ABIDE_fs-6.0.0/0051359/scripts/recon-all.log

Sat Oct  7 17:06:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051359 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_d/0051359/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051359
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-908 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:      66074808   52422368   13652440    1756396          0   49365104
-/+ buffers/cache:    3057264   63017544
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:05-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:06:06-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-908  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-6.0.0/0051359

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_d/0051359/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_d/0051359/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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/MaxMun_d/0051359/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-6.0.0/0051359/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 17:06:09 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/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-6.0.0/0051359/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 17:06:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/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-908 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:06:18 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.2629
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2629/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2629/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.2629/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:06:21 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.2629/nu0.mnc ./tmp.mri_nu_correct.mni.2629/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2629/0/ -iterations 1000 -distance 50
[ntraut@tars-908:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/] [2017-10-07 17:06:21] 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.2629/0/ ./tmp.mri_nu_correct.mni.2629/nu0.mnc ./tmp.mri_nu_correct.mni.2629/nu1.imp

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Number of iterations: 43 
CV of field change: 0.000977615
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.2629/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.2629/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.2629/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 17:07:32 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 17:07:32 CEST 2017
Ended   at Sat Oct  7 17:08:11 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 17:08:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5443, pval=0.2115 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/transforms/talairach_avi.log 

TalAviQA: 0.98108
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 17:08:13 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-6.0.0/0051359/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-908 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:08:13 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.3543
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3543/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3543/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.3543/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:08:16 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.3543/nu0.mnc ./tmp.mri_nu_correct.mni.3543/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3543/0/
[ntraut@tars-908:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/] [2017-10-07 17:08:16] 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.3543/0/ ./tmp.mri_nu_correct.mni.3543/nu0.mnc ./tmp.mri_nu_correct.mni.3543/nu1.imp

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Number of iterations: 40 
CV of field change: 0.000943115
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 17:09:06 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.3543/nu1.mnc ./tmp.mri_nu_correct.mni.3543/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.3543/1/
[ntraut@tars-908:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/] [2017-10-07 17:09:06] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.3543/1/ ./tmp.mri_nu_correct.mni.3543/nu1.mnc ./tmp.mri_nu_correct.mni.3543/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 14 
CV of field change: 0.000938669
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.3543/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3543/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-6.0.0/0051359/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.3543/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3543/ones.mgz 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.3543/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.3543/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.3543/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3543/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3543/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.3543/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3543/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3543/input.mean.dat 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.3543/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.3543/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3543/ones.mgz --i ./tmp.mri_nu_correct.mni.3543/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3543/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3543/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.3543/ones.mgz --i ./tmp.mri_nu_correct.mni.3543/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3543/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3543/output.mean.dat 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.3543/ones.mgz
Loading ./tmp.mri_nu_correct.mni.3543/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.3543/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.3543/nu2.mnc ./tmp.mri_nu_correct.mni.3543/nu2.mnc mul .95050958637479836936
Saving result to './tmp.mri_nu_correct.mni.3543/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.3543/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.3543/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.3543/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 10 seconds.
mapping (18, 152) to ( 3, 110)
 
 
Sat Oct  7 17:10:21 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 17:10:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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
 1.03888   0.02994   0.13168  -1.77400;
-0.07575   1.03505   0.07654  -2.40344;
-0.14706   0.04533   1.05288   10.55336;
 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 = 15
Starting OpenSpline(): npoints = 15
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 75 (75), valley at 35 (35)
csf peak at 38, setting threshold to 62
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 73 (73), valley at 33 (33)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 15 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 17:12:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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=6.0
skull bounding box = (53, 17, 21) --> (202, 168, 219)
using (103, 67, 120) as brain centroid...
mean wm in atlas = 108, using box (85,48,96) --> (121, 85,144) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 6.3
after smoothing, mri peak at 106, scaling input intensities by 1.019
scaling channel 0 by 1.01887
initial log_p = -4.711
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.384719 @ (-9.091, 27.273, -9.091)
max log p =    -4.314307 @ (4.545, -4.545, 4.545)
max log p =    -4.277694 @ (2.273, 2.273, -6.818)
max log p =    -4.277694 @ (0.000, 0.000, 0.000)
max log p =    -4.260400 @ (1.705, 1.705, -1.705)
max log p =    -4.260400 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, 26.7, -13.1): log p = -4.260
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.095, old_max_log_p =-4.260 (thresh=-4.3)
 1.07125   0.11999   0.00000  -23.36081;
-0.16902   1.13509   0.00000   32.30734;
 0.00000   0.00000   1.06375  -20.97263;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.095, old_max_log_p =-4.095 (thresh=-4.1)
 1.07125   0.11999   0.00000  -23.36081;
-0.16902   1.13509   0.00000   32.30734;
 0.00000   0.00000   1.06375  -20.97263;
 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=-4.011, old_max_log_p =-4.095 (thresh=-4.1)
 1.04471   0.15286  -0.03765  -18.91721;
-0.20599   1.14872  -0.06963   47.67999;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.011, old_max_log_p =-4.011 (thresh=-4.0)
 1.04471   0.15286  -0.03765  -18.91721;
-0.20599   1.14872  -0.06963   47.67999;
 0.02179   0.07505   1.02121  -23.34929;
 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=-3.997, old_max_log_p =-4.011 (thresh=-4.0)
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.997, old_max_log_p =-3.997 (thresh=-4.0)
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 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
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.997 (old=-4.711)
transform before final EM align:
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 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
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.5  tol 0.000000
final transform:
 1.04715   0.15322  -0.03774  -19.25423;
-0.20647   1.15141  -0.06980   47.45852;
 0.02179   0.07505   1.02121  -23.34929;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1202.430202
mri_em_register stimesec    1.704740
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   157598
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    118
mri_em_register ru_nivcsw   3948
registration took 10 minutes and 29 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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=129 y=82 z=123 r=67
      first estimation of the main basin volume: 1314958 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        17 found in the rest of the brain 
      global maximum in x=109, y=73, z=92, Imax=255
      CSF=15, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=9186597118 voxels, voxel volume =1.000 
                     = 9186597118 mmm3 = 9186596.864 cm3
done.
PostAnalyze...Basin Prior
 49 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=128,y=92, z=115, r=9552 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 42992
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = -1032617396
  LEFT_CER     CSF_MIN=0, CSF_intensity=9, CSF_MAX=39 , nb = -1046846564
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=60 , nb = 1061841852
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=57 , nb = 1079255874
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1064670116
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    56,      50,        49,   67
  after  analyzing :    37,      50,        50,   54
   RIGHT_CER   
  before analyzing :    31,      44,        52,   67
  after  analyzing :    31,      49,        52,   53
   LEFT_CER    
  before analyzing :    39,      43,        48,   82
  after  analyzing :    39,      46,        48,   55
  RIGHT_BRAIN  
  before analyzing :    60,      51,        48,   68
  after  analyzing :    35,      51,        51,   55
  LEFT_BRAIN   
  before analyzing :    57,      50,        48,   68
  after  analyzing :    38,      50,        50,   54
     OTHER     
  before analyzing :    3,      5,        49,   67
  after  analyzing :    3,      34,        49,   42
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...64 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 71.988, std = 6.959

