324: dt=0.224000, rms=0.528 (0.012%), neg=0, invalid=762
0325: dt=0.224000, rms=0.528 (0.012%), neg=0, invalid=762
0326: dt=0.224000, rms=0.527 (0.011%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0327: dt=0.448000, rms=0.522 (1.187%), neg=0, invalid=762
0328: dt=0.448000, rms=0.521 (0.133%), neg=0, invalid=762
0329: dt=0.448000, rms=0.521 (0.033%), neg=0, invalid=762
0330: dt=0.448000, rms=0.521 (-0.004%), 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=0.519, neg=0, invalid=762
0331: dt=0.000000, rms=0.518 (0.140%), neg=0, invalid=762
0332: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.519, neg=0, invalid=762
0333: dt=110.976000, rms=0.518 (0.159%), neg=0, invalid=762
0334: dt=295.936000, rms=0.518 (0.039%), neg=0, invalid=762
0335: dt=295.936000, rms=0.518 (-0.209%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.519, neg=0, invalid=762
0336: dt=36.288000, rms=0.518 (0.234%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0337: dt=36.288000, rms=0.517 (0.033%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0338: dt=36.288000, rms=0.517 (0.021%), neg=0, invalid=762
0339: dt=36.288000, rms=0.517 (-0.038%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.518, neg=0, invalid=762
0340: dt=76.012308, rms=0.515 (0.497%), neg=0, invalid=762
0341: dt=69.079365, rms=0.514 (0.191%), neg=0, invalid=762
0342: dt=69.079365, rms=0.514 (0.062%), neg=0, invalid=762
0343: dt=69.079365, rms=0.513 (0.220%), neg=0, invalid=762
0344: dt=69.079365, rms=0.512 (0.182%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 3 iterations, nbhd size=0, neg = 0
0345: dt=69.079365, rms=0.511 (0.171%), neg=0, invalid=762
0346: dt=69.079365, rms=0.510 (0.151%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 5 iterations, nbhd size=0, neg = 0
0347: dt=69.079365, rms=0.510 (0.093%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0348: dt=69.079365, rms=0.509 (0.130%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0349: dt=69.079365, rms=0.509 (0.065%), neg=0, invalid=762
0350: dt=69.079365, rms=0.508 (0.105%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0351: dt=69.079365, rms=0.508 (0.050%), neg=0, invalid=762
0352: dt=36.288000, rms=0.508 (0.049%), neg=0, invalid=762
0353: dt=36.288000, rms=0.508 (0.015%), neg=0, invalid=762
0354: dt=36.288000, rms=0.508 (0.018%), neg=0, invalid=762
0355: dt=36.288000, rms=0.508 (0.028%), neg=0, invalid=762
0356: dt=36.288000, rms=0.507 (0.030%), neg=0, invalid=762
0357: dt=36.288000, rms=0.507 (0.034%), neg=0, invalid=762
0358: dt=36.288000, rms=0.507 (0.030%), neg=0, invalid=762
0359: dt=36.288000, rms=0.507 (0.026%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.508, neg=0, invalid=762
0360: dt=24.479263, rms=0.507 (0.325%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0361: dt=38.400000, rms=0.506 (0.132%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
0362: dt=38.400000, rms=0.506 (0.100%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 9 iterations, nbhd size=1, neg = 0
0363: dt=38.400000, rms=0.505 (0.135%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 3 iterations, nbhd size=0, neg = 0
0364: dt=38.400000, rms=0.505 (0.080%), neg=0, invalid=762
iter 0, gcam->neg = 13
after 11 iterations, nbhd size=1, neg = 0
0365: dt=38.400000, rms=0.504 (0.167%), neg=0, invalid=762
iter 0, gcam->neg = 26
after 10 iterations, nbhd size=1, neg = 0
0366: dt=38.400000, rms=0.503 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 10 iterations, nbhd size=1, neg = 0
0367: dt=38.400000, rms=0.501 (0.339%), neg=0, invalid=762
iter 0, gcam->neg = 22
after 12 iterations, nbhd size=1, neg = 0
0368: dt=38.400000, rms=0.500 (0.237%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 11 iterations, nbhd size=1, neg = 0
0369: dt=38.400000, rms=0.499 (0.276%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0370: dt=38.400000, rms=0.498 (0.160%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 11 iterations, nbhd size=1, neg = 0
0371: dt=38.400000, rms=0.497 (0.179%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 2 iterations, nbhd size=0, neg = 0
0372: dt=38.400000, rms=0.497 (0.074%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 8 iterations, nbhd size=1, neg = 0
0373: dt=38.400000, rms=0.496 (0.047%), neg=0, invalid=762
0374: dt=38.400000, rms=0.496 (0.183%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0375: dt=25.600000, rms=0.495 (0.060%), neg=0, invalid=762
0376: dt=25.600000, rms=0.495 (0.047%), neg=0, invalid=762
0377: dt=25.600000, rms=0.495 (0.070%), neg=0, invalid=762
0378: dt=25.600000, rms=0.495 (0.037%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0379: dt=25.600000, rms=0.494 (0.041%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0380: dt=25.600000, rms=0.494 (0.025%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.495, neg=0, invalid=762
0381: dt=60.779874, rms=0.490 (0.949%), neg=0, invalid=762
0382: dt=28.167665, rms=0.489 (0.353%), neg=0, invalid=762
0383: dt=32.000000, rms=0.488 (0.195%), neg=0, invalid=762
0384: dt=32.000000, rms=0.487 (0.085%), neg=0, invalid=762
0385: dt=32.000000, rms=0.486 (0.230%), neg=0, invalid=762
0386: dt=32.000000, rms=0.486 (0.124%), neg=0, invalid=762
0387: dt=32.000000, rms=0.485 (0.116%), neg=0, invalid=762
0388: dt=25.600000, rms=0.485 (0.072%), neg=0, invalid=762
0389: dt=25.600000, rms=0.484 (0.022%), neg=0, invalid=762
0390: dt=25.600000, rms=0.484 (0.059%), neg=0, invalid=762
0391: dt=25.600000, rms=0.484 (0.039%), neg=0, invalid=762
0392: dt=25.600000, rms=0.484 (0.069%), neg=0, invalid=762
0393: dt=25.600000, rms=0.484 (0.032%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0394: dt=1.008000, rms=0.492 (0.158%), neg=0, invalid=762
0395: dt=0.144000, rms=0.491 (0.002%), neg=0, invalid=762
0396: dt=0.144000, rms=0.491 (0.000%), neg=0, invalid=762
0397: dt=0.144000, rms=0.491 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0398: dt=4.000000, rms=0.491 (0.202%), neg=0, invalid=762
0399: dt=1.008000, rms=0.491 (0.007%), neg=0, invalid=762
0400: dt=1.008000, rms=0.491 (0.006%), neg=0, invalid=762
0401: dt=1.008000, rms=0.491 (-0.004%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.504, neg=0, invalid=762
0402: dt=1.280000, rms=0.503 (0.311%), neg=0, invalid=762
0403: dt=0.256000, rms=0.503 (0.006%), neg=0, invalid=762
0404: dt=0.256000, rms=0.503 (0.000%), neg=0, invalid=762
0405: dt=0.256000, rms=0.503 (-0.021%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.503, neg=0, invalid=762
0406: dt=1.792000, rms=0.501 (0.425%), neg=0, invalid=762
0407: dt=1.536000, rms=0.501 (0.063%), neg=0, invalid=762
0408: dt=1.536000, rms=0.501 (0.010%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0409: dt=1.536000, rms=0.501 (-0.083%), 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=0.494, neg=0, invalid=762
iter 0, gcam->neg = 466
after 13 iterations, nbhd size=1, neg = 0
0410: dt=2.229940, rms=0.464 (6.105%), neg=0, invalid=762
0411: dt=0.096000, rms=0.463 (0.083%), neg=0, invalid=762
0412: dt=0.096000, rms=0.463 (-0.054%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
0413: dt=0.112000, rms=0.463 (0.262%), neg=0, invalid=762
0414: dt=0.004000, rms=0.463 (0.001%), neg=0, invalid=762
0415: dt=0.004000, rms=0.463 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.449, neg=0, invalid=762
0416: dt=0.000000, rms=0.449 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.449, neg=0, invalid=762
0417: dt=92.480000, rms=0.449 (0.016%), neg=0, invalid=762
0418: dt=129.472000, rms=0.449 (0.007%), neg=0, invalid=762
0419: dt=129.472000, rms=0.448 (0.004%), neg=0, invalid=762
0420: dt=129.472000, rms=0.448 (0.004%), neg=0, invalid=762
0421: dt=129.472000, rms=0.448 (0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.449, neg=0, invalid=762
0422: dt=1.333333, rms=0.449 (0.000%), neg=0, invalid=762
0423: dt=-0.000305, rms=0.449 (0.000%), neg=0, invalid=762
0424: dt=-0.000305, rms=0.449 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.449, neg=0, invalid=762
0425: dt=145.152000, rms=0.448 (0.125%), neg=0, invalid=762
0426: dt=103.680000, rms=0.448 (0.047%), neg=0, invalid=762
0427: dt=103.680000, rms=0.448 (0.030%), neg=0, invalid=762
0428: dt=103.680000, rms=0.447 (0.078%), neg=0, invalid=762
0429: dt=103.680000, rms=0.447 (0.040%), neg=0, invalid=762
0430: dt=103.680000, rms=0.447 (0.055%), neg=0, invalid=762
0431: dt=103.680000, rms=0.447 (0.043%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.448, neg=0, invalid=762
0432: dt=11.200000, rms=0.447 (0.065%), neg=0, invalid=762
0433: dt=2.800000, rms=0.447 (0.005%), neg=0, invalid=762
0434: dt=2.800000, rms=0.447 (0.003%), neg=0, invalid=762
0435: dt=2.800000, rms=0.447 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.447, neg=0, invalid=762
0436: dt=92.689655, rms=0.444 (0.641%), neg=0, invalid=762
0437: dt=25.600000, rms=0.443 (0.396%), neg=0, invalid=762
0438: dt=44.800000, rms=0.442 (0.142%), neg=0, invalid=762
0439: dt=44.800000, rms=0.441 (0.105%), neg=0, invalid=762
0440: dt=44.800000, rms=0.440 (0.264%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0441: dt=44.800000, rms=0.439 (0.212%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0442: dt=44.800000, rms=0.438 (0.265%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0443: dt=44.800000, rms=0.437 (0.226%), neg=0, invalid=762
0444: dt=44.800000, rms=0.436 (0.180%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0445: dt=44.800000, rms=0.436 (0.162%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0446: dt=44.800000, rms=0.435 (0.123%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0447: dt=44.800000, rms=0.435 (0.101%), neg=0, invalid=762
0448: dt=11.200000, rms=0.435 (0.015%), neg=0, invalid=762
0449: dt=11.200000, rms=0.435 (0.003%), neg=0, invalid=762
0450: dt=11.200000, rms=0.435 (0.002%), neg=0, invalid=762
0451: dt=11.200000, rms=0.435 (0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.440, neg=0, invalid=762
0452: dt=0.180000, rms=0.440 (0.000%), neg=0, invalid=762
0453: dt=0.023438, rms=0.440 (0.000%), neg=0, invalid=762
0454: dt=0.023438, rms=0.440 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.440, neg=0, invalid=762
0455: dt=2.304000, rms=0.440 (0.013%), neg=0, invalid=762
0456: dt=0.864000, rms=0.440 (0.001%), neg=0, invalid=762
0457: dt=0.864000, rms=0.440 (-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=0.450, neg=0, invalid=762
0458: dt=0.000000, rms=0.450 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.450, neg=0, invalid=762
0459: dt=0.112000, rms=0.450 (0.004%), neg=0, invalid=762
0460: dt=0.096000, rms=0.450 (0.001%), neg=0, invalid=762
0461: dt=0.096000, rms=0.450 (-0.001%), 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=0.434, neg=0, invalid=762
iter 0, gcam->neg = 450
after 12 iterations, nbhd size=1, neg = 0
0462: dt=1.406321, rms=0.423 (2.541%), neg=0, invalid=762
0463: dt=0.000013, rms=0.423 (0.000%), neg=0, invalid=762
0464: dt=0.000013, rms=0.423 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
0465: dt=0.112000, rms=0.422 (0.081%), neg=0, invalid=762
0466: dt=0.064000, rms=0.422 (0.014%), neg=0, invalid=762
0467: dt=0.064000, rms=0.422 (0.002%), neg=0, invalid=762
0468: dt=0.064000, rms=0.422 (-0.038%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 24 minutes and 2 seconds.
mri_ca_register utimesec    9508.008562
mri_ca_register stimesec    9.480558
mri_ca_register ru_maxrss   1350208
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4814646
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63160
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    8372
mri_ca_register ru_nivcsw   23027
FSRUNTIME@ mri_ca_register  2.4004 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 21:13:03 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-105
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-6.0.0/0050017/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.92
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 = 0.07991 (18)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (3185 voxels, overlap=0.814)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (3185 voxels, peak = 16), gca=16.5
gca peak = 0.17677 (13)
mri peak = 0.08954 (18)
Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (2384 voxels, overlap=0.753)
Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (2384 voxels, peak = 12), gca=12.0
gca peak = 0.28129 (95)
mri peak = 0.08170 (86)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (642 voxels, overlap=0.880)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (642 voxels, peak = 87), gca=86.9
gca peak = 0.16930 (96)
mri peak = 0.09470 (86)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (625 voxels, overlap=0.287)
Left_Pallidum (13): linear fit = 0.92 x + 0.0 (625 voxels, peak = 88), gca=87.8
gca peak = 0.24553 (55)
mri peak = 0.07859 (62)
Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (1182 voxels, overlap=1.015)
Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (1182 voxels, peak = 61), gca=61.3
gca peak = 0.30264 (59)
mri peak = 0.07306 (60)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (957 voxels, overlap=1.016)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (957 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.06743 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (50088 voxels, overlap=0.737)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (50088 voxels, peak = 106), gca=105.6
gca peak = 0.07714 (104)
mri peak = 0.07110 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (51395 voxels, overlap=0.704)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (51395 voxels, peak = 107), gca=106.6
gca peak = 0.09712 (58)
mri peak = 0.03545 (70)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (34572 voxels, overlap=0.641)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (34572 voxels, peak = 66), gca=65.8
gca peak = 0.11620 (58)
mri peak = 0.03473 (63)
Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (33419 voxels, overlap=0.656)
Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (33419 voxels, peak = 66), gca=65.8
gca peak = 0.30970 (66)
mri peak = 0.08640 (72)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (1551 voxels, overlap=1.008)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (1551 voxels, peak = 70), gca=70.3
gca peak = 0.15280 (69)
mri peak = 0.09351 (75)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1378 voxels, overlap=1.000)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1378 voxels, peak = 69), gca=69.0
gca peak = 0.13902 (56)
mri peak = 0.04110 (58)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (25977 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (25977 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.04387 (56)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (23769 voxels, overlap=0.998)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (23769 voxels, peak = 57), gca=57.5
gca peak = 0.16765 (84)
mri peak = 0.05176 (83)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5093 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5093 voxels, peak = 84), gca=83.6
gca peak = 0.18739 (84)
mri peak = 0.04764 (79)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4993 voxels, overlap=0.997)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4993 voxels, peak = 82), gca=81.9
gca peak = 0.29869 (57)
mri peak = 0.07273 (57)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (398 voxels, overlap=0.758)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (398 voxels, peak = 64), gca=63.6
gca peak = 0.33601 (57)
mri peak = 0.06173 (65)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (543 voxels, overlap=0.806)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (543 voxels, peak = 64), gca=63.6
gca peak = 0.11131 (90)
mri peak = 0.07704 (83)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5094 voxels, overlap=0.915)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5094 voxels, peak = 85), gca=85.1
gca peak = 0.11793 (83)
mri peak = 0.08929 (83)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5450 voxels, overlap=0.960)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5450 voxels, peak = 82), gca=81.8
gca peak = 0.08324 (81)
mri peak = 0.06826 (82)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1377 voxels, overlap=0.955)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1377 voxels, peak = 81), gca=81.0
gca peak = 0.10360 (77)
mri peak = 0.08672 (75)
Right_Putamen (51): linear fit = 0.98 x + 0.0 (1270 voxels, overlap=0.976)
Right_Putamen (51): linear fit = 0.98 x + 0.0 (1270 voxels, peak = 75), gca=75.1
gca peak = 0.08424 (78)
mri peak = 0.08368 (83)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8620 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8620 voxels, peak = 85), gca=85.4
gca peak = 0.12631 (89)
mri peak = 0.09465 (81)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (1617 voxels, overlap=0.822)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (1617 voxels, peak = 86), gca=85.9
gca peak = 0.14500 (87)
mri peak = 0.11062 (83)
Left_VentralDC (28): linear fit = 0.96 x + 0.0 (1825 voxels, overlap=0.913)
Left_VentralDC (28): linear fit = 0.96 x + 0.0 (1825 voxels, peak = 84), gca=84.0
gca peak = 0.14975 (24)
mri peak = 0.08898 (14)
gca peak = 0.19357 (14)
mri peak = 0.07694 (19)
Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (130 voxels, overlap=0.709)
Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (130 voxels, peak = 15), gca=15.3
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 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 1.11 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.95 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.18320 (17)
mri peak = 0.07991 (18)
Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (3185 voxels, overlap=0.948)
Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (3185 voxels, peak = 19), gca=18.8
gca peak = 0.18706 (12)
mri peak = 0.08954 (18)
Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (2384 voxels, overlap=0.838)
Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (2384 voxels, peak = 12), gca=12.4
gca peak = 0.26681 (87)
mri peak = 0.08170 (86)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (642 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (642 voxels, peak = 87), gca=86.6
gca peak = 0.17027 (89)
mri peak = 0.09470 (86)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (625 voxels, overlap=1.004)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (625 voxels, peak = 89), gca=88.6
gca peak = 0.27893 (62)
mri peak = 0.07859 (62)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1182 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1182 voxels, peak = 61), gca=61.1
gca peak = 0.27973 (59)
mri peak = 0.07306 (60)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (957 voxels, overlap=1.013)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (957 voxels, peak = 59), gca=59.0
gca peak = 0.07614 (105)
mri peak = 0.06743 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50088 voxels, overlap=0.834)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50088 voxels, peak = 104), gca=104.5
gca peak = 0.07686 (107)
mri peak = 0.07110 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51395 voxels, overlap=0.807)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51395 voxels, peak = 106), gca=106.5
gca peak = 0.08622 (66)
mri peak = 0.03545 (70)
Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (34572 voxels, overlap=0.962)
Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (34572 voxels, peak = 68), gca=68.3
gca peak = 0.10506 (66)
mri peak = 0.03473 (63)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (33419 voxels, overlap=0.966)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (33419 voxels, peak = 65), gca=65.0
gca peak = 0.26194 (71)
mri peak = 0.08640 (72)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1551 voxels, overlap=1.008)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1551 voxels, peak = 70), gca=69.9
gca peak = 0.16042 (69)
mri peak = 0.09351 (75)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1378 voxels, overlap=1.000)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1378 voxels, peak = 69), gca=69.0
gca peak = 0.13179 (57)
mri peak = 0.04110 (58)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (25977 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (25977 voxels, peak = 58), gca=58.4
gca peak = 0.14489 (57)
mri peak = 0.04387 (56)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23769 voxels, overlap=0.998)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23769 voxels, peak = 56), gca=56.1
gca peak = 0.16779 (84)
mri peak = 0.05176 (83)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5093 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5093 voxels, peak = 84), gca=83.6
gca peak = 0.18746 (82)
mri peak = 0.04764 (79)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4993 voxels, overlap=0.990)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4993 voxels, peak = 87), gca=86.5
gca peak = 0.28686 (65)
mri peak = 0.07273 (57)
Left_Amygdala (18): linear fit = 0.86 x + 0.0 (398 voxels, overlap=1.036)
Left_Amygdala (18): linear fit = 0.86 x + 0.0 (398 voxels, peak = 56), gca=55.6
gca peak = 0.32136 (64)
mri peak = 0.06173 (65)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (543 voxels, overlap=1.039)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (543 voxels, peak = 64), gca=64.0
gca peak = 0.10890 (85)
mri peak = 0.07704 (83)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5094 voxels, overlap=0.941)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5094 voxels, peak = 85), gca=85.0
gca peak = 0.10672 (79)
mri peak = 0.08929 (83)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5450 voxels, overlap=0.942)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5450 voxels, peak = 80), gca=80.2
gca peak = 0.08313 (81)
mri peak = 0.06826 (82)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1377 voxels, overlap=0.955)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1377 voxels, peak = 81), gca=81.0
gca peak = 0.10523 (75)
mri peak = 0.08672 (75)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1270 voxels, overlap=0.903)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1270 voxels, peak = 75), gca=75.0
gca peak = 0.07470 (86)
mri peak = 0.08368 (83)
Brain_Stem (16): linear fit = 0.96 x + 0.0 (8620 voxels, overlap=0.767)
Brain_Stem (16): linear fit = 0.96 x + 0.0 (8620 voxels, peak = 83), gca=83.0
gca peak = 0.11629 (81)
mri peak = 0.09465 (81)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1617 voxels, overlap=0.777)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1617 voxels, peak = 81), gca=81.0
gca peak = 0.13787 (84)
mri peak = 0.11062 (83)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1825 voxels, overlap=0.863)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1825 voxels, peak = 84), gca=83.6
gca peak = 0.16743 (24)
mri peak = 0.08898 (14)
gca peak = 0.19627 (16)
mri peak = 0.07694 (19)
Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (130 voxels, overlap=0.895)
Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (130 voxels, peak = 18), gca=17.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16507 (28)
gca peak Left_Thalamus = 0.64095 (103)
gca peak Third_Ventricle = 0.16743 (24)
gca peak CSF = 0.22075 (34)
gca peak Left_Accumbens_area = 0.57804 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24188 (26)
gca peak Right_Accumbens_area = 0.29948 (69)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65358 (30)
gca peak WM_hypointensities = 0.07828 (77)
gca peak non_WM_hypointensities = 0.07502 (56)
gca peak Optic_Chiasm = 0.71095 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.98 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.08 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
100844 voxels changed in iteration 0 of unlikely voxel relabeling
353 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
70792 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
545 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 92853 changed. image ll: -2.169, PF=0.500
pass 2: 26856 changed. image ll: -2.168, PF=0.500
pass 3: 8260 changed.
pass 4: 2910 changed.
69199 voxels changed in iteration 0 of unlikely voxel relabeling
538 voxels changed in iteration 1 of unlikely voxel relabeling
24 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
9238 voxels changed in iteration 0 of unlikely voxel relabeling
145 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
6 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
8259 voxels changed in iteration 0 of unlikely voxel relabeling
95 voxels changed in iteration 1 of unlikely voxel relabeling
42 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7070 voxels changed in iteration 0 of unlikely voxel relabeling
42 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    4125.935762
mri_ca_label stimesec    1.302801
mri_ca_label ru_maxrss   2113472
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   679939
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63152
mri_ca_label ru_oublock  528
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    308
mri_ca_label ru_nivcsw   9154
auto-labeling took 67 minutes and 59 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/transforms/cc_up.lta 0050017 

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-6.0.0/0050017/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/norm.mgz
39180 voxels in left wm, 59443 in right wm, xrange [122, 132]
searching rotation angles z=[-6  8], y=[-9  5]

searching scale 1 Z rot -6.2  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  global minimum found at slice 127.3, rotations (-2.00, 0.81)
final transformation (x=127.3, yr=-2.003, zr=0.810):
 0.99929  -0.01413  -0.03495   5.91608;
 0.01412   0.99990  -0.00049   16.26352;
 0.03495   0.00000   0.99939   21.61344;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 127
cc center is found at 127 110 102
eigenvectors:
-0.00008  -0.00378   0.99999;
-0.23287  -0.97250  -0.00369;
 0.97251  -0.23287  -0.00081;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.9 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 22:21:58 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 22:21:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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...
1635 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 72 (72), valley at 29 (29)
csf peak at 36, setting threshold to 60
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 28 (28)
csf peak at 35, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 13 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 22:25:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1825813 voxels in mask (pct= 10.88)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 22:25:14 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): 104.3 +- 5.9 [79.0 --> 125.0]
GM (72.0) : 69.4 +- 9.8 [30.0 --> 95.0]
setting bottom of white matter range to 79.2
setting top of gray matter range to 89.0
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...
6087 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3188 filled
181 bright non-wm voxels segmented.
4251 diagonally connected voxels added...
white matter segmentation took 1.7 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.56 minutes
reading wm segmentation from wm.seg.mgz...
958 voxels added to wm to prevent paths from MTL structures to cortex
3947 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 64473 voxels turned on, 12519 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  57 found -  57 modified     |    TOTAL:  57
pass   2 (xy+):   0 found -  57 modified     |    TOTAL:  57
pass   1 (xy-):  46 found -  46 modified     |    TOTAL: 103
pass   2 (xy-):   0 found -  46 modified     |    TOTAL: 103
pass   1 (yz+):  62 found -  62 modified     |    TOTAL: 165
pass   2 (yz+):   0 found -  62 modified     |    TOTAL: 165
pass   1 (yz-):  44 found -  44 modified     |    TOTAL: 209
pass   2 (yz-):   0 found -  44 modified     |    TOTAL: 209
pass   1 (xz+):  46 found -  46 modified     |    TOTAL: 255
pass   2 (xz+):   0 found -  46 modified     |    TOTAL: 255
pass   1 (xz-):  43 found -  43 modified     |    TOTAL: 298
pass   2 (xz-):   0 found -  43 modified     |    TOTAL: 298
Iteration Number : 1
pass   1 (+++):  53 found -  53 modified     |    TOTAL:  53
pass   2 (+++):   0 found -  53 modified     |    TOTAL:  53
pass   1 (+++):  80 found -  80 modified     |    TOTAL: 133
pass   2 (+++):   0 found -  80 modified     |    TOTAL: 133
pass   1 (+++):  58 found -  58 modified     |    TOTAL: 191
pass   2 (+++):   0 found -  58 modified     |    TOTAL: 191
pass   1 (+++):  49 found -  49 modified     |    TOTAL: 240
pass   2 (+++):   0 found -  49 modified     |    TOTAL: 240
Iteration Number : 1
pass   1 (++): 100 found - 100 modified     |    TOTAL: 100
pass   2 (++):   0 found - 100 modified     |    TOTAL: 100
pass   1 (+-): 115 found - 115 modified     |    TOTAL: 215
pass   2 (+-):   1 found - 116 modified     |    TOTAL: 216
pass   3 (+-):   0 found - 116 modified     |    TOTAL: 216
pass   1 (--): 117 found - 117 modified     |    TOTAL: 333
pass   2 (--):   1 found - 118 modified     |    TOTAL: 334
pass   3 (--):   0 found - 118 modified     |    TOTAL: 334
pass   1 (-+): 115 found - 115 modified     |    TOTAL: 449
pass   2 (-+):   0 found - 115 modified     |    TOTAL: 449
Iteration Number : 2
pass   1 (xy+):  12 found -  12 modified     |    TOTAL:  12
pass   2 (xy+):   0 found -  12 modified     |    TOTAL:  12
pass   1 (xy-):  10 found -  10 modified     |    TOTAL:  22
pass   2 (xy-):   0 found -  10 modified     |    TOTAL:  22
pass   1 (yz+):  16 found -  16 modified     |    TOTAL:  38
pass   2 (yz+):   0 found -  16 modified     |    TOTAL:  38
pass   1 (yz-):  23 found -  23 modified     |    TOTAL:  61
pass   2 (yz-):   0 found -  23 modified     |    TOTAL:  61
pass   1 (xz+):  12 found -  12 modified     |    TOTAL:  73
pass   2 (xz+):   0 found -  12 modified     |    TOTAL:  73
pass   1 (xz-):  19 found -  19 modified     |    TOTAL:  92
pass   2 (xz-):   0 found -  19 modified     |    TOTAL:  92
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   6
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   6
Iteration Number : 2
pass   1 (++):   7 found -   7 modified     |    TOTAL:   7
pass   2 (++):   0 found -   7 modified     |    TOTAL:   7
pass   1 (+-):   4 found -   4 modified     |    TOTAL:  11
pass   2 (+-):   0 found -   4 modified     |    TOTAL:  11
pass   1 (--):   7 found -   7 modified     |    TOTAL:  18
pass   2 (--):   0 found -   7 modified     |    TOTAL:  18
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  22
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  22
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   5
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   7
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1119 (out of 624546: 0.179170)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 22:27:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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
 1.04825   0.00347  -0.01259  -7.62717;
 0.03062   0.95477   0.35460  -42.74931;
 0.02358  -0.36394   0.87384   55.88711;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.04825   0.00347  -0.01259  -7.62717;
 0.03062   0.95477   0.35460  -42.74931;
 0.02358  -0.36394   0.87384   55.88711;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2250 (min = 350, max = 1400), aspect = 1.04 (min = 0.10, max = 0.75)
need search nearby
using seed (124, 122, 152), TAL = (4.0, 24.0, 6.0)
talairach voxel to voxel transform
 0.95363   0.00153   0.01312   6.60590;
-0.01821   0.90704  -0.36833   59.22139;
-0.03332   0.37773   0.99061  -39.46892;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (124,  122,  152) --> (4.0, 24.0, 6.0)
done.
writing output to filled.mgz...
filling took 0.6 minutes
talairach cc position changed to (4.00, 24.00, 6.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(22.00, 24.00, 6.00) SRC: (109.87, 111.96, 153.65)
search lh wm seed point around talairach space (-14.00, 24.00, 6.00), SRC: (144.20, 111.31, 152.45)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 22:28:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   7
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   8
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  11
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  11
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   2 found -   2 modified     |    TOTAL:   2
pass   2 (--):   0 found -   2 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (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 = 13 (out of 305447: 0.004256)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 30: 64 vertices, 84 faces
slice 40: 4793 vertices, 5098 faces
slice 50: 15920 vertices, 16445 faces
slice 60: 29038 vertices, 29660 faces
slice 70: 41673 vertices, 42262 faces
slice 80: 53928 vertices, 54499 faces
slice 90: 66460 vertices, 67090 faces
slice 100: 79336 vertices, 79981 faces
slice 110: 91617 vertices, 92255 faces
slice 120: 103416 vertices, 104069 faces
slice 130: 115769 vertices, 116505 faces
slice 140: 128122 vertices, 128870 faces
slice 150: 138535 vertices, 139268 faces
slice 160: 147313 vertices, 148004 faces
slice 170: 154743 vertices, 155362 faces
slice 180: 160125 vertices, 160716 faces
slice 190: 163409 vertices, 163950 faces
slice 200: 164943 vertices, 165397 faces
slice 210: 164966 vertices, 165412 faces
slice 220: 164966 vertices, 165412 faces
slice 230: 164966 vertices, 165412 faces
slice 240: 164966 vertices, 165412 faces
slice 250: 164966 vertices, 165412 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...
   164966 voxel in cpt #1: X=-446 [v=164966,e=496236,f=330824] located at (-27.890427, -24.578835, 8.906077)
For the whole surface: X=-446 [v=164966,e=496236,f=330824]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 22:28:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   6
pass   1 (yz+):   6 found -   6 modified     |    TOTAL:  12
pass   2 (yz+):   0 found -   6 modified     |    TOTAL:  12
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  15
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  15
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  16
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  16
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  18
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  18
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
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 = 20 (out of 305245: 0.006552)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 2943 vertices, 3164 faces
slice 50: 11862 vertices, 12300 faces
slice 60: 24427 vertices, 25001 faces
slice 70: 37369 vertices, 37926 faces
slice 80: 50085 vertices, 50725 faces
slice 90: 62824 vertices, 63432 faces
slice 100: 75902 vertices, 76589 faces
slice 110: 89381 vertices, 90095 faces
slice 120: 101855 vertices, 102576 faces
slice 130: 114140 vertices, 114860 faces
slice 140: 126966 vertices, 127710 faces
slice 150: 138507 vertices, 139283 faces
slice 160: 148405 vertices, 149088 faces
slice 170: 155886 vertices, 156554 faces
slice 180: 162049 vertices, 162698 faces
slice 190: 166657 vertices, 167279 faces
slice 200: 169462 vertices, 169966 faces
slice 210: 169524 vertices, 170006 faces
slice 220: 169524 vertices, 170006 faces
slice 230: 169524 vertices, 170006 faces
slice 240: 169524 vertices, 170006 faces
slice 250: 169524 vertices, 170006 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...
   169524 voxel in cpt #1: X=-482 [v=169524,e=510018,f=340012] located at (28.051685, -20.622442, 6.924996)
For the whole surface: X=-482 [v=169524,e=510018,f=340012]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 22:28:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 22:28:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