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 5.59, sigma = 7.84
      after  rotation: sse = 5.59, sigma = 7.84
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  6.42, its var is  9.13   
      before Erosion-Dilatation  3.13% of inacurate vertices
      after  Erosion-Dilatation  2.11% 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...43 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1781364 voxels, voxel volume = 1.000 mm3
           = 1781364 mmm3 = 1781.364 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    25.283156
mri_watershed stimesec    0.430934
mri_watershed ru_maxrss   819944
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   212317
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2976
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    3093
mri_watershed ru_nivcsw   153
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 17:23:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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=30.0
skull bounding box = (58, 26, 31) --> (196, 149, 207)
using (104, 67, 119) as brain centroid...
mean wm in atlas = 107, using box (87,52,97) --> (120, 82,140) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 6.3
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.626
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.879753 @ (-9.091, 27.273, -9.091)
max log p =    -3.879753 @ (0.000, 0.000, 0.000)
max log p =    -3.710522 @ (6.818, -2.273, -2.273)
max log p =    -3.678594 @ (1.136, 1.136, 3.409)
max log p =    -3.657561 @ (0.568, -0.568, -0.568)
max log p =    -3.636541 @ (-1.420, -0.852, -0.852)
Found translation: (-2.0, 24.7, -9.4): log p = -3.637
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.605, old_max_log_p =-3.637 (thresh=-3.6)
 0.99144   0.13053   0.00000  -13.23177;
-0.14032   1.06580   0.00000   36.55486;
 0.00000   0.00000   1.00000  -9.37500;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.605, old_max_log_p =-3.605 (thresh=-3.6)
 0.99144   0.13053   0.00000  -13.23177;
-0.14032   1.06580   0.00000   36.55486;
 0.00000   0.00000   1.00000  -9.37500;
 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=-3.533, old_max_log_p =-3.605 (thresh=-3.6)
 1.01001   0.13023  -0.03201  -11.91798;
-0.14524   1.08455  -0.00202   35.64795;
 0.03207   0.00654   0.96198  -7.88200;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.504, old_max_log_p =-3.533 (thresh=-3.5)
 1.01001   0.13023  -0.03201  -11.91798;
-0.14252   1.06421  -0.00198   39.09124;
 0.03207   0.00654   0.96198  -7.88200;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.502, old_max_log_p =-3.504 (thresh=-3.5)
 1.00481   0.16498  -0.03206  -14.46778;
-0.17549   1.05938  -0.00093   43.67085;
 0.03207   0.00654   0.96198  -7.88200;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.450, old_max_log_p =-3.502 (thresh=-3.5)
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.450, old_max_log_p =-3.450 (thresh=-3.4)
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 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
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.450 (old=-4.626)
transform before final EM align:
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 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
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.9  tol 0.000000
final transform:
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1232.912568
mri_em_register stimesec    1.965701
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158991
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    146
mri_em_register ru_nivcsw   3836
registration took 10 minutes and 35 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 17:34:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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=30.0
skull bounding box = (58, 26, 31) --> (196, 149, 207)
using (104, 67, 119) as brain centroid...
mean wm in atlas = 107, using box (87,52,97) --> (120, 82,140) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 6.3
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
using 246344 sample points...
INFO: compute sample coordinates transform
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 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 (122, 33, 30) --> (195, 147, 205)
Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0
0 of 33 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 29, 31) --> (136, 137, 205)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 21 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (123, 111, 53) --> (168, 156, 110)
Left_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0
2 of 6 (33.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (77, 111, 52) --> (124, 147, 112)
Right_Cerebellum_White_Matter: limiting intensities to 114.0 --> 132.0
1 of 5 (20.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (105, 103, 89) --> (142, 168, 123)
Brain_Stem: limiting intensities to 98.0 --> 132.0
6 of 14 (42.9%) samples deleted
using 79 total control points for intensity normalization...
bias field = 0.887 +- 0.083
0 of 70 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (122, 33, 30) --> (195, 147, 205)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 120 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 29, 31) --> (136, 137, 205)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 119 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (123, 111, 53) --> (168, 156, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
20 of 36 (55.6%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (77, 111, 52) --> (124, 147, 112)
Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0
53 of 59 (89.8%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (105, 103, 89) --> (142, 168, 123)
Brain_Stem: limiting intensities to 88.0 --> 132.0
26 of 37 (70.3%) samples deleted
using 371 total control points for intensity normalization...
bias field = 1.012 +- 0.063
1 of 266 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (122, 33, 30) --> (195, 147, 205)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
5 of 268 (1.9%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 29, 31) --> (136, 137, 205)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
6 of 259 (2.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (123, 111, 53) --> (168, 156, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
32 of 40 (80.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (77, 111, 52) --> (124, 147, 112)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
55 of 60 (91.7%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (105, 103, 89) --> (142, 168, 123)
Brain_Stem: limiting intensities to 88.0 --> 132.0
85 of 96 (88.5%) samples deleted
using 723 total control points for intensity normalization...
bias field = 1.028 +- 0.057
0 of 538 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 52 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 17:35:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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) = 1.05 (predicted orig area = 7.6)
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=0.807, neg=0, invalid=762
0001: dt=223.206357, rms=0.727 (9.923%), neg=0, invalid=762
0002: dt=198.511628, rms=0.701 (3.567%), neg=0, invalid=762
0003: dt=176.188235, rms=0.690 (1.496%), neg=0, invalid=762
0004: dt=164.085106, rms=0.685 (0.785%), neg=0, invalid=762
0005: dt=295.936000, rms=0.680 (0.670%), neg=0, invalid=762
0006: dt=129.472000, rms=0.677 (0.448%), neg=0, invalid=762
0007: dt=369.920000, rms=0.675 (0.379%), neg=0, invalid=762
0008: dt=129.472000, rms=0.673 (0.276%), neg=0, invalid=762
0009: dt=369.920000, rms=0.671 (0.221%), neg=0, invalid=762
0010: dt=369.920000, rms=0.671 (-0.378%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.672, neg=0, invalid=762
0011: dt=129.472000, rms=0.669 (0.396%), neg=0, invalid=762
0012: dt=517.888000, rms=0.667 (0.348%), neg=0, invalid=762
0013: dt=369.920000, rms=0.665 (0.226%), neg=0, invalid=762
0014: dt=369.920000, rms=0.664 (0.084%), neg=0, invalid=762
0015: dt=369.920000, rms=0.662 (0.325%), neg=0, invalid=762
0016: dt=369.920000, rms=0.660 (0.289%), neg=0, invalid=762
0017: dt=369.920000, rms=0.659 (0.280%), neg=0, invalid=762
0018: dt=369.920000, rms=0.657 (0.298%), neg=0, invalid=762
0019: dt=369.920000, rms=0.654 (0.347%), neg=0, invalid=762
0020: dt=369.920000, rms=0.653 (0.156%), neg=0, invalid=762
0021: dt=369.920000, rms=0.652 (0.192%), neg=0, invalid=762
0022: dt=369.920000, rms=0.651 (0.197%), neg=0, invalid=762
0023: dt=369.920000, rms=0.650 (0.150%), neg=0, invalid=762
0024: dt=369.920000, rms=0.649 (0.121%), neg=0, invalid=762
0025: dt=369.920000, rms=0.648 (0.108%), neg=0, invalid=762
0026: dt=295.936000, rms=0.648 (0.087%), neg=0, invalid=762
0027: dt=295.936000, rms=0.648 (0.011%), neg=0, invalid=762
0028: dt=295.936000, rms=0.647 (0.040%), neg=0, invalid=762
0029: dt=295.936000, rms=0.647 (0.076%), neg=0, invalid=762
0030: dt=295.936000, rms=0.647 (0.051%), neg=0, invalid=762
0031: dt=295.936000, rms=0.646 (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=0.651, neg=0, invalid=762
0032: dt=64.132505, rms=0.648 (0.423%), neg=0, invalid=762
0033: dt=331.776000, rms=0.642 (0.991%), neg=0, invalid=762
0034: dt=124.416000, rms=0.637 (0.819%), neg=0, invalid=762
0035: dt=79.151020, rms=0.633 (0.527%), neg=0, invalid=762
0036: dt=36.288000, rms=0.632 (0.130%), neg=0, invalid=762
0037: dt=36.288000, rms=0.632 (0.094%), neg=0, invalid=762
0038: dt=36.288000, rms=0.631 (0.173%), neg=0, invalid=762
0039: dt=36.288000, rms=0.629 (0.250%), neg=0, invalid=762
0040: dt=36.288000, rms=0.627 (0.314%), neg=0, invalid=762
0041: dt=36.288000, rms=0.625 (0.351%), neg=0, invalid=762
0042: dt=36.288000, rms=0.623 (0.349%), neg=0, invalid=762
0043: dt=36.288000, rms=0.621 (0.331%), neg=0, invalid=762
0044: dt=36.288000, rms=0.619 (0.319%), neg=0, invalid=762
0045: dt=36.288000, rms=0.617 (0.309%), neg=0, invalid=762
0046: dt=36.288000, rms=0.615 (0.301%), neg=0, invalid=762
0047: dt=36.288000, rms=0.613 (0.277%), neg=0, invalid=762
0048: dt=36.288000, rms=0.612 (0.240%), neg=0, invalid=762
0049: dt=36.288000, rms=0.610 (0.215%), neg=0, invalid=762
0050: dt=36.288000, rms=0.609 (0.195%), neg=0, invalid=762
0051: dt=36.288000, rms=0.608 (0.190%), neg=0, invalid=762
0052: dt=36.288000, rms=0.607 (0.189%), neg=0, invalid=762
0053: dt=36.288000, rms=0.606 (0.159%), neg=0, invalid=762
0054: dt=36.288000, rms=0.605 (0.134%), neg=0, invalid=762
0055: dt=36.288000, rms=0.605 (0.110%), neg=0, invalid=762
0056: dt=36.288000, rms=0.604 (0.099%), neg=0, invalid=762
0057: dt=145.152000, rms=0.604 (0.050%), neg=0, invalid=762
0058: dt=145.152000, rms=0.604 (-0.205%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.604, neg=0, invalid=762
0059: dt=124.416000, rms=0.602 (0.405%), neg=0, invalid=762
0060: dt=103.680000, rms=0.601 (0.107%), neg=0, invalid=762
0061: dt=103.680000, rms=0.601 (0.050%), neg=0, invalid=762
0062: dt=103.680000, rms=0.601 (0.057%), neg=0, invalid=762
0063: dt=103.680000, rms=0.600 (0.028%), neg=0, invalid=762
0064: dt=103.680000, rms=0.600 (-0.023%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.622, neg=0, invalid=762
0065: dt=8.000000, rms=0.621 (0.189%), neg=0, invalid=762
0066: dt=2.800000, rms=0.621 (0.008%), neg=0, invalid=762
0067: dt=2.800000, rms=0.621 (0.002%), neg=0, invalid=762
0068: dt=2.800000, rms=0.621 (-0.024%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.622, neg=0, invalid=762
0069: dt=0.000000, rms=0.621 (0.100%), neg=0, invalid=762
0070: dt=0.000000, rms=0.621 (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=0.677, neg=0, invalid=762
0071: dt=6.301370, rms=0.660 (2.536%), neg=0, invalid=762
0072: dt=3.456000, rms=0.659 (0.109%), neg=0, invalid=762
0073: dt=3.456000, rms=0.659 (-0.014%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.660, neg=0, invalid=762
0074: dt=0.000000, rms=0.659 (0.082%), neg=0, invalid=762
0075: dt=0.000000, rms=0.659 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.712, neg=0, invalid=762
0076: dt=0.448000, rms=0.710 (0.215%), neg=0, invalid=762
0077: dt=1.024000, rms=0.709 (0.171%), neg=0, invalid=762
0078: dt=1.024000, rms=0.707 (0.290%), neg=0, invalid=762
0079: dt=1.024000, rms=0.706 (0.178%), neg=0, invalid=762
0080: dt=1.024000, rms=0.706 (-0.232%), neg=0, invalid=762
0081: dt=1.792000, rms=0.705 (0.079%), neg=0, invalid=762
0082: dt=1.792000, rms=0.704 (0.176%), neg=0, invalid=762
0083: dt=0.000000, rms=0.704 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.704, neg=0, invalid=762
0084: dt=0.448000, rms=0.704 (0.093%), neg=0, invalid=762
0085: dt=0.448000, rms=0.704 (0.011%), neg=0, invalid=762
0086: dt=0.448000, rms=0.703 (0.009%), neg=0, invalid=762
0087: dt=0.448000, rms=0.703 (-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=0.666, neg=0, invalid=762
0088: dt=0.743590, rms=0.651 (2.243%), neg=0, invalid=762
0089: dt=0.064000, rms=0.650 (0.098%), neg=0, invalid=762
0090: dt=0.064000, rms=0.650 (-0.052%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.650, neg=0, invalid=762
0091: dt=0.028000, rms=0.650 (0.095%), neg=0, invalid=762
0092: dt=0.007000, rms=0.650 (0.001%), neg=0, invalid=762
0093: dt=0.007000, rms=0.650 (0.000%), neg=0, invalid=762
0094: dt=0.007000, rms=0.650 (-0.003%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.08595 (24)
Left_Lateral_Ventricle (4): linear fit = 1.17 x + 0.0 (648 voxels, overlap=0.838)
Left_Lateral_Ventricle (4): linear fit = 1.17 x + 0.0 (648 voxels, peak = 24), gca=23.5
gca peak = 0.15565 (16)
mri peak = 0.08571 (27)
Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (1018 voxels, overlap=0.533)
Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (1018 voxels, peak = 21), gca=21.4
gca peak = 0.26829 (96)
mri peak = 0.10278 (92)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (719 voxels, overlap=0.984)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (719 voxels, peak = 93), gca=92.6
gca peak = 0.20183 (93)
mri peak = 0.10311 (92)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (623 voxels, overlap=0.835)
Left_Pallidum (13): linear fit = 0.94 x + 0.0 (623 voxels, peak = 88), gca=87.9
gca peak = 0.21683 (55)
mri peak = 0.07184 (68)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (699 voxels, overlap=0.224)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (699 voxels, peak = 64), gca=63.5
gca peak = 0.30730 (58)
mri peak = 0.07029 (65)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (643 voxels, overlap=0.869)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (643 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.07563 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (69238 voxels, overlap=0.809)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (69238 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.07742 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (67225 voxels, overlap=0.878)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (67225 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.04009 (67)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (26771 voxels, overlap=0.566)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (26771 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.04749 (70)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (29134 voxels, overlap=0.245)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (29134 voxels, peak = 69), gca=69.3
gca peak = 0.14161 (67)
mri peak = 0.09551 (76)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (888 voxels, overlap=0.420)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (888 voxels, peak = 75), gca=74.7
gca peak = 0.15243 (71)
mri peak = 0.09056 (77)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1019 voxels, overlap=0.907)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1019 voxels, peak = 73), gca=73.5
gca peak = 0.13336 (57)
mri peak = 0.05062 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (13984 voxels, overlap=0.549)
Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (13984 voxels, peak = 66), gca=66.4
gca peak = 0.13252 (56)
mri peak = 0.04853 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (18951 voxels, overlap=0.555)
Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (18951 voxels, peak = 64), gca=63.6
gca peak = 0.18181 (84)
mri peak = 0.04055 (78)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (7440 voxels, overlap=0.993)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (7440 voxels, peak = 83), gca=82.7
gca peak = 0.20573 (83)
mri peak = 0.04375 (81)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (7640 voxels, overlap=0.996)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (7640 voxels, peak = 81), gca=80.9
gca peak = 0.21969 (57)
mri peak = 0.08775 (67)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (325 voxels, overlap=0.960)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (325 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.07950 (67)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (397 voxels, overlap=0.152)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (397 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.05794 (88)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4708 voxels, overlap=0.979)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4708 voxels, peak = 85), gca=84.6
gca peak = 0.11978 (83)
mri peak = 0.06799 (80)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3849 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3849 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.07274 (80)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1855 voxels, overlap=0.995)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1855 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.07542 (83)
Right_Putamen (51): linear fit = 1.09 x + 0.0 (2217 voxels, overlap=0.761)
Right_Putamen (51): linear fit = 1.09 x + 0.0 (2217 voxels, peak = 86), gca=85.7
gca peak = 0.10025 (80)
mri peak = 0.11828 (80)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (7755 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (7755 voxels, peak = 85), gca=85.2
gca peak = 0.13281 (86)
mri peak = 0.08128 (87)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1126 voxels, overlap=0.725)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1126 voxels, peak = 92), gca=91.6
gca peak = 0.12801 (89)
mri peak = 0.07953 (83)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1122 voxels, overlap=0.849)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1122 voxels, peak = 89), gca=88.6
gca peak = 0.20494 (23)
mri peak = 0.06378 (24)
gca peak = 0.15061 (21)
mri peak = 0.06854 (53)
Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (318 voxels, overlap=0.681)
Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (318 voxels, peak = 28), gca=28.5
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 1.14 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.29 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=0.640, neg=0, invalid=762
0095: dt=129.472000, rms=0.627 (2.098%), neg=0, invalid=762
0096: dt=221.952000, rms=0.621 (0.898%), neg=0, invalid=762
0097: dt=110.976000, rms=0.620 (0.152%), neg=0, invalid=762
0098: dt=517.888000, rms=0.617 (0.480%), neg=0, invalid=762
0099: dt=73.984000, rms=0.616 (0.145%), neg=0, invalid=762
0100: dt=517.888000, rms=0.615 (0.163%), neg=0, invalid=762
0101: dt=129.472000, rms=0.614 (0.187%), neg=0, invalid=762
0102: dt=73.984000, rms=0.614 (0.018%), neg=0, invalid=762
0103: dt=73.984000, rms=0.614 (0.023%), neg=0, invalid=762
0104: dt=73.984000, rms=0.614 (0.044%), neg=0, invalid=762
0105: dt=73.984000, rms=0.613 (0.062%), neg=0, invalid=762
0106: dt=73.984000, rms=0.613 (0.076%), neg=0, invalid=762
0107: dt=73.984000, rms=0.612 (0.080%), neg=0, invalid=762
0108: dt=73.984000, rms=0.612 (0.083%), neg=0, invalid=762
0109: dt=73.984000, rms=0.611 (0.082%), neg=0, invalid=762
0110: dt=73.984000, rms=0.611 (0.081%), neg=0, invalid=762
0111: dt=73.984000, rms=0.610 (0.081%), neg=0, invalid=762
0112: dt=73.984000, rms=0.610 (0.080%), neg=0, invalid=762
0113: dt=73.984000, rms=0.609 (0.075%), neg=0, invalid=762
0114: dt=73.984000, rms=0.609 (0.062%), neg=0, invalid=762
0115: dt=73.984000, rms=0.609 (0.054%), neg=0, invalid=762
0116: dt=73.984000, rms=0.608 (0.049%), neg=0, invalid=762
0117: dt=73.984000, rms=0.608 (0.048%), neg=0, invalid=762
0118: dt=73.984000, rms=0.608 (0.045%), neg=0, invalid=762
0119: dt=73.984000, rms=0.608 (0.043%), neg=0, invalid=762
0120: dt=73.984000, rms=0.607 (0.042%), neg=0, invalid=762
0121: dt=73.984000, rms=0.607 (0.036%), neg=0, invalid=762
0122: dt=73.984000, rms=0.607 (0.036%), neg=0, invalid=762
0123: dt=73.984000, rms=0.607 (0.041%), neg=0, invalid=762
0124: dt=73.984000, rms=0.606 (0.042%), neg=0, invalid=762
0125: dt=73.984000, rms=0.606 (0.043%), neg=0, invalid=762
0126: dt=73.984000, rms=0.606 (0.041%), neg=0, invalid=762
0127: dt=73.984000, rms=0.606 (0.038%), neg=0, invalid=762
0128: dt=73.984000, rms=0.605 (0.028%), neg=0, invalid=762
0129: dt=73.984000, rms=0.605 (0.031%), neg=0, invalid=762
0130: dt=73.984000, rms=0.605 (0.030%), neg=0, invalid=762
0131: dt=73.984000, rms=0.605 (0.033%), neg=0, invalid=762
0132: dt=73.984000, rms=0.605 (0.036%), neg=0, invalid=762
0133: dt=73.984000, rms=0.604 (0.040%), neg=0, invalid=762
0134: dt=73.984000, rms=0.604 (0.037%), neg=0, invalid=762
0135: dt=73.984000, rms=0.604 (0.033%), neg=0, invalid=762
0136: dt=73.984000, rms=0.604 (0.033%), neg=0, invalid=762
0137: dt=73.984000, rms=0.604 (0.034%), neg=0, invalid=762
0138: dt=73.984000, rms=0.603 (0.033%), neg=0, invalid=762
0139: dt=73.984000, rms=0.603 (0.027%), neg=0, invalid=762
0140: dt=73.984000, rms=0.603 (0.024%), neg=0, invalid=762
0141: dt=73.984000, rms=0.603 (0.024%), neg=0, invalid=762
0142: dt=73.984000, rms=0.603 (0.025%), neg=0, invalid=762
0143: dt=73.984000, rms=0.603 (0.027%), neg=0, invalid=762
0144: dt=73.984000, rms=0.602 (0.029%), neg=0, invalid=762
0145: dt=73.984000, rms=0.602 (0.029%), neg=0, invalid=762
0146: dt=73.984000, rms=0.602 (0.029%), neg=0, invalid=762
0147: dt=73.984000, rms=0.602 (0.028%), neg=0, invalid=762
0148: dt=73.984000, rms=0.602 (0.027%), neg=0, invalid=762
0149: dt=73.984000, rms=0.602 (0.026%), neg=0, invalid=762
0150: dt=73.984000, rms=0.601 (0.024%), neg=0, invalid=762
0151: dt=73.984000, rms=0.601 (0.027%), neg=0, invalid=762
0152: dt=73.984000, rms=0.601 (0.024%), neg=0, invalid=762
0153: dt=73.984000, rms=0.601 (0.024%), neg=0, invalid=762
0154: dt=73.984000, rms=0.601 (0.023%), neg=0, invalid=762
0155: dt=5918.720000, rms=0.600 (0.094%), neg=0, invalid=762
0156: dt=129.472000, rms=0.600 (0.050%), neg=0, invalid=762
0157: dt=129.472000, rms=0.600 (0.018%), neg=0, invalid=762
0158: dt=129.472000, rms=0.600 (0.007%), neg=0, invalid=762
0159: dt=129.472000, rms=0.600 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.600, neg=0, invalid=762
0160: dt=129.472000, rms=0.599 (0.123%), neg=0, invalid=762
0161: dt=517.888000, rms=0.599 (0.107%), neg=0, invalid=762
0162: dt=295.936000, rms=0.599 (0.046%), neg=0, invalid=762
0163: dt=295.936000, rms=0.598 (0.027%), neg=0, invalid=762
0164: dt=295.936000, rms=0.598 (0.068%), neg=0, invalid=762
0165: dt=295.936000, rms=0.598 (0.046%), neg=0, invalid=762
0166: dt=295.936000, rms=0.597 (0.047%), neg=0, invalid=762
0167: dt=295.936000, rms=0.597 (0.084%), neg=0, invalid=762
0168: dt=295.936000, rms=0.597 (0.018%), neg=0, invalid=762
0169: dt=295.936000, rms=0.596 (0.064%), neg=0, invalid=762
0170: dt=295.936000, rms=0.596 (0.045%), neg=0, invalid=762
0171: dt=295.936000, rms=0.596 (-0.024%), neg=0, invalid=762
0172: dt=32.368000, rms=0.596 (0.002%), neg=0, invalid=762
0173: dt=73.984000, rms=0.596 (0.005%), neg=0, invalid=762
0174: dt=129.472000, rms=0.596 (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=0.597, neg=0, invalid=762
0175: dt=124.416000, rms=0.594 (0.552%), neg=0, invalid=762
0176: dt=145.152000, rms=0.589 (0.762%), neg=0, invalid=762
0177: dt=82.944000, rms=0.588 (0.303%), neg=0, invalid=762
0178: dt=145.152000, rms=0.585 (0.510%), neg=0, invalid=762
0179: dt=77.042654, rms=0.583 (0.258%), neg=0, invalid=762
0180: dt=145.152000, rms=0.581 (0.440%), neg=0, invalid=762
0181: dt=83.517730, rms=0.580 (0.188%), neg=0, invalid=762
0182: dt=145.152000, rms=0.577 (0.350%), neg=0, invalid=762
0183: dt=64.984615, rms=0.577 (0.169%), neg=0, invalid=762
0184: dt=331.776000, rms=0.574 (0.502%), neg=0, invalid=762
0185: dt=36.288000, rms=0.572 (0.246%), neg=0, invalid=762
0186: dt=124.416000, rms=0.572 (0.115%), neg=0, invalid=762
0187: dt=103.680000, rms=0.570 (0.217%), neg=0, invalid=762
0188: dt=82.944000, rms=0.570 (0.104%), neg=0, invalid=762
0189: dt=145.152000, rms=0.569 (0.206%), neg=0, invalid=762
0190: dt=36.288000, rms=0.568 (0.096%), neg=0, invalid=762
0191: dt=331.776000, rms=0.567 (0.226%), neg=0, invalid=762
0192: dt=64.402516, rms=0.565 (0.235%), neg=0, invalid=762
0193: dt=145.152000, rms=0.565 (0.106%), neg=0, invalid=762
0194: dt=82.944000, rms=0.564 (0.117%), neg=0, invalid=762
0195: dt=82.944000, rms=0.564 (0.095%), neg=0, invalid=762
0196: dt=103.680000, rms=0.563 (0.088%), neg=0, invalid=762
0197: dt=82.944000, rms=0.563 (0.090%), neg=0, invalid=762
0198: dt=103.680000, rms=0.562 (0.080%), neg=0, invalid=762
0199: dt=82.944000, rms=0.562 (0.089%), neg=0, invalid=762
0200: dt=82.944000, rms=0.561 (0.069%), neg=0, invalid=762
0201: dt=82.944000, rms=0.561 (0.082%), neg=0, invalid=762
0202: dt=82.944000, rms=0.560 (0.058%), neg=0, invalid=762
0203: dt=103.680000, rms=0.560 (0.077%), neg=0, invalid=762
0204: dt=36.288000, rms=0.560 (0.046%), neg=0, invalid=762
0205: dt=36.288000, rms=0.560 (0.031%), neg=0, invalid=762
0206: dt=36.288000, rms=0.559 (0.050%), neg=0, invalid=762
0207: dt=36.288000, rms=0.559 (0.066%), neg=0, invalid=762
0208: dt=36.288000, rms=0.559 (0.077%), neg=0, invalid=762
0209: dt=36.288000, rms=0.558 (0.090%), neg=0, invalid=762
0210: dt=36.288000, rms=0.558 (0.018%), neg=0, invalid=762
0211: dt=36.288000, rms=0.558 (0.037%), neg=0, invalid=762
0212: dt=36.288000, rms=0.558 (0.021%), neg=0, invalid=762
0213: dt=36.288000, rms=0.557 (0.020%), neg=0, invalid=762
0214: dt=9.072000, rms=0.557 (0.005%), neg=0, invalid=762
0215: dt=0.035437, rms=0.557 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.558, neg=0, invalid=762
0216: dt=145.152000, rms=0.555 (0.552%), neg=0, invalid=762
0217: dt=124.416000, rms=0.554 (0.193%), neg=0, invalid=762
0218: dt=82.944000, rms=0.553 (0.113%), neg=0, invalid=762
0219: dt=145.152000, rms=0.552 (0.131%), neg=0, invalid=762
0220: dt=82.944000, rms=0.552 (0.067%), neg=0, invalid=762
0221: dt=124.416000, rms=0.552 (0.091%), neg=0, invalid=762
0222: dt=62.208000, rms=0.551 (0.050%), neg=0, invalid=762
0223: dt=62.208000, rms=0.551 (0.049%), neg=0, invalid=762
0224: dt=31.104000, rms=0.551 (0.018%), neg=0, invalid=762
0225: dt=0.030375, rms=0.551 (-0.001%), neg=0, invalid=762
0226: dt=0.035437, rms=0.551 (0.000%), neg=0, invalid=762
0227: dt=0.005670, rms=0.551 (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=0.557, neg=0, invalid=762
0228: dt=84.412304, rms=0.548 (1.632%), neg=0, invalid=762
0229: dt=71.393502, rms=0.538 (1.756%), neg=0, invalid=762
0230: dt=26.974359, rms=0.535 (0.645%), neg=0, invalid=762
0231: dt=102.400000, rms=0.531 (0.683%), neg=0, invalid=762
0232: dt=25.600000, rms=0.528 (0.538%), neg=0, invalid=762
0233: dt=78.644068, rms=0.527 (0.374%), neg=0, invalid=762
0234: dt=19.577640, rms=0.525 (0.356%), neg=0, invalid=762
0235: dt=179.200000, rms=0.521 (0.707%), neg=0, invalid=762
0236: dt=38.400000, rms=0.520 (0.247%), neg=0, invalid=762
0237: dt=32.000000, rms=0.519 (0.177%), neg=0, invalid=762
0238: dt=44.800000, rms=0.518 (0.089%), neg=0, invalid=762
0239: dt=25.600000, rms=0.518 (0.128%), neg=0, invalid=762
0240: dt=44.800000, rms=0.517 (0.083%), neg=0, invalid=762
0241: dt=32.000000, rms=0.517 (0.113%), neg=0, invalid=762
0242: dt=32.000000, rms=0.516 (0.059%), neg=0, invalid=762
0243: dt=38.400000, rms=0.516 (0.110%), neg=0, invalid=762
0244: dt=25.600000, rms=0.515 (0.047%), neg=0, invalid=762
0245: dt=25.600000, rms=0.515 (0.090%), neg=0, invalid=762
0246: dt=25.600000, rms=0.514 (0.097%), neg=0, invalid=762
0247: dt=25.600000, rms=0.514 (0.139%), neg=0, invalid=762
0248: dt=25.600000, rms=0.513 (0.179%), neg=0, invalid=762
0249: dt=25.600000, rms=0.512 (0.207%), neg=0, invalid=762
0250: dt=25.600000, rms=0.511 (0.200%), neg=0, invalid=762
0251: dt=25.600000, rms=0.510 (0.192%), neg=0, invalid=762
0252: dt=25.600000, rms=0.509 (0.210%), neg=0, invalid=762
0253: dt=25.600000, rms=0.508 (0.200%), neg=0, invalid=762
0254: dt=25.600000, rms=0.507 (0.179%), neg=0, invalid=762
0255: dt=25.600000, rms=0.506 (0.161%), neg=0, invalid=762
0256: dt=25.600000, rms=0.505 (0.154%), neg=0, invalid=762
0257: dt=25.600000, rms=0.505 (0.135%), neg=0, invalid=762
0258: dt=25.600000, rms=0.504 (0.115%), neg=0, invalid=762
0259: dt=25.600000, rms=0.503 (0.116%), neg=0, invalid=762
0260: dt=25.600000, rms=0.503 (0.109%), neg=0, invalid=762
0261: dt=25.600000, rms=0.502 (0.103%), neg=0, invalid=762
0262: dt=25.600000, rms=0.502 (0.087%), neg=0, invalid=762
0263: dt=25.600000, rms=0.502 (0.070%), neg=0, invalid=762
0264: dt=25.600000, rms=0.501 (0.070%), neg=0, invalid=762
0265: dt=25.600000, rms=0.501 (0.068%), neg=0, invalid=762
0266: dt=25.600000, rms=0.501 (0.048%), neg=0, invalid=762
0267: dt=25.600000, rms=0.500 (0.052%), neg=0, invalid=762
0268: dt=25.600000, rms=0.500 (0.053%), neg=0, invalid=762
0269: dt=25.600000, rms=0.500 (0.050%), neg=0, invalid=762
0270: dt=25.600000, rms=0.500 (0.043%), neg=0, invalid=762
0271: dt=25.600000, rms=0.499 (0.042%), neg=0, invalid=762
0272: dt=25.600000, rms=0.499 (0.044%), neg=0, invalid=762
0273: dt=25.600000, rms=0.499 (0.039%), neg=0, invalid=762
0274: dt=25.600000, rms=0.499 (0.028%), neg=0, invalid=762
0275: dt=25.600000, rms=0.499 (0.033%), neg=0, invalid=762
0276: dt=25.600000, rms=0.499 (0.026%), neg=0, invalid=762
0277: dt=25.600000, rms=0.498 (0.031%), neg=0, invalid=762
0278: dt=25.600000, rms=0.498 (0.028%), neg=0, invalid=762
0279: dt=25.600000, rms=0.498 (0.028%), neg=0, invalid=762
0280: dt=25.600000, rms=0.498 (0.024%), neg=0, invalid=762
0281: dt=25.600000, rms=0.498 (0.030%), neg=0, invalid=762
0282: dt=25.600000, rms=0.498 (0.025%), neg=0, invalid=762
0283: dt=25.600000, rms=0.498 (0.030%), neg=0, invalid=762
0284: dt=25.600000, rms=0.497 (0.024%), neg=0, invalid=762
0285: dt=25.600000, rms=0.497 (0.025%), neg=0, invalid=762
0286: dt=25.600000, rms=0.497 (0.018%), neg=0, invalid=762
0287: dt=25.600000, rms=0.497 (0.005%), neg=0, invalid=762
0288: dt=25.600000, rms=0.497 (0.002%), neg=0, invalid=762
0289: dt=25.600000, rms=0.497 (0.006%), neg=0, invalid=762
0290: dt=25.600000, rms=0.497 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.498, neg=0, invalid=762
0291: dt=44.800000, rms=0.495 (0.506%), neg=0, invalid=762
0292: dt=44.800000, rms=0.495 (0.106%), neg=0, invalid=762
0293: dt=11.200000, rms=0.495 (0.018%), neg=0, invalid=762
0294: dt=11.200000, rms=0.494 (0.024%), neg=0, invalid=762
0295: dt=11.200000, rms=0.494 (0.022%), neg=0, invalid=762
0296: dt=11.200000, rms=0.494 (0.014%), neg=0, invalid=762
0297: dt=102.400000, rms=0.494 (0.059%), neg=0, invalid=762
0298: dt=11.200000, rms=0.494 (0.002%), neg=0, invalid=762
0299: dt=11.200000, rms=0.494 (0.012%), neg=0, invalid=762
0300: dt=11.200000, rms=0.494 (0.009%), neg=0, invalid=762
0301: dt=11.200000, rms=0.494 (0.015%), neg=0, invalid=762
0302: dt=11.200000, rms=0.494 (0.010%), neg=0, invalid=762
0303: dt=11.200000, rms=0.494 (0.006%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.519, neg=0, invalid=762
0304: dt=0.000000, rms=0.518 (0.094%), neg=0, invalid=762
0305: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762
0306: dt=0.150000, rms=0.518 (-0.011%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.519, neg=0, invalid=762
0307: dt=0.000000, rms=0.518 (0.094%), neg=0, invalid=762
0308: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762
0309: dt=0.150000, rms=0.518 (-0.006%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.567, neg=0, invalid=762
0310: dt=1.915058, rms=0.559 (1.496%), neg=0, invalid=762
0311: dt=0.768000, rms=0.558 (0.091%), neg=0, invalid=762
0312: dt=0.320000, rms=0.558 (0.008%), neg=0, invalid=762
0313: dt=0.320000, rms=0.558 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.559, neg=0, invalid=762
0314: dt=1.536000, rms=0.557 (0.285%), neg=0, invalid=762
0315: dt=0.768000, rms=0.557 (0.035%), neg=0, invalid=762
0316: dt=0.768000, rms=0.557 (0.005%), neg=0, invalid=762
0317: dt=0.768000, rms=0.557 (-0.085%), 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=0.525, neg=0, invalid=762
0318: dt=0.448000, rms=0.512 (2.512%), neg=0, invalid=762
0319: dt=0.448000, rms=0.508 (0.599%), neg=0, invalid=762
0320: dt=0.448000, rms=0.507 (0.361%), neg=0, invalid=762
0321: dt=0.448000, rms=0.505 (0.240%), neg=0, invalid=762
0322: dt=0.653846, rms=0.504 (0.254%), neg=0, invalid=762
0323: dt=0.448000, rms=0.504 (0.117%), neg=0, invalid=762
0324: dt=0.448000, rms=0.503 (0.095%), neg=0, invalid=762
0325: dt=0.448000, rms=0.503 (0.077%), neg=0, invalid=762
0326: dt=0.448000, rms=0.502 (0.066%), neg=0, invalid=762
0327: dt=0.448000, rms=0.502 (0.053%), neg=0, invalid=762
0328: dt=0.448000, rms=0.502 (0.049%), neg=0, invalid=762
0329: dt=0.448000, rms=0.502 (0.038%), neg=0, invalid=762
0330: dt=0.448000, rms=0.501 (0.073%), neg=0, invalid=762
0331: dt=0.448000, rms=0.501 (0.087%), neg=0, invalid=762
0332: dt=0.448000, rms=0.500 (0.093%), neg=0, invalid=762
0333: dt=0.448000, rms=0.500 (0.006%), neg=0, invalid=762
0334: dt=0.448000, rms=0.500 (0.010%), neg=0, invalid=762
0335: dt=0.448000, rms=0.500 (0.016%), neg=0, invalid=762
0336: dt=0.448000, rms=0.500 (0.018%), neg=0, invalid=762
0337: dt=0.448000, rms=0.500 (0.026%), neg=0, invalid=762
0338: dt=0.448000, rms=0.500 (0.025%), neg=0, invalid=762
0339: dt=0.448000, rms=0.500 (0.023%), neg=0, invalid=762
0340: dt=0.448000, rms=0.500 (0.007%), neg=0, invalid=762
0341: dt=0.448000, rms=0.500 (0.000%), neg=0, invalid=762
0342: dt=0.448000, rms=0.500 (0.002%), neg=0, invalid=762
0343: dt=0.448000, rms=0.500 (0.000%), neg=0, invalid=762
0344: dt=0.448000, rms=0.500 (0.004%), neg=0, invalid=762
0345: dt=0.448000, rms=0.500 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.500, neg=0, invalid=762
0346: dt=0.448000, rms=0.495 (1.110%), neg=0, invalid=762
0347: dt=0.448000, rms=0.494 (0.138%), neg=0, invalid=762
0348: dt=0.448000, rms=0.494 (0.039%), neg=0, invalid=762
0349: dt=0.448000, rms=0.494 (0.005%), neg=0, invalid=762
0350: dt=0.448000, rms=0.494 (0.002%), neg=0, invalid=762
0351: dt=0.448000, rms=0.494 (-0.016%), 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=0.492, neg=0, invalid=762
0352: dt=0.000000, rms=0.491 (0.108%), neg=0, invalid=762
0353: dt=0.000000, rms=0.491 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0354: dt=92.480000, rms=0.491 (0.137%), neg=0, invalid=762
0355: dt=295.936000, rms=0.491 (0.068%), neg=0, invalid=762
0356: dt=295.936000, rms=0.491 (-0.607%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.491, neg=0, invalid=762
0357: dt=36.288000, rms=0.490 (0.179%), neg=0, invalid=762
0358: dt=36.288000, rms=0.490 (0.049%), neg=0, invalid=762
0359: dt=36.288000, rms=0.490 (0.041%), neg=0, invalid=762
0360: dt=36.288000, rms=0.490 (0.035%), neg=0, invalid=762
0361: dt=36.288000, rms=0.490 (-0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.490, neg=0, invalid=762
0362: dt=122.494624, rms=0.487 (0.654%), neg=0, invalid=762
0363: dt=36.288000, rms=0.486 (0.117%), neg=0, invalid=762
0364: dt=36.288000, rms=0.486 (0.050%), neg=0, invalid=762
0365: dt=36.288000, rms=0.486 (0.063%), neg=0, invalid=762
0366: dt=36.288000, rms=0.485 (0.094%), neg=0, invalid=762
0367: dt=36.288000, rms=0.485 (0.118%), neg=0, invalid=762
0368: dt=36.288000, rms=0.484 (0.131%), neg=0, invalid=762
0369: dt=36.288000, rms=0.484 (0.124%), neg=0, invalid=762
0370: dt=36.288000, rms=0.483 (0.111%), neg=0, invalid=762
0371: dt=103.680000, rms=0.483 (0.025%), neg=0, invalid=762
0372: dt=103.680000, rms=0.483 (0.041%), neg=0, invalid=762
0373: dt=103.680000, rms=0.482 (0.068%), neg=0, invalid=762
0374: dt=103.680000, rms=0.482 (0.093%), neg=0, invalid=762
0375: dt=103.680000, rms=0.481 (0.123%), neg=0, invalid=762
0376: dt=103.680000, rms=0.481 (0.120%), neg=0, invalid=762
0377: dt=103.680000, rms=0.480 (0.109%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0378: dt=32.000000, rms=0.479 (0.469%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0379: dt=44.800000, rms=0.477 (0.430%), neg=0, invalid=762
0380: dt=32.000000, rms=0.476 (0.204%), neg=0, invalid=762
0381: dt=32.000000, rms=0.475 (0.250%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0382: dt=32.000000, rms=0.473 (0.328%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0383: dt=32.000000, rms=0.472 (0.261%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0384: dt=32.000000, rms=0.471 (0.291%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 9 iterations, nbhd size=1, neg = 0
0385: dt=32.000000, rms=0.470 (0.250%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 11 iterations, nbhd size=1, neg = 0
0386: dt=32.000000, rms=0.469 (0.224%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 4 iterations, nbhd size=0, neg = 0
0387: dt=32.000000, rms=0.468 (0.195%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0388: dt=32.000000, rms=0.466 (0.283%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 11 iterations, nbhd size=1, neg = 0
0389: dt=32.000000, rms=0.465 (0.254%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0390: dt=32.000000, rms=0.464 (0.199%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0391: dt=32.000000, rms=0.464 (0.128%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0392: dt=32.000000, rms=0.463 (0.129%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0393: dt=32.000000, rms=0.463 (0.111%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0394: dt=32.000000, rms=0.462 (0.100%), neg=0, invalid=762
0395: dt=32.000000, rms=0.462 (0.080%), neg=0, invalid=762
0396: dt=32.000000, rms=0.462 (-0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.462, neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0397: dt=44.800000, rms=0.459 (0.832%), neg=0, invalid=762
0398: dt=30.141079, rms=0.457 (0.337%), neg=0, invalid=762
0399: dt=25.600000, rms=0.456 (0.178%), neg=0, invalid=762
0400: dt=25.600000, rms=0.456 (0.131%), neg=0, invalid=762
0401: dt=25.600000, rms=0.455 (0.161%), neg=0, invalid=762
0402: dt=25.600000, rms=0.454 (0.160%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0403: dt=25.600000, rms=0.454 (0.133%), neg=0, invalid=762
0404: dt=25.600000, rms=0.453 (0.088%), neg=0, invalid=762
0405: dt=25.600000, rms=0.453 (0.043%), neg=0, invalid=762
0406: dt=25.600000, rms=0.453 (0.054%), neg=0, invalid=762
0407: dt=19.200000, rms=0.452 (0.041%), neg=0, invalid=762
0408: dt=19.200000, rms=0.452 (0.027%), neg=0, invalid=762
0409: dt=19.200000, rms=0.452 (0.033%), neg=0, invalid=762
0410: dt=19.200000, rms=0.452 (0.043%), neg=0, invalid=762
0411: dt=19.200000, rms=0.452 (0.039%), neg=0, invalid=762
0412: dt=19.200000, rms=0.452 (0.034%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0413: dt=0.000000, rms=0.459 (0.126%), neg=0, invalid=762
0414: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0415: dt=1.008000, rms=0.459 (0.132%), neg=0, invalid=762
0416: dt=0.252000, rms=0.459 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.475, neg=0, invalid=762
0417: dt=1.280000, rms=0.473 (0.459%), neg=0, invalid=762
0418: dt=0.256000, rms=0.472 (0.007%), neg=0, invalid=762
0419: dt=0.256000, rms=0.472 (-0.006%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.473, neg=0, invalid=762
0420: dt=1.536000, rms=0.471 (0.338%), neg=0, invalid=762
0421: dt=0.448000, rms=0.471 (0.011%), neg=0, invalid=762
0422: dt=0.448000, rms=0.471 (-0.002%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
iter 0, gcam->neg = 393
after 13 iterations, nbhd size=1, neg = 0
0423: dt=2.234153, rms=0.433 (5.839%), neg=0, invalid=762
0424: dt=0.112000, rms=0.433 (0.113%), neg=0, invalid=762
0425: dt=0.112000, rms=0.433 (-0.093%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0426: dt=0.096000, rms=0.433 (0.210%), neg=0, invalid=762
0427: dt=0.003000, rms=0.433 (-0.001%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0428: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0429: dt=55.488000, rms=0.419 (0.005%), neg=0, invalid=762
0430: dt=92.480000, rms=0.419 (0.002%), neg=0, invalid=762
0431: dt=92.480000, rms=0.419 (0.002%), neg=0, invalid=762
0432: dt=92.480000, rms=0.419 (0.001%), neg=0, invalid=762
0433: dt=92.480000, rms=0.419 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0434: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0435: dt=124.416000, rms=0.419 (0.055%), neg=0, invalid=762
0436: dt=145.152000, rms=0.419 (0.053%), neg=0, invalid=762
0437: dt=145.152000, rms=0.419 (-0.103%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0438: dt=11.200000, rms=0.419 (0.083%), neg=0, invalid=762
0439: dt=8.000000, rms=0.419 (0.015%), neg=0, invalid=762
0440: dt=8.000000, rms=0.419 (0.000%), neg=0, invalid=762
0441: dt=8.000000, rms=0.419 (-0.040%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0442: dt=58.434783, rms=0.417 (0.612%), neg=0, invalid=762
0443: dt=25.600000, rms=0.415 (0.293%), neg=0, invalid=762
0444: dt=102.400000, rms=0.414 (0.293%), neg=0, invalid=762
0445: dt=25.600000, rms=0.413 (0.171%), neg=0, invalid=762
0446: dt=25.600000, rms=0.413 (0.070%), neg=0, invalid=762
0447: dt=25.600000, rms=0.413 (0.099%), neg=0, invalid=762
0448: dt=25.600000, rms=0.412 (0.141%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0449: dt=25.600000, rms=0.412 (0.136%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0450: dt=25.600000, rms=0.411 (0.146%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0451: dt=25.600000, rms=0.410 (0.143%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0452: dt=25.600000, rms=0.410 (0.132%), neg=0, invalid=762
0453: dt=25.600000, rms=0.409 (0.128%), neg=0, invalid=762
0454: dt=25.600000, rms=0.409 (0.106%), neg=0, invalid=762
0455: dt=25.600000, rms=0.408 (0.097%), neg=0, invalid=762
0456: dt=44.800000, rms=0.408 (0.012%), neg=0, invalid=762
0457: dt=44.800000, rms=0.408 (0.002%), neg=0, invalid=762
0458: dt=44.800000, rms=0.408 (0.023%), neg=0, invalid=762
0459: dt=44.800000, rms=0.408 (0.019%), neg=0, invalid=762
0460: dt=44.800000, rms=0.408 (0.023%), neg=0, invalid=762
0461: dt=44.800000, rms=0.408 (0.029%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0462: dt=44.800000, rms=0.408 (0.047%), neg=0, invalid=762
0463: dt=44.800000, rms=0.408 (0.049%), neg=0, invalid=762
0464: dt=44.800000, rms=0.407 (0.055%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0465: dt=44.800000, rms=0.407 (0.068%), neg=0, invalid=762
0466: dt=44.800000, rms=0.407 (0.066%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.411, neg=0, invalid=762
0467: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.411, neg=0, invalid=762
0468: dt=0.000000, rms=0.411 (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=0.420, neg=0, invalid=762
0469: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0470: dt=0.256000, rms=0.420 (0.009%), neg=0, invalid=762
0471: dt=0.028000, rms=0.420 (0.000%), neg=0, invalid=762
0472: dt=0.028000, rms=0.420 (-0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
iter 0, gcam->neg = 309
after 16 iterations, nbhd size=1, neg = 0
0473: dt=1.324410, rms=0.398 (2.032%), neg=0, invalid=762
0474: dt=0.000020, rms=0.398 (0.000%), neg=0, invalid=762
0475: dt=0.000020, rms=0.398 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.398, neg=0, invalid=762
0476: dt=0.112000, rms=0.397 (0.091%), neg=0, invalid=762
0477: dt=0.112000, rms=0.397 (0.033%), neg=0, invalid=762
0478: dt=0.112000, rms=0.397 (0.019%), neg=0, invalid=762
0479: dt=0.112000, rms=0.397 (-0.038%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 49 minutes and 43 seconds.
mri_ca_register utimesec    11112.474647
mri_ca_register stimesec    10.128460
mri_ca_register ru_maxrss   1340880
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4946242
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63312
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    6179
mri_ca_register ru_nivcsw   25531
FSRUNTIME@ mri_ca_register  2.8287 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 20:25:41 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-908
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-6.0.0/0051359/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 7.62
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 = 0.09407 (24)
Left_Lateral_Ventricle (4): linear fit = 1.16 x + 0.0 (462 voxels, overlap=0.958)
Left_Lateral_Ventricle (4): linear fit = 1.16 x + 0.0 (462 voxels, peak = 23), gca=23.3
gca peak = 0.17677 (13)
mri peak = 0.08572 (24)
Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (1259 voxels, overlap=0.486)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1259 voxels, peak = 23), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.12338 (92)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (457 voxels, overlap=1.016)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (457 voxels, peak = 91), gca=90.7
gca peak = 0.16930 (96)
mri peak = 0.11071 (92)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (560 voxels, overlap=0.836)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (560 voxels, peak = 92), gca=91.7
gca peak = 0.24553 (55)
mri peak = 0.08934 (68)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (777 voxels, overlap=0.282)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (777 voxels, peak = 66), gca=66.3
gca peak = 0.30264 (59)
mri peak = 0.07240 (62)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (729 voxels, overlap=1.012)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (729 voxels, peak = 67), gca=67.0
gca peak = 0.07580 (103)
mri peak = 0.08223 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (45055 voxels, overlap=0.737)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (45055 voxels, peak = 106), gca=105.6
gca peak = 0.07714 (104)
mri peak = 0.08363 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (46464 voxels, overlap=0.750)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (46464 voxels, peak = 106), gca=105.6
gca peak = 0.09712 (58)
mri peak = 0.04673 (67)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (33518 voxels, overlap=0.545)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (33518 voxels, peak = 66), gca=65.8
gca peak = 0.11620 (58)
mri peak = 0.04899 (67)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (35734 voxels, overlap=0.432)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (35734 voxels, peak = 68), gca=67.6
gca peak = 0.30970 (66)
mri peak = 0.09046 (76)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (1113 voxels, overlap=0.159)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (1113 voxels, peak = 76), gca=75.6
gca peak = 0.15280 (69)
mri peak = 0.09129 (78)
Left_Caudate (11): linear fit = 1.04 x + 0.0 (1056 voxels, overlap=0.927)
Left_Caudate (11): linear fit = 1.04 x + 0.0 (1056 voxels, peak = 72), gca=72.1
gca peak = 0.13902 (56)
mri peak = 0.06289 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (19400 voxels, overlap=0.721)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (19400 voxels, peak = 64), gca=63.6
gca peak = 0.14777 (55)
mri peak = 0.06290 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (23814 voxels, overlap=0.721)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (23814 voxels, peak = 64), gca=63.5
gca peak = 0.16765 (84)
mri peak = 0.07960 (83)
Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (3466 voxels, overlap=0.990)
Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (3466 voxels, peak = 82), gca=81.9
gca peak = 0.18739 (84)
mri peak = 0.07745 (82)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4053 voxels, overlap=0.994)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4053 voxels, peak = 82), gca=81.9
gca peak = 0.29869 (57)
mri peak = 0.08181 (64)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (366 voxels, overlap=0.511)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (366 voxels, peak = 64), gca=63.6
gca peak = 0.33601 (57)
mri peak = 0.08429 (68)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (385 voxels, overlap=0.049)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (385 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.06324 (82)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3526 voxels, overlap=0.995)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3526 voxels, peak = 89), gca=88.7
gca peak = 0.11793 (83)
mri peak = 0.06829 (85)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3444 voxels, overlap=0.950)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3444 voxels, peak = 84), gca=84.2
gca peak = 0.08324 (81)
mri peak = 0.06889 (80)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (1466 voxels, overlap=0.852)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (1466 voxels, peak = 84), gca=83.8
gca peak = 0.10360 (77)
mri peak = 0.07832 (83)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1757 voxels, overlap=0.750)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1757 voxels, peak = 81), gca=81.2
gca peak = 0.08424 (78)
mri peak = 0.11172 (83)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (7262 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (7262 voxels, peak = 82), gca=82.3
gca peak = 0.12631 (89)
mri peak = 0.07636 (90)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1114 voxels, overlap=0.825)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1114 voxels, peak = 90), gca=90.3
gca peak = 0.14500 (87)
mri peak = 0.07755 (87)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1054 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1054 voxels, peak = 86), gca=85.7
gca peak = 0.14975 (24)
mri peak = 0.11946 (27)
gca peak = 0.19357 (14)
mri peak = 0.10533 (26)
Fourth_Ventricle (15): linear fit = 1.48 x + 0.0 (141 voxels, overlap=0.485)
Fourth_Ventricle (15): linear fit = 1.48 x + 0.0 (141 voxels, peak = 21), gca=20.6
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 1.16 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.38 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.14868 (24)
mri peak = 0.09407 (24)
Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (462 voxels, overlap=0.921)
Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (462 voxels, peak = 26), gca=25.6
gca peak = 0.13639 (19)
mri peak = 0.08572 (24)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (1259 voxels, overlap=0.746)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (1259 voxels, peak = 23), gca=22.5
gca peak = 0.26787 (90)
mri peak = 0.12338 (92)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (457 voxels, overlap=1.013)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (457 voxels, peak = 91), gca=91.3
gca peak = 0.18687 (92)
mri peak = 0.11071 (92)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (560 voxels, overlap=1.006)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (560 voxels, peak = 93), gca=93.4
gca peak = 0.27728 (67)
mri peak = 0.08934 (68)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (777 voxels, overlap=1.003)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (777 voxels, peak = 67), gca=67.0
gca peak = 0.28669 (64)
mri peak = 0.07240 (62)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (729 voxels, overlap=1.012)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (729 voxels, peak = 61), gca=61.1
gca peak = 0.07610 (105)
mri peak = 0.08223 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45055 voxels, overlap=0.829)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45055 voxels, peak = 104), gca=104.5
gca peak = 0.07820 (106)
mri peak = 0.08363 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46464 voxels, overlap=0.811)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46464 voxels, peak = 105), gca=105.5
gca peak = 0.08609 (66)
mri peak = 0.04673 (67)
Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (33518 voxels, overlap=0.961)
Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (33518 voxels, peak = 68), gca=68.3
gca peak = 0.09798 (68)
mri peak = 0.04899 (67)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (35734 voxels, overlap=0.961)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (35734 voxels, peak = 68), gca=68.0
gca peak = 0.24442 (76)
mri peak = 0.09046 (76)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1113 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1113 voxels, peak = 75), gca=74.9
gca peak = 0.15386 (72)
mri peak = 0.09129 (78)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1056 voxels, overlap=1.002)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1056 voxels, peak = 72), gca=72.0
gca peak = 0.12599 (63)
mri peak = 0.06289 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (19400 voxels, overlap=0.996)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (19400 voxels, peak = 63), gca=63.0
gca peak = 0.13021 (63)
mri peak = 0.06290 (64)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23814 voxels, overlap=0.990)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23814 voxels, peak = 62), gca=62.1
gca peak = 0.17082 (82)
mri peak = 0.07960 (83)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3466 voxels, overlap=0.980)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3466 voxels, peak = 82), gca=82.0
gca peak = 0.18659 (82)
mri peak = 0.07745 (82)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4053 voxels, overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4053 voxels, peak = 82), gca=82.0
gca peak = 0.29916 (65)
mri peak = 0.08181 (64)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (366 voxels, overlap=1.024)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (366 voxels, peak = 66), gca=66.0
gca peak = 0.29009 (68)
mri peak = 0.08429 (68)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (385 voxels, overlap=1.008)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (385 voxels, peak = 69), gca=69.0
gca peak = 0.10448 (87)
mri peak = 0.06324 (82)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3526 voxels, overlap=0.997)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3526 voxels, peak = 87), gca=86.6
gca peak = 0.11237 (82)
mri peak = 0.06829 (85)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3444 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3444 voxels, peak = 82), gca=81.6
gca peak = 0.08250 (84)
mri peak = 0.06889 (80)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1466 voxels, overlap=0.928)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1466 voxels, peak = 83), gca=82.7
gca peak = 0.08162 (81)
mri peak = 0.07832 (83)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1757 voxels, overlap=0.930)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1757 voxels, peak = 81), gca=80.6
gca peak = 0.07687 (85)
mri peak = 0.11172 (83)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (7262 voxels, overlap=0.675)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (7262 voxels, peak = 85), gca=84.6
gca peak = 0.12482 (89)
mri peak = 0.07636 (90)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1114 voxels, overlap=0.840)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1114 voxels, peak = 88), gca=87.7
gca peak = 0.15230 (84)
mri peak = 0.07755 (87)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1054 voxels, overlap=0.894)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1054 voxels, peak = 84), gca=83.6
gca peak = 0.14011 (33)
mri peak = 0.11946 (27)
gca peak = 0.14887 (22)
mri peak = 0.10533 (26)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (141 voxels, overlap=0.759)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (141 voxels, peak = 23), gca=22.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15127 (30)
gca peak Left_Thalamus = 0.36646 (103)
gca peak Third_Ventricle = 0.14011 (33)
gca peak CSF = 0.17099 (50)
gca peak Left_Accumbens_area = 0.73262 (65)
gca peak Left_undetermined = 0.96707 (27)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.11914 (35)
gca peak Right_Inf_Lat_Vent = 0.24202 (28)
gca peak Right_Accumbens_area = 0.29834 (74)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14507 (37)
gca peak Fifth_Ventricle = 0.75707 (43)
gca peak WM_hypointensities = 0.07583 (78)
gca peak non_WM_hypointensities = 0.08683 (44)
gca peak Optic_Chiasm = 0.71117 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.09 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
96470 voxels changed in iteration 0 of unlikely voxel relabeling
277 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
2 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
67280 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels)
634 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 92845 changed. image ll: -2.138, PF=0.500
pass 2: 22865 changed. image ll: -2.137, PF=0.500
pass 3: 6109 changed.
pass 4: 2230 changed.
58203 voxels changed in iteration 0 of unlikely voxel relabeling
441 voxels changed in iteration 1 of unlikely voxel relabeling
18 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8164 voxels changed in iteration 0 of unlikely voxel relabeling
170 voxels changed in iteration 1 of unlikely voxel relabeling
10 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6367 voxels changed in iteration 0 of unlikely voxel relabeling
61 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5632 voxels changed in iteration 0 of unlikely voxel relabeling
34 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    4186.931489
mri_ca_label stimesec    2.282652
mri_ca_label ru_maxrss   2102172
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   710390
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  520
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    282
mri_ca_label ru_nivcsw   19319
auto-labeling took 69 minutes and 3 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/transforms/cc_up.lta 0051359 