Waiting for PID 17408 of (17408 17411) to complete...
Waiting for PID 17411 of (17408 17411) 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 (17408 17411) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 22:28:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 22:28:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

Waiting for PID 17452 of (17452 17455) to complete...
Waiting for PID 17455 of (17452 17455) 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 = 49.7 mm, total surface area = 82737 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 1.2 minutes

step 000: RMS=0.192 (target=0.015)   
step 005: RMS=0.153 (target=0.015)   
step 010: RMS=0.129 (target=0.015)   
step 015: RMS=0.118 (target=0.015)   
step 020: RMS=0.111 (target=0.015)   
step 025: RMS=0.106 (target=0.015)   
step 030: RMS=0.102 (target=0.015)   
step 035: RMS=0.098 (target=0.015)   
step 040: RMS=0.095 (target=0.015)   
step 045: RMS=0.094 (target=0.015)   
step 050: RMS=0.093 (target=0.015)   
step 055: RMS=0.093 (target=0.015)   
step 060: RMS=0.092 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    64.837143
mris_inflate stimesec    0.102984
mris_inflate ru_maxrss   242264
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34953
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11640
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2279
mris_inflate ru_nivcsw   5017

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 49.5 mm, total surface area = 85313 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.1 minutes

step 000: RMS=0.189 (target=0.015)   
step 005: RMS=0.151 (target=0.015)   
step 010: RMS=0.126 (target=0.015)   
step 015: RMS=0.116 (target=0.015)   
step 020: RMS=0.110 (target=0.015)   
step 025: RMS=0.105 (target=0.015)   
step 030: RMS=0.100 (target=0.015)   
step 035: RMS=0.097 (target=0.015)   
step 040: RMS=0.093 (target=0.015)   
step 045: RMS=0.092 (target=0.015)   
step 050: RMS=0.091 (target=0.015)   
step 055: RMS=0.089 (target=0.015)   
step 060: RMS=0.089 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    60.290834
mris_inflate stimesec    0.120981
mris_inflate ru_maxrss   248868
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36092
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11952
mris_inflate ru_oublock  11968
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1986
mris_inflate ru_nivcsw   5146
PIDs (17452 17455) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 22:29:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 22:29:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

Waiting for PID 17542 of (17542 17546) to complete...
Waiting for PID 17546 of (17542 17546) 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 0.89 +- 0.62 (0.00-->9.93) (max @ vno 110098 --> 111297)
face area 0.02 +- 0.04 (-0.34-->0.83)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.304...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.065, avgs=0
005/300: dt: 0.9000, rms radial error=175.805, avgs=0
010/300: dt: 0.9000, rms radial error=175.246, avgs=0
015/300: dt: 0.9000, rms radial error=174.510, avgs=0
020/300: dt: 0.9000, rms radial error=173.670, avgs=0
025/300: dt: 0.9000, rms radial error=172.771, avgs=0
030/300: dt: 0.9000, rms radial error=171.837, avgs=0
035/300: dt: 0.9000, rms radial error=170.886, avgs=0
040/300: dt: 0.9000, rms radial error=169.925, avgs=0
045/300: dt: 0.9000, rms radial error=168.961, avgs=0
050/300: dt: 0.9000, rms radial error=167.997, avgs=0
055/300: dt: 0.9000, rms radial error=167.034, avgs=0
060/300: dt: 0.9000, rms radial error=166.073, avgs=0
065/300: dt: 0.9000, rms radial error=165.129, avgs=0
070/300: dt: 0.9000, rms radial error=164.202, avgs=0
075/300: dt: 0.9000, rms radial error=163.281, avgs=0
080/300: dt: 0.9000, rms radial error=162.364, avgs=0
085/300: dt: 0.9000, rms radial error=161.452, avgs=0
090/300: dt: 0.9000, rms radial error=160.545, avgs=0
095/300: dt: 0.9000, rms radial error=159.643, avgs=0
100/300: dt: 0.9000, rms radial error=158.745, avgs=0
105/300: dt: 0.9000, rms radial error=157.852, avgs=0
110/300: dt: 0.9000, rms radial error=156.964, avgs=0
115/300: dt: 0.9000, rms radial error=156.081, avgs=0
120/300: dt: 0.9000, rms radial error=155.203, avgs=0
125/300: dt: 0.9000, rms radial error=154.329, avgs=0
130/300: dt: 0.9000, rms radial error=153.459, avgs=0
135/300: dt: 0.9000, rms radial error=152.595, avgs=0
140/300: dt: 0.9000, rms radial error=151.734, avgs=0
145/300: dt: 0.9000, rms radial error=150.878, avgs=0
150/300: dt: 0.9000, rms radial error=150.027, avgs=0
155/300: dt: 0.9000, rms radial error=149.180, avgs=0
160/300: dt: 0.9000, rms radial error=148.338, avgs=0
165/300: dt: 0.9000, rms radial error=147.501, avgs=0
170/300: dt: 0.9000, rms radial error=146.668, avgs=0
175/300: dt: 0.9000, rms radial error=145.840, avgs=0
180/300: dt: 0.9000, rms radial error=145.016, avgs=0
185/300: dt: 0.9000, rms radial error=144.200, avgs=0
190/300: dt: 0.9000, rms radial error=143.390, avgs=0
195/300: dt: 0.9000, rms radial error=142.585, avgs=0
200/300: dt: 0.9000, rms radial error=141.784, avgs=0
205/300: dt: 0.9000, rms radial error=140.988, avgs=0
210/300: dt: 0.9000, rms radial error=140.196, avgs=0
215/300: dt: 0.9000, rms radial error=139.409, avgs=0
220/300: dt: 0.9000, rms radial error=138.626, avgs=0
225/300: dt: 0.9000, rms radial error=137.847, avgs=0
230/300: dt: 0.9000, rms radial error=137.073, avgs=0
235/300: dt: 0.9000, rms radial error=136.304, avgs=0
240/300: dt: 0.9000, rms radial error=135.538, avgs=0
245/300: dt: 0.9000, rms radial error=134.777, avgs=0
250/300: dt: 0.9000, rms radial error=134.020, avgs=0
255/300: dt: 0.9000, rms radial error=133.268, avgs=0
260/300: dt: 0.9000, rms radial error=132.519, avgs=0
265/300: dt: 0.9000, rms radial error=131.775, avgs=0
270/300: dt: 0.9000, rms radial error=131.035, avgs=0
275/300: dt: 0.9000, rms radial error=130.299, avgs=0
280/300: dt: 0.9000, rms radial error=129.567, avgs=0
285/300: dt: 0.9000, rms radial error=128.840, avgs=0
290/300: dt: 0.9000, rms radial error=128.116, avgs=0
295/300: dt: 0.9000, rms radial error=127.397, avgs=0
300/300: dt: 0.9000, rms radial error=126.682, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19791.63
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 2 (K=40.0), pass 1, starting sse = 3659.45
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00023
epoch 3 (K=160.0), pass 1, starting sse = 545.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00358
epoch 4 (K=640.0), pass 1, starting sse = 96.92
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/13 = 0.00881
final distance error %30.20
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    374.813019
mris_sphere stimesec    0.175973
mris_sphere ru_maxrss   242464
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   35001
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11664
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8787
mris_sphere ru_nivcsw   25759
FSRUNTIME@ mris_sphere  0.1030 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 0.89 +- 0.63 (0.00-->8.48) (max @ vno 114934 --> 114935)
face area 0.02 +- 0.03 (-0.29-->0.53)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.300...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.974, avgs=0
005/300: dt: 0.9000, rms radial error=175.711, avgs=0
010/300: dt: 0.9000, rms radial error=175.151, avgs=0
015/300: dt: 0.9000, rms radial error=174.416, avgs=0
020/300: dt: 0.9000, rms radial error=173.579, avgs=0
025/300: dt: 0.9000, rms radial error=172.685, avgs=0
030/300: dt: 0.9000, rms radial error=171.762, avgs=0
035/300: dt: 0.9000, rms radial error=170.828, avgs=0
040/300: dt: 0.9000, rms radial error=169.889, avgs=0
045/300: dt: 0.9000, rms radial error=168.948, avgs=0
050/300: dt: 0.9000, rms radial error=168.008, avgs=0
055/300: dt: 0.9000, rms radial error=167.070, avgs=0
060/300: dt: 0.9000, rms radial error=166.139, avgs=0
065/300: dt: 0.9000, rms radial error=165.212, avgs=0
070/300: dt: 0.9000, rms radial error=164.290, avgs=0
075/300: dt: 0.9000, rms radial error=163.372, avgs=0
080/300: dt: 0.9000, rms radial error=162.458, avgs=0
085/300: dt: 0.9000, rms radial error=161.549, avgs=0
090/300: dt: 0.9000, rms radial error=160.644, avgs=0
095/300: dt: 0.9000, rms radial error=159.745, avgs=0
100/300: dt: 0.9000, rms radial error=158.851, avgs=0
105/300: dt: 0.9000, rms radial error=157.961, avgs=0
110/300: dt: 0.9000, rms radial error=157.077, avgs=0
115/300: dt: 0.9000, rms radial error=156.197, avgs=0
120/300: dt: 0.9000, rms radial error=155.322, avgs=0
125/300: dt: 0.9000, rms radial error=154.453, avgs=0
130/300: dt: 0.9000, rms radial error=153.588, avgs=0
135/300: dt: 0.9000, rms radial error=152.728, avgs=0
140/300: dt: 0.9000, rms radial error=151.873, avgs=0
145/300: dt: 0.9000, rms radial error=151.023, avgs=0
150/300: dt: 0.9000, rms radial error=150.177, avgs=0
155/300: dt: 0.9000, rms radial error=149.336, avgs=0
160/300: dt: 0.9000, rms radial error=148.500, avgs=0
165/300: dt: 0.9000, rms radial error=147.668, avgs=0
170/300: dt: 0.9000, rms radial error=146.842, avgs=0
175/300: dt: 0.9000, rms radial error=146.020, avgs=0
180/300: dt: 0.9000, rms radial error=145.203, avgs=0
185/300: dt: 0.9000, rms radial error=144.390, avgs=0
190/300: dt: 0.9000, rms radial error=143.581, avgs=0
195/300: dt: 0.9000, rms radial error=142.777, avgs=0
200/300: dt: 0.9000, rms radial error=141.977, avgs=0
205/300: dt: 0.9000, rms radial error=141.182, avgs=0
210/300: dt: 0.9000, rms radial error=140.391, avgs=0
215/300: dt: 0.9000, rms radial error=139.604, avgs=0
220/300: dt: 0.9000, rms radial error=138.822, avgs=0
225/300: dt: 0.9000, rms radial error=138.044, avgs=0
230/300: dt: 0.9000, rms radial error=137.270, avgs=0
235/300: dt: 0.9000, rms radial error=136.501, avgs=0
240/300: dt: 0.9000, rms radial error=135.735, avgs=0
245/300: dt: 0.9000, rms radial error=134.974, avgs=0
250/300: dt: 0.9000, rms radial error=134.218, avgs=0
255/300: dt: 0.9000, rms radial error=133.465, avgs=0
260/300: dt: 0.9000, rms radial error=132.717, avgs=0
265/300: dt: 0.9000, rms radial error=131.972, avgs=0
270/300: dt: 0.9000, rms radial error=131.232, avgs=0
275/300: dt: 0.9000, rms radial error=130.496, avgs=0
280/300: dt: 0.9000, rms radial error=129.764, avgs=0
285/300: dt: 0.9000, rms radial error=129.037, avgs=0
290/300: dt: 0.9000, rms radial error=128.313, avgs=0
295/300: dt: 0.9000, rms radial error=127.593, avgs=0
300/300: dt: 0.9000, rms radial error=126.877, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20399.15
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 = 3782.57
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 3 (K=160.0), pass 1, starting sse = 560.04
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00279
epoch 4 (K=640.0), pass 1, starting sse = 92.57
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00667
final distance error %31.10
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    349.595853
mris_sphere stimesec    0.167974
mris_sphere ru_maxrss   249072
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   36141
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11952
mris_sphere ru_oublock  11992
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    7598
mris_sphere ru_nivcsw   24974
FSRUNTIME@ mris_sphere  0.0984 hours 1 threads
PIDs (17542 17546) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 22:36:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 22:36:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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


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

#@# Fix Topology lh Sat Oct  7 22:36:04 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050017 lh 

#@# Fix Topology rh Sat Oct  7 22:36:04 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050017 rh 

Waiting for PID 18164 of (18164 18167) to complete...
Waiting for PID 18167 of (18164 18167) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050017 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=-446 (nv=164966, nf=330824, ne=496236, g=224)
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...
52759 ambiguous faces found in tessellation
segmenting defects...
148 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 6 into 0
      -merging segment 27 into 2
      -merging segment 13 into 4
      -merging segment 9 into 5
      -merging segment 7 into 5
      -merging segment 8 into 5
      -merging segment 33 into 29
      -merging segment 50 into 49
      -merging segment 88 into 67
      -merging segment 74 into 72
      -merging segment 82 into 79
      -merging segment 85 into 79
      -merging segment 99 into 79
      -merging segment 101 into 79
      -merging segment 114 into 79
      -merging segment 118 into 79
      -merging segment 117 into 116
      -merging segment 125 into 116
      -merging segment 134 into 128
      -merging segment 146 into 143
128 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.0145  (-4.5072)
      -vertex     loglikelihood: -6.0889  (-3.0445)
      -normal dot loglikelihood: -3.5736  (-3.5736)
      -quad curv  loglikelihood: -6.1394  (-3.0697)
      Total Loglikelihood : -24.8163

CORRECTING DEFECT 0 (vertices=610, convex hull=359, v0=0)
After retessellation of defect 0 (v0=0), euler #=-128 (134979,397184,262077) : difference with theory (-125) = 3 

CORRECTING DEFECT 1 (vertices=115, convex hull=100, v0=107)
After retessellation of defect 1 (v0=107), euler #=-127 (135008,397319,262184) : difference with theory (-124) = 3 

CORRECTING DEFECT 2 (vertices=5729, convex hull=1646, v0=151)
XL defect detected...
After retessellation of defect 2 (v0=151), euler #=-131 (135927,401031,264973) : difference with theory (-123) = 8 

CORRECTING DEFECT 3 (vertices=41, convex hull=91, v0=477)
After retessellation of defect 3 (v0=477), euler #=-130 (135951,401139,265058) : difference with theory (-122) = 8 

CORRECTING DEFECT 4 (vertices=403, convex hull=508, v0=1101)
L defect detected...
After retessellation of defect 4 (v0=1101), euler #=-128 (136186,402105,265791) : difference with theory (-121) = 7 

CORRECTING DEFECT 5 (vertices=449, convex hull=437, v0=1556)
After retessellation of defect 5 (v0=1556), euler #=-125 (136412,403025,266488) : difference with theory (-120) = 5 

CORRECTING DEFECT 6 (vertices=129, convex hull=44, v0=3642)
After retessellation of defect 6 (v0=3642), euler #=-124 (136417,403056,266515) : difference with theory (-119) = 5 

CORRECTING DEFECT 7 (vertices=55, convex hull=80, v0=4213)
After retessellation of defect 7 (v0=4213), euler #=-123 (136435,403143,266585) : difference with theory (-118) = 5 

CORRECTING DEFECT 8 (vertices=163, convex hull=157, v0=4843)
After retessellation of defect 8 (v0=4843), euler #=-122 (136498,403403,266783) : difference with theory (-117) = 5 

CORRECTING DEFECT 9 (vertices=14, convex hull=28, v0=5535)
After retessellation of defect 9 (v0=5535), euler #=-121 (136499,403415,266795) : difference with theory (-116) = 5 

CORRECTING DEFECT 10 (vertices=39, convex hull=32, v0=6179)
After retessellation of defect 10 (v0=6179), euler #=-120 (136502,403436,266814) : difference with theory (-115) = 5 

CORRECTING DEFECT 11 (vertices=53, convex hull=105, v0=6699)
After retessellation of defect 11 (v0=6699), euler #=-119 (136532,403574,266923) : difference with theory (-114) = 5 

CORRECTING DEFECT 12 (vertices=19, convex hull=34, v0=7350)
After retessellation of defect 12 (v0=7350), euler #=-118 (136533,403592,266941) : difference with theory (-113) = 5 

CORRECTING DEFECT 13 (vertices=34, convex hull=84, v0=9177)
After retessellation of defect 13 (v0=9177), euler #=-117 (136552,403682,267013) : difference with theory (-112) = 5 

CORRECTING DEFECT 14 (vertices=32, convex hull=37, v0=10145)
After retessellation of defect 14 (v0=10145), euler #=-116 (136558,403714,267040) : difference with theory (-111) = 5 

CORRECTING DEFECT 15 (vertices=390, convex hull=219, v0=10439)
After retessellation of defect 15 (v0=10439), euler #=-115 (136597,403958,267246) : difference with theory (-110) = 5 

CORRECTING DEFECT 16 (vertices=184, convex hull=70, v0=10820)
After retessellation of defect 16 (v0=10820), euler #=-114 (136615,404043,267314) : difference with theory (-109) = 5 

CORRECTING DEFECT 17 (vertices=41, convex hull=79, v0=10928)
After retessellation of defect 17 (v0=10928), euler #=-113 (136643,404159,267403) : difference with theory (-108) = 5 

CORRECTING DEFECT 18 (vertices=46, convex hull=68, v0=11617)
After retessellation of defect 18 (v0=11617), euler #=-112 (136660,404237,267465) : difference with theory (-107) = 5 

CORRECTING DEFECT 19 (vertices=60, convex hull=27, v0=12749)
After retessellation of defect 19 (v0=12749), euler #=-111 (136663,404255,267481) : difference with theory (-106) = 5 

CORRECTING DEFECT 20 (vertices=45, convex hull=43, v0=13099)
After retessellation of defect 20 (v0=13099), euler #=-110 (136669,404286,267507) : difference with theory (-105) = 5 

CORRECTING DEFECT 21 (vertices=112, convex hull=93, v0=15182)
After retessellation of defect 21 (v0=15182), euler #=-109 (136702,404428,267617) : difference with theory (-104) = 5 

CORRECTING DEFECT 22 (vertices=6, convex hull=25, v0=19296)
After retessellation of defect 22 (v0=19296), euler #=-108 (136703,404438,267627) : difference with theory (-103) = 5 

CORRECTING DEFECT 23 (vertices=108, convex hull=40, v0=20547)
After retessellation of defect 23 (v0=20547), euler #=-106 (136710,404472,267656) : difference with theory (-102) = 4 

CORRECTING DEFECT 24 (vertices=46, convex hull=88, v0=21472)
After retessellation of defect 24 (v0=21472), euler #=-105 (136725,404551,267721) : difference with theory (-101) = 4 

CORRECTING DEFECT 25 (vertices=336, convex hull=194, v0=24778)
After retessellation of defect 25 (v0=24778), euler #=-104 (136821,404938,268013) : difference with theory (-100) = 4 

CORRECTING DEFECT 26 (vertices=16, convex hull=29, v0=25739)
After retessellation of defect 26 (v0=25739), euler #=-103 (136825,404958,268030) : difference with theory (-99) = 4 

CORRECTING DEFECT 27 (vertices=271, convex hull=199, v0=27317)
After retessellation of defect 27 (v0=27317), euler #=-102 (136920,405325,268303) : difference with theory (-98) = 4 

CORRECTING DEFECT 28 (vertices=36, convex hull=75, v0=27733)
After retessellation of defect 28 (v0=27733), euler #=-101 (136941,405419,268377) : difference with theory (-97) = 4 

CORRECTING DEFECT 29 (vertices=15, convex hull=27, v0=28779)
After retessellation of defect 29 (v0=28779), euler #=-100 (136943,405435,268392) : difference with theory (-96) = 4 

CORRECTING DEFECT 30 (vertices=109, convex hull=89, v0=32357)
After retessellation of defect 30 (v0=32357), euler #=-99 (136972,405563,268492) : difference with theory (-95) = 4 

CORRECTING DEFECT 31 (vertices=192, convex hull=47, v0=32660)
After retessellation of defect 31 (v0=32660), euler #=-98 (136984,405619,268537) : difference with theory (-94) = 4 

CORRECTING DEFECT 32 (vertices=47, convex hull=90, v0=36032)
After retessellation of defect 32 (v0=36032), euler #=-97 (137011,405738,268630) : difference with theory (-93) = 4 

CORRECTING DEFECT 33 (vertices=15, convex hull=20, v0=37487)
After retessellation of defect 33 (v0=37487), euler #=-96 (137012,405747,268639) : difference with theory (-92) = 4 

CORRECTING DEFECT 34 (vertices=6, convex hull=17, v0=37576)
After retessellation of defect 34 (v0=37576), euler #=-95 (137013,405753,268645) : difference with theory (-91) = 4 

CORRECTING DEFECT 35 (vertices=51, convex hull=35, v0=38811)
After retessellation of defect 35 (v0=38811), euler #=-94 (137019,405784,268671) : difference with theory (-90) = 4 

CORRECTING DEFECT 36 (vertices=28, convex hull=15, v0=39418)
After retessellation of defect 36 (v0=39418), euler #=-93 (137019,405789,268677) : difference with theory (-89) = 4 

CORRECTING DEFECT 37 (vertices=81, convex hull=94, v0=39938)
After retessellation of defect 37 (v0=39938), euler #=-92 (137062,405954,268800) : difference with theory (-88) = 4 

CORRECTING DEFECT 38 (vertices=64, convex hull=95, v0=40759)
After retessellation of defect 38 (v0=40759), euler #=-91 (137100,406113,268922) : difference with theory (-87) = 4 

CORRECTING DEFECT 39 (vertices=78, convex hull=79, v0=40791)
After retessellation of defect 39 (v0=40791), euler #=-90 (137150,406294,269054) : difference with theory (-86) = 4 

CORRECTING DEFECT 40 (vertices=125, convex hull=130, v0=41093)
After retessellation of defect 40 (v0=41093), euler #=-89 (137213,406542,269240) : difference with theory (-85) = 4 

CORRECTING DEFECT 41 (vertices=49, convex hull=74, v0=45148)
After retessellation of defect 41 (v0=45148), euler #=-88 (137239,406653,269326) : difference with theory (-84) = 4 

CORRECTING DEFECT 42 (vertices=207, convex hull=152, v0=45352)
After retessellation of defect 42 (v0=45352), euler #=-86 (137259,406782,269437) : difference with theory (-83) = 3 

CORRECTING DEFECT 43 (vertices=6, convex hull=19, v0=50036)
After retessellation of defect 43 (v0=50036), euler #=-85 (137260,406789,269444) : difference with theory (-82) = 3 

CORRECTING DEFECT 44 (vertices=52, convex hull=94, v0=50127)
After retessellation of defect 44 (v0=50127), euler #=-84 (137298,406943,269561) : difference with theory (-81) = 3 

CORRECTING DEFECT 45 (vertices=32, convex hull=32, v0=51366)
After retessellation of defect 45 (v0=51366), euler #=-83 (137300,406962,269579) : difference with theory (-80) = 3 

CORRECTING DEFECT 46 (vertices=37, convex hull=57, v0=52191)
After retessellation of defect 46 (v0=52191), euler #=-82 (137315,407028,269631) : difference with theory (-79) = 3 

CORRECTING DEFECT 47 (vertices=230, convex hull=122, v0=52461)
After retessellation of defect 47 (v0=52461), euler #=-81 (137368,407242,269793) : difference with theory (-78) = 3 

CORRECTING DEFECT 48 (vertices=48, convex hull=104, v0=54504)
After retessellation of defect 48 (v0=54504), euler #=-80 (137399,407380,269901) : difference with theory (-77) = 3 

CORRECTING DEFECT 49 (vertices=22, convex hull=49, v0=55542)
After retessellation of defect 49 (v0=55542), euler #=-79 (137408,407426,269939) : difference with theory (-76) = 3 

CORRECTING DEFECT 50 (vertices=35, convex hull=53, v0=60025)
After retessellation of defect 50 (v0=60025), euler #=-78 (137422,407487,269987) : difference with theory (-75) = 3 

CORRECTING DEFECT 51 (vertices=70, convex hull=85, v0=60749)
After retessellation of defect 51 (v0=60749), euler #=-77 (137447,407594,270070) : difference with theory (-74) = 3 

CORRECTING DEFECT 52 (vertices=281, convex hull=290, v0=60890)
After retessellation of defect 52 (v0=60890), euler #=-76 (137589,408164,270499) : difference with theory (-73) = 3 

CORRECTING DEFECT 53 (vertices=189, convex hull=75, v0=61229)
After retessellation of defect 53 (v0=61229), euler #=-75 (137629,408312,270608) : difference with theory (-72) = 3 

CORRECTING DEFECT 54 (vertices=257, convex hull=123, v0=63829)
After retessellation of defect 54 (v0=63829), euler #=-74 (137660,408461,270727) : difference with theory (-71) = 3 

CORRECTING DEFECT 55 (vertices=105, convex hull=95, v0=63923)
After retessellation of defect 55 (v0=63923), euler #=-75 (137685,408588,270828) : difference with theory (-70) = 5 

CORRECTING DEFECT 56 (vertices=22, convex hull=25, v0=65925)
After retessellation of defect 56 (v0=65925), euler #=-74 (137688,408607,270845) : difference with theory (-69) = 5 

CORRECTING DEFECT 57 (vertices=25, convex hull=63, v0=66491)
After retessellation of defect 57 (v0=66491), euler #=-73 (137697,408663,270893) : difference with theory (-68) = 5 