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-6.0.0/0051359/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/norm.mgz
93088 voxels in left wm, 125263 in right wm, xrange [119, 139]
searching rotation angles z=[-14 -0], y=[-10  4]

searching scale 1 Z rot -14.4  
searching scale 1 Z rot -14.1  
searching scale 1 Z rot -13.9  
searching scale 1 Z rot -13.6  
searching scale 1 Z rot -13.4  
searching scale 1 Z rot -13.1  
searching scale 1 Z rot -12.9  
searching scale 1 Z rot -12.6  
searching scale 1 Z rot -12.4  
searching scale 1 Z rot -12.1  
searching scale 1 Z rot -11.9  
searching scale 1 Z rot -11.6  
searching scale 1 Z rot -11.4  
searching scale 1 Z rot -11.1  
searching scale 1 Z rot -10.9  
searching scale 1 Z rot -10.6  
searching scale 1 Z rot -10.4  
searching scale 1 Z rot -10.1  
searching scale 1 Z rot -9.9  
searching scale 1 Z rot -9.6  
searching scale 1 Z rot -9.4  
searching scale 1 Z rot -9.1  
searching scale 1 Z rot -8.9  
searching scale 1 Z rot -8.6  
searching scale 1 Z rot -8.4  
searching scale 1 Z rot -8.1  
searching scale 1 Z rot -7.9  
searching scale 1 Z rot -7.6  
searching scale 1 Z rot -7.4  
searching scale 1 Z rot -7.1  
searching scale 1 Z rot -6.9  
searching scale 1 Z rot -6.6  
searching scale 1 Z rot -6.4  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.4  global minimum found at slice 131.0, rotations (-2.33, -7.14)
final transformation (x=131.0, yr=-2.331, zr=-7.136):
 0.99143   0.12423  -0.04035  -6.30908;
-0.12413   0.99225   0.00505   70.23754;
 0.04067   0.00000   0.99917   4.77026;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [124, 132] in xformed coordinates
best xformed slice 129
cc center is found at 129 74 118
eigenvectors:
 0.00016  -0.00631   0.99998;
 0.15872  -0.98730  -0.00626;
 0.98732   0.15872   0.00084;
error in mid anterior detected - correcting...
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/aseg.auto.mgz...
corpus callosum segmentation took 2.7 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 21:37:26 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 21:37:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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...
2336 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 74 (74), valley at 31 (31)
csf peak at 37, setting threshold to 61
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 72 (72), valley at  0 (-1)
csf peak at 36, setting threshold to 60
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 39 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 21:41:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1754354 voxels in mask (pct= 10.46)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 21:41:08 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 104.0 +- 6.6 [79.0 --> 125.0]
GM (72.0) : 69.9 +- 9.2 [30.0 --> 95.0]
setting bottom of white matter range to 79.2
setting top of gray matter range to 88.4
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...
21412 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5121 filled
560 bright non-wm voxels segmented.
9437 diagonally connected voxels added...
white matter segmentation took 1.9 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...
368 voxels added to wm to prevent paths from MTL structures to cortex
2728 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 45209 voxels turned on, 29939 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  38 found -  38 modified     |    TOTAL:  38
pass   2 (xy+):   0 found -  38 modified     |    TOTAL:  38
pass   1 (xy-):  50 found -  50 modified     |    TOTAL:  88
pass   2 (xy-):   0 found -  50 modified     |    TOTAL:  88
pass   1 (yz+):  38 found -  38 modified     |    TOTAL: 126
pass   2 (yz+):   0 found -  38 modified     |    TOTAL: 126
pass   1 (yz-):  54 found -  54 modified     |    TOTAL: 180
pass   2 (yz-):   0 found -  54 modified     |    TOTAL: 180
pass   1 (xz+):  41 found -  41 modified     |    TOTAL: 221
pass   2 (xz+):   0 found -  41 modified     |    TOTAL: 221
pass   1 (xz-):  32 found -  32 modified     |    TOTAL: 253
pass   2 (xz-):   0 found -  32 modified     |    TOTAL: 253
Iteration Number : 1
pass   1 (+++):  36 found -  36 modified     |    TOTAL:  36
pass   2 (+++):   0 found -  36 modified     |    TOTAL:  36
pass   1 (+++):  43 found -  43 modified     |    TOTAL:  79
pass   2 (+++):   0 found -  43 modified     |    TOTAL:  79
pass   1 (+++):  61 found -  61 modified     |    TOTAL: 140
pass   2 (+++):   0 found -  61 modified     |    TOTAL: 140
pass   1 (+++):  49 found -  49 modified     |    TOTAL: 189
pass   2 (+++):   0 found -  49 modified     |    TOTAL: 189
Iteration Number : 1
pass   1 (++): 217 found - 217 modified     |    TOTAL: 217
pass   2 (++):   0 found - 217 modified     |    TOTAL: 217
pass   1 (+-): 222 found - 222 modified     |    TOTAL: 439
pass   2 (+-):   0 found - 222 modified     |    TOTAL: 439
pass   1 (--): 210 found - 210 modified     |    TOTAL: 649
pass   2 (--):   0 found - 210 modified     |    TOTAL: 649
pass   1 (-+): 270 found - 270 modified     |    TOTAL: 919
pass   2 (-+):   0 found - 270 modified     |    TOTAL: 919
Iteration Number : 2
pass   1 (xy+):  16 found -  16 modified     |    TOTAL:  16
pass   2 (xy+):   0 found -  16 modified     |    TOTAL:  16
pass   1 (xy-):  21 found -  21 modified     |    TOTAL:  37
pass   2 (xy-):   0 found -  21 modified     |    TOTAL:  37
pass   1 (yz+):  20 found -  20 modified     |    TOTAL:  57
pass   2 (yz+):   0 found -  20 modified     |    TOTAL:  57
pass   1 (yz-):  33 found -  33 modified     |    TOTAL:  90
pass   2 (yz-):   0 found -  33 modified     |    TOTAL:  90
pass   1 (xz+):  21 found -  21 modified     |    TOTAL: 111
pass   2 (xz+):   0 found -  21 modified     |    TOTAL: 111
pass   1 (xz-):  20 found -  20 modified     |    TOTAL: 131
pass   2 (xz-):   0 found -  20 modified     |    TOTAL: 131
Iteration Number : 2
pass   1 (+++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   8
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  12
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  12
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  18
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  18
Iteration Number : 2
pass   1 (++):  13 found -  13 modified     |    TOTAL:  13
pass   2 (++):   0 found -  13 modified     |    TOTAL:  13
pass   1 (+-):   5 found -   5 modified     |    TOTAL:  18
pass   2 (+-):   0 found -   5 modified     |    TOTAL:  18
pass   1 (--):   7 found -   7 modified     |    TOTAL:  25
pass   2 (--):   0 found -   7 modified     |    TOTAL:  25
pass   1 (-+):  12 found -  12 modified     |    TOTAL:  37
pass   2 (-+):   0 found -  12 modified     |    TOTAL:  37
Iteration Number : 3
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   6
pass   1 (yz-):   5 found -   5 modified     |    TOTAL:  11
pass   2 (yz-):   0 found -   5 modified     |    TOTAL:  11
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  14
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  14
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  17
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  17
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 : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   1 found -   1 modified     |    TOTAL:   3
pass   2 (--):   0 found -   1 modified     |    TOTAL:   3
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   4
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1571 (out of 631112: 0.248926)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 21:43:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.00742   0.16527  -0.02427  -15.71089;
-0.17432   1.05563   0.01475   41.16247;
 0.02666  -0.01213   0.96097  -5.33792;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1107 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75)
no need to search
using seed (127, 115, 93), TAL = (1.0, -35.0, 13.0)
talairach voxel to voxel transform
 0.96582  -0.15090   0.02671   21.52802;
 0.15984   0.92216  -0.01012  -35.50129;
-0.02478   0.01583   1.03974   4.50923;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  115,  93) --> (1.0, -35.0, 13.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (1.00, -35.00, 13.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, -35.00, 13.00) SRC: (111.93, 87.03, 100.32)
search lh wm seed point around talairach space (-17.00, -35.00, 13.00), SRC: (146.70, 92.78, 99.43)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 21:44:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   4
pass   1 (yz+):   8 found -   8 modified     |    TOTAL:  12
pass   2 (yz+):   0 found -   8 modified     |    TOTAL:  12
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:  12
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  13
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  13
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  14
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  14
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   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 = 16 (out of 305619: 0.005235)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 3580 vertices, 3804 faces
slice 50: 11717 vertices, 12017 faces
slice 60: 21737 vertices, 22094 faces
slice 70: 33052 vertices, 33459 faces
slice 80: 45679 vertices, 46023 faces
slice 90: 57606 vertices, 58041 faces
slice 100: 70528 vertices, 71056 faces
slice 110: 85453 vertices, 85962 faces
slice 120: 99891 vertices, 100417 faces
slice 130: 113092 vertices, 113623 faces
slice 140: 126069 vertices, 126599 faces
slice 150: 136885 vertices, 137376 faces
slice 160: 146767 vertices, 147257 faces
slice 170: 156007 vertices, 156461 faces
slice 180: 163420 vertices, 163838 faces
slice 190: 170437 vertices, 170837 faces
slice 200: 174719 vertices, 174972 faces
slice 210: 175092 vertices, 175264 faces
slice 220: 175092 vertices, 175264 faces
slice 230: 175092 vertices, 175264 faces
slice 240: 175092 vertices, 175264 faces
slice 250: 175092 vertices, 175264 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...
   175092 voxel in cpt #1: X=-172 [v=175092,e=525792,f=350528] located at (-28.656517, -16.306513, 37.135593)
For the whole surface: X=-172 [v=175092,e=525792,f=350528]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 21:44:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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


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

Total Number of Modified Voxels = 0 (out of 306083: 0.000000)
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: 458 vertices, 512 faces
slice 50: 4662 vertices, 4865 faces
slice 60: 12182 vertices, 12472 faces
slice 70: 21964 vertices, 22352 faces
slice 80: 33866 vertices, 34281 faces
slice 90: 46898 vertices, 47277 faces
slice 100: 59254 vertices, 59664 faces
slice 110: 73798 vertices, 74319 faces
slice 120: 88926 vertices, 89483 faces
slice 130: 104055 vertices, 104598 faces
slice 140: 118711 vertices, 119276 faces
slice 150: 131391 vertices, 131915 faces
slice 160: 141261 vertices, 141709 faces
slice 170: 151157 vertices, 151681 faces
slice 180: 160087 vertices, 160551 faces
slice 190: 167616 vertices, 168049 faces
slice 200: 173621 vertices, 173975 faces
slice 210: 174794 vertices, 174990 faces
slice 220: 174794 vertices, 174990 faces
slice 230: 174794 vertices, 174990 faces
slice 240: 174794 vertices, 174990 faces
slice 250: 174794 vertices, 174990 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...
   174794 voxel in cpt #1: X=-196 [v=174794,e=524970,f=349980] located at (27.222256, -9.238996, 45.054539)
For the whole surface: X=-196 [v=174794,e=524970,f=349980]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 21:44:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 21:44:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

Waiting for PID 16742 of (16742 16745) to complete...
Waiting for PID 16745 of (16742 16745) 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 (16742 16745) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 21:44:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 21:44:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

Waiting for PID 16791 of (16791 16794) to complete...
Waiting for PID 16794 of (16791 16794) 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 = 49.4 mm, total surface area = 88685 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.165 (target=0.015)   
step 005: RMS=0.127 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.085 (target=0.015)   
step 020: RMS=0.074 (target=0.015)   
step 025: RMS=0.068 (target=0.015)   
step 030: RMS=0.061 (target=0.015)   
step 035: RMS=0.058 (target=0.015)   
step 040: RMS=0.056 (target=0.015)   
step 045: RMS=0.053 (target=0.015)   
step 050: RMS=0.052 (target=0.015)   
step 055: RMS=0.052 (target=0.015)   
step 060: RMS=0.051 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    52.210062
mris_inflate stimesec    0.145977
mris_inflate ru_maxrss   256272
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36922
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12328
mris_inflate ru_oublock  12344
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2049
mris_inflate ru_nivcsw   4066

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.1 mm, total surface area = 88277 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.2 minutes

step 000: RMS=0.168 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.099 (target=0.015)   
step 015: RMS=0.085 (target=0.015)   
step 020: RMS=0.076 (target=0.015)   
step 025: RMS=0.069 (target=0.015)   
step 030: RMS=0.062 (target=0.015)   
step 035: RMS=0.057 (target=0.015)   
step 040: RMS=0.054 (target=0.015)   
step 045: RMS=0.053 (target=0.015)   
step 050: RMS=0.051 (target=0.015)   
step 055: RMS=0.050 (target=0.015)   
step 060: RMS=0.050 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    70.437291
mris_inflate stimesec    0.143978
mris_inflate ru_maxrss   256112
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36881
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12304
mris_inflate ru_oublock  12320
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1989
mris_inflate ru_nivcsw   5860
PIDs (16791 16794) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 21:46:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 21:46:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

Waiting for PID 16916 of (16916 16920) to complete...
Waiting for PID 16920 of (16916 16920) 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 0.87 +- 0.55 (0.00-->6.50) (max @ vno 57151 --> 58343)
face area 0.02 +- 0.03 (-0.28-->0.72)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.282...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.968, avgs=0
005/300: dt: 0.9000, rms radial error=176.714, avgs=0
010/300: dt: 0.9000, rms radial error=176.168, avgs=0
015/300: dt: 0.9000, rms radial error=175.450, avgs=0
020/300: dt: 0.9000, rms radial error=174.621, avgs=0
025/300: dt: 0.9000, rms radial error=173.734, avgs=0
030/300: dt: 0.9000, rms radial error=172.814, avgs=0
035/300: dt: 0.9000, rms radial error=171.877, avgs=0
040/300: dt: 0.9000, rms radial error=170.932, avgs=0
045/300: dt: 0.9000, rms radial error=169.985, avgs=0
050/300: dt: 0.9000, rms radial error=169.038, avgs=0
055/300: dt: 0.9000, rms radial error=168.094, avgs=0
060/300: dt: 0.9000, rms radial error=167.154, avgs=0
065/300: dt: 0.9000, rms radial error=166.217, avgs=0
070/300: dt: 0.9000, rms radial error=165.286, avgs=0
075/300: dt: 0.9000, rms radial error=164.359, avgs=0
080/300: dt: 0.9000, rms radial error=163.437, avgs=0
085/300: dt: 0.9000, rms radial error=162.519, avgs=0
090/300: dt: 0.9000, rms radial error=161.607, avgs=0
095/300: dt: 0.9000, rms radial error=160.700, avgs=0
100/300: dt: 0.9000, rms radial error=159.797, avgs=0
105/300: dt: 0.9000, rms radial error=158.900, avgs=0
110/300: dt: 0.9000, rms radial error=158.007, avgs=0
115/300: dt: 0.9000, rms radial error=157.120, avgs=0
120/300: dt: 0.9000, rms radial error=156.237, avgs=0
125/300: dt: 0.9000, rms radial error=155.359, avgs=0
130/300: dt: 0.9000, rms radial error=154.486, avgs=0
135/300: dt: 0.9000, rms radial error=153.617, avgs=0
140/300: dt: 0.9000, rms radial error=152.753, avgs=0
145/300: dt: 0.9000, rms radial error=151.894, avgs=0
150/300: dt: 0.9000, rms radial error=151.039, avgs=0
155/300: dt: 0.9000, rms radial error=150.189, avgs=0
160/300: dt: 0.9000, rms radial error=149.344, avgs=0
165/300: dt: 0.9000, rms radial error=148.503, avgs=0
170/300: dt: 0.9000, rms radial error=147.667, avgs=0
175/300: dt: 0.9000, rms radial error=146.835, avgs=0
180/300: dt: 0.9000, rms radial error=146.008, avgs=0
185/300: dt: 0.9000, rms radial error=145.186, avgs=0
190/300: dt: 0.9000, rms radial error=144.368, avgs=0
195/300: dt: 0.9000, rms radial error=143.555, avgs=0
200/300: dt: 0.9000, rms radial error=142.746, avgs=0
205/300: dt: 0.9000, rms radial error=141.941, avgs=0
210/300: dt: 0.9000, rms radial error=141.141, avgs=0
215/300: dt: 0.9000, rms radial error=140.345, avgs=0
220/300: dt: 0.9000, rms radial error=139.554, avgs=0
225/300: dt: 0.9000, rms radial error=138.767, avgs=0
230/300: dt: 0.9000, rms radial error=137.985, avgs=0
235/300: dt: 0.9000, rms radial error=137.206, avgs=0
240/300: dt: 0.9000, rms radial error=136.432, avgs=0
245/300: dt: 0.9000, rms radial error=135.663, avgs=0
250/300: dt: 0.9000, rms radial error=134.897, avgs=0
255/300: dt: 0.9000, rms radial error=134.136, avgs=0
260/300: dt: 0.9000, rms radial error=133.379, avgs=0
265/300: dt: 0.9000, rms radial error=132.627, avgs=0
270/300: dt: 0.9000, rms radial error=131.878, avgs=0
275/300: dt: 0.9000, rms radial error=131.134, avgs=0
280/300: dt: 0.9000, rms radial error=130.394, avgs=0
285/300: dt: 0.9000, rms radial error=129.658, avgs=0
290/300: dt: 0.9000, rms radial error=128.926, avgs=0
295/300: dt: 0.9000, rms radial error=128.199, avgs=0
300/300: dt: 0.9000, rms radial error=127.475, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 21243.82
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 2 (K=40.0), pass 1, starting sse = 3862.31
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 476.43
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/11 = 0.00484
epoch 4 (K=640.0), pass 1, starting sse = 40.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/13 = 0.00680
final distance error %29.69
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    399.068332
mris_sphere stimesec    0.245962
mris_sphere ru_maxrss   256476
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   36970
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  12328
mris_sphere ru_oublock  12368
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8806
mris_sphere ru_nivcsw   24461
FSRUNTIME@ mris_sphere  0.1013 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 0.88 +- 0.53 (0.00-->6.72) (max @ vno 58954 --> 60241)
face area 0.02 +- 0.03 (-0.13-->0.60)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.287...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.817, avgs=0
005/300: dt: 0.9000, rms radial error=176.557, avgs=0
010/300: dt: 0.9000, rms radial error=176.000, avgs=0
015/300: dt: 0.9000, rms radial error=175.270, avgs=0
020/300: dt: 0.9000, rms radial error=174.440, avgs=0
025/300: dt: 0.9000, rms radial error=173.552, avgs=0
030/300: dt: 0.9000, rms radial error=172.632, avgs=0
035/300: dt: 0.9000, rms radial error=171.696, avgs=0
040/300: dt: 0.9000, rms radial error=170.751, avgs=0
045/300: dt: 0.9000, rms radial error=169.804, avgs=0
050/300: dt: 0.9000, rms radial error=168.858, avgs=0
055/300: dt: 0.9000, rms radial error=167.914, avgs=0
060/300: dt: 0.9000, rms radial error=166.974, avgs=0
065/300: dt: 0.9000, rms radial error=166.038, avgs=0
070/300: dt: 0.9000, rms radial error=165.107, avgs=0
075/300: dt: 0.9000, rms radial error=164.180, avgs=0
080/300: dt: 0.9000, rms radial error=163.258, avgs=0
085/300: dt: 0.9000, rms radial error=162.341, avgs=0
090/300: dt: 0.9000, rms radial error=161.429, avgs=0
095/300: dt: 0.9000, rms radial error=160.522, avgs=0
100/300: dt: 0.9000, rms radial error=159.620, avgs=0
105/300: dt: 0.9000, rms radial error=158.723, avgs=0
110/300: dt: 0.9000, rms radial error=157.831, avgs=0
115/300: dt: 0.9000, rms radial error=156.943, avgs=0
120/300: dt: 0.9000, rms radial error=156.060, avgs=0
125/300: dt: 0.9000, rms radial error=155.183, avgs=0
130/300: dt: 0.9000, rms radial error=154.309, avgs=0
135/300: dt: 0.9000, rms radial error=153.441, avgs=0
140/300: dt: 0.9000, rms radial error=152.577, avgs=0
145/300: dt: 0.9000, rms radial error=151.718, avgs=0
150/300: dt: 0.9000, rms radial error=150.863, avgs=0
155/300: dt: 0.9000, rms radial error=150.013, avgs=0
160/300: dt: 0.9000, rms radial error=149.168, avgs=0
165/300: dt: 0.9000, rms radial error=148.328, avgs=0
170/300: dt: 0.9000, rms radial error=147.492, avgs=0
175/300: dt: 0.9000, rms radial error=146.661, avgs=0
180/300: dt: 0.9000, rms radial error=145.834, avgs=0
185/300: dt: 0.9000, rms radial error=145.012, avgs=0
190/300: dt: 0.9000, rms radial error=144.195, avgs=0
195/300: dt: 0.9000, rms radial error=143.382, avgs=0
200/300: dt: 0.9000, rms radial error=142.573, avgs=0
205/300: dt: 0.9000, rms radial error=141.769, avgs=0
210/300: dt: 0.9000, rms radial error=140.970, avgs=0
215/300: dt: 0.9000, rms radial error=140.175, avgs=0
220/300: dt: 0.9000, rms radial error=139.384, avgs=0
225/300: dt: 0.9000, rms radial error=138.598, avgs=0
230/300: dt: 0.9000, rms radial error=137.816, avgs=0
235/300: dt: 0.9000, rms radial error=137.038, avgs=0
240/300: dt: 0.9000, rms radial error=136.265, avgs=0
245/300: dt: 0.9000, rms radial error=135.496, avgs=0
250/300: dt: 0.9000, rms radial error=134.731, avgs=0
255/300: dt: 0.9000, rms radial error=133.971, avgs=0
260/300: dt: 0.9000, rms radial error=133.215, avgs=0
265/300: dt: 0.9000, rms radial error=132.463, avgs=0
270/300: dt: 0.9000, rms radial error=131.715, avgs=0
275/300: dt: 0.9000, rms radial error=130.972, avgs=0
280/300: dt: 0.9000, rms radial error=130.232, avgs=0
285/300: dt: 0.9000, rms radial error=129.497, avgs=0
290/300: dt: 0.9000, rms radial error=128.766, avgs=0
295/300: dt: 0.9000, rms radial error=128.039, avgs=0
300/300: dt: 0.9000, rms radial error=127.316, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 21087.46
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 2 (K=40.0), pass 1, starting sse = 3749.92
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
epoch 3 (K=160.0), pass 1, starting sse = 439.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00372
epoch 4 (K=640.0), pass 1, starting sse = 39.03
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00679
final distance error %27.69
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    304.799663
mris_sphere stimesec    0.223965
mris_sphere ru_maxrss   256320
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   36930
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  12304
mris_sphere ru_oublock  12344
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    7980
mris_sphere ru_nivcsw   23026
FSRUNTIME@ mris_sphere  0.0855 hours 1 threads
PIDs (16916 16920) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 21:52:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 21:52:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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


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

#@# Fix Topology lh Sat Oct  7 21:52:10 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051359 lh 

#@# Fix Topology rh Sat Oct  7 21:52:10 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051359 rh 

Waiting for PID 17328 of (17328 17331) to complete...
Waiting for PID 17331 of (17328 17331) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051359 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=-172 (nv=175092, nf=350528, ne=525792, g=87)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
11881 ambiguous faces found in tessellation
segmenting defects...
77 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 40 into 39
      -merging segment 41 into 39
      -merging segment 60 into 50
      -merging segment 63 into 62
      -merging segment 49 into 66
72 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5381  (-4.7690)
      -vertex     loglikelihood: -6.1888  (-3.0944)
      -normal dot loglikelihood: -3.6301  (-3.6301)
      -quad curv  loglikelihood: -6.6189  (-3.3095)
      Total Loglikelihood : -25.9758

CORRECTING DEFECT 0 (vertices=393, convex hull=78, v0=1255)
After retessellation of defect 0 (v0=1255), euler #=-66 (167945,501112,333101) : difference with theory (-69) = -3 

CORRECTING DEFECT 1 (vertices=32, convex hull=59, v0=4384)
After retessellation of defect 1 (v0=4384), euler #=-65 (167964,501187,333158) : difference with theory (-68) = -3 

CORRECTING DEFECT 2 (vertices=21, convex hull=36, v0=12635)
After retessellation of defect 2 (v0=12635), euler #=-64 (167967,501205,333174) : difference with theory (-67) = -3 

CORRECTING DEFECT 3 (vertices=232, convex hull=232, v0=13122)
After retessellation of defect 3 (v0=13122), euler #=-63 (168050,501558,333445) : difference with theory (-66) = -3 

CORRECTING DEFECT 4 (vertices=90, convex hull=115, v0=31954)
After retessellation of defect 4 (v0=31954), euler #=-62 (168086,501712,333564) : difference with theory (-65) = -3 

CORRECTING DEFECT 5 (vertices=31, convex hull=66, v0=34896)
After retessellation of defect 5 (v0=34896), euler #=-61 (168103,501789,333625) : difference with theory (-64) = -3 

CORRECTING DEFECT 6 (vertices=69, convex hull=105, v0=35264)
After retessellation of defect 6 (v0=35264), euler #=-60 (168146,501969,333763) : difference with theory (-63) = -3 

CORRECTING DEFECT 7 (vertices=55, convex hull=89, v0=36837)
After retessellation of defect 7 (v0=36837), euler #=-59 (168169,502075,333847) : difference with theory (-62) = -3 

CORRECTING DEFECT 8 (vertices=9, convex hull=32, v0=43058)
After retessellation of defect 8 (v0=43058), euler #=-58 (168171,502093,333864) : difference with theory (-61) = -3 

CORRECTING DEFECT 9 (vertices=21, convex hull=33, v0=51295)
After retessellation of defect 9 (v0=51295), euler #=-57 (168180,502129,333892) : difference with theory (-60) = -3 

CORRECTING DEFECT 10 (vertices=28, convex hull=51, v0=51361)
After retessellation of defect 10 (v0=51361), euler #=-56 (168198,502202,333948) : difference with theory (-59) = -3 

CORRECTING DEFECT 11 (vertices=63, convex hull=97, v0=53068)
After retessellation of defect 11 (v0=53068), euler #=-55 (168220,502306,334031) : difference with theory (-58) = -3 

CORRECTING DEFECT 12 (vertices=23, convex hull=67, v0=53951)
After retessellation of defect 12 (v0=53951), euler #=-54 (168233,502368,334081) : difference with theory (-57) = -3 

CORRECTING DEFECT 13 (vertices=33, convex hull=65, v0=53979)
After retessellation of defect 13 (v0=53979), euler #=-53 (168253,502452,334146) : difference with theory (-56) = -3 

CORRECTING DEFECT 14 (vertices=28, convex hull=68, v0=55054)
After retessellation of defect 14 (v0=55054), euler #=-52 (168272,502536,334212) : difference with theory (-55) = -3 

CORRECTING DEFECT 15 (vertices=40, convex hull=33, v0=55867)
After retessellation of defect 15 (v0=55867), euler #=-51 (168275,502555,334229) : difference with theory (-54) = -3 

CORRECTING DEFECT 16 (vertices=57, convex hull=34, v0=57341)
After retessellation of defect 16 (v0=57341), euler #=-50 (168287,502604,334267) : difference with theory (-53) = -3 

CORRECTING DEFECT 17 (vertices=265, convex hull=232, v0=59689)
After retessellation of defect 17 (v0=59689), euler #=-49 (168331,502845,334465) : difference with theory (-52) = -3 

CORRECTING DEFECT 18 (vertices=32, convex hull=49, v0=61241)
After retessellation of defect 18 (v0=61241), euler #=-48 (168345,502906,334513) : difference with theory (-51) = -3 

CORRECTING DEFECT 19 (vertices=126, convex hull=143, v0=61273)
After retessellation of defect 19 (v0=61273), euler #=-48 (168405,503153,334700) : difference with theory (-50) = -2 

CORRECTING DEFECT 20 (vertices=32, convex hull=89, v0=62959)
After retessellation of defect 20 (v0=62959), euler #=-47 (168425,503253,334781) : difference with theory (-49) = -2 

CORRECTING DEFECT 21 (vertices=23, convex hull=45, v0=63851)
After retessellation of defect 21 (v0=63851), euler #=-46 (168435,503302,334821) : difference with theory (-48) = -2 

CORRECTING DEFECT 22 (vertices=25, convex hull=56, v0=64615)
After retessellation of defect 22 (v0=64615), euler #=-45 (168453,503379,334881) : difference with theory (-47) = -2 

CORRECTING DEFECT 23 (vertices=20, convex hull=46, v0=78861)
After retessellation of defect 23 (v0=78861), euler #=-44 (168465,503431,334922) : difference with theory (-46) = -2 

CORRECTING DEFECT 24 (vertices=20, convex hull=22, v0=79247)
After retessellation of defect 24 (v0=79247), euler #=-43 (168467,503446,334936) : difference with theory (-45) = -2 

CORRECTING DEFECT 25 (vertices=25, convex hull=26, v0=80776)
After retessellation of defect 25 (v0=80776), euler #=-42 (168470,503464,334952) : difference with theory (-44) = -2 

CORRECTING DEFECT 26 (vertices=233, convex hull=142, v0=82336)
After retessellation of defect 26 (v0=82336), euler #=-42 (168560,503815,335213) : difference with theory (-43) = -1 

CORRECTING DEFECT 27 (vertices=50, convex hull=55, v0=88152)
After retessellation of defect 27 (v0=88152), euler #=-41 (168575,503880,335264) : difference with theory (-42) = -1 

CORRECTING DEFECT 28 (vertices=20, convex hull=22, v0=93381)
After retessellation of defect 28 (v0=93381), euler #=-40 (168580,503900,335280) : difference with theory (-41) = -1 

CORRECTING DEFECT 29 (vertices=58, convex hull=52, v0=99860)
After retessellation of defect 29 (v0=99860), euler #=-39 (168589,503954,335326) : difference with theory (-40) = -1 

CORRECTING DEFECT 30 (vertices=252, convex hull=158, v0=99881)
After retessellation of defect 30 (v0=99881), euler #=-38 (168619,504124,335467) : difference with theory (-39) = -1 

CORRECTING DEFECT 31 (vertices=31, convex hull=59, v0=101623)
After retessellation of defect 31 (v0=101623), euler #=-37 (168635,504197,335525) : difference with theory (-38) = -1 

CORRECTING DEFECT 32 (vertices=63, convex hull=31, v0=102042)
After retessellation of defect 32 (v0=102042), euler #=-38 (168639,504230,335553) : difference with theory (-37) = 1 

CORRECTING DEFECT 33 (vertices=8, convex hull=19, v0=104649)
After retessellation of defect 33 (v0=104649), euler #=-37 (168640,504240,335563) : difference with theory (-36) = 1 

CORRECTING DEFECT 34 (vertices=34, convex hull=38, v0=106153)
After retessellation of defect 34 (v0=106153), euler #=-36 (168643,504262,335583) : difference with theory (-35) = 1 

CORRECTING DEFECT 35 (vertices=6, convex hull=10, v0=107148)
After retessellation of defect 35 (v0=107148), euler #=-35 (168643,504265,335587) : difference with theory (-34) = 1 

CORRECTING DEFECT 36 (vertices=12, convex hull=24, v0=107308)
After retessellation of defect 36 (v0=107308), euler #=-34 (168644,504273,335595) : difference with theory (-33) = 1 

CORRECTING DEFECT 37 (vertices=44, convex hull=74, v0=107664)
After retessellation of defect 37 (v0=107664), euler #=-33 (168671,504383,335679) : difference with theory (-32) = 1 

CORRECTING DEFECT 38 (vertices=8, convex hull=32, v0=108432)
After retessellation of defect 38 (v0=108432), euler #=-32 (168673,504398,335693) : difference with theory (-31) = 1 

CORRECTING DEFECT 39 (vertices=682, convex hull=347, v0=110105)
After retessellation of defect 39 (v0=110105), euler #=-30 (168832,505054,336192) : difference with theory (-30) = 0 

CORRECTING DEFECT 40 (vertices=57, convex hull=50, v0=112647)
After retessellation of defect 40 (v0=112647), euler #=-29 (168844,505110,336237) : difference with theory (-29) = 0 

CORRECTING DEFECT 41 (vertices=42, convex hull=27, v0=114208)
After retessellation of defect 41 (v0=114208), euler #=-28 (168850,505136,336258) : difference with theory (-28) = 0 

CORRECTING DEFECT 42 (vertices=390, convex hull=258, v0=114307)
After retessellation of defect 42 (v0=114307), euler #=-28 (168984,505680,336668) : difference with theory (-27) = 1 

CORRECTING DEFECT 43 (vertices=19, convex hull=59, v0=118196)
After retessellation of defect 43 (v0=118196), euler #=-27 (168995,505735,336713) : difference with theory (-26) = 1 

CORRECTING DEFECT 44 (vertices=39, convex hull=96, v0=118295)
After retessellation of defect 44 (v0=118295), euler #=-26 (169015,505833,336792) : difference with theory (-25) = 1 

CORRECTING DEFECT 45 (vertices=20, convex hull=21, v0=119054)
After retessellation of defect 45 (v0=119054), euler #=-25 (169021,505857,336811) : difference with theory (-24) = 1 

CORRECTING DEFECT 46 (vertices=251, convex hull=216, v0=119448)
After retessellation of defect 46 (v0=119448), euler #=-24 (169108,506220,337088) : difference with theory (-23) = 1 

CORRECTING DEFECT 47 (vertices=867, convex hull=520, v0=122213)
L defect detected...
After retessellation of defect 47 (v0=122213), euler #=-22 (169326,507147,337799) : difference with theory (-22) = 0 

CORRECTING DEFECT 48 (vertices=46, convex hull=32, v0=123066)
After retessellation of defect 48 (v0=123066), euler #=-21 (169333,507178,337824) : difference with theory (-21) = 0 

CORRECTING DEFECT 49 (vertices=6, convex hull=23, v0=123391)
After retessellation of defect 49 (v0=123391), euler #=-20 (169334,507187,337833) : difference with theory (-20) = 0 

CORRECTING DEFECT 50 (vertices=85, convex hull=126, v0=125605)
After retessellation of defect 50 (v0=125605), euler #=-19 (169383,507396,337994) : difference with theory (-19) = 0 

CORRECTING DEFECT 51 (vertices=39, convex hull=37, v0=129096)
After retessellation of defect 51 (v0=129096), euler #=-18 (169390,507428,338020) : difference with theory (-18) = 0 

CORRECTING DEFECT 52 (vertices=39, convex hull=38, v0=129273)
After retessellation of defect 52 (v0=129273), euler #=-17 (169400,507469,338052) : difference with theory (-17) = 0 

CORRECTING DEFECT 53 (vertices=28, convex hull=81, v0=132826)
After retessellation of defect 53 (v0=132826), euler #=-16 (169416,507548,338116) : difference with theory (-16) = 0 

CORRECTING DEFECT 54 (vertices=5, convex hull=24, v0=133584)
After retessellation of defect 54 (v0=133584), euler #=-15 (169416,507554,338123) : difference with theory (-15) = 0 

CORRECTING DEFECT 55 (vertices=34, convex hull=52, v0=134496)
After retessellation of defect 55 (v0=134496), euler #=-14 (169431,507622,338177) : difference with theory (-14) = 0 

CORRECTING DEFECT 56 (vertices=23, convex hull=49, v0=134785)
After retessellation of defect 56 (v0=134785), euler #=-13 (169436,507655,338206) : difference with theory (-13) = 0 

CORRECTING DEFECT 57 (vertices=77, convex hull=49, v0=137644)
After retessellation of defect 57 (v0=137644), euler #=-12 (169451,507717,338254) : difference with theory (-12) = 0 

CORRECTING DEFECT 58 (vertices=67, convex hull=101, v0=140525)
After retessellation of defect 58 (v0=140525), euler #=-10 (169468,507817,338339) : difference with theory (-11) = -1 

CORRECTING DEFECT 59 (vertices=21, convex hull=60, v0=142490)
After retessellation of defect 59 (v0=142490), euler #=-9 (169479,507875,338387) : difference with theory (-10) = -1 

CORRECTING DEFECT 60 (vertices=6, convex hull=23, v0=144401)
After retessellation of defect 60 (v0=144401), euler #=-8 (169480,507884,338396) : difference with theory (-9) = -1 

CORRECTING DEFECT 61 (vertices=1006, convex hull=396, v0=144675)
After retessellation of defect 61 (v0=144675), euler #=-7 (169647,508579,338925) : difference with theory (-8) = -1 

CORRECTING DEFECT 62 (vertices=397, convex hull=296, v0=145781)
After retessellation of defect 62 (v0=145781), euler #=-7 (169776,509143,339360) : difference with theory (-7) = 0 

CORRECTING DEFECT 63 (vertices=13, convex hull=18, v0=146822)
After retessellation of defect 63 (v0=146822), euler #=-6 (169777,509151,339368) : difference with theory (-6) = 0 

CORRECTING DEFECT 64 (vertices=13, convex hull=22, v0=147371)
After retessellation of defect 64 (v0=147371), euler #=-5 (169779,509163,339379) : difference with theory (-5) = 0 