CORRECTING DEFECT 58 (vertices=122, convex hull=168, v0=67411)
After retessellation of defect 58 (v0=67411), euler #=-73 (137710,408784,271001) : difference with theory (-67) = 6 

CORRECTING DEFECT 59 (vertices=2128, convex hull=859, v0=67479)
XL defect detected...
After retessellation of defect 59 (v0=67479), euler #=-71 (138347,411162,272744) : difference with theory (-66) = 5 

CORRECTING DEFECT 60 (vertices=13, convex hull=25, v0=67546)
After retessellation of defect 60 (v0=67546), euler #=-70 (138350,411183,272763) : difference with theory (-65) = 5 

CORRECTING DEFECT 61 (vertices=10, convex hull=23, v0=68580)
After retessellation of defect 61 (v0=68580), euler #=-69 (138356,411206,272781) : difference with theory (-64) = 5 

CORRECTING DEFECT 62 (vertices=17, convex hull=35, v0=69953)
After retessellation of defect 62 (v0=69953), euler #=-68 (138357,411225,272800) : difference with theory (-63) = 5 

CORRECTING DEFECT 63 (vertices=39, convex hull=89, v0=70027)
After retessellation of defect 63 (v0=70027), euler #=-67 (138374,411308,272867) : difference with theory (-62) = 5 

CORRECTING DEFECT 64 (vertices=453, convex hull=243, v0=72461)
After retessellation of defect 64 (v0=72461), euler #=-65 (138502,411817,273250) : difference with theory (-61) = 4 

CORRECTING DEFECT 65 (vertices=18, convex hull=27, v0=72971)
After retessellation of defect 65 (v0=72971), euler #=-64 (138503,411830,273263) : difference with theory (-60) = 4 

CORRECTING DEFECT 66 (vertices=33, convex hull=89, v0=75515)
After retessellation of defect 66 (v0=75515), euler #=-63 (138517,411909,273329) : difference with theory (-59) = 4 

CORRECTING DEFECT 67 (vertices=8, convex hull=24, v0=76516)
After retessellation of defect 67 (v0=76516), euler #=-62 (138521,411927,273344) : difference with theory (-58) = 4 

CORRECTING DEFECT 68 (vertices=148, convex hull=169, v0=76519)
After retessellation of defect 68 (v0=76519), euler #=-61 (138589,412212,273562) : difference with theory (-57) = 4 

CORRECTING DEFECT 69 (vertices=68, convex hull=94, v0=78090)
After retessellation of defect 69 (v0=78090), euler #=-60 (138616,412337,273661) : difference with theory (-56) = 4 

CORRECTING DEFECT 70 (vertices=9505, convex hull=2572, v0=79916)
XL defect detected...
After retessellation of defect 70 (v0=79916), euler #=-58 (139600,416746,277088) : difference with theory (-55) = 3 

CORRECTING DEFECT 71 (vertices=26, convex hull=27, v0=81455)
After retessellation of defect 71 (v0=81455), euler #=-57 (139603,416762,277102) : difference with theory (-54) = 3 

CORRECTING DEFECT 72 (vertices=24, convex hull=58, v0=83006)
After retessellation of defect 72 (v0=83006), euler #=-56 (139619,416830,277155) : difference with theory (-53) = 3 

CORRECTING DEFECT 73 (vertices=68, convex hull=82, v0=88028)
After retessellation of defect 73 (v0=88028), euler #=-55 (139659,416987,277273) : difference with theory (-52) = 3 

CORRECTING DEFECT 74 (vertices=93, convex hull=109, v0=89145)
After retessellation of defect 74 (v0=89145), euler #=-54 (139696,417147,277397) : difference with theory (-51) = 3 

CORRECTING DEFECT 75 (vertices=67, convex hull=112, v0=91672)
After retessellation of defect 75 (v0=91672), euler #=-53 (139737,417318,277528) : difference with theory (-50) = 3 

CORRECTING DEFECT 76 (vertices=478, convex hull=190, v0=96428)
After retessellation of defect 76 (v0=96428), euler #=-53 (139810,417633,277770) : difference with theory (-49) = 4 

CORRECTING DEFECT 77 (vertices=47, convex hull=25, v0=102290)
After retessellation of defect 77 (v0=102290), euler #=-52 (139813,417650,277785) : difference with theory (-48) = 4 

CORRECTING DEFECT 78 (vertices=41, convex hull=92, v0=102840)
After retessellation of defect 78 (v0=102840), euler #=-51 (139841,417770,277878) : difference with theory (-47) = 4 

CORRECTING DEFECT 79 (vertices=9, convex hull=19, v0=103994)
After retessellation of defect 79 (v0=103994), euler #=-50 (139842,417779,277887) : difference with theory (-46) = 4 

CORRECTING DEFECT 80 (vertices=20, convex hull=57, v0=104929)
After retessellation of defect 80 (v0=104929), euler #=-49 (139852,417830,277929) : difference with theory (-45) = 4 

CORRECTING DEFECT 81 (vertices=207, convex hull=43, v0=110245)
After retessellation of defect 81 (v0=110245), euler #=-48 (139868,417894,277978) : difference with theory (-44) = 4 

CORRECTING DEFECT 82 (vertices=18, convex hull=29, v0=111200)
After retessellation of defect 82 (v0=111200), euler #=-47 (139870,417912,277995) : difference with theory (-43) = 4 

CORRECTING DEFECT 83 (vertices=354, convex hull=206, v0=113580)
After retessellation of defect 83 (v0=113580), euler #=-46 (139939,418220,278235) : difference with theory (-42) = 4 

CORRECTING DEFECT 84 (vertices=50, convex hull=35, v0=116108)
After retessellation of defect 84 (v0=116108), euler #=-45 (139947,418254,278262) : difference with theory (-41) = 4 

CORRECTING DEFECT 85 (vertices=130, convex hull=65, v0=116779)
After retessellation of defect 85 (v0=116779), euler #=-44 (139973,418364,278347) : difference with theory (-40) = 4 

CORRECTING DEFECT 86 (vertices=33, convex hull=63, v0=117351)
After retessellation of defect 86 (v0=117351), euler #=-43 (139983,418418,278392) : difference with theory (-39) = 4 

CORRECTING DEFECT 87 (vertices=45, convex hull=89, v0=118398)
After retessellation of defect 87 (v0=118398), euler #=-42 (140005,418519,278472) : difference with theory (-38) = 4 

CORRECTING DEFECT 88 (vertices=36, convex hull=70, v0=120892)
After retessellation of defect 88 (v0=120892), euler #=-41 (140025,418605,278539) : difference with theory (-37) = 4 

CORRECTING DEFECT 89 (vertices=73, convex hull=74, v0=122677)
After retessellation of defect 89 (v0=122677), euler #=-40 (140063,418751,278648) : difference with theory (-36) = 4 

CORRECTING DEFECT 90 (vertices=44, convex hull=72, v0=123084)
After retessellation of defect 90 (v0=123084), euler #=-39 (140078,418822,278705) : difference with theory (-35) = 4 

CORRECTING DEFECT 91 (vertices=34, convex hull=29, v0=125683)
After retessellation of defect 91 (v0=125683), euler #=-38 (140084,418848,278726) : difference with theory (-34) = 4 

CORRECTING DEFECT 92 (vertices=43, convex hull=59, v0=125862)
After retessellation of defect 92 (v0=125862), euler #=-37 (140111,418951,278803) : difference with theory (-33) = 4 

CORRECTING DEFECT 93 (vertices=22, convex hull=64, v0=126021)
After retessellation of defect 93 (v0=126021), euler #=-36 (140122,419007,278849) : difference with theory (-32) = 4 

CORRECTING DEFECT 94 (vertices=54, convex hull=48, v0=126473)
After retessellation of defect 94 (v0=126473), euler #=-35 (140132,419060,278893) : difference with theory (-31) = 4 

CORRECTING DEFECT 95 (vertices=36, convex hull=30, v0=126837)
After retessellation of defect 95 (v0=126837), euler #=-34 (140140,419096,278922) : difference with theory (-30) = 4 

CORRECTING DEFECT 96 (vertices=58, convex hull=83, v0=128061)
After retessellation of defect 96 (v0=128061), euler #=-33 (140167,419209,279009) : difference with theory (-29) = 4 

CORRECTING DEFECT 97 (vertices=35, convex hull=66, v0=128914)
After retessellation of defect 97 (v0=128914), euler #=-32 (140192,419316,279092) : difference with theory (-28) = 4 

CORRECTING DEFECT 98 (vertices=19, convex hull=24, v0=129823)
After retessellation of defect 98 (v0=129823), euler #=-31 (140196,419334,279107) : difference with theory (-27) = 4 

CORRECTING DEFECT 99 (vertices=75, convex hull=99, v0=130736)
After retessellation of defect 99 (v0=130736), euler #=-30 (140248,419530,279252) : difference with theory (-26) = 4 

CORRECTING DEFECT 100 (vertices=8, convex hull=30, v0=132156)
After retessellation of defect 100 (v0=132156), euler #=-29 (140250,419547,279268) : difference with theory (-25) = 4 

CORRECTING DEFECT 101 (vertices=756, convex hull=604, v0=134048)
L defect detected...
After retessellation of defect 101 (v0=134048), euler #=-26 (140451,420461,279984) : difference with theory (-24) = 2 

CORRECTING DEFECT 102 (vertices=36, convex hull=26, v0=137889)
After retessellation of defect 102 (v0=137889), euler #=-25 (140459,420494,280010) : difference with theory (-23) = 2 

CORRECTING DEFECT 103 (vertices=164, convex hull=156, v0=140605)
After retessellation of defect 103 (v0=140605), euler #=-24 (140524,420763,280215) : difference with theory (-22) = 2 

CORRECTING DEFECT 104 (vertices=42, convex hull=86, v0=141062)
After retessellation of defect 104 (v0=141062), euler #=-23 (140546,420864,280295) : difference with theory (-21) = 2 

CORRECTING DEFECT 105 (vertices=34, convex hull=85, v0=146562)
After retessellation of defect 105 (v0=146562), euler #=-22 (140568,420963,280373) : difference with theory (-20) = 2 

CORRECTING DEFECT 106 (vertices=237, convex hull=68, v0=146825)
After retessellation of defect 106 (v0=146825), euler #=-21 (140587,421045,280437) : difference with theory (-19) = 2 

CORRECTING DEFECT 107 (vertices=317, convex hull=93, v0=147554)
After retessellation of defect 107 (v0=147554), euler #=-20 (140613,421166,280533) : difference with theory (-18) = 2 

CORRECTING DEFECT 108 (vertices=81, convex hull=50, v0=148910)
After retessellation of defect 108 (v0=148910), euler #=-19 (140620,421202,280563) : difference with theory (-17) = 2 

CORRECTING DEFECT 109 (vertices=64, convex hull=80, v0=149143)
After retessellation of defect 109 (v0=149143), euler #=-18 (140632,421272,280622) : difference with theory (-16) = 2 

CORRECTING DEFECT 110 (vertices=331, convex hull=98, v0=153480)
After retessellation of defect 110 (v0=153480), euler #=-16 (140642,421359,280701) : difference with theory (-15) = 1 

CORRECTING DEFECT 111 (vertices=85, convex hull=80, v0=153948)
After retessellation of defect 111 (v0=153948), euler #=-15 (140656,421432,280761) : difference with theory (-14) = 1 

CORRECTING DEFECT 112 (vertices=44, convex hull=75, v0=154180)
After retessellation of defect 112 (v0=154180), euler #=-14 (140684,421543,280845) : difference with theory (-13) = 1 

CORRECTING DEFECT 113 (vertices=90, convex hull=84, v0=154696)
After retessellation of defect 113 (v0=154696), euler #=-13 (140728,421712,280971) : difference with theory (-12) = 1 

CORRECTING DEFECT 114 (vertices=128, convex hull=99, v0=155021)
After retessellation of defect 114 (v0=155021), euler #=-12 (140763,421863,281088) : difference with theory (-11) = 1 

CORRECTING DEFECT 115 (vertices=54, convex hull=90, v0=155550)
After retessellation of defect 115 (v0=155550), euler #=-11 (140777,421943,281155) : difference with theory (-10) = 1 

CORRECTING DEFECT 116 (vertices=54, convex hull=60, v0=159560)
After retessellation of defect 116 (v0=159560), euler #=-10 (140794,422020,281216) : difference with theory (-9) = 1 

CORRECTING DEFECT 117 (vertices=166, convex hull=87, v0=159646)
After retessellation of defect 117 (v0=159646), euler #=-9 (140833,422173,281331) : difference with theory (-8) = 1 

CORRECTING DEFECT 118 (vertices=16, convex hull=29, v0=159828)
After retessellation of defect 118 (v0=159828), euler #=-8 (140833,422185,281344) : difference with theory (-7) = 1 

CORRECTING DEFECT 119 (vertices=68, convex hull=124, v0=161207)
After retessellation of defect 119 (v0=161207), euler #=-7 (140875,422370,281488) : difference with theory (-6) = 1 

CORRECTING DEFECT 120 (vertices=29, convex hull=71, v0=161449)
After retessellation of defect 120 (v0=161449), euler #=-6 (140886,422429,281537) : difference with theory (-5) = 1 

CORRECTING DEFECT 121 (vertices=24, convex hull=70, v0=162104)
After retessellation of defect 121 (v0=162104), euler #=-5 (140903,422508,281600) : difference with theory (-4) = 1 

CORRECTING DEFECT 122 (vertices=176, convex hull=121, v0=162471)
After retessellation of defect 122 (v0=162471), euler #=-4 (140936,422668,281728) : difference with theory (-3) = 1 

CORRECTING DEFECT 123 (vertices=17, convex hull=22, v0=163529)
After retessellation of defect 123 (v0=163529), euler #=-3 (140937,422682,281742) : difference with theory (-2) = 1 

CORRECTING DEFECT 124 (vertices=140, convex hull=195, v0=163757)
After retessellation of defect 124 (v0=163757), euler #=-1 (140992,422937,281944) : difference with theory (-1) = 0 

CORRECTING DEFECT 125 (vertices=26, convex hull=36, v0=163851)
After retessellation of defect 125 (v0=163851), euler #=0 (140993,422954,281961) : difference with theory (0) = 0 

CORRECTING DEFECT 126 (vertices=33, convex hull=25, v0=164139)
After retessellation of defect 126 (v0=164139), euler #=1 (140995,422968,281974) : difference with theory (1) = 0 

CORRECTING DEFECT 127 (vertices=25, convex hull=31, v0=164894)
After retessellation of defect 127 (v0=164894), euler #=2 (140996,422982,281988) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.90 +- 0.37 (0.03-->22.09) (max @ vno 92683 --> 106908)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.90 +- 0.37 (0.03-->22.09) (max @ vno 92683 --> 106908)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
334 mutations (32.1%), 707 crossovers (67.9%), 2458 vertices were eliminated
building final representation...
23970 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=140996, nf=281988, ne=422982, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 812.7 minutes
0 defective edges
removing intersecting faces
000: 1870 intersecting
001: 104 intersecting
002: 23 intersecting
003: 5 intersecting
004: 3 intersecting
expanding nbhd size to 2
005: 3 intersecting
expanding nbhd size to 3
006: 6 intersecting
expanding nbhd size to 4
007: 7 intersecting
mris_fix_topology utimesec    48371.060481
mris_fix_topology stimesec    2.247658
mris_fix_topology ru_maxrss   1140072
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   105088
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23144
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    755
mris_fix_topology ru_nivcsw   144880
FSRUNTIME@ mris_fix_topology lh 13.5442 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050017 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=-482 (nv=169524, nf=340012, ne=510018, g=242)
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...
53847 ambiguous faces found in tessellation
segmenting defects...
169 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 5 into 4
      -merging segment 10 into 4
      -merging segment 38 into 4
      -merging segment 32 into 19
      -merging segment 42 into 24
      -merging segment 41 into 37
      -merging segment 47 into 46
      -merging segment 81 into 61
      -merging segment 107 into 78
      -merging segment 109 into 78
      -merging segment 111 into 78
      -merging segment 124 into 78
      -merging segment 114 into 78
      -merging segment 122 into 116
      -merging segment 162 into 128
      -merging segment 147 into 142
      -merging segment 154 into 148
      -merging segment 156 into 148
      -merging segment 164 into 161
150 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -8.9206  (-4.4603)
      -vertex     loglikelihood: -6.0486  (-3.0243)
      -normal dot loglikelihood: -3.5303  (-3.5303)
      -quad curv  loglikelihood: -6.2155  (-3.1078)
      Total Loglikelihood : -24.7149

CORRECTING DEFECT 0 (vertices=924, convex hull=407, v0=8)
L defect detected...
After retessellation of defect 0 (v0=8), euler #=-143 (138798,407954,269013) : difference with theory (-147) = -4 

CORRECTING DEFECT 1 (vertices=54, convex hull=44, v0=127)
After retessellation of defect 1 (v0=127), euler #=-142 (138801,407982,269039) : difference with theory (-146) = -4 

CORRECTING DEFECT 2 (vertices=39, convex hull=63, v0=764)
After retessellation of defect 2 (v0=764), euler #=-141 (138811,408037,269085) : difference with theory (-145) = -4 

CORRECTING DEFECT 3 (vertices=107, convex hull=144, v0=802)
After retessellation of defect 3 (v0=802), euler #=-140 (138862,408249,269247) : difference with theory (-144) = -4 

CORRECTING DEFECT 4 (vertices=4663, convex hull=1368, v0=896)
XL defect detected...
After retessellation of defect 4 (v0=896), euler #=-147 (139858,412170,272165) : difference with theory (-143) = 4 

CORRECTING DEFECT 5 (vertices=335, convex hull=279, v0=2697)
After retessellation of defect 5 (v0=2697), euler #=-146 (140016,412776,272614) : difference with theory (-142) = 4 

CORRECTING DEFECT 6 (vertices=49, convex hull=101, v0=3723)
After retessellation of defect 6 (v0=3723), euler #=-145 (140044,412908,272719) : difference with theory (-141) = 4 

CORRECTING DEFECT 7 (vertices=76, convex hull=73, v0=5874)
After retessellation of defect 7 (v0=5874), euler #=-145 (140063,413002,272794) : difference with theory (-140) = 5 

CORRECTING DEFECT 8 (vertices=12, convex hull=25, v0=7198)
After retessellation of defect 8 (v0=7198), euler #=-144 (140064,413014,272806) : difference with theory (-139) = 5 

CORRECTING DEFECT 9 (vertices=53, convex hull=25, v0=9258)
After retessellation of defect 9 (v0=9258), euler #=-143 (140070,413038,272825) : difference with theory (-138) = 5 

CORRECTING DEFECT 10 (vertices=7, convex hull=19, v0=9561)
After retessellation of defect 10 (v0=9561), euler #=-142 (140071,413046,272833) : difference with theory (-137) = 5 

CORRECTING DEFECT 11 (vertices=20, convex hull=51, v0=11275)
After retessellation of defect 11 (v0=11275), euler #=-141 (140077,413082,272864) : difference with theory (-136) = 5 

CORRECTING DEFECT 12 (vertices=92, convex hull=141, v0=12954)
After retessellation of defect 12 (v0=12954), euler #=-140 (140141,413338,273057) : difference with theory (-135) = 5 

CORRECTING DEFECT 13 (vertices=6, convex hull=25, v0=14631)
After retessellation of defect 13 (v0=14631), euler #=-139 (140141,413345,273065) : difference with theory (-134) = 5 

CORRECTING DEFECT 14 (vertices=174, convex hull=153, v0=16184)
After retessellation of defect 14 (v0=16184), euler #=-138 (140220,413645,273287) : difference with theory (-133) = 5 

CORRECTING DEFECT 15 (vertices=96, convex hull=94, v0=17198)
After retessellation of defect 15 (v0=17198), euler #=-137 (140264,413821,273420) : difference with theory (-132) = 5 

CORRECTING DEFECT 16 (vertices=77, convex hull=86, v0=17687)
After retessellation of defect 16 (v0=17687), euler #=-136 (140288,413929,273505) : difference with theory (-131) = 5 

CORRECTING DEFECT 17 (vertices=275, convex hull=184, v0=19435)
After retessellation of defect 17 (v0=19435), euler #=-134 (140399,414355,273822) : difference with theory (-130) = 4 

CORRECTING DEFECT 18 (vertices=37, convex hull=75, v0=19570)
After retessellation of defect 18 (v0=19570), euler #=-133 (140416,414435,273886) : difference with theory (-129) = 4 

CORRECTING DEFECT 19 (vertices=27, convex hull=54, v0=20929)
After retessellation of defect 19 (v0=20929), euler #=-132 (140425,414483,273926) : difference with theory (-128) = 4 

CORRECTING DEFECT 20 (vertices=59, convex hull=47, v0=23845)
After retessellation of defect 20 (v0=23845), euler #=-131 (140439,414545,273975) : difference with theory (-127) = 4 

CORRECTING DEFECT 21 (vertices=109, convex hull=76, v0=23918)
After retessellation of defect 21 (v0=23918), euler #=-130 (140453,414625,274042) : difference with theory (-126) = 4 

CORRECTING DEFECT 22 (vertices=339, convex hull=285, v0=24321)
After retessellation of defect 22 (v0=24321), euler #=-128 (140617,415255,274510) : difference with theory (-125) = 3 

CORRECTING DEFECT 23 (vertices=24, convex hull=24, v0=25543)
After retessellation of defect 23 (v0=25543), euler #=-127 (140617,415264,274520) : difference with theory (-124) = 3 

CORRECTING DEFECT 24 (vertices=11, convex hull=22, v0=26721)
After retessellation of defect 24 (v0=26721), euler #=-126 (140620,415279,274533) : difference with theory (-123) = 3 

CORRECTING DEFECT 25 (vertices=60, convex hull=103, v0=27292)
After retessellation of defect 25 (v0=27292), euler #=-125 (140661,415447,274661) : difference with theory (-122) = 3 

CORRECTING DEFECT 26 (vertices=77, convex hull=98, v0=27946)
After retessellation of defect 26 (v0=27946), euler #=-124 (140709,415631,274798) : difference with theory (-121) = 3 

CORRECTING DEFECT 27 (vertices=135, convex hull=219, v0=28499)
After retessellation of defect 27 (v0=28499), euler #=-123 (140815,416054,275116) : difference with theory (-120) = 3 

CORRECTING DEFECT 28 (vertices=40, convex hull=76, v0=31077)
After retessellation of defect 28 (v0=31077), euler #=-122 (140835,416144,275187) : difference with theory (-119) = 3 

CORRECTING DEFECT 29 (vertices=60, convex hull=58, v0=31283)
After retessellation of defect 29 (v0=31283), euler #=-121 (140857,416231,275253) : difference with theory (-118) = 3 

CORRECTING DEFECT 30 (vertices=598, convex hull=455, v0=32846)
L defect detected...
After retessellation of defect 30 (v0=32846), euler #=-120 (141057,417057,275880) : difference with theory (-117) = 3 

CORRECTING DEFECT 31 (vertices=74, convex hull=50, v0=33183)
After retessellation of defect 31 (v0=33183), euler #=-119 (141068,417110,275923) : difference with theory (-116) = 3 

CORRECTING DEFECT 32 (vertices=38, convex hull=48, v0=33407)
After retessellation of defect 32 (v0=33407), euler #=-118 (141081,417164,275965) : difference with theory (-115) = 3 

CORRECTING DEFECT 33 (vertices=162, convex hull=130, v0=33574)
After retessellation of defect 33 (v0=33574), euler #=-117 (141144,417412,276151) : difference with theory (-114) = 3 

CORRECTING DEFECT 34 (vertices=291, convex hull=268, v0=34485)
After retessellation of defect 34 (v0=34485), euler #=-115 (141307,418027,276605) : difference with theory (-113) = 2 

CORRECTING DEFECT 35 (vertices=25, convex hull=33, v0=35489)
After retessellation of defect 35 (v0=35489), euler #=-114 (141312,418051,276625) : difference with theory (-112) = 2 

CORRECTING DEFECT 36 (vertices=99, convex hull=95, v0=36895)
After retessellation of defect 36 (v0=36895), euler #=-113 (141365,418250,276772) : difference with theory (-111) = 2 

CORRECTING DEFECT 37 (vertices=93, convex hull=103, v0=38745)
After retessellation of defect 37 (v0=38745), euler #=-112 (141418,418455,276925) : difference with theory (-110) = 2 

CORRECTING DEFECT 38 (vertices=21, convex hull=28, v0=40779)
After retessellation of defect 38 (v0=40779), euler #=-111 (141421,418470,276938) : difference with theory (-109) = 2 

CORRECTING DEFECT 39 (vertices=129, convex hull=103, v0=41831)
After retessellation of defect 39 (v0=41831), euler #=-110 (141493,418732,277129) : difference with theory (-108) = 2 

CORRECTING DEFECT 40 (vertices=366, convex hull=141, v0=43149)
After retessellation of defect 40 (v0=43149), euler #=-108 (141551,418977,277318) : difference with theory (-107) = 1 

CORRECTING DEFECT 41 (vertices=23, convex hull=40, v0=43413)
After retessellation of defect 41 (v0=43413), euler #=-107 (141560,419019,277352) : difference with theory (-106) = 1 

CORRECTING DEFECT 42 (vertices=57, convex hull=81, v0=45985)
After retessellation of defect 42 (v0=45985), euler #=-106 (141570,419078,277402) : difference with theory (-105) = 1 

CORRECTING DEFECT 43 (vertices=67, convex hull=90, v0=47160)
After retessellation of defect 43 (v0=47160), euler #=-106 (141611,419246,277529) : difference with theory (-104) = 2 

CORRECTING DEFECT 44 (vertices=171, convex hull=111, v0=48674)
After retessellation of defect 44 (v0=48674), euler #=-105 (141653,419426,277668) : difference with theory (-103) = 2 

CORRECTING DEFECT 45 (vertices=274, convex hull=179, v0=50079)
After retessellation of defect 45 (v0=50079), euler #=-104 (141725,419725,277896) : difference with theory (-102) = 2 

CORRECTING DEFECT 46 (vertices=26, convex hull=56, v0=51070)
After retessellation of defect 46 (v0=51070), euler #=-103 (141735,419775,277937) : difference with theory (-101) = 2 

CORRECTING DEFECT 47 (vertices=21, convex hull=63, v0=57106)
After retessellation of defect 47 (v0=57106), euler #=-102 (141744,419827,277981) : difference with theory (-100) = 2 

CORRECTING DEFECT 48 (vertices=41, convex hull=76, v0=58416)
After retessellation of defect 48 (v0=58416), euler #=-101 (141769,419934,278064) : difference with theory (-99) = 2 

CORRECTING DEFECT 49 (vertices=2055, convex hull=668, v0=60146)
XL defect detected...
After retessellation of defect 49 (v0=60146), euler #=-100 (142025,421057,278932) : difference with theory (-98) = 2 

CORRECTING DEFECT 50 (vertices=38, convex hull=54, v0=61273)
After retessellation of defect 50 (v0=61273), euler #=-99 (142046,421138,278993) : difference with theory (-97) = 2 

CORRECTING DEFECT 51 (vertices=15, convex hull=23, v0=64071)
After retessellation of defect 51 (v0=64071), euler #=-98 (142048,421154,279008) : difference with theory (-96) = 2 

CORRECTING DEFECT 52 (vertices=19, convex hull=22, v0=64786)
After retessellation of defect 52 (v0=64786), euler #=-97 (142050,421166,279019) : difference with theory (-95) = 2 

CORRECTING DEFECT 53 (vertices=52, convex hull=53, v0=65886)
After retessellation of defect 53 (v0=65886), euler #=-96 (142055,421198,279047) : difference with theory (-94) = 2 

CORRECTING DEFECT 54 (vertices=1392, convex hull=463, v0=67539)
L defect detected...
After retessellation of defect 54 (v0=67539), euler #=-94 (142380,422410,279936) : difference with theory (-93) = 1 

CORRECTING DEFECT 55 (vertices=20, convex hull=24, v0=67939)
After retessellation of defect 55 (v0=67939), euler #=-93 (142383,422424,279948) : difference with theory (-92) = 1 

CORRECTING DEFECT 56 (vertices=54, convex hull=37, v0=69229)
After retessellation of defect 56 (v0=69229), euler #=-92 (142388,422454,279974) : difference with theory (-91) = 1 

CORRECTING DEFECT 57 (vertices=11, convex hull=21, v0=70227)
After retessellation of defect 57 (v0=70227), euler #=-91 (142389,422462,279982) : difference with theory (-90) = 1 

CORRECTING DEFECT 58 (vertices=48, convex hull=22, v0=71050)
After retessellation of defect 58 (v0=71050), euler #=-90 (142397,422495,280008) : difference with theory (-89) = 1 

CORRECTING DEFECT 59 (vertices=298, convex hull=363, v0=71123)
After retessellation of defect 59 (v0=71123), euler #=-90 (142550,423136,280496) : difference with theory (-88) = 2 

CORRECTING DEFECT 60 (vertices=44, convex hull=96, v0=71391)
After retessellation of defect 60 (v0=71391), euler #=-89 (142561,423211,280561) : difference with theory (-87) = 2 