CORRECTING DEFECT 65 (vertices=37, convex hull=96, v0=149571)
After retessellation of defect 65 (v0=149571), euler #=-4 (169801,509265,339460) : difference with theory (-4) = 0 

CORRECTING DEFECT 66 (vertices=16, convex hull=57, v0=152034)
After retessellation of defect 66 (v0=152034), euler #=-3 (169809,509312,339500) : difference with theory (-3) = 0 

CORRECTING DEFECT 67 (vertices=32, convex hull=33, v0=153155)
After retessellation of defect 67 (v0=153155), euler #=-2 (169814,509342,339526) : difference with theory (-2) = 0 

CORRECTING DEFECT 68 (vertices=30, convex hull=55, v0=157257)
After retessellation of defect 68 (v0=157257), euler #=-1 (169823,509389,339565) : difference with theory (-1) = 0 

CORRECTING DEFECT 69 (vertices=33, convex hull=64, v0=158755)
After retessellation of defect 69 (v0=158755), euler #=0 (169839,509461,339622) : difference with theory (0) = 0 

CORRECTING DEFECT 70 (vertices=79, convex hull=51, v0=160460)
After retessellation of defect 70 (v0=160460), euler #=1 (169849,509510,339662) : difference with theory (1) = 0 

CORRECTING DEFECT 71 (vertices=35, convex hull=76, v0=168218)
After retessellation of defect 71 (v0=168218), euler #=2 (169870,509604,339736) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.87 +- 0.25 (0.06-->8.25) (max @ vno 21581 --> 22591)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.87 +- 0.25 (0.06-->8.25) (max @ vno 21581 --> 22591)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
238 mutations (35.0%), 442 crossovers (65.0%), 482 vertices were eliminated
building final representation...
5222 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=169870, nf=339736, ne=509604, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 84.7 minutes
0 defective edges
removing intersecting faces
000: 647 intersecting
001: 14 intersecting
002: 2 intersecting
mris_fix_topology utimesec    5084.253076
mris_fix_topology stimesec    0.359945
mris_fix_topology ru_maxrss   549576
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   64839
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  35368
mris_fix_topology ru_oublock  16608
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    418
mris_fix_topology ru_nivcsw   13028
FSRUNTIME@ mris_fix_topology lh  1.4121 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051359 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=-196 (nv=174794, nf=349980, ne=524970, g=99)
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 12 iterations
marking ambiguous vertices...
12333 ambiguous faces found in tessellation
segmenting defects...
92 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 14 into 13
      -merging segment 34 into 26
      -merging segment 57 into 47
      -merging segment 62 into 52
      -merging segment 59 into 53
      -merging segment 63 into 60
      -merging segment 77 into 72
      -merging segment 91 into 90
84 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4010  (-4.7005)
      -vertex     loglikelihood: -6.1089  (-3.0544)
      -normal dot loglikelihood: -3.5678  (-3.5678)
      -quad curv  loglikelihood: -6.5060  (-3.2530)
      Total Loglikelihood : -25.5836

CORRECTING DEFECT 0 (vertices=153, convex hull=163, v0=2174)
After retessellation of defect 0 (v0=2174), euler #=-84 (167375,499362,331903) : difference with theory (-81) = 3 

CORRECTING DEFECT 1 (vertices=152, convex hull=175, v0=2336)
After retessellation of defect 1 (v0=2336), euler #=-83 (167436,499625,332106) : difference with theory (-80) = 3 

CORRECTING DEFECT 2 (vertices=6, convex hull=21, v0=9350)
After retessellation of defect 2 (v0=9350), euler #=-82 (167437,499633,332114) : difference with theory (-79) = 3 

CORRECTING DEFECT 3 (vertices=24, convex hull=27, v0=10512)
After retessellation of defect 3 (v0=10512), euler #=-81 (167443,499662,332138) : difference with theory (-78) = 3 

CORRECTING DEFECT 4 (vertices=31, convex hull=78, v0=12964)
After retessellation of defect 4 (v0=12964), euler #=-80 (167451,499719,332188) : difference with theory (-77) = 3 

CORRECTING DEFECT 5 (vertices=28, convex hull=73, v0=21925)
After retessellation of defect 5 (v0=21925), euler #=-79 (167460,499776,332237) : difference with theory (-76) = 3 

CORRECTING DEFECT 6 (vertices=6, convex hull=25, v0=33917)
After retessellation of defect 6 (v0=33917), euler #=-78 (167461,499785,332246) : difference with theory (-75) = 3 

CORRECTING DEFECT 7 (vertices=26, convex hull=60, v0=42725)
After retessellation of defect 7 (v0=42725), euler #=-77 (167470,499837,332290) : difference with theory (-74) = 3 

CORRECTING DEFECT 8 (vertices=25, convex hull=61, v0=49958)
After retessellation of defect 8 (v0=49958), euler #=-76 (167479,499886,332331) : difference with theory (-73) = 3 

CORRECTING DEFECT 9 (vertices=38, convex hull=48, v0=52654)
After retessellation of defect 9 (v0=52654), euler #=-75 (167497,499959,332387) : difference with theory (-72) = 3 

CORRECTING DEFECT 10 (vertices=53, convex hull=80, v0=55334)
After retessellation of defect 10 (v0=55334), euler #=-74 (167530,500091,332487) : difference with theory (-71) = 3 

CORRECTING DEFECT 11 (vertices=35, convex hull=57, v0=55560)
After retessellation of defect 11 (v0=55560), euler #=-73 (167550,500176,332553) : difference with theory (-70) = 3 

CORRECTING DEFECT 12 (vertices=24, convex hull=23, v0=56684)
After retessellation of defect 12 (v0=56684), euler #=-72 (167555,500197,332570) : difference with theory (-69) = 3 

CORRECTING DEFECT 13 (vertices=932, convex hull=386, v0=57716)
L defect detected...
After retessellation of defect 13 (v0=57716), euler #=-72 (167575,500492,332845) : difference with theory (-68) = 4 

CORRECTING DEFECT 14 (vertices=53, convex hull=93, v0=59236)
After retessellation of defect 14 (v0=59236), euler #=-71 (167588,500576,332917) : difference with theory (-67) = 4 

CORRECTING DEFECT 15 (vertices=23, convex hull=60, v0=61939)
After retessellation of defect 15 (v0=61939), euler #=-70 (167599,500632,332963) : difference with theory (-66) = 4 

CORRECTING DEFECT 16 (vertices=35, convex hull=70, v0=65525)
After retessellation of defect 16 (v0=65525), euler #=-69 (167608,500684,333007) : difference with theory (-65) = 4 

CORRECTING DEFECT 17 (vertices=9, convex hull=38, v0=67293)
After retessellation of defect 17 (v0=67293), euler #=-68 (167612,500708,333028) : difference with theory (-64) = 4 

CORRECTING DEFECT 18 (vertices=39, convex hull=56, v0=68334)
After retessellation of defect 18 (v0=68334), euler #=-67 (167629,500782,333086) : difference with theory (-63) = 4 

CORRECTING DEFECT 19 (vertices=31, convex hull=52, v0=72224)
After retessellation of defect 19 (v0=72224), euler #=-66 (167645,500849,333138) : difference with theory (-62) = 4 

CORRECTING DEFECT 20 (vertices=26, convex hull=58, v0=73761)
After retessellation of defect 20 (v0=73761), euler #=-65 (167659,500910,333186) : difference with theory (-61) = 4 

CORRECTING DEFECT 21 (vertices=68, convex hull=107, v0=74298)
After retessellation of defect 21 (v0=74298), euler #=-64 (167699,501078,333315) : difference with theory (-60) = 4 

CORRECTING DEFECT 22 (vertices=18, convex hull=28, v0=79273)
After retessellation of defect 22 (v0=79273), euler #=-63 (167702,501094,333329) : difference with theory (-59) = 4 

CORRECTING DEFECT 23 (vertices=25, convex hull=64, v0=82113)
After retessellation of defect 23 (v0=82113), euler #=-62 (167711,501145,333372) : difference with theory (-58) = 4 

CORRECTING DEFECT 24 (vertices=5, convex hull=22, v0=82337)
After retessellation of defect 24 (v0=82337), euler #=-61 (167713,501156,333382) : difference with theory (-57) = 4 

CORRECTING DEFECT 25 (vertices=684, convex hull=321, v0=82662)
After retessellation of defect 25 (v0=82662), euler #=-59 (167803,501597,333735) : difference with theory (-56) = 3 

CORRECTING DEFECT 26 (vertices=29, convex hull=45, v0=83220)
After retessellation of defect 26 (v0=83220), euler #=-58 (167814,501645,333773) : difference with theory (-55) = 3 

CORRECTING DEFECT 27 (vertices=27, convex hull=32, v0=83670)
After retessellation of defect 27 (v0=83670), euler #=-57 (167819,501672,333796) : difference with theory (-54) = 3 

CORRECTING DEFECT 28 (vertices=122, convex hull=51, v0=87312)
After retessellation of defect 28 (v0=87312), euler #=-56 (167834,501742,333852) : difference with theory (-53) = 3 

CORRECTING DEFECT 29 (vertices=24, convex hull=55, v0=87501)
After retessellation of defect 29 (v0=87501), euler #=-55 (167848,501801,333898) : difference with theory (-52) = 3 

CORRECTING DEFECT 30 (vertices=40, convex hull=28, v0=91739)
After retessellation of defect 30 (v0=91739), euler #=-54 (167855,501829,333920) : difference with theory (-51) = 3 

CORRECTING DEFECT 31 (vertices=25, convex hull=57, v0=92378)
After retessellation of defect 31 (v0=92378), euler #=-53 (167870,501900,333977) : difference with theory (-50) = 3 

CORRECTING DEFECT 32 (vertices=10, convex hull=30, v0=92780)
After retessellation of defect 32 (v0=92780), euler #=-52 (167873,501917,333992) : difference with theory (-49) = 3 

CORRECTING DEFECT 33 (vertices=29, convex hull=42, v0=93390)
After retessellation of defect 33 (v0=93390), euler #=-51 (167881,501958,334026) : difference with theory (-48) = 3 

CORRECTING DEFECT 34 (vertices=19, convex hull=55, v0=94159)
After retessellation of defect 34 (v0=94159), euler #=-50 (167887,501995,334058) : difference with theory (-47) = 3 

CORRECTING DEFECT 35 (vertices=10, convex hull=26, v0=94812)
After retessellation of defect 35 (v0=94812), euler #=-49 (167889,502008,334070) : difference with theory (-46) = 3 

CORRECTING DEFECT 36 (vertices=44, convex hull=82, v0=101135)
After retessellation of defect 36 (v0=101135), euler #=-48 (167911,502108,334149) : difference with theory (-45) = 3 

CORRECTING DEFECT 37 (vertices=47, convex hull=41, v0=103820)
After retessellation of defect 37 (v0=103820), euler #=-47 (167916,502135,334172) : difference with theory (-44) = 3 

CORRECTING DEFECT 38 (vertices=95, convex hull=96, v0=103899)
After retessellation of defect 38 (v0=103899), euler #=-46 (167933,502226,334247) : difference with theory (-43) = 3 

CORRECTING DEFECT 39 (vertices=6, convex hull=28, v0=104039)
After retessellation of defect 39 (v0=104039), euler #=-45 (167934,502236,334257) : difference with theory (-42) = 3 

CORRECTING DEFECT 40 (vertices=38, convex hull=44, v0=104911)
After retessellation of defect 40 (v0=104911), euler #=-44 (167944,502284,334296) : difference with theory (-41) = 3 

CORRECTING DEFECT 41 (vertices=11, convex hull=33, v0=105073)
After retessellation of defect 41 (v0=105073), euler #=-43 (167948,502307,334316) : difference with theory (-40) = 3 

CORRECTING DEFECT 42 (vertices=34, convex hull=48, v0=105137)
After retessellation of defect 42 (v0=105137), euler #=-42 (167963,502371,334366) : difference with theory (-39) = 3 

CORRECTING DEFECT 43 (vertices=8, convex hull=27, v0=106359)
After retessellation of defect 43 (v0=106359), euler #=-41 (167966,502387,334380) : difference with theory (-38) = 3 

CORRECTING DEFECT 44 (vertices=100, convex hull=45, v0=107960)
After retessellation of defect 44 (v0=107960), euler #=-40 (167992,502482,334450) : difference with theory (-37) = 3 

CORRECTING DEFECT 45 (vertices=44, convex hull=76, v0=108466)
After retessellation of defect 45 (v0=108466), euler #=-38 (168016,502584,334530) : difference with theory (-36) = 2 

CORRECTING DEFECT 46 (vertices=36, convex hull=48, v0=108477)
After retessellation of defect 46 (v0=108477), euler #=-37 (168026,502629,334566) : difference with theory (-35) = 2 

CORRECTING DEFECT 47 (vertices=24, convex hull=47, v0=109457)
After retessellation of defect 47 (v0=109457), euler #=-36 (168035,502673,334602) : difference with theory (-34) = 2 

CORRECTING DEFECT 48 (vertices=6, convex hull=21, v0=110172)
After retessellation of defect 48 (v0=110172), euler #=-35 (168037,502685,334613) : difference with theory (-33) = 2 

CORRECTING DEFECT 49 (vertices=533, convex hull=228, v0=111467)
After retessellation of defect 49 (v0=111467), euler #=-36 (168194,503287,335057) : difference with theory (-32) = 4 

CORRECTING DEFECT 50 (vertices=588, convex hull=376, v0=112532)
After retessellation of defect 50 (v0=112532), euler #=-34 (168390,504086,335662) : difference with theory (-31) = 3 

CORRECTING DEFECT 51 (vertices=42, convex hull=84, v0=113771)
After retessellation of defect 51 (v0=113771), euler #=-32 (168404,504164,335728) : difference with theory (-30) = 2 

CORRECTING DEFECT 52 (vertices=48, convex hull=86, v0=114258)
After retessellation of defect 52 (v0=114258), euler #=-31 (168420,504245,335794) : difference with theory (-29) = 2 

CORRECTING DEFECT 53 (vertices=32, convex hull=68, v0=115035)
After retessellation of defect 53 (v0=115035), euler #=-30 (168441,504332,335861) : difference with theory (-28) = 2 

CORRECTING DEFECT 54 (vertices=21, convex hull=64, v0=115191)
After retessellation of defect 54 (v0=115191), euler #=-29 (168450,504379,335900) : difference with theory (-27) = 2 

CORRECTING DEFECT 55 (vertices=15, convex hull=25, v0=116734)
After retessellation of defect 55 (v0=116734), euler #=-28 (168454,504398,335916) : difference with theory (-26) = 2 

CORRECTING DEFECT 56 (vertices=293, convex hull=97, v0=118387)
After retessellation of defect 56 (v0=118387), euler #=-26 (168473,504512,336013) : difference with theory (-25) = 1 

CORRECTING DEFECT 57 (vertices=18, convex hull=17, v0=118711)
After retessellation of defect 57 (v0=118711), euler #=-25 (168475,504521,336021) : difference with theory (-24) = 1 

CORRECTING DEFECT 58 (vertices=108, convex hull=71, v0=122044)
After retessellation of defect 58 (v0=122044), euler #=-24 (168495,504610,336091) : difference with theory (-23) = 1 

CORRECTING DEFECT 59 (vertices=32, convex hull=20, v0=122833)
After retessellation of defect 59 (v0=122833), euler #=-23 (168500,504629,336106) : difference with theory (-22) = 1 

CORRECTING DEFECT 60 (vertices=56, convex hull=73, v0=126100)
After retessellation of defect 60 (v0=126100), euler #=-22 (168516,504708,336170) : difference with theory (-21) = 1 

CORRECTING DEFECT 61 (vertices=15, convex hull=33, v0=126249)
After retessellation of defect 61 (v0=126249), euler #=-21 (168520,504727,336186) : difference with theory (-20) = 1 

CORRECTING DEFECT 62 (vertices=67, convex hull=66, v0=127598)
After retessellation of defect 62 (v0=127598), euler #=-20 (168538,504808,336250) : difference with theory (-19) = 1 

CORRECTING DEFECT 63 (vertices=53, convex hull=96, v0=128547)
After retessellation of defect 63 (v0=128547), euler #=-19 (168574,504958,336365) : difference with theory (-18) = 1 

CORRECTING DEFECT 64 (vertices=107, convex hull=88, v0=128868)
After retessellation of defect 64 (v0=128868), euler #=-18 (168605,505084,336461) : difference with theory (-17) = 1 

CORRECTING DEFECT 65 (vertices=31, convex hull=37, v0=128912)
After retessellation of defect 65 (v0=128912), euler #=-17 (168613,505120,336490) : difference with theory (-16) = 1 

CORRECTING DEFECT 66 (vertices=408, convex hull=251, v0=130159)
After retessellation of defect 66 (v0=130159), euler #=-16 (168735,505642,336891) : difference with theory (-15) = 1 

CORRECTING DEFECT 67 (vertices=25, convex hull=36, v0=130169)
After retessellation of defect 67 (v0=130169), euler #=-15 (168735,505658,336908) : difference with theory (-14) = 1 

CORRECTING DEFECT 68 (vertices=50, convex hull=84, v0=131020)
After retessellation of defect 68 (v0=131020), euler #=-14 (168756,505754,336984) : difference with theory (-13) = 1 

CORRECTING DEFECT 69 (vertices=7, convex hull=17, v0=132039)
After retessellation of defect 69 (v0=132039), euler #=-13 (168758,505764,336993) : difference with theory (-12) = 1 

CORRECTING DEFECT 70 (vertices=27, convex hull=36, v0=132161)
After retessellation of defect 70 (v0=132161), euler #=-12 (168764,505796,337020) : difference with theory (-11) = 1 

CORRECTING DEFECT 71 (vertices=22, convex hull=43, v0=135875)
After retessellation of defect 71 (v0=135875), euler #=-11 (168771,505832,337050) : difference with theory (-10) = 1 

CORRECTING DEFECT 72 (vertices=73, convex hull=72, v0=136354)
After retessellation of defect 72 (v0=136354), euler #=-10 (168782,505896,337104) : difference with theory (-9) = 1 

CORRECTING DEFECT 73 (vertices=9, convex hull=21, v0=139246)
After retessellation of defect 73 (v0=139246), euler #=-9 (168784,505907,337114) : difference with theory (-8) = 1 

CORRECTING DEFECT 74 (vertices=66, convex hull=85, v0=139698)
After retessellation of defect 74 (v0=139698), euler #=-8 (168798,505983,337177) : difference with theory (-7) = 1 

CORRECTING DEFECT 75 (vertices=19, convex hull=64, v0=140336)
After retessellation of defect 75 (v0=140336), euler #=-7 (168808,506033,337218) : difference with theory (-6) = 1 

CORRECTING DEFECT 76 (vertices=947, convex hull=361, v0=142083)
After retessellation of defect 76 (v0=142083), euler #=-6 (168964,506677,337707) : difference with theory (-5) = 1 

CORRECTING DEFECT 77 (vertices=20, convex hull=45, v0=143903)
After retessellation of defect 77 (v0=143903), euler #=-5 (168972,506716,337739) : difference with theory (-4) = 1 

CORRECTING DEFECT 78 (vertices=45, convex hull=87, v0=156913)
After retessellation of defect 78 (v0=156913), euler #=-4 (168996,506821,337821) : difference with theory (-3) = 1 

CORRECTING DEFECT 79 (vertices=48, convex hull=88, v0=159877)
After retessellation of defect 79 (v0=159877), euler #=-3 (169018,506923,337902) : difference with theory (-2) = 1 

CORRECTING DEFECT 80 (vertices=29, convex hull=42, v0=166157)
After retessellation of defect 80 (v0=166157), euler #=-2 (169027,506966,337937) : difference with theory (-1) = 1 

CORRECTING DEFECT 81 (vertices=36, convex hull=86, v0=169401)
After retessellation of defect 81 (v0=169401), euler #=-1 (169044,507049,338004) : difference with theory (0) = 1 

CORRECTING DEFECT 82 (vertices=67, convex hull=68, v0=170517)
After retessellation of defect 82 (v0=170517), euler #=0 (169061,507130,338069) : difference with theory (1) = 1 

CORRECTING DEFECT 83 (vertices=103, convex hull=104, v0=171388)
After retessellation of defect 83 (v0=171388), euler #=2 (169093,507273,338182) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.87 +- 0.26 (0.01-->12.58) (max @ vno 60889 --> 62212)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.87 +- 0.26 (0.01-->12.58) (max @ vno 60889 --> 62212)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
287 mutations (35.7%), 516 crossovers (64.3%), 598 vertices were eliminated
building final representation...
5701 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=169093, nf=338182, ne=507273, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 79.6 minutes
0 defective edges
removing intersecting faces
000: 637 intersecting
001: 16 intersecting
mris_fix_topology utimesec    4776.104921
mris_fix_topology stimesec    0.944856
mris_fix_topology ru_maxrss   542476
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   61781
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  35344
mris_fix_topology ru_oublock  16584
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    678
mris_fix_topology ru_nivcsw   16749
FSRUNTIME@ mris_fix_topology rh  1.3271 hours 1 threads
PIDs (17328 17331) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 169870 - 509604 + 339736 = 2 --> 0 holes
      F =2V-4:          339736 = 339740-4 (0)
      2E=3F:            1019208 = 1019208 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 169093 - 507273 + 338182 = 2 --> 0 holes
      F =2V-4:          338182 = 338186-4 (0)
      2E=3F:            1014546 = 1014546 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 111 intersecting
001: 14 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 80 intersecting
001: 4 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 23:17:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051359 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 23:17:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051359 rh 

Waiting for PID 20284 of (20284 20287) to complete...
Waiting for PID 20287 of (20284 20287) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051359 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-6.0.0/0051359/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
41371 bright wm thresholded.
694 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.orig...
computing class statistics...
border white:    322490 voxels (1.92%)
border gray      366609 voxels (2.19%)
WM (96.0): 96.9 +- 8.5 [70.0 --> 110.0]
GM (74.0) : 72.8 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.0 (was 70)
setting MAX_BORDER_WHITE to 109.5 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.0 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.80 +- 0.23 (0.01-->4.18) (max @ vno 32331 --> 168076)
face area 0.27 +- 0.13 (0.00-->3.60)
mean absolute distance = 0.67 +- 0.85
4144 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=101+-7.8,    GM=72+-6.1
mean inside = 92.8, mean outside = 76.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=81.9, 72 (72) missing vertices, mean dist 0.2 [0.6 (%40.3)->0.7 (%59.7))]
%71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.26 (0.08-->4.59) (max @ vno 119330 --> 119354)
face area 0.27 +- 0.13 (0.00-->3.26)
mean absolute distance = 0.38 +- 0.58
5568 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3042644.8, rms=8.408
001: dt: 0.5000, sse=1746791.1, rms=5.771 (31.362%)
002: dt: 0.5000, sse=1253207.6, rms=4.294 (25.584%)
003: dt: 0.5000, sse=1090579.2, rms=3.593 (16.329%)
004: dt: 0.5000, sse=998277.7, rms=3.275 (8.846%)
005: dt: 0.5000, sse=972456.4, rms=3.146 (3.953%)
006: dt: 0.5000, sse=958652.6, rms=3.086 (1.890%)
rms = 3.06, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=959305.7, rms=3.064 (0.734%)
008: dt: 0.2500, sse=811462.4, rms=2.099 (31.481%)
009: dt: 0.2500, sse=776213.1, rms=1.843 (12.195%)
rms = 1.80, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=771944.8, rms=1.801 (2.318%)
011: dt: 0.1250, sse=765494.6, rms=1.747 (2.978%)
rms = 1.74, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=765251.5, rms=1.739 (0.444%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=84.9, 111 (26) missing vertices, mean dist -0.2 [0.4 (%72.4)->0.3 (%27.6))]
%82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.25 (0.04-->4.08) (max @ vno 168539 --> 168551)
face area 0.33 +- 0.16 (0.00-->3.89)
mean absolute distance = 0.28 +- 0.40
4838 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1421264.5, rms=4.289
013: dt: 0.5000, sse=1087914.0, rms=2.821 (34.225%)
014: dt: 0.5000, sse=1062655.2, rms=2.765 (1.970%)
rms = 2.85, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=958570.8, rms=2.078 (24.866%)
016: dt: 0.2500, sse=921082.6, rms=1.686 (18.872%)
017: dt: 0.2500, sse=907682.0, rms=1.591 (5.626%)
rms = 1.56, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=903718.8, rms=1.557 (2.107%)
rms = 1.51, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=898137.2, rms=1.508 (3.160%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=86.7, 124 (13) missing vertices, mean dist -0.1 [0.3 (%65.3)->0.2 (%34.7))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.87 +- 0.25 (0.05-->4.35) (max @ vno 168539 --> 168551)
face area 0.32 +- 0.16 (0.00-->4.58)
mean absolute distance = 0.25 +- 0.34
4988 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1040690.1, rms=2.718
020: dt: 0.5000, sse=993698.8, rms=2.362 (13.104%)
rms = 2.58, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=906127.1, rms=1.758 (25.575%)
022: dt: 0.2500, sse=878805.0, rms=1.480 (15.800%)
023: dt: 0.2500, sse=873342.9, rms=1.426 (3.647%)
rms = 1.42, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=867660.4, rms=1.415 (0.767%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=865526.8, rms=1.375 (2.854%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=87.4, 147 (13) missing vertices, mean dist -0.0 [0.3 (%54.7)->0.2 (%45.3))]
%91 local maxima, % 5 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-6.0.0/0051359/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=885066.1, rms=1.665
026: dt: 0.5000, sse=868745.5, rms=1.522 (8.591%)
rms = 2.27, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=829101.4, rms=1.118 (26.565%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
rms = 1.08, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=824251.6, rms=1.083 (3.056%)
positioning took 0.7 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 8059 vertices
erasing segment 1 (vno[0] = 71746)
erasing segment 2 (vno[0] = 88774)
erasing segment 3 (vno[0] = 98874)
erasing segment 4 (vno[0] = 105194)
erasing segment 5 (vno[0] = 121558)
erasing segment 6 (vno[0] = 121602)
erasing segment 7 (vno[0] = 124549)
erasing segment 8 (vno[0] = 126157)
erasing segment 9 (vno[0] = 126185)
erasing segment 10 (vno[0] = 127100)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.area
vertex spacing 0.87 +- 0.26 (0.01-->4.59) (max @ vno 119330 --> 119354)
face area 0.32 +- 0.16 (0.00-->4.79)
refinement took 7.1 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051359 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-6.0.0/0051359/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
41371 bright wm thresholded.
694 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.orig...
computing class statistics...
border white:    322490 voxels (1.92%)
border gray      366609 voxels (2.19%)
WM (96.0): 96.9 +- 8.5 [70.0 --> 110.0]
GM (74.0) : 72.8 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.0 (was 70)
setting MAX_BORDER_WHITE to 110.5 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 53.0 (was 40)
setting MAX_GRAY to 93.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.80 +- 0.23 (0.03-->5.95) (max @ vno 67823 --> 69241)
face area 0.27 +- 0.13 (0.00-->4.23)
mean absolute distance = 0.66 +- 0.86
4505 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-8.7,    GM=73+-6.1
mean inside = 93.0, mean outside = 76.8
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=82.6, 136 (136) missing vertices, mean dist 0.1 [0.6 (%42.1)->0.7 (%57.9))]
%72 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.26 (0.03-->6.64) (max @ vno 69241 --> 67823)
face area 0.27 +- 0.13 (0.00-->6.55)
mean absolute distance = 0.37 +- 0.59
5038 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2870005.5, rms=8.110
001: dt: 0.5000, sse=1652503.8, rms=5.521 (31.931%)
002: dt: 0.5000, sse=1200947.0, rms=4.107 (25.613%)
003: dt: 0.5000, sse=1043255.9, rms=3.464 (15.644%)
004: dt: 0.5000, sse=978299.6, rms=3.179 (8.230%)
005: dt: 0.5000, sse=957690.6, rms=3.079 (3.138%)
006: dt: 0.5000, sse=946221.6, rms=3.020 (1.932%)
rms = 3.01, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=945343.9, rms=3.011 (0.308%)
008: dt: 0.2500, sse=799731.4, rms=2.039 (32.264%)
009: dt: 0.2500, sse=769383.0, rms=1.800 (11.730%)
rms = 1.76, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=766287.7, rms=1.764 (2.028%)
rms = 1.71, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=760722.8, rms=1.714 (2.825%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=85.5, 162 (47) missing vertices, mean dist -0.2 [0.4 (%73.0)->0.3 (%27.0))]
%83 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.25 (0.07-->7.06) (max @ vno 69241 --> 67823)
face area 0.33 +- 0.17 (0.00-->8.91)
mean absolute distance = 0.28 +- 0.41
5281 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1358578.1, rms=4.073
012: dt: 0.5000, sse=1052967.1, rms=2.666 (34.541%)
rms = 2.69, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=965478.1, rms=2.122 (20.422%)
014: dt: 0.2500, sse=928595.4, rms=1.749 (17.580%)
015: dt: 0.2500, sse=905732.9, rms=1.612 (7.814%)
rms = 1.57, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=899662.6, rms=1.565 (2.910%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=900568.0, rms=1.523 (2.674%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=87.2, 177 (25) missing vertices, mean dist -0.1 [0.3 (%65.4)->0.2 (%34.6))]
%89 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.87 +- 0.26 (0.03-->7.09) (max @ vno 69241 --> 67823)
face area 0.32 +- 0.17 (0.00-->8.83)
mean absolute distance = 0.25 +- 0.35
4994 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1030358.1, rms=2.641
018: dt: 0.5000, sse=989292.6, rms=2.337 (11.531%)
rms = 2.55, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=903408.7, rms=1.755 (24.910%)
020: dt: 0.2500, sse=874927.9, rms=1.485 (15.362%)
021: dt: 0.2500, sse=867097.3, rms=1.427 (3.940%)
rms = 1.42, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=870363.1, rms=1.417 (0.663%)
rms = 1.38, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=861542.1, rms=1.379 (2.679%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=87.8, 221 (23) missing vertices, mean dist -0.0 [0.3 (%54.0)->0.2 (%46.0))]
%91 local maxima, % 5 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-6.0.0/0051359/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=875952.9, rms=1.620
024: dt: 0.5000, sse=863467.5, rms=1.479 (8.689%)
rms = 2.20, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=829403.2, rms=1.119 (24.360%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
rms = 1.09, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=825291.1, rms=1.091 (2.524%)
positioning took 0.7 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 7148 vertices
erasing segment 1 (vno[0] = 100446)
erasing segment 2 (vno[0] = 105987)
erasing segment 3 (vno[0] = 114404)
erasing segment 4 (vno[0] = 115459)
erasing segment 5 (vno[0] = 117465)
erasing segment 6 (vno[0] = 117782)
erasing segment 7 (vno[0] = 120255)
erasing segment 8 (vno[0] = 121471)
erasing segment 9 (vno[0] = 122625)
erasing segment 10 (vno[0] = 122641)
erasing segment 11 (vno[0] = 123788)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.area
vertex spacing 0.87 +- 0.26 (0.02-->7.33) (max @ vno 67814 --> 67823)
face area 0.32 +- 0.16 (0.00-->8.75)
refinement took 7.5 minutes
PIDs (20284 20287) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 23:24:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 23:24:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

Waiting for PID 20542 of (20542 20545) to complete...
Waiting for PID 20545 of (20542 20545) 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 (20542 20545) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 23:24:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 23:24:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 20592 of (20592 20595) to complete...
Waiting for PID 20595 of (20592 20595) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.4 mm, total surface area = 97570 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.182 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.080 (target=0.015)   
step 020: RMS=0.066 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.046 (target=0.015)   
step 035: RMS=0.039 (target=0.015)   
step 040: RMS=0.034 (target=0.015)   
step 045: RMS=0.031 (target=0.015)   
step 050: RMS=0.028 (target=0.015)   
step 055: RMS=0.026 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 1.6 minutes
mris_inflate utimesec    96.204374
mris_inflate stimesec    0.210967
mris_inflate ru_maxrss   248880
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35713
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  13296
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2018
mris_inflate ru_nivcsw   7476

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.2 mm, total surface area = 97155 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.184 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.056 (target=0.015)   
step 030: RMS=0.048 (target=0.015)   
step 035: RMS=0.040 (target=0.015)   
step 040: RMS=0.035 (target=0.015)   
step 045: RMS=0.031 (target=0.015)   
step 050: RMS=0.028 (target=0.015)   
step 055: RMS=0.026 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 2.0 minutes
mris_inflate utimesec    131.832958
mris_inflate stimesec    0.172973
mris_inflate ru_maxrss   247840
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35964
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  13240
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1996
mris_inflate ru_nivcsw   7811
PIDs (20592 20595) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 23:26:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sat Oct  7 23:26:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 20720 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20723 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20726 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20729 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20732 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20735 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20738 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20741 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20744 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20747 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20750 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...
Waiting for PID 20753 of (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 4.523*4pi (56.837) --> -4 handles
ICI = 266.1, FI = 2359.4, variation=38701.074
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
217 vertices thresholded to be in k1 ~ [-0.27 0.23], k2 ~ [-0.14 0.07]
total integrated curvature = 0.434*4pi (5.453) --> 1 handles
ICI = 1.6, FI = 11.1, variation=187.397
176 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
169 vertices thresholded to be in [-0.17 0.11]
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 = -0.148*4pi (-1.859) --> 1 handles
ICI = 272.3, FI = 2437.6, variation=39944.607
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
234 vertices thresholded to be in k1 ~ [-0.21 0.97], k2 ~ [-0.13 0.08]
total integrated curvature = 0.504*4pi (6.338) --> 0 handles
ICI = 1.6, FI = 10.5, variation=178.586
168 vertices thresholded to be in [-0.04 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
139 vertices thresholded to be in [-0.13 0.20]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022
done.
PIDs (20720 20723 20726 20729 20732 20735 20738 20741 20744 20747 20750 20753) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 23:28:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051359 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      [ 0051359/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                      [ 319 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.318407
WARN:    S explicit min:                          0.000000	vertex = 187

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 23:29:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051359 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      [ 0051359/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                      [ 324 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.306980
WARN:    S explicit min:                          0.000000	vertex = 181
#--------------------------------------------
#@# Sphere lh Sat Oct  7 23:29:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 23:29:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 20917 of (20917 20921) to complete...
Waiting for PID 20921 of (20917 20921) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0.265...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.84
pass 1: epoch 2 of 3 starting distance error %20.80
unfolding complete - removing small folds...
starting distance error %20.71
removing remaining folds...
final distance error %20.72
MRISunfold() return, current seed 1234
-01: dt=0.0000, 384 negative triangles
179: dt=0.9900, 384 negative triangles
180: dt=0.9900, 188 negative triangles
181: dt=0.9900, 152 negative triangles
182: dt=0.9900, 118 negative triangles
183: dt=0.9900, 107 negative triangles
184: dt=0.9900, 96 negative triangles
185: dt=0.9900, 77 negative triangles
186: dt=0.9900, 71 negative triangles
187: dt=0.9900, 78 negative triangles
188: dt=0.9900, 68 negative triangles
189: dt=0.9900, 49 negative triangles
190: dt=0.9900, 43 negative triangles
191: dt=0.9900, 38 negative triangles
192: dt=0.9900, 43 negative triangles
193: dt=0.9900, 34 negative triangles
194: dt=0.9900, 40 negative triangles
195: dt=0.9900, 23 negative triangles
196: dt=0.9900, 24 negative triangles
197: dt=0.9900, 23 negative triangles
198: dt=0.9900, 20 negative triangles
199: dt=0.9900, 18 negative triangles
200: dt=0.9900, 17 negative triangles
201: dt=0.9900, 13 negative triangles
202: dt=0.9900, 14 negative triangles
203: dt=0.9900, 11 negative triangles
204: dt=0.9900, 9 negative triangles
205: dt=0.9900, 11 negative triangles
206: dt=0.9900, 9 negative triangles
207: dt=0.9900, 7 negative triangles
208: dt=0.9900, 4 negative triangles
209: dt=0.9900, 10 negative triangles
210: dt=0.9900, 6 negative triangles
211: dt=0.9900, 3 negative triangles
212: dt=0.9900, 8 negative triangles
213: dt=0.9900, 4 negative triangles
214: dt=0.9900, 2 negative triangles
215: dt=0.9900, 3 negative triangles
216: dt=0.9900, 1 negative triangles
217: dt=0.9900, 1 negative triangles
218: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 2.11 hours
mris_sphere utimesec    7987.099776
mris_sphere stimesec    4.140370
mris_sphere ru_maxrss   348828
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   60836
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12000
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    135062
mris_sphere ru_nivcsw   604300
FSRUNTIME@ mris_sphere  2.1058 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0.270...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.16
pass 1: epoch 2 of 3 starting distance error %20.07
unfolding complete - removing small folds...
starting distance error %20.03
removing remaining folds...
final distance error %20.04
MRISunfold() return, current seed 1234
-01: dt=0.0000, 353 negative triangles
183: dt=0.9900, 353 negative triangles
184: dt=0.9900, 154 negative triangles
185: dt=0.9900, 112 negative triangles
186: dt=0.9900, 95 negative triangles
187: dt=0.9900, 100 negative triangles
188: dt=0.9900, 83 negative triangles
189: dt=0.9900, 90 negative triangles
190: dt=0.9900, 75 negative triangles
191: dt=0.9900, 76 negative triangles
192: dt=0.9900, 68 negative triangles
193: dt=0.9900, 58 negative triangles
194: dt=0.9900, 60 negative triangles
195: dt=0.9900, 60 negative triangles
196: dt=0.9900, 64 negative triangles
197: dt=0.9900, 58 negative triangles
198: dt=0.9900, 57 negative triangles
199: dt=0.9900, 54 negative triangles
200: dt=0.9900, 53 negative triangles
201: dt=0.9900, 48 negative triangles
202: dt=0.9900, 49 negative triangles
203: dt=0.9900, 44 negative triangles
204: dt=0.9900, 37 negative triangles
205: dt=0.9900, 42 negative triangles
206: dt=0.9900, 33 negative triangles
207: dt=0.9900, 36 negative triangles
208: dt=0.9900, 32 negative triangles
209: dt=0.9900, 38 negative triangles
210: dt=0.9900, 32 negative triangles
211: dt=0.9900, 27 negative triangles
212: dt=0.9900, 27 negative triangles
213: dt=0.9900, 27 negative triangles
214: dt=0.9900, 28 negative triangles
215: dt=0.9900, 26 negative triangles
216: dt=0.9900, 17 negative triangles
217: dt=0.9900, 17 negative triangles
218: dt=0.9900, 22 negative triangles
219: dt=0.9900, 17 negative triangles
220: dt=0.9900, 14 negative triangles
221: dt=0.9900, 16 negative triangles
222: dt=0.9900, 19 negative triangles
223: dt=0.9900, 16 negative triangles
224: dt=0.9900, 16 negative triangles
225: dt=0.9900, 16 negative triangles
226: dt=0.9900, 23 negative triangles
227: dt=0.9900, 16 negative triangles
228: dt=0.9900, 13 negative triangles
229: dt=0.9900, 15 negative triangles
230: dt=0.9900, 10 negative triangles
231: dt=0.9900, 9 negative triangles
232: dt=0.9900, 9 negative triangles
233: dt=0.9900, 7 negative triangles
234: dt=0.9900, 6 negative triangles
235: dt=0.9900, 5 negative triangles
236: dt=0.9900, 3 negative triangles
237: dt=0.9900, 6 negative triangles
238: dt=0.9900, 2 negative triangles
239: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.95 hours
mris_sphere utimesec    7000.128818
mris_sphere stimesec    4.178364
mris_sphere ru_maxrss   347276
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   60972
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11984
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    143605
mris_sphere ru_nivcsw   598828
FSRUNTIME@ mris_sphere  1.9496 hours 1 threads
PIDs (20917 20921) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 01:35:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 01:35:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 30890 of (30890 30893) to complete...
Waiting for PID 30893 of (30890 30893) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 5.488
curvature mean = 0.038, std = 0.820
curvature mean = 0.027, std = 0.840
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 393166.3, tmin=2.5198
  d=32.00 min @ (8.00, 0.00, -8.00) sse = 315977.9, tmin=4.6541
  d=16.00 min @ (-4.00, 0.00, 4.00) sse = 299677.9, tmin=6.7253
  d=8.00 min @ (2.00, 0.00, -2.00) sse = 294119.0, tmin=8.7800
  d=4.00 min @ (0.00, 0.00, 1.00) sse = 292448.9, tmin=10.8712
  d=2.00 min @ (-0.50, -0.50, 0.00) sse = 291828.9, tmin=13.0115
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 291812.6, tmin=17.3321
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  17.33 min
curvature mean = 0.013, std = 0.835
curvature mean = 0.009, std = 0.933
curvature mean = 0.012, std = 0.845
curvature mean = 0.003, std = 0.969
curvature mean = 0.010, std = 0.846
curvature mean = 0.001, std = 0.986
2 Reading smoothwm
curvature mean = -0.030, std = 0.337
curvature mean = 0.043, std = 0.248
curvature mean = 0.069, std = 0.282
curvature mean = 0.039, std = 0.304
curvature mean = 0.042, std = 0.443
curvature mean = 0.039, std = 0.329
curvature mean = 0.025, std = 0.577
curvature mean = 0.039, std = 0.341
curvature mean = 0.010, std = 0.692
MRISregister() return, current seed 0
-01: dt=0.0000, 79 negative triangles
136: dt=0.9900, 79 negative triangles
expanding nbhd size to 1
137: dt=0.9900, 98 negative triangles
138: dt=0.9900, 70 negative triangles
139: dt=0.9900, 60 negative triangles
140: dt=0.9900, 68 negative triangles
141: dt=0.9900, 58 negative triangles
142: dt=0.9900, 48 negative triangles
143: dt=0.9900, 48 negative triangles
144: dt=0.9900, 48 negative triangles
145: dt=0.9900, 39 negative triangles
146: dt=0.9900, 33 negative triangles
147: dt=0.9900, 27 negative triangles
148: dt=0.9900, 26 negative triangles
149: dt=0.9900, 21 negative triangles
150: dt=0.9900, 18 negative triangles
151: dt=0.9900, 19 negative triangles
152: dt=0.9900, 12 negative triangles
153: dt=0.9900, 18 negative triangles
154: dt=0.9900, 11 negative triangles
155: dt=0.9900, 10 negative triangles
156: dt=0.9900, 11 negative triangles
157: dt=0.9900, 9 negative triangles
158: dt=0.9900, 6 negative triangles
159: dt=0.9900, 4 negative triangles
160: dt=0.9900, 3 negative triangles
161: dt=0.9900, 4 negative triangles
162: dt=0.9900, 3 negative triangles
163: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 3.53 hours
mris_register utimesec    12640.611334
mris_register stimesec    9.889496
mris_register ru_maxrss   302644
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   43929
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  11952
mris_register ru_oublock  12048
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    371560
mris_register ru_nivcsw   875195
FSRUNTIME@ mris_register  3.5282 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 5.544
curvature mean = 0.037, std = 0.811
curvature mean = 0.028, std = 0.841
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 390980.3, tmin=2.2989
  d=32.00 min @ (8.00, 0.00, 0.00) sse = 332044.0, tmin=4.0923
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 331908.9, tmin=5.8131
  d=8.00 min @ (0.00, 2.00, -2.00) sse = 321280.8, tmin=7.5048
  d=4.00 min @ (-1.00, -1.00, -1.00) sse = 318762.9, tmin=9.2084
  d=2.00 min @ (0.00, 0.00, 0.50) sse = 318353.2, tmin=10.9201
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 318323.3, tmin=14.4129
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  14.41 min
curvature mean = 0.008, std = 0.813
curvature mean = 0.010, std = 0.933
curvature mean = 0.003, std = 0.818
curvature mean = 0.004, std = 0.970
curvature mean = 0.002, std = 0.818
curvature mean = 0.001, std = 0.986
2 Reading smoothwm
curvature mean = -0.031, std = 0.337
curvature mean = 0.034, std = 0.235
curvature mean = 0.076, std = 0.279
curvature mean = 0.032, std = 0.292
curvature mean = 0.045, std = 0.448
curvature mean = 0.031, std = 0.318
curvature mean = 0.027, std = 0.581
curvature mean = 0.032, std = 0.328
curvature mean = 0.011, std = 0.694
MRISregister() return, current seed 0
-01: dt=0.0000, 122 negative triangles
130: dt=0.9900, 122 negative triangles
expanding nbhd size to 1
131: dt=0.9900, 162 negative triangles
132: dt=0.9900, 115 negative triangles
133: dt=0.9900, 111 negative triangles
134: dt=0.9900, 106 negative triangles
135: dt=0.9900, 102 negative triangles
136: dt=0.9900, 100 negative triangles
137: dt=0.9900, 93 negative triangles
138: dt=0.9900, 91 negative triangles
139: dt=0.9900, 81 negative triangles
140: dt=0.9900, 79 negative triangles
141: dt=0.9900, 80 negative triangles
142: dt=0.9900, 74 negative triangles
143: dt=0.9900, 67 negative triangles
144: dt=0.9900, 65 negative triangles
145: dt=0.9900, 64 negative triangles
146: dt=0.9900, 56 negative triangles
147: dt=0.9900, 54 negative triangles
148: dt=0.9900, 48 negative triangles
149: dt=0.9900, 46 negative triangles
150: dt=0.9900, 45 negative triangles
151: dt=0.9900, 43 negative triangles
152: dt=0.9900, 45 negative triangles
153: dt=0.9900, 40 negative triangles
154: dt=0.9900, 40 negative triangles
155: dt=0.9900, 36 negative triangles
156: dt=0.9900, 34 negative triangles
157: dt=0.9900, 30 negative triangles
158: dt=0.9900, 32 negative triangles
159: dt=0.9900, 26 negative triangles
160: dt=0.9900, 24 negative triangles
161: dt=0.9900, 28 negative triangles
162: dt=0.9900, 23 negative triangles
163: dt=0.9900, 26 negative triangles
164: dt=0.9900, 21 negative triangles
165: dt=0.9900, 23 negative triangles
166: dt=0.9900, 17 negative triangles
167: dt=0.9900, 17 negative triangles
168: dt=0.9900, 14 negative triangles
169: dt=0.9900, 14 negative triangles
170: dt=0.9900, 14 negative triangles
171: dt=0.9900, 13 negative triangles
172: dt=0.9900, 13 negative triangles
173: dt=0.9900, 11 negative triangles
174: dt=0.9900, 10 negative triangles
175: dt=0.9900, 12 negative triangles
176: dt=0.9900, 11 negative triangles
177: dt=0.9900, 10 negative triangles
178: dt=0.9900, 11 negative triangles
179: dt=0.9900, 10 negative triangles
180: dt=0.9900, 12 negative triangles
181: dt=0.9900, 12 negative triangles
182: dt=0.9900, 11 negative triangles
183: dt=0.9900, 8 negative triangles
184: dt=0.9900, 10 negative triangles
185: dt=0.9900, 10 negative triangles
186: dt=0.9900, 9 negative triangles
187: dt=0.9900, 7 negative triangles
188: dt=0.9900, 9 negative triangles
189: dt=0.9900, 5 negative triangles
190: dt=0.9900, 8 negative triangles
191: dt=0.9900, 7 negative triangles
192: dt=0.9900, 4 negative triangles
193: dt=0.9900, 5 negative triangles
194: dt=0.9900, 3 negative triangles
195: dt=0.9900, 4 negative triangles
196: dt=0.9900, 6 negative triangles
197: dt=0.9900, 3 negative triangles
198: dt=0.9900, 4 negative triangles
199: dt=0.9900, 3 negative triangles
200: dt=0.9900, 3 negative triangles
201: dt=0.9900, 3 negative triangles
202: dt=0.9900, 4 negative triangles
203: dt=0.9900, 3 negative triangles
204: dt=0.9900, 2 negative triangles
205: dt=0.9900, 3 negative triangles
206: dt=0.9900, 2 negative triangles
207: dt=0.9900, 2 negative triangles
208: dt=0.9900, 2 negative triangles
209: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 3.51 hours
mris_register utimesec    12527.813482
mris_register stimesec    9.020628
mris_register ru_maxrss   300552
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   42766
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  12016
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    322961
mris_register ru_nivcsw   937159
FSRUNTIME@ mris_register  3.5078 hours 1 threads
PIDs (30890 30893) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 05:07:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 05:07:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