CORRECTING DEFECT 61 (vertices=94, convex hull=52, v0=71636)
After retessellation of defect 61 (v0=71636), euler #=-88 (142568,423252,280596) : difference with theory (-86) = 2 

CORRECTING DEFECT 62 (vertices=23, convex hull=36, v0=72409)
After retessellation of defect 62 (v0=72409), euler #=-87 (142575,423286,280624) : difference with theory (-85) = 2 

CORRECTING DEFECT 63 (vertices=25, convex hull=44, v0=72413)
After retessellation of defect 63 (v0=72413), euler #=-86 (142589,423344,280669) : difference with theory (-84) = 2 

CORRECTING DEFECT 64 (vertices=579, convex hull=506, v0=74943)
L defect detected...
After retessellation of defect 64 (v0=74943), euler #=-85 (142824,424293,281384) : difference with theory (-83) = 2 

CORRECTING DEFECT 65 (vertices=11, convex hull=38, v0=77210)
After retessellation of defect 65 (v0=77210), euler #=-84 (142824,424307,281399) : difference with theory (-82) = 2 

CORRECTING DEFECT 66 (vertices=210, convex hull=133, v0=78443)
After retessellation of defect 66 (v0=78443), euler #=-83 (142873,424517,281561) : difference with theory (-81) = 2 

CORRECTING DEFECT 67 (vertices=282, convex hull=193, v0=79567)
After retessellation of defect 67 (v0=79567), euler #=-82 (142936,424797,281779) : difference with theory (-80) = 2 

CORRECTING DEFECT 68 (vertices=6, convex hull=38, v0=81958)
After retessellation of defect 68 (v0=81958), euler #=-81 (142939,424816,281796) : difference with theory (-79) = 2 

CORRECTING DEFECT 69 (vertices=28, convex hull=27, v0=82324)
After retessellation of defect 69 (v0=82324), euler #=-80 (142939,424826,281807) : difference with theory (-78) = 2 

CORRECTING DEFECT 70 (vertices=166, convex hull=113, v0=82413)
After retessellation of defect 70 (v0=82413), euler #=-79 (143002,425069,281988) : difference with theory (-77) = 2 

CORRECTING DEFECT 71 (vertices=6952, convex hull=2186, v0=83430)
XL defect detected...
After retessellation of defect 71 (v0=83430), euler #=-77 (143821,428755,284857) : difference with theory (-76) = 1 

CORRECTING DEFECT 72 (vertices=75, convex hull=78, v0=83988)
After retessellation of defect 72 (v0=83988), euler #=-76 (143856,428891,284959) : difference with theory (-75) = 1 

CORRECTING DEFECT 73 (vertices=8, convex hull=24, v0=89674)
After retessellation of defect 73 (v0=89674), euler #=-75 (143857,428900,284968) : difference with theory (-74) = 1 

CORRECTING DEFECT 74 (vertices=213, convex hull=130, v0=92901)
After retessellation of defect 74 (v0=92901), euler #=-74 (143898,429087,285115) : difference with theory (-73) = 1 

CORRECTING DEFECT 75 (vertices=67, convex hull=28, v0=93295)
After retessellation of defect 75 (v0=93295), euler #=-73 (143904,429113,285136) : difference with theory (-72) = 1 

CORRECTING DEFECT 76 (vertices=6, convex hull=34, v0=94210)
After retessellation of defect 76 (v0=94210), euler #=-72 (143907,429133,285154) : difference with theory (-71) = 1 

CORRECTING DEFECT 77 (vertices=5, convex hull=22, v0=94972)
After retessellation of defect 77 (v0=94972), euler #=-71 (143907,429139,285161) : difference with theory (-70) = 1 

CORRECTING DEFECT 78 (vertices=49, convex hull=19, v0=98230)
After retessellation of defect 78 (v0=98230), euler #=-70 (143911,429156,285175) : difference with theory (-69) = 1 

CORRECTING DEFECT 79 (vertices=30, convex hull=73, v0=98457)
After retessellation of defect 79 (v0=98457), euler #=-69 (143929,429239,285241) : difference with theory (-68) = 1 

CORRECTING DEFECT 80 (vertices=24, convex hull=61, v0=100521)
After retessellation of defect 80 (v0=100521), euler #=-69 (143941,429301,285291) : difference with theory (-67) = 2 

CORRECTING DEFECT 81 (vertices=99, convex hull=90, v0=101937)
After retessellation of defect 81 (v0=101937), euler #=-68 (143983,429468,285417) : difference with theory (-66) = 2 

CORRECTING DEFECT 82 (vertices=26, convex hull=45, v0=108220)
After retessellation of defect 82 (v0=108220), euler #=-67 (143996,429523,285460) : difference with theory (-65) = 2 

CORRECTING DEFECT 83 (vertices=32, convex hull=61, v0=109092)
After retessellation of defect 83 (v0=109092), euler #=-66 (144010,429584,285508) : difference with theory (-64) = 2 

CORRECTING DEFECT 84 (vertices=84, convex hull=147, v0=109769)
After retessellation of defect 84 (v0=109769), euler #=-65 (144069,429828,285694) : difference with theory (-63) = 2 

CORRECTING DEFECT 85 (vertices=5, convex hull=24, v0=110319)
After retessellation of defect 85 (v0=110319), euler #=-64 (144069,429833,285700) : difference with theory (-62) = 2 

CORRECTING DEFECT 86 (vertices=328, convex hull=94, v0=110346)
After retessellation of defect 86 (v0=110346), euler #=-63 (144101,429968,285804) : difference with theory (-61) = 2 

CORRECTING DEFECT 87 (vertices=67, convex hull=38, v0=112744)
After retessellation of defect 87 (v0=112744), euler #=-62 (144109,430005,285834) : difference with theory (-60) = 2 

CORRECTING DEFECT 88 (vertices=54, convex hull=64, v0=112858)
After retessellation of defect 88 (v0=112858), euler #=-61 (144134,430104,285909) : difference with theory (-59) = 2 

CORRECTING DEFECT 89 (vertices=86, convex hull=39, v0=113964)
After retessellation of defect 89 (v0=113964), euler #=-60 (144140,430139,285939) : difference with theory (-58) = 2 

CORRECTING DEFECT 90 (vertices=60, convex hull=69, v0=114066)
After retessellation of defect 90 (v0=114066), euler #=-59 (144161,430233,286013) : difference with theory (-57) = 2 

CORRECTING DEFECT 91 (vertices=20, convex hull=28, v0=114119)
After retessellation of defect 91 (v0=114119), euler #=-58 (144162,430247,286027) : difference with theory (-56) = 2 

CORRECTING DEFECT 92 (vertices=74, convex hull=80, v0=114159)
After retessellation of defect 92 (v0=114159), euler #=-57 (144205,430412,286150) : difference with theory (-55) = 2 

CORRECTING DEFECT 93 (vertices=16, convex hull=56, v0=116160)
After retessellation of defect 93 (v0=116160), euler #=-56 (144215,430460,286189) : difference with theory (-54) = 2 

CORRECTING DEFECT 94 (vertices=33, convex hull=67, v0=116742)
After retessellation of defect 94 (v0=116742), euler #=-55 (144234,430545,286256) : difference with theory (-53) = 2 

CORRECTING DEFECT 95 (vertices=157, convex hull=137, v0=117071)
After retessellation of defect 95 (v0=117071), euler #=-54 (144305,430820,286461) : difference with theory (-52) = 2 

CORRECTING DEFECT 96 (vertices=196, convex hull=152, v0=117353)
After retessellation of defect 96 (v0=117353), euler #=-55 (144330,430974,286589) : difference with theory (-51) = 4 

CORRECTING DEFECT 97 (vertices=25, convex hull=45, v0=118011)
After retessellation of defect 97 (v0=118011), euler #=-54 (144339,431019,286626) : difference with theory (-50) = 4 

CORRECTING DEFECT 98 (vertices=116, convex hull=127, v0=118123)
After retessellation of defect 98 (v0=118123), euler #=-53 (144401,431258,286804) : difference with theory (-49) = 4 

CORRECTING DEFECT 99 (vertices=22, convex hull=32, v0=120412)
After retessellation of defect 99 (v0=120412), euler #=-52 (144405,431281,286824) : difference with theory (-48) = 4 

CORRECTING DEFECT 100 (vertices=574, convex hull=238, v0=122899)
After retessellation of defect 100 (v0=122899), euler #=-52 (144595,431974,287327) : difference with theory (-47) = 5 

CORRECTING DEFECT 101 (vertices=197, convex hull=74, v0=125693)
After retessellation of defect 101 (v0=125693), euler #=-51 (144622,432082,287409) : difference with theory (-46) = 5 

CORRECTING DEFECT 102 (vertices=26, convex hull=27, v0=126419)
After retessellation of defect 102 (v0=126419), euler #=-50 (144627,432104,287427) : difference with theory (-45) = 5 

CORRECTING DEFECT 103 (vertices=18, convex hull=21, v0=127146)
After retessellation of defect 103 (v0=127146), euler #=-49 (144627,432112,287436) : difference with theory (-44) = 5 

CORRECTING DEFECT 104 (vertices=153, convex hull=141, v0=127514)
After retessellation of defect 104 (v0=127514), euler #=-47 (144654,432257,287556) : difference with theory (-43) = 4 

CORRECTING DEFECT 105 (vertices=260, convex hull=82, v0=129214)
After retessellation of defect 105 (v0=129214), euler #=-46 (144682,432377,287649) : difference with theory (-42) = 4 

CORRECTING DEFECT 106 (vertices=201, convex hull=167, v0=131486)
After retessellation of defect 106 (v0=131486), euler #=-45 (144747,432646,287854) : difference with theory (-41) = 4 

CORRECTING DEFECT 107 (vertices=76, convex hull=95, v0=132851)
After retessellation of defect 107 (v0=132851), euler #=-44 (144777,432776,287955) : difference with theory (-40) = 4 

CORRECTING DEFECT 108 (vertices=403, convex hull=97, v0=133165)
After retessellation of defect 108 (v0=133165), euler #=-43 (144827,432974,288104) : difference with theory (-39) = 4 

CORRECTING DEFECT 109 (vertices=21, convex hull=41, v0=134262)
After retessellation of defect 109 (v0=134262), euler #=-42 (144840,433027,288145) : difference with theory (-38) = 4 

CORRECTING DEFECT 110 (vertices=77, convex hull=54, v0=134371)
After retessellation of defect 110 (v0=134371), euler #=-41 (144852,433082,288189) : difference with theory (-37) = 4 

CORRECTING DEFECT 111 (vertices=37, convex hull=31, v0=138014)
After retessellation of defect 111 (v0=138014), euler #=-40 (144859,433112,288213) : difference with theory (-36) = 4 

CORRECTING DEFECT 112 (vertices=7, convex hull=23, v0=138834)
After retessellation of defect 112 (v0=138834), euler #=-39 (144860,433121,288222) : difference with theory (-35) = 4 

CORRECTING DEFECT 113 (vertices=27, convex hull=71, v0=139508)
After retessellation of defect 113 (v0=139508), euler #=-38 (144874,433190,288278) : difference with theory (-34) = 4 

CORRECTING DEFECT 114 (vertices=1309, convex hull=448, v0=140329)
L defect detected...
After retessellation of defect 114 (v0=140329), euler #=-36 (145051,433974,288887) : difference with theory (-33) = 3 

CORRECTING DEFECT 115 (vertices=30, convex hull=78, v0=140941)
After retessellation of defect 115 (v0=140941), euler #=-35 (145069,434060,288956) : difference with theory (-32) = 3 

CORRECTING DEFECT 116 (vertices=76, convex hull=103, v0=141294)
After retessellation of defect 116 (v0=141294), euler #=-34 (145111,434229,289084) : difference with theory (-31) = 3 

CORRECTING DEFECT 117 (vertices=236, convex hull=119, v0=141803)
After retessellation of defect 117 (v0=141803), euler #=-33 (145156,434415,289226) : difference with theory (-30) = 3 

CORRECTING DEFECT 118 (vertices=13, convex hull=35, v0=145573)
After retessellation of defect 118 (v0=145573), euler #=-32 (145157,434429,289240) : difference with theory (-29) = 3 

CORRECTING DEFECT 119 (vertices=59, convex hull=33, v0=146935)
After retessellation of defect 119 (v0=146935), euler #=-31 (145160,434449,289258) : difference with theory (-28) = 3 

CORRECTING DEFECT 120 (vertices=41, convex hull=78, v0=147623)
After retessellation of defect 120 (v0=147623), euler #=-30 (145180,434540,289330) : difference with theory (-27) = 3 

CORRECTING DEFECT 121 (vertices=37, convex hull=92, v0=148681)
After retessellation of defect 121 (v0=148681), euler #=-29 (145203,434648,289416) : difference with theory (-26) = 3 

CORRECTING DEFECT 122 (vertices=59, convex hull=27, v0=149855)
After retessellation of defect 122 (v0=149855), euler #=-28 (145207,434667,289432) : difference with theory (-25) = 3 

CORRECTING DEFECT 123 (vertices=40, convex hull=59, v0=152475)
After retessellation of defect 123 (v0=152475), euler #=-27 (145216,434717,289474) : difference with theory (-24) = 3 

CORRECTING DEFECT 124 (vertices=52, convex hull=53, v0=152949)
After retessellation of defect 124 (v0=152949), euler #=-26 (145219,434747,289502) : difference with theory (-23) = 3 

CORRECTING DEFECT 125 (vertices=102, convex hull=119, v0=153140)
After retessellation of defect 125 (v0=153140), euler #=-25 (145273,434963,289665) : difference with theory (-22) = 3 

CORRECTING DEFECT 126 (vertices=57, convex hull=100, v0=154812)
After retessellation of defect 126 (v0=154812), euler #=-24 (145301,435087,289762) : difference with theory (-21) = 3 

CORRECTING DEFECT 127 (vertices=51, convex hull=91, v0=155511)
After retessellation of defect 127 (v0=155511), euler #=-23 (145328,435209,289858) : difference with theory (-20) = 3 

CORRECTING DEFECT 128 (vertices=184, convex hull=177, v0=156506)
After retessellation of defect 128 (v0=156506), euler #=-22 (145402,435534,290110) : difference with theory (-19) = 3 

CORRECTING DEFECT 129 (vertices=35, convex hull=59, v0=156748)
After retessellation of defect 129 (v0=156748), euler #=-21 (145420,435612,290171) : difference with theory (-18) = 3 

CORRECTING DEFECT 130 (vertices=27, convex hull=29, v0=156834)
After retessellation of defect 130 (v0=156834), euler #=-20 (145422,435627,290185) : difference with theory (-17) = 3 

CORRECTING DEFECT 131 (vertices=37, convex hull=97, v0=157352)
After retessellation of defect 131 (v0=157352), euler #=-19 (145444,435731,290268) : difference with theory (-16) = 3 

CORRECTING DEFECT 132 (vertices=23, convex hull=71, v0=158172)
After retessellation of defect 132 (v0=158172), euler #=-18 (145455,435797,290324) : difference with theory (-15) = 3 

CORRECTING DEFECT 133 (vertices=316, convex hull=219, v0=159770)
After retessellation of defect 133 (v0=159770), euler #=-15 (145542,436174,290617) : difference with theory (-14) = 1 

CORRECTING DEFECT 134 (vertices=138, convex hull=102, v0=159917)
After retessellation of defect 134 (v0=159917), euler #=-14 (145570,436305,290721) : difference with theory (-13) = 1 

CORRECTING DEFECT 135 (vertices=61, convex hull=22, v0=160269)
After retessellation of defect 135 (v0=160269), euler #=-13 (145573,436322,290736) : difference with theory (-12) = 1 

CORRECTING DEFECT 136 (vertices=6, convex hull=33, v0=160840)
After retessellation of defect 136 (v0=160840), euler #=-12 (145574,436336,290750) : difference with theory (-11) = 1 

CORRECTING DEFECT 137 (vertices=15, convex hull=28, v0=161113)
After retessellation of defect 137 (v0=161113), euler #=-11 (145576,436352,290765) : difference with theory (-10) = 1 

CORRECTING DEFECT 138 (vertices=171, convex hull=111, v0=162067)
After retessellation of defect 138 (v0=162067), euler #=-10 (145620,436530,290900) : difference with theory (-9) = 1 

CORRECTING DEFECT 139 (vertices=31, convex hull=68, v0=163224)
After retessellation of defect 139 (v0=163224), euler #=-9 (145634,436601,290958) : difference with theory (-8) = 1 

CORRECTING DEFECT 140 (vertices=28, convex hull=38, v0=163928)
After retessellation of defect 140 (v0=163928), euler #=-8 (145636,436623,290979) : difference with theory (-7) = 1 

CORRECTING DEFECT 141 (vertices=8, convex hull=27, v0=164696)
After retessellation of defect 141 (v0=164696), euler #=-7 (145636,436630,290987) : difference with theory (-6) = 1 

CORRECTING DEFECT 142 (vertices=36, convex hull=71, v0=165083)
After retessellation of defect 142 (v0=165083), euler #=-6 (145658,436723,291059) : difference with theory (-5) = 1 

CORRECTING DEFECT 143 (vertices=170, convex hull=121, v0=165219)
After retessellation of defect 143 (v0=165219), euler #=-5 (145691,436874,291178) : difference with theory (-4) = 1 

CORRECTING DEFECT 144 (vertices=258, convex hull=191, v0=165821)
After retessellation of defect 144 (v0=165821), euler #=-3 (145771,437215,291441) : difference with theory (-3) = 0 

CORRECTING DEFECT 145 (vertices=42, convex hull=80, v0=166101)
After retessellation of defect 145 (v0=166101), euler #=-2 (145793,437315,291520) : difference with theory (-2) = 0 

CORRECTING DEFECT 146 (vertices=42, convex hull=44, v0=168239)
After retessellation of defect 146 (v0=168239), euler #=-1 (145800,437352,291551) : difference with theory (-1) = 0 

CORRECTING DEFECT 147 (vertices=28, convex hull=30, v0=168990)
After retessellation of defect 147 (v0=168990), euler #=0 (145802,437366,291564) : difference with theory (0) = 0 

CORRECTING DEFECT 148 (vertices=39, convex hull=52, v0=169022)
After retessellation of defect 148 (v0=169022), euler #=1 (145818,437436,291619) : difference with theory (1) = 0 

CORRECTING DEFECT 149 (vertices=37, convex hull=37, v0=169131)
After retessellation of defect 149 (v0=169131), euler #=2 (145822,437460,291640) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.91 +- 0.37 (0.04-->31.29) (max @ vno 88556 --> 113803)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.91 +- 0.37 (0.04-->31.29) (max @ vno 88556 --> 113803)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
422 mutations (35.9%), 753 crossovers (64.1%), 1964 vertices were eliminated
building final representation...
23702 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=145822, nf=291640, ne=437460, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 433.4 minutes
0 defective edges
removing intersecting faces
000: 2132 intersecting
001: 131 intersecting
002: 12 intersecting
003: 4 intersecting
expanding nbhd size to 2
004: 7 intersecting
005: 4 intersecting
006: 2 intersecting
mris_fix_topology utimesec    25606.375239
mris_fix_topology stimesec    1.774730
mris_fix_topology ru_maxrss   882820
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   173717
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23472
mris_fix_topology ru_oublock  15096
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    582
mris_fix_topology ru_nivcsw   73107
FSRUNTIME@ mris_fix_topology rh  7.2237 hours 1 threads
PIDs (18164 18167) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 140996 - 422982 + 281988 = 2 --> 0 holes
      F =2V-4:          281988 = 281992-4 (0)
      2E=3F:            845964 = 845964 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 145822 - 437460 + 291640 = 2 --> 0 holes
      F =2V-4:          291640 = 291644-4 (0)
      2E=3F:            874920 = 874920 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 604 intersecting
001: 38 intersecting
002: 15 intersecting
expanding nbhd size to 2
003: 16 intersecting
004: 5 intersecting
005: 2 intersecting
expanding nbhd size to 3
006: 3 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 558 intersecting
001: 61 intersecting
002: 14 intersecting
003: 6 intersecting
004: 4 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 12:09:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050017 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 12:09:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050017 rh 

Waiting for PID 29976 of (29976 29979) to complete...
Waiting for PID 29979 of (29976 29979) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050017 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-6.0.0/0050017/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
18499 bright wm thresholded.
612 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.orig...
computing class statistics...
border white:    300590 voxels (1.79%)
border gray      366883 voxels (2.19%)
WM (94.0): 94.6 +- 8.0 [70.0 --> 110.0]
GM (72.0) : 71.1 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70)
setting MAX_BORDER_WHITE to 105.0 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 49.3 (was 40)
setting MAX_GRAY to 89.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.27 (0.03-->10.30) (max @ vno 94608 --> 138851)
face area 0.28 +- 0.16 (0.00-->11.23)
mean absolute distance = 0.74 +- 0.94
3993 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=97+-6.1,    GM=70+-7.0
mean inside = 90.8, mean outside = 75.8
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=81.0, 304 (304) missing vertices, mean dist 0.2 [0.7 (%39.4)->0.8 (%60.6))]
%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 0.92 +- 0.29 (0.04-->9.79) (max @ vno 94608 --> 138851)
face area 0.28 +- 0.16 (0.00-->8.70)
mean absolute distance = 0.41 +- 0.73
5048 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2577439.8, rms=8.424
001: dt: 0.5000, sse=1539327.6, rms=5.995 (28.829%)
002: dt: 0.5000, sse=1122845.6, rms=4.531 (24.423%)
003: dt: 0.5000, sse=950111.3, rms=3.778 (16.624%)
004: dt: 0.5000, sse=879623.7, rms=3.425 (9.326%)
005: dt: 0.5000, sse=851988.2, rms=3.270 (4.527%)
006: dt: 0.5000, sse=839901.0, rms=3.202 (2.080%)
rms = 3.16, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=834527.9, rms=3.163 (1.212%)
008: dt: 0.2500, sse=725189.9, rms=2.342 (25.971%)
009: dt: 0.2500, sse=705660.4, rms=2.175 (7.113%)
rms = 2.14, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=702585.6, rms=2.140 (1.613%)
rms = 2.11, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=697668.2, rms=2.107 (1.556%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.0, 413 (101) missing vertices, mean dist -0.2 [0.5 (%62.2)->0.3 (%37.8))]
%70 local maxima, %25 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 +- 0.29 (0.06-->9.69) (max @ vno 94608 --> 138851)
face area 0.35 +- 0.20 (0.00-->11.13)
mean absolute distance = 0.35 +- 0.53
4822 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1073074.1, rms=3.605
012: dt: 0.5000, sse=929255.4, rms=2.626 (27.177%)
013: dt: 0.5000, sse=888918.1, rms=2.530 (3.623%)
rms = 2.60, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=840511.1, rms=2.102 (16.920%)
015: dt: 0.2500, sse=821446.6, rms=1.893 (9.944%)
rms = 1.85, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=824781.6, rms=1.850 (2.284%)
rms = 1.82, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=811607.4, rms=1.819 (1.700%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=84.4, 490 (66) missing vertices, mean dist -0.1 [0.4 (%58.9)->0.3 (%41.1))]
%77 local maxima, %18 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 +- 0.29 (0.03-->9.59) (max @ vno 94608 --> 138851)
face area 0.34 +- 0.20 (0.00-->11.21)
mean absolute distance = 0.32 +- 0.44
3969 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=910984.3, rms=2.723
018: dt: 0.5000, sse=869885.3, rms=2.233 (17.981%)
rms = 2.26, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=810459.4, rms=1.892 (15.288%)
020: dt: 0.2500, sse=799428.4, rms=1.718 (9.215%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=791730.0, rms=1.676 (2.439%)
rms = 1.65, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=783817.9, rms=1.645 (1.806%)
positioning took 0.6 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 3 vertex label from ripped group
mean border=85.2, 569 (50) missing vertices, mean dist -0.1 [0.4 (%53.3)->0.3 (%46.7))]
%82 local maxima, %13 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-6.0.0/0050017/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=807104.3, rms=1.953
023: dt: 0.5000, sse=822241.5, rms=1.673 (14.338%)
rms = 2.02, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=773631.4, rms=1.411 (15.702%)
025: dt: 0.2500, sse=767515.6, rms=1.350 (4.278%)
rms = 1.31, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=752892.7, rms=1.308 (3.108%)
rms = 1.29, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=744553.6, rms=1.294 (1.061%)
positioning took 0.6 minutes
generating cortex label...
16 non-cortical segments detected
only using segment with 6918 vertices
erasing segment 0 (vno[0] = 26174)
erasing segment 1 (vno[0] = 27210)
erasing segment 2 (vno[0] = 28312)
erasing segment 3 (vno[0] = 50056)
erasing segment 5 (vno[0] = 59450)
erasing segment 6 (vno[0] = 59467)
erasing segment 7 (vno[0] = 76363)
erasing segment 8 (vno[0] = 96777)
erasing segment 9 (vno[0] = 98603)
erasing segment 10 (vno[0] = 99516)
erasing segment 11 (vno[0] = 101520)
erasing segment 12 (vno[0] = 103289)
erasing segment 13 (vno[0] = 103305)
erasing segment 14 (vno[0] = 105119)
erasing segment 15 (vno[0] = 139875)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.area
vertex spacing 0.90 +- 0.29 (0.04-->9.53) (max @ vno 94608 --> 138851)
face area 0.34 +- 0.20 (0.00-->11.59)
refinement took 4.7 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050017 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-6.0.0/0050017/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
18499 bright wm thresholded.
612 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.orig...
computing class statistics...
border white:    300590 voxels (1.79%)
border gray      366883 voxels (2.19%)
WM (94.0): 94.6 +- 8.0 [70.0 --> 110.0]
GM (72.0) : 71.1 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70)
setting MAX_BORDER_WHITE to 106.0 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 49.3 (was 40)
setting MAX_GRAY to 90.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.28 (0.02-->12.49) (max @ vno 88556 --> 113803)
face area 0.28 +- 0.18 (0.00-->15.07)
mean absolute distance = 0.72 +- 0.93
3934 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=98+-7.0,    GM=70+-7.0
mean inside = 91.0, mean outside = 76.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=81.2, 236 (236) missing vertices, mean dist 0.2 [0.7 (%38.8)->0.7 (%61.2))]
%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 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.30 (0.05-->11.98) (max @ vno 88556 --> 113803)
face area 0.28 +- 0.17 (0.00-->11.13)
mean absolute distance = 0.40 +- 0.70
4878 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2591885.5, rms=8.333
001: dt: 0.5000, sse=1560179.5, rms=5.887 (29.353%)
002: dt: 0.5000, sse=1130329.6, rms=4.402 (25.216%)
003: dt: 0.5000, sse=960304.6, rms=3.634 (17.445%)
004: dt: 0.5000, sse=901602.0, rms=3.286 (9.578%)
005: dt: 0.5000, sse=863698.1, rms=3.146 (4.275%)
006: dt: 0.5000, sse=852507.1, rms=3.080 (2.086%)
rms = 3.05, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=856014.2, rms=3.049 (1.009%)
008: dt: 0.2500, sse=739473.8, rms=2.206 (27.639%)
009: dt: 0.2500, sse=720271.4, rms=2.039 (7.574%)
rms = 2.01, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=717263.6, rms=2.012 (1.355%)
rms = 1.98, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=713502.5, rms=1.983 (1.405%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.0, 302 (52) missing vertices, mean dist -0.2 [0.5 (%61.2)->0.3 (%38.8))]
%71 local maxima, %24 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 +- 0.30 (0.08-->11.77) (max @ vno 88556 --> 113803)
face area 0.35 +- 0.21 (0.00-->13.63)
mean absolute distance = 0.35 +- 0.52
4817 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1092109.5, rms=3.510
012: dt: 0.5000, sse=927923.5, rms=2.510 (28.490%)
013: dt: 0.5000, sse=912733.7, rms=2.403 (4.247%)
rms = 2.50, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=858110.2, rms=1.977 (17.722%)
015: dt: 0.2500, sse=839092.4, rms=1.779 (10.042%)
rms = 1.74, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=833464.4, rms=1.743 (2.033%)
rms = 1.71, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=828854.6, rms=1.715 (1.588%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=84.4, 326 (33) missing vertices, mean dist -0.1 [0.4 (%57.9)->0.3 (%42.1))]
%77 local maxima, %17 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 +- 0.30 (0.05-->11.72) (max @ vno 88556 --> 113803)
face area 0.35 +- 0.21 (0.00-->13.92)
mean absolute distance = 0.33 +- 0.45
4197 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=929385.0, rms=2.618
018: dt: 0.5000, sse=905390.2, rms=2.131 (18.611%)
rms = 2.17, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=831268.8, rms=1.798 (15.620%)
020: dt: 0.2500, sse=822229.1, rms=1.626 (9.563%)
rms = 1.59, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=809633.1, rms=1.589 (2.279%)
rms = 1.56, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=814567.7, rms=1.558 (1.957%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=85.2, 414 (28) missing vertices, mean dist -0.1 [0.4 (%53.1)->0.3 (%46.9))]
%82 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-6.0.0/0050017/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=844507.6, rms=1.924
023: dt: 0.5000, sse=820673.0, rms=1.601 (16.801%)
rms = 1.95, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=783681.9, rms=1.329 (17.013%)
025: dt: 0.2500, sse=776508.5, rms=1.273 (4.185%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=773808.1, rms=1.229 (3.458%)
rms = 1.22, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=769530.8, rms=1.217 (0.932%)
positioning took 0.6 minutes
generating cortex label...
22 non-cortical segments detected
only using segment with 7740 vertices
erasing segment 0 (vno[0] = 37680)
erasing segment 1 (vno[0] = 38782)
erasing segment 2 (vno[0] = 40059)
erasing segment 3 (vno[0] = 42399)
erasing segment 4 (vno[0] = 46708)
erasing segment 6 (vno[0] = 58527)
erasing segment 7 (vno[0] = 59662)
erasing segment 8 (vno[0] = 62027)
erasing segment 9 (vno[0] = 68155)
erasing segment 10 (vno[0] = 69642)
erasing segment 11 (vno[0] = 93187)
erasing segment 12 (vno[0] = 97113)
erasing segment 13 (vno[0] = 100425)
erasing segment 14 (vno[0] = 101437)
erasing segment 15 (vno[0] = 102420)
erasing segment 16 (vno[0] = 103491)
erasing segment 17 (vno[0] = 105210)
erasing segment 18 (vno[0] = 107015)
erasing segment 19 (vno[0] = 107073)
erasing segment 20 (vno[0] = 141786)
erasing segment 21 (vno[0] = 144220)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.area
vertex spacing 0.90 +- 0.30 (0.05-->11.69) (max @ vno 88556 --> 113803)
face area 0.34 +- 0.21 (0.00-->14.46)
refinement took 4.9 minutes
PIDs (29976 29979) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 12:13:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 12:13:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

Waiting for PID 30194 of (30194 30197) to complete...
Waiting for PID 30197 of (30194 30197) 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 (30194 30197) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 12:14:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 12:14:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 30240 of (30240 30243) to complete...
Waiting for PID 30243 of (30240 30243) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.4 mm, total surface area = 84609 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.197 (target=0.015)   
step 005: RMS=0.140 (target=0.015)   
step 010: RMS=0.112 (target=0.015)   
step 015: RMS=0.095 (target=0.015)   
step 020: RMS=0.081 (target=0.015)   
step 025: RMS=0.069 (target=0.015)   
step 030: RMS=0.060 (target=0.015)   
step 035: RMS=0.052 (target=0.015)   
step 040: RMS=0.046 (target=0.015)   
step 045: RMS=0.041 (target=0.015)   
step 050: RMS=0.038 (target=0.015)   
step 055: RMS=0.036 (target=0.015)   
step 060: RMS=0.035 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    42.495539
mris_inflate stimesec    0.092985
mris_inflate ru_maxrss   208164
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30647
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  9920
mris_inflate ru_oublock  11040
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    6152
mris_inflate ru_nivcsw   5036

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 49.0 mm, total surface area = 88141 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.195 (target=0.015)   
step 005: RMS=0.139 (target=0.015)   
step 010: RMS=0.111 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.081 (target=0.015)   
step 025: RMS=0.069 (target=0.015)   
step 030: RMS=0.059 (target=0.015)   
step 035: RMS=0.051 (target=0.015)   
step 040: RMS=0.045 (target=0.015)   
step 045: RMS=0.040 (target=0.015)   
step 050: RMS=0.036 (target=0.015)   
step 055: RMS=0.034 (target=0.015)   
step 060: RMS=0.033 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    44.559225
mris_inflate stimesec    0.122981
mris_inflate ru_maxrss   215368
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31425
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11424
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5858
mris_inflate ru_nivcsw   5139
PIDs (30240 30243) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 12:14:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 12:14:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 30350 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30353 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30356 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30359 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30362 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30365 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30368 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30371 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30374 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30377 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30381 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...
Waiting for PID 30385 of (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 34.270*4pi (430.643) --> -33 handles
ICI = 308.5, FI = 1986.4, variation=35235.977
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
158 vertices thresholded to be in k1 ~ [-0.32 0.46], k2 ~ [-0.16 0.11]
total integrated curvature = 0.073*4pi (0.919) --> 1 handles
ICI = 1.3, FI = 8.8, variation=156.627
138 vertices thresholded to be in [-0.03 0.03]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
137 vertices thresholded to be in [-0.18 0.20]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 28.232*4pi (354.768) --> -27 handles
ICI = 310.6, FI = 2040.8, variation=36095.537
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
202 vertices thresholded to be in k1 ~ [-0.26 0.79], k2 ~ [-0.14 0.14]
total integrated curvature = 0.165*4pi (2.069) --> 1 handles
ICI = 1.3, FI = 9.2, variation=157.245
164 vertices thresholded to be in [-0.05 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
132 vertices thresholded to be in [-0.15 0.33]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023
done.
PIDs (30350 30353 30356 30359 30362 30365 30368 30371 30374 30377 30381 30385) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 12:16:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050017 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      [ 0050017/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                      [ 315 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.512018
WARN:    S explicit min:                          0.000000	vertex = 17

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 12:16:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050017 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      [ 0050017/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                      [ 356 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.524785
WARN:    S explicit min:                          0.000000	vertex = 201
#--------------------------------------------
#@# Sphere lh Sun Oct  8 12:16:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 12:16:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 30543 of (30543 30546) to complete...
Waiting for PID 30546 of (30543 30546) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0.292...
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 %19.94
pass 1: epoch 2 of 3 starting distance error %19.78
unfolding complete - removing small folds...
starting distance error %19.34
removing remaining folds...
final distance error %19.39
MRISunfold() return, current seed 1234
-01: dt=0.0000, 390 negative triangles
300: dt=0.9900, 390 negative triangles
301: dt=0.9900, 171 negative triangles
302: dt=0.9900, 110 negative triangles
303: dt=0.9900, 101 negative triangles
304: dt=0.9900, 76 negative triangles
305: dt=0.9900, 70 negative triangles
306: dt=0.9900, 74 negative triangles
307: dt=0.9900, 77 negative triangles
308: dt=0.9900, 68 negative triangles
309: dt=0.9900, 71 negative triangles
310: dt=0.9900, 70 negative triangles
311: dt=0.9900, 66 negative triangles
312: dt=0.9900, 50 negative triangles
313: dt=0.9900, 53 negative triangles
314: dt=0.9900, 54 negative triangles
315: dt=0.9900, 52 negative triangles
316: dt=0.9900, 54 negative triangles
317: dt=0.9900, 50 negative triangles
318: dt=0.9900, 38 negative triangles
319: dt=0.9900, 41 negative triangles
320: dt=0.9900, 36 negative triangles
321: dt=0.9900, 35 negative triangles
322: dt=0.9900, 39 negative triangles
323: dt=0.9900, 39 negative triangles
324: dt=0.9900, 31 negative triangles
325: dt=0.9900, 37 negative triangles
326: dt=0.9900, 25 negative triangles
327: dt=0.9900, 28 negative triangles
328: dt=0.9900, 25 negative triangles
329: dt=0.9900, 26 negative triangles
330: dt=0.9900, 17 negative triangles
331: dt=0.9900, 19 negative triangles
332: dt=0.9900, 15 negative triangles
333: dt=0.9900, 17 negative triangles
334: dt=0.9900, 18 negative triangles
335: dt=0.9900, 16 negative triangles
336: dt=0.9900, 15 negative triangles
337: dt=0.9900, 10 negative triangles
338: dt=0.9900, 13 negative triangles
339: dt=0.9900, 10 negative triangles
340: dt=0.9900, 8 negative triangles
341: dt=0.9900, 10 negative triangles
342: dt=0.9900, 10 negative triangles
343: dt=0.9900, 9 negative triangles
344: dt=0.9900, 3 negative triangles
345: dt=0.9900, 4 negative triangles
346: dt=0.9900, 5 negative triangles
347: dt=0.9900, 3 negative triangles
348: dt=0.9900, 1 negative triangles
349: dt=0.9900, 1 negative triangles
350: dt=0.9900, 1 negative triangles
351: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.16 hours
mris_sphere utimesec    4177.137978
mris_sphere stimesec    0.864868
mris_sphere ru_maxrss   290768
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   50907
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9976
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    165745
mris_sphere ru_nivcsw   365160
FSRUNTIME@ mris_sphere  1.1599 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0.284...
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 %21.92
pass 1: epoch 2 of 3 starting distance error %21.75
unfolding complete - removing small folds...
starting distance error %21.27
removing remaining folds...
final distance error %21.32
MRISunfold() return, current seed 1234
-01: dt=0.0000, 351 negative triangles
341: dt=0.9900, 351 negative triangles
342: dt=0.9900, 178 negative triangles
343: dt=0.9900, 166 negative triangles
344: dt=0.9900, 147 negative triangles
345: dt=0.9900, 156 negative triangles
346: dt=0.9900, 150 negative triangles
347: dt=0.9900, 123 negative triangles
348: dt=0.9900, 117 negative triangles
349: dt=0.9900, 107 negative triangles
350: dt=0.9900, 103 negative triangles
351: dt=0.9900, 97 negative triangles
352: dt=0.9900, 95 negative triangles
353: dt=0.9900, 90 negative triangles
354: dt=0.9900, 81 negative triangles
355: dt=0.9900, 62 negative triangles
356: dt=0.9900, 66 negative triangles
357: dt=0.9900, 49 negative triangles
358: dt=0.9900, 36 negative triangles
359: dt=0.9900, 36 negative triangles
360: dt=0.9900, 36 negative triangles
361: dt=0.9900, 25 negative triangles
362: dt=0.9900, 27 negative triangles
363: dt=0.9900, 26 negative triangles
364: dt=0.9900, 19 negative triangles
365: dt=0.9900, 22 negative triangles
366: dt=0.9900, 17 negative triangles
367: dt=0.9900, 19 negative triangles
368: dt=0.9900, 15 negative triangles
369: dt=0.9900, 15 negative triangles
370: dt=0.9900, 12 negative triangles
371: dt=0.9900, 18 negative triangles
372: dt=0.9900, 12 negative triangles
373: dt=0.9900, 13 negative triangles
374: dt=0.9900, 15 negative triangles
375: dt=0.9900, 11 negative triangles
376: dt=0.9900, 13 negative triangles
377: dt=0.9900, 16 negative triangles
378: dt=0.9900, 11 negative triangles
379: dt=0.9900, 7 negative triangles
380: dt=0.9900, 6 negative triangles
381: dt=0.9900, 3 negative triangles
382: dt=0.9900, 6 negative triangles
383: dt=0.9900, 3 negative triangles
384: dt=0.9900, 2 negative triangles
385: dt=0.9900, 2 negative triangles
386: dt=0.9900, 1 negative triangles
387: dt=0.9900, 1 negative triangles
388: dt=0.9900, 1 negative triangles
389: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.21 hours
mris_sphere utimesec    4511.832097
mris_sphere stimesec    1.379790
mris_sphere ru_maxrss   300548
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   52811
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10304
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    174359
mris_sphere ru_nivcsw   364052
FSRUNTIME@ mris_sphere  1.2149 hours 1 threads
PIDs (30543 30546) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 13:29:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 13:29:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 712 of (712 715) to complete...
Waiting for PID 715 of (712 715) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 5.492
curvature mean = 0.036, std = 0.820
curvature mean = 0.017, std = 0.866
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 348879.0, tmin=1.0311
  d=32.00 min @ (0.00, 0.00, -8.00) sse = 331990.8, tmin=2.0846
  d=16.00 min @ (-4.00, -4.00, 0.00) sse = 314161.1, tmin=3.1467
  d=8.00 min @ (0.00, 0.00, 2.00) sse = 311942.2, tmin=4.2420
  d=4.00 min @ (0.00, -1.00, 0.00) sse = 311035.1, tmin=5.3478
  d=2.00 min @ (0.50, 0.00, -0.50) sse = 310908.9, tmin=6.4539
  d=1.00 min @ (-0.25, 0.25, 0.00) sse = 310847.8, tmin=7.5592
  d=0.50 min @ (0.00, -0.12, 0.12) sse = 310806.3, tmin=8.6621
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   8.66 min
curvature mean = 0.003, std = 0.835
curvature mean = 0.005, std = 0.947
curvature mean = -0.003, std = 0.844
curvature mean = 0.001, std = 0.978
curvature mean = -0.003, std = 0.847
curvature mean = 0.000, std = 0.990
2 Reading smoothwm
curvature mean = -0.043, std = 0.336
curvature mean = 0.038, std = 0.243
curvature mean = 0.068, std = 0.312
curvature mean = 0.032, std = 0.301
curvature mean = 0.059, std = 0.460
curvature mean = 0.031, std = 0.327
curvature mean = 0.037, std = 0.595
curvature mean = 0.031, std = 0.337
curvature mean = 0.015, std = 0.714
MRISregister() return, current seed 0
-01: dt=0.0000, 353 negative triangles
144: dt=0.9900, 353 negative triangles
expanding nbhd size to 1
145: dt=0.9900, 419 negative triangles
146: dt=0.9900, 320 negative triangles
147: dt=0.9900, 304 negative triangles
148: dt=0.9900, 307 negative triangles
149: dt=0.9900, 292 negative triangles
150: dt=0.9900, 272 negative triangles
151: dt=0.9900, 247 negative triangles
152: dt=0.9900, 229 negative triangles
153: dt=0.9900, 203 negative triangles
154: dt=0.9900, 192 negative triangles
155: dt=0.9900, 177 negative triangles
156: dt=0.9900, 171 negative triangles
157: dt=0.9900, 159 negative triangles
158: dt=0.9900, 151 negative triangles
159: dt=0.9900, 138 negative triangles
160: dt=0.9900, 124 negative triangles
161: dt=0.9900, 114 negative triangles
162: dt=0.9900, 123 negative triangles
163: dt=0.9900, 107 negative triangles
164: dt=0.9900, 98 negative triangles
165: dt=0.9900, 88 negative triangles
166: dt=0.9900, 82 negative triangles
167: dt=0.9900, 89 negative triangles
168: dt=0.9900, 94 negative triangles
169: dt=0.9900, 84 negative triangles
170: dt=0.9900, 71 negative triangles
171: dt=0.9900, 72 negative triangles
172: dt=0.9900, 66 negative triangles
173: dt=0.9900, 64 negative triangles
174: dt=0.9900, 66 negative triangles
175: dt=0.9900, 61 negative triangles
176: dt=0.9900, 61 negative triangles
177: dt=0.9900, 53 negative triangles
178: dt=0.9900, 52 negative triangles
179: dt=0.9900, 49 negative triangles
180: dt=0.9900, 50 negative triangles
181: dt=0.9900, 47 negative triangles
182: dt=0.9900, 43 negative triangles
183: dt=0.9900, 44 negative triangles
184: dt=0.9900, 44 negative triangles
185: dt=0.9900, 44 negative triangles
186: dt=0.9900, 39 negative triangles
187: dt=0.9900, 39 negative triangles
188: dt=0.9900, 37 negative triangles
189: dt=0.9900, 33 negative triangles
190: dt=0.9900, 29 negative triangles
191: dt=0.9900, 25 negative triangles
192: dt=0.9900, 21 negative triangles
193: dt=0.9900, 23 negative triangles
194: dt=0.9900, 20 negative triangles
195: dt=0.9900, 18 negative triangles
196: dt=0.9900, 18 negative triangles
197: dt=0.9900, 19 negative triangles
198: dt=0.9900, 21 negative triangles
199: dt=0.9900, 18 negative triangles
200: dt=0.9900, 15 negative triangles
201: dt=0.9900, 15 negative triangles
202: dt=0.9900, 14 negative triangles
203: dt=0.9900, 13 negative triangles
204: dt=0.9900, 14 negative triangles
205: dt=0.9900, 16 negative triangles
206: dt=0.9900, 13 negative triangles
207: dt=0.9900, 10 negative triangles
208: dt=0.9900, 8 negative triangles
209: dt=0.9900, 10 negative triangles
210: dt=0.9900, 9 negative triangles
211: dt=0.9900, 8 negative triangles
212: dt=0.9900, 9 negative triangles
213: dt=0.9900, 7 negative triangles
214: dt=0.9900, 4 negative triangles
215: dt=0.9900, 5 negative triangles
216: dt=0.9900, 5 negative triangles
217: dt=0.9900, 6 negative triangles
218: dt=0.9900, 4 negative triangles
219: dt=0.9900, 5 negative triangles
220: dt=0.9900, 5 negative triangles
221: dt=0.9900, 4 negative triangles
222: dt=0.9900, 5 negative triangles
223: dt=0.9900, 4 negative triangles
224: dt=0.9405, 4 negative triangles
225: dt=0.9405, 5 negative triangles
226: dt=0.9405, 5 negative triangles
227: dt=0.9405, 4 negative triangles
228: dt=0.9405, 4 negative triangles
229: dt=0.9405, 6 negative triangles
230: dt=0.9405, 5 negative triangles
231: dt=0.9405, 4 negative triangles
232: dt=0.9405, 4 negative triangles
233: dt=0.9405, 4 negative triangles
234: dt=0.8935, 5 negative triangles
235: dt=0.8935, 4 negative triangles
236: dt=0.8935, 4 negative triangles
237: dt=0.8935, 3 negative triangles
238: dt=0.8935, 3 negative triangles
239: dt=0.8935, 3 negative triangles
240: dt=0.8935, 3 negative triangles
241: dt=0.8935, 3 negative triangles
242: dt=0.8935, 4 negative triangles
243: dt=0.8935, 2 negative triangles
244: dt=0.8935, 2 negative triangles
245: dt=0.8935, 2 negative triangles
246: dt=0.8935, 3 negative triangles
247: dt=0.8935, 2 negative triangles
248: dt=0.8935, 1 negative triangles
249: dt=0.8935, 2 negative triangles
250: dt=0.8935, 1 negative triangles
251: dt=0.8935, 1 negative triangles
252: dt=0.8935, 1 negative triangles
253: dt=0.8935, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.65 hours
mris_register utimesec    5941.106814
mris_register stimesec    5.359185
mris_register ru_maxrss   262956
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   37960
mris_register ru_majflt   1
mris_register ru_nswap    0
mris_register ru_inblock  11904
mris_register ru_oublock  10040
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    479882
mris_register ru_nivcsw   304563
FSRUNTIME@ mris_register  1.6514 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 5.582
curvature mean = 0.008, std = 0.810
curvature mean = 0.016, std = 0.857
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 331187.7, tmin=2.5741
  d=16.00 min @ (4.00, 4.00, 0.00) sse = 328670.7, tmin=3.8777
  d=8.00 min @ (-4.00, -2.00, 0.00) sse = 324968.0, tmin=5.2169
  d=4.00 min @ (1.00, 1.00, 0.00) sse = 324326.7, tmin=6.5790
  d=2.00 min @ (0.00, -0.50, 0.50) sse = 324139.9, tmin=7.9523
  d=1.00 min @ (0.00, 0.25, -0.25) sse = 324066.9, tmin=9.3139
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  10.68 min
curvature mean = -0.020, std = 0.821
curvature mean = 0.006, std = 0.944
curvature mean = -0.025, std = 0.827
curvature mean = 0.002, std = 0.976
curvature mean = -0.026, std = 0.829
curvature mean = 0.000, std = 0.989
2 Reading smoothwm
curvature mean = -0.043, std = 0.538
curvature mean = 0.031, std = 0.236
curvature mean = 0.042, std = 0.193
curvature mean = 0.022, std = 0.295
curvature mean = 0.037, std = 0.280
curvature mean = 0.021, std = 0.321
curvature mean = 0.023, std = 0.364
curvature mean = 0.021, std = 0.331
curvature mean = 0.008, std = 0.466
MRISregister() return, current seed 0
-01: dt=0.0000, 345 negative triangles
135: dt=0.9900, 345 negative triangles
expanding nbhd size to 1
136: dt=0.9900, 404 negative triangles
137: dt=0.9900, 315 negative triangles
138: dt=0.9900, 319 negative triangles
139: dt=0.9900, 320 negative triangles
140: dt=0.9900, 315 negative triangles
141: dt=0.9900, 302 negative triangles
142: dt=0.9900, 318 negative triangles
143: dt=0.9900, 289 negative triangles
144: dt=0.9900, 258 negative triangles
145: dt=0.9900, 258 negative triangles
146: dt=0.9900, 242 negative triangles
147: dt=0.9900, 244 negative triangles
148: dt=0.9900, 232 negative triangles
149: dt=0.9900, 217 negative triangles
150: dt=0.9900, 214 negative triangles
151: dt=0.9900, 208 negative triangles
152: dt=0.9900, 194 negative triangles
153: dt=0.9900, 184 negative triangles
154: dt=0.9900, 171 negative triangles
155: dt=0.9900, 166 negative triangles
156: dt=0.9900, 141 negative triangles
157: dt=0.9900, 141 negative triangles
158: dt=0.9900, 136 negative triangles
159: dt=0.9900, 123 negative triangles
160: dt=0.9900, 124 negative triangles
161: dt=0.9900, 115 negative triangles
162: dt=0.9900, 110 negative triangles
163: dt=0.9900, 99 negative triangles
164: dt=0.9900, 97 negative triangles
165: dt=0.9900, 88 negative triangles
166: dt=0.9900, 85 negative triangles
167: dt=0.9900, 85 negative triangles
168: dt=0.9900, 68 negative triangles
169: dt=0.9900, 74 negative triangles
170: dt=0.9900, 67 negative triangles
171: dt=0.9900, 58 negative triangles
172: dt=0.9900, 54 negative triangles
173: dt=0.9900, 50 negative triangles
174: dt=0.9900, 45 negative triangles
175: dt=0.9900, 41 negative triangles
176: dt=0.9900, 39 negative triangles
177: dt=0.9900, 37 negative triangles
178: dt=0.9900, 33 negative triangles
179: dt=0.9900, 25 negative triangles
180: dt=0.9900, 22 negative triangles
181: dt=0.9900, 19 negative triangles
182: dt=0.9900, 13 negative triangles
183: dt=0.9900, 13 negative triangles
184: dt=0.9900, 11 negative triangles
185: dt=0.9900, 9 negative triangles
186: dt=0.9900, 7 negative triangles
187: dt=0.9900, 10 negative triangles
188: dt=0.9900, 6 negative triangles
189: dt=0.9900, 4 negative triangles
190: dt=0.9900, 5 negative triangles
191: dt=0.9900, 6 negative triangles
192: dt=0.9900, 5 negative triangles
193: dt=0.9900, 4 negative triangles
194: dt=0.9900, 3 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 2.16 hours
mris_register utimesec    8178.586665
mris_register stimesec    2.823570
mris_register ru_maxrss   268700
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   40277
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10352
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    445679
mris_register ru_nivcsw   378564
FSRUNTIME@ mris_register  2.1585 hours 1 threads
PIDs (712 715) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 15:38:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 15:38:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

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

Waiting for PID 5104 of (5104 5107) to complete...
Waiting for PID 5107 of (5104 5107) 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 (5104 5107) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 15:38:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 15:38:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 5150 of (5150 5153) to complete...
Waiting for PID 5153 of (5150 5153) 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 (5150 5153) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 15:38:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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 15:38:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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 5194 of (5194 5197) to complete...
Waiting for PID 5197 of (5194 5197) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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...
1489 labels changed using aseg
relabeling using gibbs priors...
000:   3298 changed, 140996 examined...
001:    812 changed, 13687 examined...
002:    217 changed, 4432 examined...
003:     72 changed, 1281 examined...
004:     24 changed, 417 examined...
005:     11 changed, 144 examined...
006:      1 changed, 70 examined...
007:      0 changed, 7 examined...
303 labels changed using aseg
000: 141 total segments, 99 labels (510 vertices) changed
001: 43 total segments, 1 labels (2 vertices) changed
002: 42 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2790 vertices marked for relabeling...
2790 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 0050017 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...
975 labels changed using aseg
relabeling using gibbs priors...
000:   2939 changed, 145822 examined...
001:    781 changed, 12644 examined...
002:    181 changed, 4295 examined...
003:     58 changed, 1097 examined...
004:     21 changed, 352 examined...
005:      8 changed, 131 examined...
006:      8 changed, 54 examined...
007:      2 changed, 45 examined...
008:      1 changed, 8 examined...
009:      1 changed, 5 examined...
010:      0 changed, 6 examined...
230 labels changed using aseg
000: 121 total segments, 81 labels (512 vertices) changed
001: 40 total segments, 2 labels (11 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1750 vertices marked for relabeling...
1750 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 19 seconds.
PIDs (5194 5197) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 15:39:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050017 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 15:39:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050017 rh 

Waiting for PID 5241 of (5241 5244) to complete...
Waiting for PID 5244 of (5241 5244) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050017 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-6.0.0/0050017/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
18499 bright wm thresholded.
612 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.orig...
computing class statistics...
border white:    300590 voxels (1.79%)
border gray      366883 voxels (2.19%)
WM (94.0): 94.6 +- 8.0 [70.0 --> 110.0]
GM (72.0) : 71.1 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70)
setting MAX_BORDER_WHITE to 105.0 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 49.3 (was 40)
setting MAX_GRAY to 89.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=97+-6.1,    GM=70+-7.0
mean inside = 90.8, mean outside = 75.8
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 +- 0.29 (0.04-->9.53) (max @ vno 94608 --> 138851)
face area 0.34 +- 0.20 (0.00-->11.53)
mean absolute distance = 0.59 +- 0.92
3601 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 42 points - only 0.00% unknown
deleting segment 1 with 7 points - only 0.00% unknown
deleting segment 2 with 11 points - only 0.00% unknown
deleting segment 3 with 35 points - only 0.00% unknown
deleting segment 5 with 30 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 64 points - only 0.00% unknown
deleting segment 8 with 32 points - only 0.00% unknown
deleting segment 9 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
deleting segment 11 with 9 points - only 0.00% unknown
deleting segment 12 with 9 points - only 0.00% unknown
deleting segment 13 with 22 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
mean border=81.1, 401 (393) missing vertices, mean dist 0.3 [0.8 (%21.4)->0.5 (%78.6))]
%63 local maxima, %32 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 +- 0.30 (0.10-->9.58) (max @ vno 94608 --> 138851)
face area 0.34 +- 0.20 (0.00-->10.32)
mean absolute distance = 0.40 +- 0.72
5176 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1610895.4, rms=5.822
001: dt: 0.5000, sse=1106128.6, rms=3.881 (33.339%)
002: dt: 0.5000, sse=967522.7, rms=3.167 (18.401%)
003: dt: 0.5000, sse=941133.0, rms=3.041 (3.983%)
004: dt: 0.5000, sse=937440.9, rms=2.951 (2.937%)
rms = 3.01, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=859415.6, rms=2.434 (17.520%)
006: dt: 0.2500, sse=836432.8, rms=2.196 (9.803%)
007: dt: 0.2500, sse=828686.9, rms=2.139 (2.606%)
rms = 2.12, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=824966.3, rms=2.124 (0.699%)
rms = 2.10, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=821169.2, rms=2.096 (1.279%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 42 points - only 0.00% unknown
deleting segment 1 with 9 points - only 0.00% unknown
deleting segment 2 with 15 points - only 0.00% unknown
deleting segment 3 with 50 points - only 0.00% unknown
deleting segment 4 with 25 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 88 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 12 points - only 0.00% unknown
mean border=82.9, 430 (124) missing vertices, mean dist -0.2 [0.5 (%61.4)->0.3 (%38.6))]
%69 local maxima, %26 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 +- 0.30 (0.09-->9.39) (max @ vno 94608 --> 138851)
face area 0.35 +- 0.21 (0.00-->11.00)
mean absolute distance = 0.35 +- 0.53
4865 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1058277.5, rms=3.480
010: dt: 0.5000, sse=917713.3, rms=2.576 (25.983%)
011: dt: 0.5000, sse=894605.6, rms=2.474 (3.942%)
rms = 2.56, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=845376.1, rms=2.064 (16.572%)
013: dt: 0.2500, sse=832391.2, rms=1.863 (9.737%)
rms = 1.82, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=824470.2, rms=1.819 (2.361%)
rms = 1.79, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=819424.6, rms=1.787 (1.779%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 40 points - only 0.00% unknown
deleting segment 1 with 15 points - only 0.00% unknown
deleting segment 2 with 42 points - only 0.00% unknown
deleting segment 3 with 25 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 102 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
deleting segment 7 with 36 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
mean border=84.4, 474 (77) missing vertices, mean dist -0.1 [0.4 (%59.0)->0.3 (%41.0))]
%77 local maxima, %18 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 +- 0.30 (0.03-->9.35) (max @ vno 94608 --> 138851)
face area 0.35 +- 0.21 (0.00-->11.22)
mean absolute distance = 0.32 +- 0.43
3859 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=916127.1, rms=2.709
016: dt: 0.5000, sse=858842.2, rms=2.214 (18.285%)
rms = 2.24, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=813781.5, rms=1.870 (15.531%)
018: dt: 0.2500, sse=801065.9, rms=1.695 (9.373%)
rms = 1.65, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=796329.8, rms=1.654 (2.379%)
rms = 1.63, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=789537.5, rms=1.628 (1.586%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 40 points - only 0.00% unknown
deleting segment 1 with 15 points - only 0.00% unknown
deleting segment 2 with 30 points - only 0.00% unknown
deleting segment 3 with 25 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 101 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
deleting segment 7 with 36 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 16 points - only 0.00% unknown
mean border=85.1, 546 (61) missing vertices, mean dist -0.1 [0.4 (%53.3)->0.3 (%46.7))]
%82 local maxima, %13 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-6.0.0/0050017/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=812827.6, rms=1.942
021: dt: 0.5000, sse=789991.1, rms=1.666 (14.194%)
rms = 2.02, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=761198.6, rms=1.402 (15.852%)
023: dt: 0.2500, sse=775722.0, rms=1.351 (3.665%)
rms = 1.31, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=753370.2, rms=1.309 (3.128%)
rms = 1.30, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=750472.5, rms=1.298 (0.799%)
positioning took 0.6 minutes
generating cortex label...
14 non-cortical segments detected
only using segment with 6916 vertices
erasing segment 0 (vno[0] = 26174)
erasing segment 2 (vno[0] = 52558)
erasing segment 3 (vno[0] = 76363)
erasing segment 4 (vno[0] = 93644)
erasing segment 5 (vno[0] = 96777)
erasing segment 6 (vno[0] = 98617)
erasing segment 7 (vno[0] = 99516)
erasing segment 8 (vno[0] = 101438)
erasing segment 9 (vno[0] = 101520)
erasing segment 10 (vno[0] = 102336)
erasing segment 11 (vno[0] = 103305)
erasing segment 12 (vno[0] = 105106)
erasing segment 13 (vno[0] = 105119)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.area
vertex spacing 0.90 +- 0.30 (0.03-->9.37) (max @ vno 94608 --> 138851)
face area 0.34 +- 0.20 (0.00-->11.33)
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 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
deleting segment 2 with 51 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 6 with 8 points - only 0.00% unknown
deleting segment 7 with 22 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 8 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=58.5, 403 (403) missing vertices, mean dist 1.7 [1.4 (%0.0)->2.9 (%100.0))]
%15 local maxima, %42 large gradients and %39 min vals, 621 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=20780742.0, rms=27.323
001: dt: 0.0500, sse=18690048.0, rms=25.861 (5.349%)
002: dt: 0.0500, sse=17162230.0, rms=24.738 (4.342%)
003: dt: 0.0500, sse=15969312.0, rms=23.825 (3.693%)
004: dt: 0.0500, sse=14986892.0, rms=23.045 (3.273%)
005: dt: 0.0500, sse=14147938.0, rms=22.357 (2.983%)
006: dt: 0.0500, sse=13411279.0, rms=21.736 (2.781%)
007: dt: 0.0500, sse=12752004.0, rms=21.164 (2.631%)
008: dt: 0.0500, sse=12153498.0, rms=20.631 (2.519%)
009: dt: 0.0500, sse=11602821.0, rms=20.128 (2.438%)
010: dt: 0.0500, sse=11092877.0, rms=19.650 (2.371%)
positioning took 1.0 minutes
mean border=58.3, 321 (187) missing vertices, mean dist 1.4 [0.7 (%0.0)->2.4 (%100.0))]
%16 local maxima, %42 large gradients and %38 min vals, 573 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=11845573.0, rms=20.343
011: dt: 0.0500, sse=11365306.0, rms=19.899 (2.181%)
012: dt: 0.0500, sse=10915583.0, rms=19.474 (2.134%)
013: dt: 0.0500, sse=10492876.0, rms=19.067 (2.095%)
014: dt: 0.0500, sse=10094498.0, rms=18.674 (2.059%)
015: dt: 0.0500, sse=9718865.0, rms=18.296 (2.024%)
016: dt: 0.0500, sse=9364541.0, rms=17.932 (1.989%)
017: dt: 0.0500, sse=9030267.0, rms=17.582 (1.954%)
018: dt: 0.0500, sse=8714499.0, rms=17.244 (1.920%)
019: dt: 0.0500, sse=8416380.0, rms=16.919 (1.885%)
020: dt: 0.0500, sse=8134714.0, rms=16.606 (1.850%)
positioning took 1.0 minutes
mean border=58.2, 338 (122) missing vertices, mean dist 1.2 [0.1 (%1.1)->2.1 (%98.9))]
%16 local maxima, %42 large gradients and %38 min vals, 602 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=8247621.5, rms=16.736
021: dt: 0.0500, sse=7974598.0, rms=16.429 (1.832%)
022: dt: 0.0500, sse=7717184.5, rms=16.135 (1.793%)
023: dt: 0.0500, sse=7472883.0, rms=15.850 (1.764%)
024: dt: 0.0500, sse=7242927.5, rms=15.577 (1.721%)
025: dt: 0.0500, sse=7026490.5, rms=15.316 (1.677%)
026: dt: 0.0500, sse=6822377.0, rms=15.065 (1.637%)
027: dt: 0.0500, sse=6629511.0, rms=14.824 (1.599%)
028: dt: 0.0500, sse=6445487.0, rms=14.591 (1.576%)
029: dt: 0.0500, sse=6269729.0, rms=14.364 (1.554%)
030: dt: 0.0500, sse=6101163.5, rms=14.143 (1.538%)
positioning took 1.0 minutes
mean border=58.1, 377 (89) missing vertices, mean dist 1.1 [0.1 (%10.2)->1.9 (%89.8))]
%16 local maxima, %42 large gradients and %37 min vals, 589 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=6191621.5, rms=14.261
031: dt: 0.5000, sse=4964174.5, rms=12.554 (11.965%)
032: dt: 0.5000, sse=4149186.2, rms=11.271 (10.220%)
033: dt: 0.5000, sse=3566678.2, rms=10.258 (8.994%)
034: dt: 0.5000, sse=3149882.0, rms=9.458 (7.796%)
035: dt: 0.5000, sse=2839113.8, rms=8.816 (6.787%)
036: dt: 0.5000, sse=2603400.8, rms=8.293 (5.932%)
037: dt: 0.5000, sse=2416092.0, rms=7.854 (5.290%)
038: dt: 0.5000, sse=2270885.5, rms=7.494 (4.583%)
039: dt: 0.5000, sse=2152397.5, rms=7.190 (4.055%)
040: dt: 0.5000, sse=2062311.2, rms=6.947 (3.388%)
041: dt: 0.5000, sse=1982449.5, rms=6.727 (3.170%)
042: dt: 0.5000, sse=1917626.8, rms=6.539 (2.786%)
043: dt: 0.5000, sse=1862316.0, rms=6.377 (2.478%)
044: dt: 0.5000, sse=1819341.2, rms=6.246 (2.057%)
045: dt: 0.5000, sse=1782732.6, rms=6.136 (1.767%)
046: dt: 0.5000, sse=1755196.0, rms=6.048 (1.428%)
047: dt: 0.5000, sse=1729645.1, rms=5.968 (1.322%)
rms = 5.92, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1715014.4, rms=5.919 (0.816%)
049: dt: 0.2500, sse=1644459.2, rms=5.654 (4.481%)
050: dt: 0.2500, sse=1624302.6, rms=5.585 (1.224%)
rms = 5.57, time step reduction 2 of 3 to 0.125...
051: dt: 0.2500, sse=1620461.0, rms=5.570 (0.258%)
rms = 5.53, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1609870.8, rms=5.530 (0.728%)
positioning took 2.9 minutes
mean border=57.0, 2561 (38) missing vertices, mean dist 0.3 [0.2 (%45.7)->0.9 (%54.3))]
%26 local maxima, %35 large gradients and %32 min vals, 346 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=1806272.1, rms=5.619
053: dt: 0.5000, sse=1683968.2, rms=5.209 (7.303%)
054: dt: 0.5000, sse=1630462.1, rms=5.042 (3.201%)
rms = 5.03, time step reduction 1 of 3 to 0.250...
055: dt: 0.5000, sse=1625327.4, rms=5.031 (0.226%)
056: dt: 0.2500, sse=1538742.0, rms=4.644 (7.677%)
057: dt: 0.2500, sse=1515789.4, rms=4.549 (2.056%)
rms = 4.53, time step reduction 2 of 3 to 0.125...
058: dt: 0.2500, sse=1510852.9, rms=4.528 (0.463%)
059: dt: 0.1250, sse=1498221.6, rms=4.469 (1.294%)
rms = 4.45, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1494391.9, rms=4.454 (0.347%)
positioning took 1.3 minutes
mean border=56.4, 3203 (31) missing vertices, mean dist 0.2 [0.2 (%49.1)->0.7 (%50.9))]
%34 local maxima, %28 large gradients and %31 min vals, 385 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=1561572.4, rms=4.668
rms = 4.71, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1535973.6, rms=4.561 (2.278%)
062: dt: 0.2500, sse=1516626.6, rms=4.488 (1.613%)
rms = 4.44, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1503057.5, rms=4.439 (1.092%)
064: dt: 0.1250, sse=1491869.9, rms=4.387 (1.172%)
rms = 4.36, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1485975.1, rms=4.364 (0.520%)
positioning took 1.0 minutes
mean border=55.8, 5892 (28) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.5 (%52.7))]
%39 local maxima, %22 large gradients and %30 min vals, 410 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-6.0.0/0050017/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1513806.8, rms=4.447
rms = 4.41, time step reduction 1 of 3 to 0.250...
066: dt: 0.5000, sse=1495695.9, rms=4.409 (0.859%)
067: dt: 0.2500, sse=1442498.4, rms=4.173 (5.347%)
068: dt: 0.2500, sse=1420282.0, rms=4.080 (2.231%)
rms = 4.03, time step reduction 2 of 3 to 0.125...
069: dt: 0.2500, sse=1409441.4, rms=4.034 (1.127%)
070: dt: 0.1250, sse=1394302.5, rms=3.958 (1.894%)
rms = 3.93, time step reduction 3 of 3 to 0.062...
071: dt: 0.1250, sse=1388877.2, rms=3.935 (0.572%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.area.pial
vertex spacing 1.02 +- 0.48 (0.04-->9.12) (max @ vno 137876 --> 137877)
face area 0.41 +- 0.37 (0.00-->9.72)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 140996 vertices processed
25000 of 140996 vertices processed
50000 of 140996 vertices processed
75000 of 140996 vertices processed
100000 of 140996 vertices processed
125000 of 140996 vertices processed
0 of 140996 vertices processed
25000 of 140996 vertices processed
50000 of 140996 vertices processed
75000 of 140996 vertices processed
100000 of 140996 vertices processed
125000 of 140996 vertices processed
thickness calculation complete, 714:1625 truncations.
25472 vertices at 0 distance
85377 vertices at 1 distance
85147 vertices at 2 distance
44489 vertices at 3 distance
17616 vertices at 4 distance
6438 vertices at 5 distance
2714 vertices at 6 distance
1142 vertices at 7 distance
531 vertices at 8 distance
276 vertices at 9 distance
157 vertices at 10 distance
101 vertices at 11 distance
78 vertices at 12 distance
47 vertices at 13 distance
45 vertices at 14 distance
59 vertices at 15 distance
45 vertices at 16 distance
38 vertices at 17 distance
19 vertices at 18 distance
12 vertices at 19 distance
13 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 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-6.0.0/0050017/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
18499 bright wm thresholded.
612 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.orig...
computing class statistics...
border white:    300590 voxels (1.79%)
border gray      366883 voxels (2.19%)
WM (94.0): 94.6 +- 8.0 [70.0 --> 110.0]
GM (72.0) : 71.1 +- 10.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70)
setting MAX_BORDER_WHITE to 106.0 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 49.3 (was 40)
setting MAX_GRAY to 90.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=98+-7.0,    GM=70+-7.0
mean inside = 91.0, mean outside = 76.0
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 +- 0.30 (0.05-->11.69) (max @ vno 88556 --> 113803)
face area 0.34 +- 0.21 (0.00-->14.39)
mean absolute distance = 0.56 +- 0.88
3767 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 269 points - only 0.00% unknown
deleting segment 1 with 31 points - only 0.00% unknown
deleting segment 3 with 24 points - only 0.00% unknown
deleting segment 4 with 46 points - only 0.00% unknown
deleting segment 5 with 193 points - only 0.00% unknown
deleting segment 6 with 16 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 11 with 26 points - only 0.00% unknown
deleting segment 12 with 37 points - only 0.00% unknown
deleting segment 13 with 12 points - only 0.00% unknown
mean border=81.2, 281 (272) missing vertices, mean dist 0.3 [0.7 (%21.5)->0.5 (%78.5))]
%66 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.31 (0.11-->11.45) (max @ vno 88556 --> 113803)
face area 0.34 +- 0.21 (0.00-->12.94)
mean absolute distance = 0.39 +- 0.71
4818 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1645894.5, rms=5.738
001: dt: 0.5000, sse=1131321.8, rms=3.790 (33.947%)
002: dt: 0.5000, sse=991551.9, rms=3.083 (18.651%)
003: dt: 0.5000, sse=971991.3, rms=2.937 (4.731%)
004: dt: 0.5000, sse=954647.3, rms=2.861 (2.586%)
rms = 2.91, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=880653.6, rms=2.330 (18.568%)
006: dt: 0.2500, sse=857433.4, rms=2.077 (10.844%)
007: dt: 0.2500, sse=857687.4, rms=2.020 (2.737%)
rms = 2.00, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=846973.1, rms=2.002 (0.917%)
rms = 1.98, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=842858.7, rms=1.975 (1.323%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 298 points - only 0.00% unknown
deleting segment 1 with 36 points - only 0.00% unknown
deleting segment 2 with 17 points - only 0.00% unknown
deleting segment 3 with 55 points - only 0.00% unknown
deleting segment 4 with 143 points - only 0.00% unknown
deleting segment 5 with 11 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
deleting segment 12 with 29 points - only 0.00% unknown
deleting segment 13 with 12 points - only 0.00% unknown
mean border=83.0, 279 (79) missing vertices, mean dist -0.2 [0.5 (%60.8)->0.3 (%39.2))]
%71 local maxima, %24 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 +- 0.31 (0.07-->11.42) (max @ vno 88556 --> 113803)
face area 0.35 +- 0.22 (0.00-->13.74)
mean absolute distance = 0.35 +- 0.53
4738 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1078682.6, rms=3.375
010: dt: 0.5000, sse=929689.9, rms=2.446 (27.543%)
011: dt: 0.5000, sse=912179.7, rms=2.350 (3.909%)
rms = 2.48, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=864534.8, rms=1.944 (17.266%)
013: dt: 0.2500, sse=858131.0, rms=1.763 (9.338%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=845931.9, rms=1.735 (1.588%)
rms = 1.71, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=846220.8, rms=1.710 (1.423%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 299 points - only 0.00% unknown
deleting segment 1 with 33 points - only 0.00% unknown
deleting segment 2 with 16 points - only 0.00% unknown
deleting segment 3 with 52 points - only 0.00% unknown
deleting segment 4 with 137 points - only 0.00% unknown
deleting segment 5 with 16 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 11 with 8 points - only 0.00% unknown
deleting segment 12 with 30 points - only 0.00% unknown
deleting segment 13 with 11 points - only 0.00% unknown
mean border=84.4, 346 (58) missing vertices, mean dist -0.1 [0.4 (%58.1)->0.3 (%41.9))]
%78 local maxima, %17 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 +- 0.30 (0.08-->11.59) (max @ vno 88556 --> 113803)
face area 0.35 +- 0.22 (0.00-->13.85)
mean absolute distance = 0.33 +- 0.44
4181 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=942000.7, rms=2.611
016: dt: 0.5000, sse=884242.1, rms=2.130 (18.408%)
rms = 2.16, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=841113.8, rms=1.799 (15.571%)
018: dt: 0.2500, sse=828788.8, rms=1.630 (9.390%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=824415.8, rms=1.597 (1.998%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=818567.3, rms=1.568 (1.801%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 342 points - only 0.00% unknown
deleting segment 1 with 20 points - only 0.00% unknown
deleting segment 2 with 52 points - only 0.00% unknown
deleting segment 3 with 141 points - only 0.00% unknown
deleting segment 4 with 17 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 6 with 9 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
deleting segment 11 with 33 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
mean border=85.2, 422 (48) missing vertices, mean dist -0.1 [0.4 (%53.0)->0.3 (%47.0))]
%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-6.0.0/0050017/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=845823.0, rms=1.912
021: dt: 0.5000, sse=827825.0, rms=1.610 (15.796%)
rms = 1.95, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=794121.8, rms=1.342 (16.612%)
023: dt: 0.2500, sse=792975.8, rms=1.292 (3.778%)
rms = 1.25, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=784550.2, rms=1.248 (3.389%)
rms = 1.24, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=782256.3, rms=1.238 (0.801%)
positioning took 0.6 minutes
generating cortex label...
23 non-cortical segments detected
only using segment with 7719 vertices
erasing segment 0 (vno[0] = 33010)
erasing segment 1 (vno[0] = 37664)
erasing segment 2 (vno[0] = 38758)
erasing segment 4 (vno[0] = 55201)
erasing segment 5 (vno[0] = 58528)
erasing segment 6 (vno[0] = 69642)
erasing segment 7 (vno[0] = 91754)
erasing segment 8 (vno[0] = 95030)
erasing segment 9 (vno[0] = 97134)
erasing segment 10 (vno[0] = 100425)
erasing segment 11 (vno[0] = 101410)
erasing segment 12 (vno[0] = 101437)
erasing segment 13 (vno[0] = 102420)
erasing segment 14 (vno[0] = 102429)
erasing segment 15 (vno[0] = 102558)
erasing segment 16 (vno[0] = 103506)
erasing segment 17 (vno[0] = 105210)
erasing segment 18 (vno[0] = 107015)
erasing segment 19 (vno[0] = 108004)
erasing segment 20 (vno[0] = 108835)
erasing segment 21 (vno[0] = 141788)
erasing segment 22 (vno[0] = 144220)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.area
vertex spacing 0.90 +- 0.31 (0.05-->11.74) (max @ vno 88556 --> 113803)
face area 0.35 +- 0.22 (0.00-->14.00)
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 9 points - only 0.00% unknown
deleting segment 1 with 7 points - only 0.00% unknown
deleting segment 2 with 29 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 10 points - only 0.00% unknown
deleting segment 5 with 194 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=58.5, 300 (300) missing vertices, mean dist 1.7 [1.7 (%0.0)->2.9 (%100.0))]
%14 local maxima, %40 large gradients and %41 min vals, 714 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=21547290.0, rms=27.386
001: dt: 0.0500, sse=19384980.0, rms=25.924 (5.336%)
002: dt: 0.0500, sse=17810962.0, rms=24.806 (4.313%)
003: dt: 0.0500, sse=16583635.0, rms=23.898 (3.662%)
004: dt: 0.0500, sse=15574806.0, rms=23.124 (3.236%)
005: dt: 0.0500, sse=14712355.0, rms=22.442 (2.951%)
006: dt: 0.0500, sse=13954502.0, rms=21.825 (2.751%)
007: dt: 0.0500, sse=13275590.0, rms=21.256 (2.604%)
008: dt: 0.0500, sse=12657846.0, rms=20.726 (2.497%)
009: dt: 0.0500, sse=12089237.0, rms=20.225 (2.417%)
010: dt: 0.0500, sse=11562156.0, rms=19.749 (2.352%)
positioning took 1.0 minutes
mean border=58.4, 304 (181) missing vertices, mean dist 1.4 [0.7 (%0.1)->2.4 (%99.9))]
%15 local maxima, %40 large gradients and %40 min vals, 662 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=12353829.0, rms=20.459
011: dt: 0.0500, sse=11857897.0, rms=20.017 (2.159%)
012: dt: 0.0500, sse=11393152.0, rms=19.594 (2.114%)
013: dt: 0.0500, sse=10956098.0, rms=19.188 (2.074%)
014: dt: 0.0500, sse=10545123.0, rms=18.798 (2.034%)
015: dt: 0.0500, sse=10157674.0, rms=18.422 (1.998%)
016: dt: 0.0500, sse=9792709.0, rms=18.061 (1.960%)
017: dt: 0.0500, sse=9448308.0, rms=17.714 (1.924%)
018: dt: 0.0500, sse=9123566.0, rms=17.379 (1.886%)
019: dt: 0.0500, sse=8817052.0, rms=17.058 (1.850%)
020: dt: 0.0500, sse=8528417.0, rms=16.749 (1.808%)
positioning took 1.0 minutes
mean border=58.2, 353 (125) missing vertices, mean dist 1.2 [0.1 (%1.1)->2.1 (%98.9))]
%15 local maxima, %41 large gradients and %40 min vals, 618 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=8634043.0, rms=16.867
021: dt: 0.0500, sse=8355287.0, rms=16.565 (1.786%)
022: dt: 0.0500, sse=8093042.0, rms=16.277 (1.742%)
023: dt: 0.0500, sse=7844602.5, rms=15.999 (1.709%)
024: dt: 0.0500, sse=7611305.5, rms=15.733 (1.662%)
025: dt: 0.0500, sse=7391530.5, rms=15.478 (1.619%)
026: dt: 0.0500, sse=7184710.0, rms=15.234 (1.574%)
027: dt: 0.0500, sse=6989174.5, rms=15.000 (1.537%)
028: dt: 0.0500, sse=6803289.5, rms=14.774 (1.507%)
029: dt: 0.0500, sse=6625553.5, rms=14.555 (1.486%)
030: dt: 0.0500, sse=6456229.5, rms=14.342 (1.459%)
positioning took 1.0 minutes
mean border=58.1, 421 (101) missing vertices, mean dist 1.1 [0.1 (%10.2)->2.0 (%89.8))]
%15 local maxima, %41 large gradients and %39 min vals, 587 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=6557613.5, rms=14.469
031: dt: 0.5000, sse=5320721.0, rms=12.830 (11.325%)
032: dt: 0.5000, sse=4497661.0, rms=11.604 (9.560%)
033: dt: 0.5000, sse=3909792.5, rms=10.642 (8.284%)
034: dt: 0.5000, sse=3480828.5, rms=9.874 (7.215%)
035: dt: 0.5000, sse=3148320.5, rms=9.237 (6.457%)
036: dt: 0.5000, sse=2876789.2, rms=8.679 (6.044%)
037: dt: 0.5000, sse=2643940.5, rms=8.172 (5.832%)
038: dt: 0.5000, sse=2456478.5, rms=7.738 (5.315%)
039: dt: 0.5000, sse=2300860.2, rms=7.362 (4.867%)
040: dt: 0.5000, sse=2187903.8, rms=7.072 (3.930%)
041: dt: 0.5000, sse=2098680.0, rms=6.838 (3.317%)
042: dt: 0.5000, sse=2034453.5, rms=6.661 (2.585%)
043: dt: 0.5000, sse=1986241.4, rms=6.526 (2.021%)
044: dt: 0.5000, sse=1949022.4, rms=6.418 (1.665%)
045: dt: 0.5000, sse=1923602.1, rms=6.344 (1.143%)
046: dt: 0.5000, sse=1899813.2, rms=6.271 (1.148%)
047: dt: 0.5000, sse=1882691.4, rms=6.221 (0.797%)
048: dt: 0.5000, sse=1863818.2, rms=6.163 (0.935%)
rms = 6.13, time step reduction 1 of 3 to 0.250...
049: dt: 0.5000, sse=1853523.1, rms=6.132 (0.509%)
050: dt: 0.2500, sse=1785298.0, rms=5.890 (3.946%)
051: dt: 0.2500, sse=1763285.6, rms=5.820 (1.184%)
rms = 5.81, time step reduction 2 of 3 to 0.125...
052: dt: 0.2500, sse=1761426.0, rms=5.812 (0.138%)
rms = 5.77, time step reduction 3 of 3 to 0.062...
053: dt: 0.1250, sse=1750003.1, rms=5.771 (0.701%)
positioning took 3.2 minutes
mean border=57.2, 3032 (43) missing vertices, mean dist 0.3 [0.2 (%46.5)->0.9 (%53.5))]
%24 local maxima, %35 large gradients and %34 min vals, 344 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=1907729.0, rms=5.698
054: dt: 0.5000, sse=1794988.4, rms=5.342 (6.243%)
055: dt: 0.5000, sse=1739733.9, rms=5.177 (3.090%)
rms = 5.17, time step reduction 1 of 3 to 0.250...
056: dt: 0.5000, sse=1734456.2, rms=5.168 (0.180%)
057: dt: 0.2500, sse=1649807.2, rms=4.811 (6.899%)
058: dt: 0.2500, sse=1625142.4, rms=4.717 (1.950%)
rms = 4.69, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1619613.0, rms=4.694 (0.500%)
060: dt: 0.1250, sse=1606051.8, rms=4.634 (1.265%)
rms = 4.62, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1602108.8, rms=4.619 (0.330%)
positioning took 1.3 minutes
mean border=56.7, 3677 (35) missing vertices, mean dist 0.2 [0.2 (%48.6)->0.7 (%51.4))]
%32 local maxima, %28 large gradients and %34 min vals, 443 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=1654519.4, rms=4.770
rms = 4.81, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1631328.1, rms=4.679 (1.913%)
063: dt: 0.2500, sse=1615019.8, rms=4.622 (1.216%)
rms = 4.58, time step reduction 2 of 3 to 0.125...
064: dt: 0.2500, sse=1602872.2, rms=4.581 (0.882%)
065: dt: 0.1250, sse=1590757.6, rms=4.528 (1.146%)
rms = 4.51, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1585131.0, rms=4.509 (0.427%)
positioning took 1.0 minutes
mean border=56.2, 6753 (34) missing vertices, mean dist 0.1 [0.2 (%46.7)->0.5 (%53.3))]
%37 local maxima, %22 large gradients and %32 min vals, 493 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-6.0.0/0050017/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1609565.0, rms=4.575
067: dt: 0.5000, sse=1586897.4, rms=4.523 (1.126%)
rms = 4.57, time step reduction 1 of 3 to 0.250...
068: dt: 0.2500, sse=1545949.8, rms=4.345 (3.934%)
069: dt: 0.2500, sse=1517444.0, rms=4.234 (2.570%)
rms = 4.18, time step reduction 2 of 3 to 0.125...
070: dt: 0.2500, sse=1504936.9, rms=4.185 (1.158%)
071: dt: 0.1250, sse=1490510.1, rms=4.117 (1.622%)
rms = 4.09, time step reduction 3 of 3 to 0.062...
072: dt: 0.1250, sse=1483473.8, rms=4.089 (0.667%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.area.pial
vertex spacing 1.02 +- 0.50 (0.05-->10.99) (max @ vno 88556 --> 113803)
face area 0.41 +- 0.39 (0.00-->17.09)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 145822 vertices processed
25000 of 145822 vertices processed
50000 of 145822 vertices processed
75000 of 145822 vertices processed
100000 of 145822 vertices processed
125000 of 145822 vertices processed
0 of 145822 vertices processed
25000 of 145822 vertices processed
50000 of 145822 vertices processed
75000 of 145822 vertices processed
100000 of 145822 vertices processed
125000 of 145822 vertices processed
thickness calculation complete, 567:1477 truncations.
26558 vertices at 0 distance
88357 vertices at 1 distance
87105 vertices at 2 distance
45242 vertices at 3 distance
18262 vertices at 4 distance
6964 vertices at 5 distance
2857 vertices at 6 distance
1267 vertices at 7 distance
562 vertices at 8 distance
284 vertices at 9 distance
185 vertices at 10 distance
114 vertices at 11 distance
89 vertices at 12 distance
65 vertices at 13 distance
51 vertices at 14 distance
50 vertices at 15 distance
33 vertices at 16 distance
32 vertices at 17 distance
28 vertices at 18 distance
31 vertices at 19 distance
40 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.thickness
positioning took 17.2 minutes
PIDs (5241 5244) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 15:56:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/lh.cortex.label
Total face volume 250267
Total vertex volume 247972 (mask=0)
#@# 0050017 lh 247972
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 15:56:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/rh.cortex.label
Total face volume 259357
Total vertex volume 256444 (mask=0)
#@# 0050017 rh 256444
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 15:56:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 

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 = 42
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/ribbon.mgz
mris_volmask took 12.74 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 16:09:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 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 0050017 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 16:09:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 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 0050017 rh pial 

Waiting for PID 6330 of (6330 6333 6336 6339) to complete...
Waiting for PID 6333 of (6330 6333 6336 6339) to complete...
Waiting for PID 6336 of (6330 6333 6336 6339) to complete...
Waiting for PID 6339 of (6330 6333 6336 6339) 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 0050017 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 250267
Total vertex volume 247972 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1074    761   1744  2.287 0.510     0.101     0.024        6     1.0  bankssts
 1034    708   2183  3.042 0.639     0.142     0.029       15     1.1  caudalanteriorcingulate
 4743   3115   7827  2.404 0.618     0.132     0.042       54     8.1  caudalmiddlefrontal
 1096    819   1598  1.866 0.468     0.164     0.049       16     2.4  cuneus
  641    427   1711  2.941 0.905     0.151     0.071       12     1.9  entorhinal
 3791   2809   8891  2.408 0.788     0.167     0.068       77    11.4  fusiform
 7583   5070  12689  2.276 0.590     0.139     0.048      103    15.0  inferiorparietal
 5310   3730  10702  2.331 0.734     0.163     0.066      105    16.2  inferiortemporal
 1661   1071   3178  2.920 0.727     0.135     0.049       21     3.2  isthmuscingulate
 6785   4756  11958  2.114 0.675     0.178     0.080      139    23.0  lateraloccipital
 3292   2268   6230  2.460 0.694     0.152     0.061       53     8.6  lateralorbitofrontal
 3288   2475   6332  2.214 0.748     0.191     0.083       72    12.9  lingual
 2508   1749   6684  3.053 0.987     0.153     0.058       39     5.9  medialorbitofrontal
 3864   2592   8677  2.617 0.796     0.149     0.055       71     8.8  middletemporal
  996    821   2378  2.502 0.746     0.164     0.054       12     2.6  parahippocampal
 2678   1740   4192  2.343 0.602     0.118     0.036       23     4.1  paracentral
 2780   1863   5687  2.580 0.676     0.134     0.047       39     5.1  parsopercularis
 1016    648   2576  2.764 0.813     0.157     0.067       21     2.8  parsorbitalis
 1814   1249   3618  2.526 0.588     0.137     0.041       23     2.8  parstriangularis
 1090    778   1600  2.086 0.576     0.182     0.075       18     3.5  pericalcarine
 7896   4973  11541  2.129 0.640     0.122     0.040       89    12.2  postcentral
 2050   1394   3910  2.782 0.685     0.140     0.036       28     3.0  posteriorcingulate
10428   6683  15761  2.285 0.621     0.134     0.048      116    21.7  precentral
 5829   4097  10698  2.309 0.609     0.141     0.042       81    10.4  precuneus
 1339    919   2482  2.613 0.810     0.152     0.051       23     2.6  rostralanteriorcingulate
 8826   5992  17201  2.499 0.636     0.155     0.059      133    22.0  rostralmiddlefrontal
12577   8111  24910  2.694 0.794     0.133     0.047      144    24.4  superiorfrontal
 9095   5984  13074  2.103 0.511     0.136     0.040      108    14.7  superiorparietal
 4850   3430  11087  2.679 0.731     0.142     0.046       65     9.6  superiortemporal
 7101   4740  12186  2.404 0.586     0.150     0.051      108    14.1  supramarginal
  375    298   1188  2.760 0.804     0.224     0.126       11     2.3  frontalpole
  646    493   2167  2.846 0.965     0.175     0.066       12     1.8  temporalpole
  685    540   1292  2.508 0.493     0.146     0.035        8     0.9  transversetemporal
 4857   3781  10013  2.682 0.869     0.163     0.064       91    13.5  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 0050017 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 250267
Total vertex volume 247972 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1074    766   1744  2.287 0.510     0.144     0.047       13     2.3  bankssts
 1034    816   2183  3.042 0.639     0.178     0.054       40     2.3  caudalanteriorcingulate
 4743   3319   7827  2.404 0.618     0.134     0.038       64     8.0  caudalmiddlefrontal
 1096    940   1598  1.866 0.468     0.155     0.042       15     2.1  cuneus
  641    763   1711  2.941 0.905     0.242     0.068       13     2.1  entorhinal
 3791   4214   8891  2.408 0.788     0.230     0.075      106    12.7  fusiform
 7583   6117  12689  2.276 0.590     0.155     0.041      104    14.2  inferiorparietal
 5310   5562  10702  2.331 0.734     0.203     0.056       88    14.1  inferiortemporal
 1661   1173   3178  2.920 0.727     0.143     0.041       37     2.9  isthmuscingulate
 6785   6314  11958  2.114 0.675     0.195     0.086      190    33.1  lateraloccipital
 3292   2759   6230  2.460 0.694     0.188     0.059       72     9.1  lateralorbitofrontal
 3288   3112   6332  2.214 0.748     0.194     0.064       78     9.5  lingual
 2508   2437   6684  3.053 0.987     0.202     0.058       56     7.0  medialorbitofrontal
 3864   3822   8677  2.617 0.796     0.185     0.048       72     8.9  middletemporal
  996   1134   2378  2.502 0.746     0.220     0.054       19     2.7  parahippocampal
 2678   1922   4192  2.343 0.602     0.114     0.027       25     3.4  paracentral
 2780   2449   5687  2.580 0.676     0.158     0.041       40     5.3  parsopercularis
 1016   1054   2576  2.764 0.813     0.191     0.048       18     2.0  parsorbitalis
 1814   1611   3618  2.526 0.588     0.162     0.041       26     3.2  parstriangularis
 1090    836   1600  2.086 0.576     0.163     0.056       41     2.7  pericalcarine
 7896   5927  11541  2.129 0.640     0.130     0.033      110    12.2  postcentral
 2050   1518   3910  2.782 0.685     0.145     0.041       41     3.7  posteriorcingulate
10428   7003  15761  2.285 0.621     0.120     0.034      147    15.6  precentral
 5829   5188  10698  2.309 0.609     0.165     0.045       89    12.7  precuneus
 1339   1129   2482  2.613 0.810     0.208     0.076       72     4.0  rostralanteriorcingulate
 8826   7737  17201  2.499 0.636     0.180     0.077      273    38.8  rostralmiddlefrontal
12577   9725  24910  2.694 0.794     0.140     0.039      162    22.4  superiorfrontal
 9095   6567  13074  2.103 0.511     0.136     0.036      130    14.5  superiorparietal
 4850   4706  11087  2.679 0.731     0.177     0.047      103    11.2  superiortemporal
 7101   5332  12186  2.404 0.586     0.151     0.044      130    14.5  supramarginal
  375    476   1188  2.760 0.804     0.200     0.043        4     0.8  frontalpole
  646    993   2167  2.846 0.965     0.246     0.053        8     1.8  temporalpole
  685    508   1292  2.508 0.493     0.136     0.036       16     1.0  transversetemporal
 4857   3701  10013  2.682 0.869     0.171     0.063      150    14.2  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 0050017 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 259357
Total vertex volume 256444 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1285    895   2037  2.380 0.518     0.122     0.038       11     2.4  bankssts
  965    626   1794  2.651 0.684     0.148     0.037       16     1.4  caudalanteriorcingulate
 4142   2678   7121  2.434 0.584     0.137     0.052       46     9.0  caudalmiddlefrontal
 2082   1613   3361  1.933 0.667     0.192     0.065       38     6.5  cuneus
  479    336   1419  2.829 0.952     0.184     0.093       10     1.9  entorhinal
 3281   2350   7230  2.465 0.790     0.151     0.051       51     6.9  fusiform
 8964   6161  16046  2.342 0.663     0.146     0.049      141    16.7  inferiorparietal
 5389   3690  11247  2.355 0.749     0.164     0.072      127    17.1  inferiortemporal
 1352    862   2603  2.723 0.884     0.148     0.053       20     2.8  isthmuscingulate
 7254   5165  13556  2.235 0.760     0.169     0.072      118    21.7  lateraloccipital
 3219   2224   6009  2.401 0.838     0.154     0.058       56     8.1  lateralorbitofrontal
 3025   2465   6877  2.382 0.815     0.197     0.074       63    10.9  lingual
 2961   2105   6742  2.764 1.157     0.153     0.057       56     6.3  medialorbitofrontal
 4891   3441  12341  2.877 0.820     0.151     0.049       74    10.2  middletemporal
  807    541   1499  2.430 0.926     0.130     0.035        9     1.1  parahippocampal
 2375   1560   3901  2.451 0.582     0.113     0.035       17     3.3  paracentral
 2219   1473   4354  2.705 0.649     0.118     0.038       21     3.4  parsopercularis
 1295    886   2908  2.538 0.668     0.156     0.075       89     3.3  parsorbitalis
 3327   2213   5846  2.395 0.671     0.139     0.048       44     6.8  parstriangularis
 2056   1627   2755  1.852 0.540     0.182     0.071       38     6.8  pericalcarine
 8102   5299  12044  2.148 0.717     0.128     0.043       90    14.5  postcentral
 1538   1043   3204  2.985 0.679     0.153     0.045       23     2.9  posteriorcingulate
10328   6756  16563  2.339 0.609     0.135     0.045      117    20.0  precentral
 7166   5029  12345  2.346 0.709     0.154     0.049      104    14.9  precuneus
  580    376   1023  2.743 0.643     0.139     0.052        8     1.3  rostralanteriorcingulate
10733   7140  19291  2.451 0.660     0.149     0.058      158    25.9  rostralmiddlefrontal
11886   8003  23782  2.657 0.707     0.138     0.047      155    23.3  superiorfrontal
 8829   5761  12405  2.009 0.521     0.134     0.043       97    15.0  superiorparietal
 4871   3862  11978  2.697 0.729     0.141     0.043       92     8.9  superiortemporal
 7745   5074  13221  2.353 0.599     0.136     0.046       95    14.0  supramarginal
  632    450   2014  2.843 0.685     0.221     0.086       20     2.8  frontalpole
  654    616   2789  2.937 0.864     0.212     0.073       13     2.4  temporalpole
  487    377   1011  2.556 0.593     0.157     0.038        6     0.8  transversetemporal
 2628   1871   5000  2.836 0.800     0.146     0.055       34     6.1  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 0050017 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 259357
Total vertex volume 256444 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1285    825   2037  2.380 0.518     0.152     0.049       25     2.9  bankssts
  965    735   1794  2.651 0.684     0.170     0.048       84     1.8  caudalanteriorcingulate
 4142   3000   7121  2.434 0.584     0.135     0.038       68     6.9  caudalmiddlefrontal
 2082   1984   3361  1.933 0.667     0.167     0.047       24     4.5  cuneus
  479    651   1419  2.829 0.952     0.247     0.063        7     1.4  entorhinal
 3281   3399   7230  2.465 0.790     0.209     0.057       54     9.1  fusiform
 8964   7429  16046  2.342 0.663     0.159     0.043      168    17.5  inferiorparietal
 5389   5845  11247  2.355 0.749     0.234     0.069      134    18.4  inferiortemporal
 1352   1030   2603  2.723 0.884     0.151     0.047       38     2.3  isthmuscingulate
 7254   6605  13556  2.235 0.760     0.176     0.051      155    17.0  lateraloccipital
 3219   2857   6009  2.401 0.838     0.208     0.076      126    11.6  lateralorbitofrontal
 3025   3347   6877  2.382 0.815     0.217     0.066       56     9.1  lingual
 2961   2691   6742  2.764 1.157     0.187     0.064       88     8.1  medialorbitofrontal
 4891   5147  12341  2.877 0.820     0.195     0.052       84    13.0  middletemporal
  807    693   1499  2.430 0.926     0.180     0.046       15     1.6  parahippocampal
 2375   1626   3901  2.451 0.582     0.105     0.023       28     2.5  paracentral
 2219   1731   4354  2.705 0.649     0.146     0.038       34     3.7  parsopercularis
 1295   1349   2908  2.538 0.668     0.188     0.066       22     3.0  parsorbitalis
 3327   2642   5846  2.395 0.671     0.143     0.040       48     5.9  parstriangularis
 2056   1528   2755  1.852 0.540     0.175     0.150      317     4.8  pericalcarine
 8102   6134  12044  2.148 0.717     0.136     0.037       98    13.6  postcentral
 1538   1225   3204  2.985 0.679     0.174     0.057       65     3.4  posteriorcingulate
10328   7450  16563  2.339 0.609     0.126     0.035      152    16.1  precentral
 7166   5382  12345  2.346 0.709     0.148     0.042      113    13.4  precuneus
  580    466   1023  2.743 0.643     0.185     0.060       13     1.5  rostralanteriorcingulate
10733   8346  19291  2.451 0.660     0.153     0.044      162    21.6  rostralmiddlefrontal
11886   9678  23782  2.657 0.707     0.151     0.044      205    23.4  superiorfrontal
 8829   6685  12405  2.009 0.521     0.140     0.038      108    14.5  superiorparietal
 4871   4916  11978  2.697 0.729     0.182     0.049       85    10.9  superiortemporal
 7745   6086  13221  2.353 0.599     0.148     0.044      114    15.7  supramarginal
  632    954   2014  2.843 0.685     0.268     0.052       11     1.5  frontalpole
  654   1088   2789  2.937 0.864     0.275     0.067       16     2.0  temporalpole
  487    431   1011  2.556 0.593     0.157     0.049       10     0.9  transversetemporal
 2628   1788   5000  2.836 0.800     0.167     0.059       81     7.3  insula
PIDs (6330 6333 6336 6339) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 16:10:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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 16:10:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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 6440 of (6440 6443) to complete...
Waiting for PID 6443 of (6440 6443) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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...
90 labels changed using aseg
relabeling using gibbs priors...
000:   9749 changed, 140996 examined...
001:   2325 changed, 37588 examined...
002:    677 changed, 12006 examined...
003:    278 changed, 3842 examined...
004:    148 changed, 1536 examined...
005:     83 changed, 813 examined...
006:     43 changed, 457 examined...
007:     20 changed, 231 examined...
008:     12 changed, 120 examined...
009:      6 changed, 60 examined...
010:      2 changed, 30 examined...
011:      0 changed, 16 examined...
12 labels changed using aseg
000: 318 total segments, 232 labels (3253 vertices) changed
001: 95 total segments, 9 labels (30 vertices) changed
002: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 42 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
2006 vertices marked for relabeling...
2006 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 31 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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...
167 labels changed using aseg
relabeling using gibbs priors...
000:   9790 changed, 145822 examined...
001:   2333 changed, 38201 examined...
002:    656 changed, 11999 examined...
003:    269 changed, 3734 examined...
004:    145 changed, 1554 examined...
005:     81 changed, 808 examined...
006:     35 changed, 446 examined...
007:     23 changed, 213 examined...
008:      7 changed, 130 examined...
009:      5 changed, 45 examined...
010:      4 changed, 27 examined...
011:      1 changed, 19 examined...
012:      0 changed, 8 examined...
69 labels changed using aseg
000: 304 total segments, 222 labels (2910 vertices) changed
001: 93 total segments, 13 labels (53 vertices) changed
002: 80 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 48 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1360 vertices marked for relabeling...
1360 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 23 seconds.
PIDs (6440 6443) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 16:11:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 16:11:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 rh white 

Waiting for PID 6502 of (6502 6505) to complete...
Waiting for PID 6505 of (6502 6505) 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 0050017 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 250267
Total vertex volume 247972 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1391    994   2902  2.650 0.604     0.172     0.063       25     3.8  G&S_frontomargin
 1530   1140   3591  2.374 0.672     0.176     0.080       26     5.0  G&S_occipital_inf
 2177   1346   3413  2.196 0.656     0.127     0.045       24     4.0  G&S_paracentral
 1861   1265   3904  2.726 0.602     0.155     0.056       32     3.9  G&S_subcentral
  785    552   1857  2.540 0.765     0.206     0.111       22     3.8  G&S_transv_frontopol
 2337   1631   4794  2.767 0.697     0.131     0.040       26     3.7  G&S_cingul-Ant
 1389    975   2800  2.897 0.599     0.127     0.028       13     1.4  G&S_cingul-Mid-Ant
 1591   1103   3002  2.745 0.570     0.129     0.029       16     1.9  G&S_cingul-Mid-Post
  690    467   1746  3.149 0.593     0.146     0.051        9     1.4  G_cingul-Post-dorsal
  346    230    860  3.164 0.645     0.168     0.084        8     1.0  G_cingul-Post-ventral
 1062    802   1738  1.918 0.518     0.179     0.062       18     2.8  G_cuneus
 1855   1171   4008  2.539 0.812     0.148     0.064       33     4.8  G_front_inf-Opercular
  438    292    946  2.359 0.684     0.181     0.075       11     1.2  G_front_inf-Orbital
 1116    744   2472  2.612 0.582     0.141     0.051       16     2.2  G_front_inf-Triangul
 5168   3319  10492  2.418 0.698     0.156     0.066       92    14.4  G_front_middle
 8702   5398  18460  2.744 0.859     0.138     0.053      115    19.2  G_front_sup
  828    784   2102  2.689 0.837     0.198     0.077       18     2.8  G_Ins_lg&S_cent_ins
 1430   1003   3490  2.743 1.046     0.187     0.102       44     6.5  G_insular_short
 2154   1464   4368  2.282 0.704     0.179     0.082       52     7.2  G_occipital_middle
 1021    658   1492  2.051 0.546     0.164     0.072       18     3.3  G_occipital_sup
 1465   1065   3992  2.383 0.802     0.184     0.088       41     5.8  G_oc-temp_lat-fusifor
 2310   1772   4506  2.141 0.677     0.198     0.085       59     9.2  G_oc-temp_med-Lingual
 1470    993   3588  2.787 0.813     0.145     0.058       24     3.8  G_oc-temp_med-Parahip
 2274   1490   5706  2.634 0.809     0.170     0.085       55     8.3  G_orbital
 3173   2011   5481  2.195 0.589     0.152     0.058       52     7.6  G_pariet_inf-Angular
 3705   2493   7176  2.479 0.546     0.166     0.060       72     8.9  G_pariet_inf-Supramar
 3923   2550   5926  2.062 0.497     0.139     0.039       50     6.4  G_parietal_sup
 3141   1801   4529  2.132 0.547     0.125     0.046       39     5.9  G_postcentral
 3973   2354   6409  2.265 0.641     0.140     0.061       55    11.1  G_precentral
 3655   2485   7639  2.336 0.586     0.157     0.055       70     8.4  G_precuneus
 1004    753   3610  3.171 1.071     0.183     0.080       20     3.4  G_rectus
  861    527   1542  2.664 1.066     0.123     0.066       17     1.6  G_subcallosal
  490    366   1010  2.669 0.499     0.132     0.028        4     0.6  G_temp_sup-G_T_transv
 1795   1194   5159  2.838 0.914     0.169     0.070       40     5.5  G_temp_sup-Lateral
  527    417   1811  3.035 0.862     0.150     0.038        6     0.8  G_temp_sup-Plan_polar
  869    578   1455  2.415 0.595     0.104     0.030        7     1.1  G_temp_sup-Plan_tempo
 3262   2216   7620  2.467 0.682     0.190     0.089       89    13.6  G_temporal_inf
 2228   1506   5847  2.667 0.779     0.165     0.067       50     6.3  G_temporal_middle
  225    168    541  2.848 0.527     0.128     0.030        3     0.3  Lat_Fis-ant-Horizont
  250    178    401  2.750 0.622     0.120     0.030        2     0.3  Lat_Fis-ant-Vertical
 1261    881   1921  2.647 0.531     0.137     0.035       12     1.8  Lat_Fis-post
 1842   1301   3059  1.923 0.595     0.194     0.085       40     7.1  Pole_occipital
 1674   1125   4564  2.709 0.990     0.160     0.066       34     4.6  Pole_temporal
 1345    935   2139  2.444 0.727     0.158     0.058       18     3.6  S_calcarine
 4233   2860   4623  1.865 0.486     0.118     0.031       30     5.3  S_central
 1363    931   1933  2.173 0.540     0.103     0.022        8     1.2  S_cingul-Marginalis
  498    353    808  2.725 0.565     0.134     0.041        4     0.9  S_circular_insula_ant
 1492   1407   3329  2.531 0.602     0.161     0.040       15     2.5  S_circular_insula_inf
 2196   1490   3160  2.560 0.605     0.123     0.029       15     3.1  S_circular_insula_sup
  906    664   1391  2.127 0.686     0.118     0.027        7     1.2  S_collat_transv_ant
  427    348    896  2.328 0.776     0.172     0.074        6     1.3  S_collat_transv_post
 2779   1913   4327  2.422 0.536     0.122     0.031       22     3.5  S_front_inf
 1491   1047   2732  2.589 0.623     0.148     0.046       17     3.2  S_front_middle
 3479   2475   5487  2.393 0.546     0.128     0.039       28     5.3  S_front_sup
  139    100    177  2.018 0.477     0.162     0.046        2     0.3  S_interm_prim-Jensen
 3527   2380   4553  2.084 0.534     0.121     0.028       31     3.7  S_intrapariet&P_trans
  845    596   1228  2.138 0.677     0.183     0.078       16     2.7  S_oc_middle&Lunatus
 1214    832   1612  2.115 0.492     0.138     0.054       16     2.6  S_oc_sup&transversal
  791    561    904  1.893 0.503     0.130     0.035        5     1.3  S_occipital_ant
  771    552   1295  2.577 0.856     0.120     0.034        5     1.0  S_oc-temp_lat
 1703   1411   3268  2.208 0.755     0.188     0.074       31     6.4  S_oc-temp_med&Lingual
  329    239    470  2.236 0.381     0.135     0.032        3     0.4  S_orbital_lateral
  520    383    898  2.632 0.748     0.128     0.029        5     0.5  S_orbital_med-olfact
 1054    723   1771  2.372 0.709     0.138     0.037       10     1.6  S_orbital-H_Shaped
  998    760   1525  2.127 0.626     0.129     0.029        8     1.2  S_parieto_occipital
 1490    894   1784  2.732 0.848     0.140     0.042       26     2.5  S_pericallosal
 3735   2532   5109  2.226 0.542     0.127     0.034       34     5.0  S_postcentral
 2262   1510   3871  2.607 0.501     0.125     0.035       21     2.9  S_precentral-inf-part
 1885   1258   2549  2.319 0.578     0.121     0.033       15     2.6  S_precentral-sup-part
  679    465   1480  3.107 0.797     0.147     0.045        9     1.3  S_suborbital
 1263    910   1903  2.436 0.620     0.127     0.031       11     1.6  S_subparietal
 1533   1131   2108  2.083 0.613     0.128     0.028       15     1.8  S_temporal_inf
 5115   3454   8208  2.424 0.588     0.114     0.034       44     6.7  S_temporal_sup
  293    212    505  2.527 0.504     0.098     0.020        2     0.2  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050017 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 259357
Total vertex volume 256444 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
  936    652   2149  2.694 0.650     0.155     0.057       15     2.2  G&S_frontomargin
 1221    903   2864  2.616 0.821     0.185     0.082       23     4.0  G&S_occipital_inf
 1963   1163   3040  2.263 0.558     0.118     0.043       17     3.4  G&S_paracentral
 1673   1111   3571  2.788 0.746     0.145     0.047       26     3.5  G&S_subcentral
 1503    992   3061  2.426 0.569     0.164     0.067       29     4.4  G&S_transv_frontopol
 2988   2082   6156  2.789 0.682     0.138     0.045       37     5.3  G&S_cingul-Ant
 1346    940   2635  2.691 0.628     0.130     0.037       15     2.1  G&S_cingul-Mid-Ant
 1314    907   2564  2.693 0.572     0.122     0.030       10     1.7  G&S_cingul-Mid-Post
  528    332   1317  3.119 0.623     0.171     0.066       11     1.4  G_cingul-Post-dorsal
  334    222    917  3.146 0.999     0.162     0.053        5     0.7  G_cingul-Post-ventral
 1905   1506   3145  1.908 0.704     0.202     0.072       39     6.8  G_cuneus
 1430    910   3449  2.735 0.725     0.131     0.048       20     2.7  G_front_inf-Opercular
  477    306   1053  2.454 0.647     0.187     0.111       76     1.7  G_front_inf-Orbital
 1845   1215   3465  2.398 0.764     0.157     0.058       32     4.5  G_front_inf-Triangul
 5869   3627  11349  2.409 0.714     0.161     0.076      112    18.9  G_front_middle
 7778   5134  17540  2.813 0.753     0.149     0.055      116    17.7  G_front_sup
  413    293    975  3.056 0.711     0.164     0.065        5     1.3  G_Ins_lg&S_cent_ins
  671    439   1150  2.253 0.895     0.168     0.088       14     2.2  G_insular_short
 2356   1607   5014  2.465 0.658     0.169     0.071       44     7.2  G_occipital_middle
 1461    938   2199  2.028 0.572     0.147     0.051       18     3.1  G_occipital_sup
 1378    979   3876  2.747 0.824     0.176     0.067       29     3.9  G_oc-temp_lat-fusifor
 1917   1515   4897  2.415 0.893     0.190     0.073       43     6.5  G_oc-temp_med-Lingual
 1014    675   2483  2.661 0.925     0.161     0.067       18     2.6  G_oc-temp_med-Parahip
 2525   1739   5710  2.506 0.688     0.164     0.068       47     7.6  G_orbital
 4221   2707   7688  2.231 0.669     0.152     0.054       71     9.0  G_pariet_inf-Angular
 4072   2637   7856  2.398 0.664     0.145     0.054       59     8.7  G_pariet_inf-Supramar
 3284   2052   5209  2.085 0.535     0.138     0.050       44     6.3  G_parietal_sup
 3004   1866   4846  2.178 0.695     0.133     0.055       38     6.6  G_postcentral
 4065   2595   7223  2.294 0.693     0.153     0.062       66    11.1  G_precentral
 3287   2195   6864  2.476 0.666     0.162     0.058       59     7.9  G_precuneus
  579    479   2158  3.205 1.019     0.197     0.068       16     1.3  G_rectus
  862    539    709  1.476 1.182     0.151     0.081       23     2.9  G_subcallosal
  299    287    998  2.684 0.615     0.214     0.043        6     0.5  G_temp_sup-G_T_transv
 1836   1290   4607  2.695 0.757     0.158     0.065       31     5.3  G_temp_sup-Lateral
  955    899   2779  2.458 1.102     0.190     0.059       53     2.4  G_temp_sup-Plan_polar
  989    694   1955  2.482 0.648     0.132     0.045       11     1.9  G_temp_sup-Plan_tempo
 3123   2091   7282  2.342 0.831     0.180     0.084       85    11.6  G_temporal_inf
 3040   2151   9214  3.062 0.814     0.168     0.059       58     7.8  G_temporal_middle
  470    306    594  2.312 0.493     0.092     0.020        2     0.4  Lat_Fis-ant-Horizont
  242    183    401  2.555 0.453     0.110     0.022        1     0.2  Lat_Fis-ant-Vertical
 1481    972   2260  2.854 0.578     0.115     0.029       10     1.7  Lat_Fis-post
 3230   2342   5827  2.050 0.743     0.184     0.081       63    11.2  Pole_occipital
 1558   1237   4692  2.593 0.884     0.185     0.080       33     5.8  Pole_temporal
 2315   2012   3500  2.175 0.759     0.203     0.072       40     8.4  S_calcarine
 4001   2772   4599  1.979 0.533     0.119     0.030       29     4.9  S_central
 1297    904   1930  2.274 0.557     0.106     0.026        9     1.3  S_cingul-Marginalis
  317    209    445  2.325 0.606     0.120     0.046        3     0.6  S_circular_insula_ant
  843    883   2337  2.933 0.752     0.159     0.037        9     1.3  S_circular_insula_inf
 1413    964   2292  2.894 0.564     0.108     0.022        8     1.3  S_circular_insula_sup
 1038    719   1508  2.191 0.555     0.102     0.020        5     0.9  S_collat_transv_ant
  363    252    435  1.803 0.720     0.142     0.070        5     1.2  S_collat_transv_post
 2752   1891   4245  2.450 0.566     0.128     0.040       25     4.4  S_front_inf
 2650   1855   4337  2.490 0.569     0.136     0.041       27     4.5  S_front_middle
 3068   2090   4697  2.366 0.556     0.118     0.033       26     4.2  S_front_sup
  476    321    569  2.404 0.476     0.121     0.030        4     0.6  S_interm_prim-Jensen
 3470   2346   4401  2.025 0.504     0.125     0.034       30     4.5  S_intrapariet&P_trans
 1157    863   1722  2.050 0.528     0.163     0.058       14     3.0  S_oc_middle&Lunatus
  957    661   1095  1.904 0.427     0.128     0.037        8     1.3  S_oc_sup&transversal
  728    518   1175  2.452 0.775     0.131     0.038        7     1.1  S_occipital_ant
  892    628   1553  2.527 0.649     0.152     0.071       22     2.7  S_oc-temp_lat
 1171    869   2131  2.300 0.812     0.120     0.027        9     1.2  S_oc-temp_med&Lingual
  535    367    904  2.618 0.681     0.117     0.037        4     0.5  S_orbital_lateral
  714    542   1332  2.414 0.702     0.151     0.063       13     1.8  S_orbital_med-olfact
 1116    785   2153  2.560 0.774     0.140     0.046       20     2.1  S_orbital-H_Shaped
 2403   1696   2960  1.938 0.525     0.154     0.049       31     4.9  S_parieto_occipital
 1050    635    959  2.410 0.818     0.158     0.043       21     1.8  S_pericallosal
 3696   2529   4806  2.058 0.459     0.120     0.030       29     4.9  S_postcentral
 2017   1348   3174  2.438 0.522     0.121     0.038       17     3.0  S_precentral-inf-part
 1985   1352   2837  2.469 0.491     0.126     0.034       15     2.9  S_precentral-sup-part
  435    308    964  3.266 0.917     0.142     0.029        4     0.5  S_suborbital
 1709   1184   2833  2.563 0.740     0.130     0.034       17     2.4  S_subparietal
 1595   1116   2578  2.434 0.652     0.130     0.032       14     2.1  S_temporal_inf
 5753   4106   9774  2.514 0.587     0.121     0.034       65     6.9  S_temporal_sup
  256    189    456  2.398 0.512     0.091     0.018        1     0.2  S_temporal_transverse
PIDs (6502 6505) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 16:12:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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 16:12:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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 6577 of (6577 6580) to complete...
Waiting for PID 6580 of (6577 6580) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 383 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1240 labels changed using aseg
relabeling using gibbs priors...
000:   2165 changed, 140996 examined...
001:    527 changed, 9847 examined...
002:    166 changed, 2986 examined...
003:     85 changed, 947 examined...
004:     37 changed, 450 examined...
005:     17 changed, 183 examined...
006:     12 changed, 106 examined...
007:      7 changed, 69 examined...
008:      7 changed, 53 examined...
009:      3 changed, 40 examined...
010:      2 changed, 23 examined...
011:      0 changed, 11 examined...
297 labels changed using aseg
000: 84 total segments, 51 labels (823 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1478 vertices marked for relabeling...
1478 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050017 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...
1574 labels changed using aseg
relabeling using gibbs priors...
000:   2167 changed, 145822 examined...
001:    519 changed, 9948 examined...
002:    177 changed, 2877 examined...
003:     98 changed, 1001 examined...
004:     49 changed, 518 examined...
005:     27 changed, 269 examined...
006:     16 changed, 160 examined...
007:     13 changed, 90 examined...
008:     13 changed, 71 examined...
009:     11 changed, 56 examined...
010:     13 changed, 64 examined...
011:     10 changed, 65 examined...
012:      4 changed, 62 examined...
013:      2 changed, 28 examined...
014:      2 changed, 14 examined...
015:      2 changed, 14 examined...
016:      2 changed, 11 examined...
017:      3 changed, 16 examined...
018:      0 changed, 22 examined...
409 labels changed using aseg
000: 83 total segments, 50 labels (693 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
847 vertices marked for relabeling...
847 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 19 seconds.
PIDs (6577 6580) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 16:12:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 16:12:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 rh white 

Waiting for PID 6631 of (6631 6634) to complete...
Waiting for PID 6634 of (6631 6634) 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 0050017 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 250267
Total vertex volume 247972 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1811   1229   3774  3.027 0.612     0.138     0.032       24     2.2  caudalanteriorcingulate
 5032   3320   8328  2.411 0.615     0.132     0.041       56     8.5  caudalmiddlefrontal
 1397   1020   2063  1.930 0.487     0.157     0.046       19     2.7  cuneus
  696    442   1723  2.938 0.834     0.158     0.070       14     2.1  entorhinal
 3349   2493   7156  2.308 0.735     0.161     0.066       65     9.7  fusiform
 7661   5103  12672  2.241 0.587     0.139     0.049      106    15.4  inferiorparietal
 5335   3751  11594  2.403 0.768     0.167     0.069      113    16.8  inferiortemporal
 1674   1087   3254  2.927 0.726     0.136     0.050       23     3.3  isthmuscingulate
 6770   4720  11948  2.106 0.674     0.179     0.081      135    23.4  lateraloccipital
 4223   2893   8634  2.519 0.772     0.159     0.068       80    12.7  lateralorbitofrontal
 3404   2580   6711  2.217 0.754     0.194     0.085       80    13.9  lingual
 2248   1616   6364  3.049 1.046     0.164     0.070       44     6.1  medialorbitofrontal
 5252   3587  10931  2.516 0.740     0.141     0.048       81    10.6  middletemporal
 1020    836   2435  2.512 0.751     0.162     0.054       12     2.7  parahippocampal
 3209   2082   5003  2.333 0.612     0.121     0.038       29     5.2  paracentral
 2649   1774   5395  2.590 0.680     0.132     0.046       36     4.7  parsopercularis
  989    691   2156  2.613 0.665     0.151     0.054       18     2.1  parsorbitalis
 2338   1567   4426  2.509 0.560     0.141     0.044       31     3.7  parstriangularis
 1109    796   1640  2.098 0.585     0.183     0.074       19     3.5  pericalcarine
 9019   5716  13086  2.152 0.638     0.126     0.041      101    14.5  postcentral
 2201   1500   4126  2.757 0.659     0.139     0.036       29     3.2  posteriorcingulate
10311   6582  15617  2.292 0.624     0.134     0.048      117    21.6  precentral
 5910   4164  10827  2.292 0.611     0.143     0.043       84    10.8  precuneus
 1975   1322   3724  2.644 0.835     0.139     0.047       30     3.5  rostralanteriorcingulate
 6205   4211  12015  2.474 0.652     0.154     0.057       89    15.5  rostralmiddlefrontal
13182   8583  26683  2.678 0.792     0.138     0.052      165    28.9  superiorfrontal
 7627   5020  10768  2.082 0.504     0.132     0.038       85    11.6  superiorparietal
 6535   4697  15444  2.715 0.776     0.144     0.047       88    13.2  superiortemporal
 6553   4376  11132  2.410 0.573     0.150     0.050       99    12.8  supramarginal
  667    530   1275  2.490 0.485     0.145     0.033        8     0.8  transversetemporal
 3252   2597   7066  2.747 0.786     0.159     0.062       56     8.6  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050017 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 259357
Total vertex volume 256444 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1106    722   2138  2.678 0.686     0.151     0.040       19     1.9  caudalanteriorcingulate
 4230   2731   7119  2.420 0.578     0.133     0.051       45     8.8  caudalmiddlefrontal
 2692   2004   3997  1.894 0.626     0.182     0.064       46     8.1  cuneus
  436    298   1294  2.768 0.887     0.180     0.088        9     1.6  entorhinal
 2902   2097   6617  2.512 0.791     0.150     0.050       43     5.8  fusiform
 9125   6242  16147  2.334 0.661     0.147     0.047      126    17.4  inferiorparietal
 5788   3965  12092  2.357 0.753     0.164     0.072      135    18.3  inferiortemporal
 1381    876   2607  2.708 0.880     0.147     0.053       20     2.9  isthmuscingulate
 7175   5119  13293  2.229 0.743     0.170     0.070      115    20.7  lateraloccipital
 3548   2481   7110  2.467 0.769     0.156     0.059       65     9.1  lateralorbitofrontal
 2995   2402   6676  2.360 0.836     0.194     0.076       63    11.1  lingual
 2176   1556   4848  2.618 1.331     0.155     0.059       44     4.9  medialorbitofrontal
 5761   4070  13797  2.806 0.793     0.145     0.050       97    11.2  middletemporal
  843    565   1635  2.518 0.990     0.130     0.037        9     1.3  parahippocampal
 2579   1677   4253  2.483 0.606     0.114     0.034       19     3.6  paracentral
 2803   1877   5504  2.690 0.630     0.121     0.039       28     4.4  parsopercularis
  995    673   2104  2.397 0.650     0.146     0.076       82     2.5  parsorbitalis
 3377   2219   5854  2.380 0.679     0.143     0.052       48     7.3  parstriangularis
 2032   1618   2736  1.847 0.541     0.185     0.072       38     6.9  pericalcarine
 9048   5919  13680  2.183 0.720     0.129     0.043      101    16.0  postcentral
 1585   1079   3231  2.975 0.664     0.152     0.045       24     2.9  posteriorcingulate
 9733   6402  15754  2.341 0.604     0.136     0.045      112    19.0  precentral
 7274   5124  12754  2.343 0.714     0.154     0.049      105    15.2  precuneus
  876    574   1412  2.683 0.775     0.130     0.048       12     1.6  rostralanteriorcingulate
 7982   5262  14541  2.485 0.674     0.151     0.060      121    19.9  rostralmiddlefrontal
15382  10413  30991  2.620 0.706     0.143     0.050      210    31.9  superiorfrontal
 7316   4778  10238  2.004 0.511     0.134     0.042       82    12.2  superiorparietal
 6300   5013  15935  2.664 0.751     0.149     0.048      116    13.4  superiortemporal
 7233   4733  12366  2.355 0.595     0.135     0.046       88    13.2  supramarginal
  462    373   1032  2.563 0.606     0.168     0.040        6     0.8  transversetemporal
 2479   1761   4687  2.851 0.799     0.145     0.055       33     5.7  insula
PIDs (6631 6634) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 16:13:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 pctsurfcon --s 0050017 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 16:13:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts

 pctsurfcon --s 0050017 --rh-only 

Waiting for PID 6701 of (6701 6708) to complete...
Waiting for PID 6708 of (6701 6708) to complete...

 pctsurfcon --s 0050017 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts/pctsurfcon.log
Sun Oct  8 16:13:40 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-6.0.0/0050017/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-105 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-6.0.0/0050017/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6701/lh.wm.mgh --regheader 0050017 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050017/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 72207
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6701/lh.wm.mgh
Dim: 140996 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6701/lh.gm.mgh --projfrac 0.3 --regheader 0050017 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050017/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 85095
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6701/lh.gm.mgh
Dim: 140996 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6701/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6701/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.w-g.pct.mgh --annot 0050017 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/lh.w-g.pct.mgh --annot 0050017 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/lh.w-g.pct.mgh
Vertex Area is 0.680501 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 0050017 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/scripts/pctsurfcon.log
Sun Oct  8 16:13:40 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-6.0.0/0050017/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-105 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-6.0.0/0050017/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6708/rh.wm.mgh --regheader 0050017 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050017/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 75151
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6708/rh.wm.mgh
Dim: 145822 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6708/rh.gm.mgh --projfrac 0.3 --regheader 0050017 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050017/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 88044
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6708/rh.gm.mgh
Dim: 145822 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6708/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/tmp.pctsurfcon.6708/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.w-g.pct.mgh --annot 0050017 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.w-g.pct.mgh --annot 0050017 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.w-g.pct.mgh
Vertex Area is 0.687227 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 (6701 6708) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 16:13:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
3715 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2939 voxels changed to hypointensity...
6438 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 16:14:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017

 mri_aparc2aseg --s 0050017 --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 16:14:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017

 mri_aparc2aseg --s 0050017 --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 16:14:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017

 mri_aparc2aseg --s 0050017 --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 6860 of (6860 6863 6866) to complete...
Waiting for PID 6863 of (6860 6863 6866) to complete...
Waiting for PID 6866 of (6860 6863 6866) to complete...

 mri_aparc2aseg --s 0050017 --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 0050017
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/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-6.0.0/0050017/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.92
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 19
rescaling Left_Inf_Lat_Vent from 34 --> 28
rescaling Left_Cerebellum_White_Matter from 86 --> 84
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 81
rescaling Left_Pallidum from 98 --> 89
rescaling Third_Ventricle from 25 --> 26
rescaling Fourth_Ventricle from 22 --> 18
rescaling Brain_Stem from 81 --> 83
rescaling Left_Hippocampus from 57 --> 59
rescaling Left_Amygdala from 56 --> 56
rescaling CSF from 32 --> 37
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 84
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 12
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 56
rescaling Right_Thalamus_Proper from 85 --> 80
rescaling Right_Caudate from 62 --> 70
rescaling Right_Putamen from 80 --> 75
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 68
rescaling Right_VentralDC from 86 --> 81
rescaling Fifth_Ventricle from 40 --> 32
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 56
  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 = 495754
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 253 changed.
pass 2: 38 changed.
pass 3: 13 changed.
pass 4: 7 changed.
pass 5: 1 changed.
pass 6: 1 changed.
pass 7: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050017 --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 0050017
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/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-6.0.0/0050017/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.92
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 19
rescaling Left_Inf_Lat_Vent from 34 --> 28
rescaling Left_Cerebellum_White_Matter from 86 --> 84
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 81
rescaling Left_Pallidum from 98 --> 89
rescaling Third_Ventricle from 25 --> 26
rescaling Fourth_Ventricle from 22 --> 18
rescaling Brain_Stem from 81 --> 83
rescaling Left_Hippocampus from 57 --> 59
rescaling Left_Amygdala from 56 --> 56
rescaling CSF from 32 --> 37
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 84
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 12
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 56
rescaling Right_Thalamus_Proper from 85 --> 80
rescaling Right_Caudate from 62 --> 70
rescaling Right_Putamen from 80 --> 75
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 68
rescaling Right_VentralDC from 86 --> 81
rescaling Fifth_Ventricle from 40 --> 32
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 56
  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 = 495849
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 253 changed.
pass 2: 38 changed.
pass 3: 13 changed.
pass 4: 7 changed.
pass 5: 1 changed.
pass 6: 1 changed.
pass 7: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050017 --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 0050017
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/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-6.0.0/0050017/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.92
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 19
rescaling Left_Inf_Lat_Vent from 34 --> 28
rescaling Left_Cerebellum_White_Matter from 86 --> 84
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 81
rescaling Left_Pallidum from 98 --> 89
rescaling Third_Ventricle from 25 --> 26
rescaling Fourth_Ventricle from 22 --> 18
rescaling Brain_Stem from 81 --> 83
rescaling Left_Hippocampus from 57 --> 59
rescaling Left_Amygdala from 56 --> 56
rescaling CSF from 32 --> 37
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 84
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 12
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 56
rescaling Right_Thalamus_Proper from 85 --> 80
rescaling Right_Caudate from 62 --> 70
rescaling Right_Putamen from 80 --> 75
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 68
rescaling Right_VentralDC from 86 --> 81
rescaling Fifth_Ventricle from 40 --> 32
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 56
  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 = 495849
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 253 changed.
pass 2: 38 changed.
pass 3: 13 changed.
pass 4: 7 changed.
pass 5: 1 changed.
pass 6: 1 changed.
pass 7: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (6860 6863 6866) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 16:23:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri

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

Sun Oct  8 16:23:20 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-6.0.0/0050017/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-105 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-6.0.0/0050017/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-105
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 16:23:20 CEST 2017 
Ended   at Sun Oct  8 16:23:26 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 16:23:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017

 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 0050017 


$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 0050017 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1864638 mm^3    (det: 1.044763 )
Computing euler number
orig.nofix lheno = -446, rheno = -482
orig.nofix lhholes =  224, rhholes = 242
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
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 16:26:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017

 mri_aparc2aseg --s 0050017 --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 0050017
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-6.0.0/0050017/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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-6.0.0/0050017/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7398 vertices from left hemi
Ripped 8275 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-6.0.0/0050017/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 = 995606
Used brute-force search on 11 voxels
Fixing Parahip LH WM
  Found 10 clusters
     0 k 1057.000000
     1 k 587.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 4.000000
     8 k 1.000000
     9 k 18.000000
Fixing Parahip RH WM
  Found 4 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1221.000000
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 0050017 --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 0050017 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-105
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1864638 mm^3    (det: 1.044763 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
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-6.0.0/0050017/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 16:35:38 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 7793 of (7793 7799 7805 7811 7817) to complete...
Waiting for PID 7799 of (7793 7799 7805 7811 7817) to complete...
Waiting for PID 7805 of (7793 7799 7805 7811 7817) to complete...
Waiting for PID 7811 of (7793 7799 7805 7811 7817) to complete...
Waiting for PID 7817 of (7793 7799 7805 7811 7817) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 756
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4885
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 1228
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9137
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 436
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4513
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 809
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6792
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 1134
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6918
mri_label2label: Done

PIDs (7793 7799 7805 7811 7817) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 7859 of (7859 7865 7870 7874) to complete...
Waiting for PID 7865 of (7859 7865 7870 7874) to complete...
Waiting for PID 7870 of (7859 7865 7870 7874) to complete...
Waiting for PID 7874 of (7859 7865 7870 7874) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 655
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4725
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 3466
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 17055
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 802
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4983
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 772
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4194
mri_label2label: Done

PIDs (7859 7865 7870 7874) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 7931 of (7931 7937 7943 7946 7955) to complete...
Waiting for PID 7937 of (7931 7937 7943 7946 7955) to complete...
Waiting for PID 7943 of (7931 7937 7943 7946 7955) to complete...
Waiting for PID 7946 of (7931 7937 7943 7946 7955) to complete...
Waiting for PID 7955 of (7931 7937 7943 7946 7955) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 627
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5268
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 1546
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 9660
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 785
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2803
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 94
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1384
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 65
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1264
mri_label2label: Done

PIDs (7931 7937 7943 7946 7955) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 8000 of (8000 8006 8012 8015 8021) to complete...
Waiting for PID 8006 of (8000 8006 8012 8015 8021) to complete...
Waiting for PID 8012 of (8000 8006 8012 8015 8021) to complete...
Waiting for PID 8015 of (8000 8006 8012 8015 8021) to complete...
Waiting for PID 8021 of (8000 8006 8012 8015 8021) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1188
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 393
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2485
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 107
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1611
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 237
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2233
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 465
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2784
mri_label2label: Done

PIDs (8000 8006 8012 8015 8021) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 8084 of (8084 8090 8094 8099) to complete...
Waiting for PID 8090 of (8084 8090 8094 8099) to complete...
Waiting for PID 8094 of (8084 8090 8094 8099) to complete...
Waiting for PID 8099 of (8084 8090 8094 8099) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 303
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1852
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 1483
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8518
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 284
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2196
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 258
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1409
mri_label2label: Done

PIDs (8084 8090 8094 8099) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 8146 of (8146 8152 8157 8164 8170) to complete...
Waiting for PID 8152 of (8146 8152 8157 8164 8170) to complete...
Waiting for PID 8157 of (8146 8152 8157 8164 8170) to complete...
Waiting for PID 8164 of (8146 8152 8157 8164 8170) to complete...
Waiting for PID 8170 of (8146 8152 8157 8164 8170) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 449
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 3854
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 552
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 3886
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 178
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 691
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 38
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 508
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 140996
Number of reverse mapping hits = 22
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 472
mri_label2label: Done

PIDs (8146 8152 8157 8164 8170) completed and logs appended.

 mris_label2annot --s 0050017 --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-6.0.0/0050017/label
cmdline mris_label2annot --s 0050017 --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-105
machine  x86_64
user     ntraut

subject 0050017
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-6.0.0/0050017/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 95751 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050017 --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-6.0.0/0050017/label
cmdline mris_label2annot --s 0050017 --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-105
machine  x86_64
user     ntraut

subject 0050017
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-6.0.0/0050017/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 115088 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 250267
Total vertex volume 247972 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1400    792   2082  2.087 0.505     0.146     0.059       24     3.2  BA1_exvivo
 5117   3306   7290  2.267 0.542     0.127     0.039       53     8.0  BA2_exvivo
 1340    905   1292  1.826 0.421     0.147     0.038       15     1.9  BA3a_exvivo
 2918   1920   4040  1.988 0.652     0.119     0.037       32     4.0  BA3b_exvivo
 2293   1430   3773  2.395 0.647     0.126     0.041       23     4.1  BA4a_exvivo
 1831   1221   2460  2.115 0.604     0.120     0.038       13     3.1  BA4p_exvivo
12899   8004  20686  2.372 0.629     0.131     0.050      151    27.6  BA6_exvivo
 2949   1995   5819  2.536 0.635     0.137     0.050       40     5.9  BA44_exvivo
 3069   2049   5925  2.524 0.614     0.139     0.048       42     5.7  BA45_exvivo
 2199   1572   3475  2.014 0.554     0.189     0.077       44     7.2  V1_exvivo
 5716   4230  10174  2.109 0.712     0.180     0.072      106    19.0  V2_exvivo
 2402   1682   4820  2.387 0.690     0.168     0.069       44     6.9  MT_exvivo
  532    382   1452  2.646 0.716     0.160     0.076       10     1.9  perirhinal_exvivo
  580    422   1616  2.918 0.860     0.127     0.035        7     0.6  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050017 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 250267
Total vertex volume 247972 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
  921    481   1267  2.030 0.432     0.142     0.060       17     2.0  BA1_exvivo
 2075   1291   2936  2.262 0.537     0.104     0.028       14     2.4  BA2_exvivo
 1116    764   1022  1.803 0.404     0.154     0.041       13     1.7  BA3a_exvivo
 1732   1146   1968  1.675 0.406     0.101     0.029       15     1.9  BA3b_exvivo
 2296   1458   3628  2.318 0.655     0.128     0.044       23     4.5  BA4a_exvivo
 1548   1030   1937  2.045 0.584     0.123     0.036       11     2.6  BA4p_exvivo
 7005   4205  11392  2.415 0.652     0.128     0.051       82    15.2  BA6_exvivo
 1742   1173   3760  2.578 0.586     0.139     0.051       25     3.2  BA44_exvivo
 1197    789   2578  2.656 0.607     0.142     0.053       17     2.5  BA45_exvivo
 2349   1676   3713  2.011 0.562     0.195     0.082       51     8.7  V1_exvivo
 2720   1957   4131  2.005 0.620     0.171     0.066       42     8.1  V2_exvivo
  629    419   1066  2.246 0.671     0.152     0.062       11     1.5  MT_exvivo
  271    188    731  2.678 0.726     0.135     0.064        4     0.7  perirhinal_exvivo
  307    212    764  2.994 0.898     0.108     0.026        2     0.3  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 16:39:20 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 8288 of (8288 8294 8299 8302 8309) to complete...
Waiting for PID 8294 of (8288 8294 8299 8302 8309) to complete...
Waiting for PID 8299 of (8288 8294 8299 8302 8309) to complete...
Waiting for PID 8302 of (8288 8294 8299 8302 8309) to complete...
Waiting for PID 8309 of (8288 8294 8299 8302 8309) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 814
Checking for and removing duplicates
Writing label file ./rh.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/rh.BA2_exvivo.label --trgsubject 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 1176
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7863
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 356
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4336
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 583
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5105
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 957
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6704
mri_label2label: Done

PIDs (8288 8294 8299 8302 8309) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 8357 of (8357 8363 8368 8372) to complete...
Waiting for PID 8363 of (8357 8363 8368 8372) to complete...
Waiting for PID 8368 of (8357 8363 8368 8372) to complete...
Waiting for PID 8372 of (8357 8363 8368 8372) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 640
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5113
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 2630
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14886
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 1991
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8903
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 2428
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7783
mri_label2label: Done

PIDs (8357 8363 8368 8372) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 8432 of (8432 8438 8443 8447 8454) to complete...
Waiting for PID 8438 of (8432 8438 8443 8447 8454) to complete...
Waiting for PID 8443 of (8432 8438 8443 8447 8454) to complete...
Waiting for PID 8447 of (8432 8438 8443 8447 8454) to complete...
Waiting for PID 8454 of (8432 8438 8443 8447 8454) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 1806
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6533
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 2275
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10291
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 491
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2423
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 124
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1162
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 89
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 841
mri_label2label: Done

PIDs (8432 8438 8443 8447 8454) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 8515 of (8515 8521 8525 8529 8537) to complete...
Waiting for PID 8521 of (8515 8521 8525 8529 8537) to complete...
Waiting for PID 8525 of (8515 8521 8525 8529 8537) to complete...
Waiting for PID 8529 of (8515 8521 8525 8529 8537) to complete...
Waiting for PID 8537 of (8515 8521 8525 8529 8537) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 254
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1130
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 486
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3174
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 129
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1827
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 257
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2440
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 175
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1563
mri_label2label: Done

PIDs (8515 8521 8525 8529 8537) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 8584 of (8584 8590 8594 8598) to complete...
Waiting for PID 8590 of (8584 8590 8594 8598) to complete...
Waiting for PID 8594 of (8584 8590 8594 8598) to complete...
Waiting for PID 8598 of (8584 8590 8594 8598) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 214
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1703
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 1597
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8556
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 170
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1182
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 599
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1777
mri_label2label: Done

PIDs (8584 8590 8594 8598) 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 0050017 --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 0050017 --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 0050017 --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 0050017 --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 0050017 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 8656 of (8656 8662 8667 8670 8677) to complete...
Waiting for PID 8662 of (8656 8662 8667 8670 8677) to complete...
Waiting for PID 8667 of (8656 8662 8667 8670 8677) to complete...
Waiting for PID 8670 of (8656 8662 8667 8670 8677) to complete...
Waiting for PID 8677 of (8656 8662 8667 8670 8677) 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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 1203
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4435
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 1023
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4460
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 373
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 82
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 776
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 0050017 --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 = 0050017
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-6.0.0/0050017/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 145822
Number of reverse mapping hits = 10
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 301
mri_label2label: Done

PIDs (8656 8662 8667 8670 8677) completed and logs appended.

 mris_label2annot --s 0050017 --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-6.0.0/0050017/label
cmdline mris_label2annot --s 0050017 --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-105
machine  x86_64
user     ntraut

subject 0050017
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-6.0.0/0050017/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 98803 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050017 --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-6.0.0/0050017/label
cmdline mris_label2annot --s 0050017 --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-105
machine  x86_64
user     ntraut

subject 0050017
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-6.0.0/0050017/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 119311 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/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 0050017 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 259357
Total vertex volume 256444 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
 1246    753   2101  2.160 0.582     0.148     0.057       17     3.0  BA1_exvivo
 4568   3010   6622  2.162 0.596     0.124     0.043       47     7.6  BA2_exvivo
 1388    957   1436  1.975 0.524     0.141     0.039       13     2.1  BA3a_exvivo
 2426   1629   3174  1.791 0.536     0.115     0.031       21     3.2  BA3b_exvivo
 2018   1260   3116  2.333 0.610     0.120     0.042       17     3.5  BA4a_exvivo
 1654   1130   2354  2.240 0.534     0.123     0.038       12     2.8  BA4p_exvivo
10404   6823  18528  2.490 0.640     0.137     0.049      130    21.7  BA6_exvivo
 4168   2842   7868  2.567 0.605     0.128     0.038       43     6.3  BA44_exvivo
 5961   3934  10719  2.419 0.669     0.145     0.058      153    14.0  BA45_exvivo
 3653   2958   6505  2.047 0.736     0.199     0.083       80    14.4  V1_exvivo
 6553   5041  12002  2.120 0.773     0.189     0.073      120    21.8  V2_exvivo
 2103   1477   3799  2.356 0.646     0.147     0.049       27     4.1  MT_exvivo
  555    363   1472  2.808 0.890     0.174     0.081       12     1.7  perirhinal_exvivo
  322    234    583  2.436 1.046     0.155     0.055        5     0.9  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 0050017 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050017/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 259357
Total vertex volume 256444 (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) = 1864638 mm^3    (det: 1.044763 )
lhCtxGM: 245239.636 244370.000  diff=  869.6  pctdiff= 0.355
rhCtxGM: 253177.745 252329.000  diff=  848.7  pctdiff= 0.335
lhCtxWM: 248836.637 250190.000  diff=-1353.4  pctdiff=-0.544
rhCtxWM: 252193.096 252679.000  diff= -485.9  pctdiff=-0.193
SubCortGMVol  66742.000
SupraTentVol  1093418.114 (1091702.000) diff=1716.114 pctdiff=0.157
SupraTentVolNotVent  1068027.114 (1066311.000) diff=1716.114 pctdiff=0.161
BrainSegVol  1248433.000 (1245921.000) diff=2512.000 pctdiff=0.201
BrainSegVolNotVent  1219466.000 (1219111.114) diff=354.886 pctdiff=0.029
BrainSegVolNotVent  1219466.000
CerebellumVol 152921.000
VentChorVol   25391.000
3rd4th5thCSF   3576.000
CSFVol  1064.000, OptChiasmVol   234.000
MaskVol 1862828.000
  921    580   1528  2.023 0.660     0.164     0.082       16     3.3  BA1_exvivo
 2629   1716   3813  2.161 0.560     0.124     0.039       26     4.1  BA2_exvivo
 1258    859   1226  1.991 0.544     0.138     0.035       11     1.7  BA3a_exvivo
 1889   1310   2167  1.649 0.396     0.107     0.026       13     2.1  BA3b_exvivo
 1174    681   2032  2.604 0.587     0.122     0.051       12     2.2  BA4a_exvivo
 1354    933   1824  2.203 0.519     0.122     0.035       10     2.0  BA4p_exvivo
 6798   4439  12024  2.441 0.663     0.140     0.052       90    14.9  BA6_exvivo
  962    642   2135  2.562 0.714     0.132     0.045       12     1.8  BA44_exvivo
 1633   1102   3486  2.593 0.691     0.145     0.055       24     3.4  BA45_exvivo
 3517   2857   6141  2.030 0.713     0.199     0.082       78    13.6  V1_exvivo
 3485   2768   7470  2.195 0.819     0.204     0.078       72    12.5  V2_exvivo
  356    230    763  2.458 0.646     0.140     0.044        5     0.7  MT_exvivo
  343    222   1000  2.834 0.844     0.183     0.080        8     1.3  perirhinal_exvivo
  192    142    407  2.805 1.098     0.142     0.057        2     0.4  entorhinal_exvivo

Started at Sat Oct 7 18:15:24 CEST 2017 
Ended   at Sun Oct 8 16:42:58 CEST 2017
#@#%# recon-all-run-time-hours 22.459
recon-all -s 0050017 finished without error at Sun Oct  8 16:42:58 CEST 2017