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

Waiting for PID 5992 of (5992 5995) to complete...
Waiting for PID 5995 of (5992 5995) 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 (5992 5995) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 05:07:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 05:07:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 6038 of (6038 6041) to complete...
Waiting for PID 6041 of (6038 6041) 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 (6038 6041) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 05:07:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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 05:07:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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 6086 of (6086 6089) to complete...
Waiting for PID 6089 of (6086 6089) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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...
1329 labels changed using aseg
relabeling using gibbs priors...
000:   3730 changed, 169870 examined...
001:    818 changed, 15660 examined...
002:    203 changed, 4543 examined...
003:     67 changed, 1222 examined...
004:     24 changed, 394 examined...
005:     12 changed, 146 examined...
006:      7 changed, 71 examined...
007:      1 changed, 39 examined...
008:      1 changed, 11 examined...
009:      0 changed, 5 examined...
244 labels changed using aseg
000: 143 total segments, 100 labels (422 vertices) changed
001: 46 total segments, 8 labels (29 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 10 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1997 vertices marked for relabeling...
1997 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 27 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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...
1375 labels changed using aseg
relabeling using gibbs priors...
000:   3311 changed, 169093 examined...
001:    791 changed, 14331 examined...
002:    187 changed, 4481 examined...
003:     53 changed, 1125 examined...
004:     20 changed, 343 examined...
005:      7 changed, 132 examined...
006:      3 changed, 50 examined...
007:      0 changed, 20 examined...
185 labels changed using aseg
000: 120 total segments, 82 labels (378 vertices) changed
001: 39 total segments, 1 labels (1 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2108 vertices marked for relabeling...
2108 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 31 seconds.
PIDs (6086 6089) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 05:07:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051359 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 05:07:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051359 rh 

Waiting for PID 6152 of (6152 6155) to complete...
Waiting for PID 6155 of (6152 6155) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051359 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-6.0.0/0051359/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
41371 bright wm thresholded.
694 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.orig...
computing class statistics...
border white:    322490 voxels (1.92%)
border gray      366609 voxels (2.19%)
WM (96.0): 96.9 +- 8.5 [70.0 --> 110.0]
GM (74.0) : 72.8 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.0 (was 70)
setting MAX_BORDER_WHITE to 109.5 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.0 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.8,    GM=72+-6.1
mean inside = 92.8, mean outside = 76.3
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 0.87 +- 0.26 (0.01-->4.59) (max @ vno 119330 --> 119354)
face area 0.32 +- 0.16 (0.00-->4.80)
mean absolute distance = 0.63 +- 0.82
3604 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 221 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
deleting segment 6 with 28 points - only 0.00% unknown
deleting segment 7 with 65 points - only 23.08% unknown
deleting segment 8 with 8 points - only 0.00% unknown
mean border=81.8, 152 (152) missing vertices, mean dist 0.4 [0.9 (%12.8)->0.6 (%87.2))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.26 (0.06-->4.77) (max @ vno 168539 --> 168551)
face area 0.32 +- 0.16 (0.00-->5.17)
mean absolute distance = 0.37 +- 0.57
4828 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2498017.5, rms=7.231
001: dt: 0.5000, sse=1399641.4, rms=4.309 (40.407%)
002: dt: 0.5000, sse=1131687.1, rms=3.227 (25.123%)
003: dt: 0.5000, sse=1085698.6, rms=3.062 (5.100%)
004: dt: 0.5000, sse=1051461.4, rms=2.910 (4.959%)
rms = 3.02, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=943831.0, rms=2.222 (23.646%)
006: dt: 0.2500, sse=903826.3, rms=1.895 (14.723%)
007: dt: 0.2500, sse=895507.3, rms=1.820 (3.954%)
rms = 1.80, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=893936.3, rms=1.797 (1.261%)
rms = 1.76, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=888587.5, rms=1.759 (2.141%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 17 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 5 with 162 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 22 points - only 27.27% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
mean border=84.9, 129 (46) missing vertices, mean dist -0.2 [0.4 (%73.2)->0.2 (%26.8))]
%82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.26 (0.07-->4.94) (max @ vno 168539 --> 168551)
face area 0.34 +- 0.17 (0.00-->6.09)
mean absolute distance = 0.28 +- 0.40
4625 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1405936.6, rms=4.203
010: dt: 0.5000, sse=1083415.4, rms=2.769 (34.122%)
011: dt: 0.5000, sse=1063160.2, rms=2.706 (2.272%)
rms = 2.81, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=960284.2, rms=2.008 (25.784%)
013: dt: 0.2500, sse=917337.0, rms=1.612 (19.753%)
014: dt: 0.2500, sse=907405.6, rms=1.523 (5.476%)
rms = 1.50, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=907263.2, rms=1.501 (1.450%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=904508.4, rms=1.458 (2.886%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
deleting segment 1 with 17 points - only 0.00% unknown
deleting segment 2 with 146 points - only 0.00% unknown
deleting segment 3 with 35 points - only 0.00% unknown
deleting segment 4 with 15 points - only 0.00% unknown
deleting segment 5 with 53 points - only 15.09% unknown
mean border=86.7, 149 (32) missing vertices, mean dist -0.1 [0.3 (%65.4)->0.2 (%34.6))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.87 +- 0.26 (0.06-->5.03) (max @ vno 168539 --> 168551)
face area 0.32 +- 0.17 (0.00-->6.28)
mean absolute distance = 0.25 +- 0.34
4957 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1040044.4, rms=2.681
017: dt: 0.5000, sse=1007344.0, rms=2.332 (13.025%)
rms = 2.55, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=916039.6, rms=1.718 (26.334%)
019: dt: 0.2500, sse=874434.7, rms=1.440 (16.144%)
rms = 1.39, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=870545.6, rms=1.391 (3.397%)
021: dt: 0.1250, sse=864422.2, rms=1.340 (3.678%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=863890.6, rms=1.344 (-0.316%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
deleting segment 1 with 152 points - only 0.00% unknown
deleting segment 2 with 47 points - only 0.00% unknown
deleting segment 3 with 19 points - only 0.00% unknown
deleting segment 4 with 65 points - only 20.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
mean border=87.4, 165 (27) missing vertices, mean dist -0.0 [0.3 (%54.6)->0.2 (%45.4))]
%91 local maxima, % 5 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-6.0.0/0051359/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=885114.6, rms=1.644
023: dt: 0.5000, sse=870740.6, rms=1.497 (8.951%)
rms = 2.26, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=833488.2, rms=1.098 (26.625%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
rms = 1.07, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=828942.4, rms=1.065 (2.982%)
positioning took 0.6 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 8035 vertices
erasing segment 1 (vno[0] = 68453)
erasing segment 2 (vno[0] = 71746)
erasing segment 3 (vno[0] = 88774)
erasing segment 4 (vno[0] = 89535)
erasing segment 5 (vno[0] = 98874)
erasing segment 6 (vno[0] = 105194)
erasing segment 7 (vno[0] = 119336)
erasing segment 8 (vno[0] = 121605)
erasing segment 9 (vno[0] = 124549)
erasing segment 10 (vno[0] = 126157)
erasing segment 11 (vno[0] = 126185)
erasing segment 12 (vno[0] = 127100)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.area
vertex spacing 0.88 +- 0.26 (0.01-->5.08) (max @ vno 168539 --> 168551)
face area 0.32 +- 0.17 (0.00-->6.27)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 4 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=60.3, 153 (153) missing vertices, mean dist 1.7 [0.1 (%0.0)->3.2 (%100.0))]
%14 local maxima, %37 large gradients and %46 min vals, 296 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=26380246.0, rms=27.970
001: dt: 0.0500, sse=23246214.0, rms=26.201 (6.323%)
002: dt: 0.0500, sse=21037298.0, rms=24.879 (5.047%)
003: dt: 0.0500, sse=19370796.0, rms=23.833 (4.206%)
004: dt: 0.0500, sse=18045912.0, rms=22.967 (3.633%)
005: dt: 0.0500, sse=16952286.0, rms=22.226 (3.223%)
006: dt: 0.0500, sse=16019637.0, rms=21.575 (2.931%)
007: dt: 0.0500, sse=15205167.0, rms=20.990 (2.714%)
008: dt: 0.0500, sse=14482073.0, rms=20.456 (2.544%)
009: dt: 0.0500, sse=13830922.0, rms=19.963 (2.410%)
010: dt: 0.0500, sse=13238772.0, rms=19.503 (2.300%)
positioning took 1.4 minutes
mean border=60.2, 98 (72) missing vertices, mean dist 1.4 [0.1 (%0.1)->2.6 (%99.9))]
%15 local maxima, %37 large gradients and %44 min vals, 281 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=14111549.0, rms=20.183
011: dt: 0.0500, sse=13564039.0, rms=19.763 (2.078%)
012: dt: 0.0500, sse=13059082.0, rms=19.369 (1.998%)
013: dt: 0.0500, sse=12591489.0, rms=18.996 (1.926%)
014: dt: 0.0500, sse=12156902.0, rms=18.642 (1.860%)
015: dt: 0.0500, sse=11752798.0, rms=18.307 (1.796%)
016: dt: 0.0500, sse=11375861.0, rms=17.989 (1.737%)
017: dt: 0.0500, sse=11022943.0, rms=17.686 (1.684%)
018: dt: 0.0500, sse=10692825.0, rms=17.398 (1.630%)
019: dt: 0.0500, sse=10382930.0, rms=17.123 (1.581%)
020: dt: 0.0500, sse=10092157.0, rms=16.861 (1.531%)
positioning took 1.3 minutes
mean border=60.1, 106 (50) missing vertices, mean dist 1.2 [0.1 (%0.5)->2.3 (%99.5))]
%16 local maxima, %37 large gradients and %44 min vals, 254 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=10209592.0, rms=16.974
021: dt: 0.0500, sse=9931820.0, rms=16.722 (1.489%)
022: dt: 0.0500, sse=9670714.0, rms=16.480 (1.442%)
023: dt: 0.0500, sse=9423268.0, rms=16.249 (1.407%)
024: dt: 0.0500, sse=9189834.0, rms=16.027 (1.365%)
025: dt: 0.0500, sse=8968763.0, rms=15.814 (1.329%)
026: dt: 0.0500, sse=8759074.0, rms=15.609 (1.295%)
027: dt: 0.0500, sse=8558825.0, rms=15.411 (1.270%)
028: dt: 0.0500, sse=8366692.0, rms=15.218 (1.251%)
029: dt: 0.0500, sse=8181863.5, rms=15.030 (1.234%)
030: dt: 0.0500, sse=8004111.0, rms=14.847 (1.217%)
positioning took 1.3 minutes
mean border=60.0, 127 (31) missing vertices, mean dist 1.1 [0.1 (%3.5)->2.0 (%96.5))]
%16 local maxima, %37 large gradients and %43 min vals, 260 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=8098087.5, rms=14.945
031: dt: 0.5000, sse=6808444.5, rms=13.554 (9.304%)
032: dt: 0.5000, sse=5831220.0, rms=12.391 (8.581%)
033: dt: 0.5000, sse=5014732.5, rms=11.328 (8.578%)
034: dt: 0.5000, sse=4307244.0, rms=10.316 (8.937%)
035: dt: 0.5000, sse=3695726.0, rms=9.354 (9.322%)
036: dt: 0.5000, sse=3167688.5, rms=8.435 (9.831%)
037: dt: 0.5000, sse=2716367.2, rms=7.563 (10.332%)
038: dt: 0.5000, sse=2353720.8, rms=6.780 (10.349%)
039: dt: 0.5000, sse=2083929.6, rms=6.137 (9.492%)
040: dt: 0.5000, sse=1908484.0, rms=5.676 (7.511%)
041: dt: 0.5000, sse=1794556.1, rms=5.358 (5.598%)
042: dt: 0.5000, sse=1724757.0, rms=5.151 (3.872%)
043: dt: 0.5000, sse=1679960.0, rms=5.015 (2.640%)
044: dt: 0.5000, sse=1647505.5, rms=4.910 (2.086%)
045: dt: 0.5000, sse=1625972.4, rms=4.842 (1.392%)
046: dt: 0.5000, sse=1607727.5, rms=4.782 (1.239%)
rms = 4.76, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1600234.2, rms=4.758 (0.506%)
048: dt: 0.2500, sse=1479698.6, rms=4.293 (9.764%)
049: dt: 0.2500, sse=1441859.2, rms=4.155 (3.213%)
rms = 4.16, time step reduction 2 of 3 to 0.125...
rms = 4.11, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1432000.1, rms=4.115 (0.971%)
positioning took 3.8 minutes
mean border=59.0, 3283 (11) missing vertices, mean dist 0.1 [0.2 (%45.3)->0.6 (%54.7))]
%28 local maxima, %28 large gradients and %39 min vals, 181 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=1759814.4, rms=4.496
051: dt: 0.5000, sse=1698457.4, rms=4.292 (4.542%)
052: dt: 0.5000, sse=1636781.8, rms=4.100 (4.466%)
rms = 4.26, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1515783.8, rms=3.562 (13.120%)
054: dt: 0.2500, sse=1482343.6, rms=3.392 (4.780%)
rms = 3.37, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1477760.4, rms=3.369 (0.691%)
056: dt: 0.1250, sse=1450839.1, rms=3.231 (4.086%)
rms = 3.20, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1444735.6, rms=3.202 (0.905%)
positioning took 1.8 minutes
mean border=58.4, 3520 (11) missing vertices, mean dist 0.1 [0.2 (%45.4)->0.4 (%54.6))]
%39 local maxima, %18 large gradients and %38 min vals, 193 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=1483194.5, rms=3.405
rms = 3.80, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1453255.6, rms=3.259 (4.267%)
rms = 3.23, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1446733.5, rms=3.235 (0.763%)
060: dt: 0.1250, sse=1435351.0, rms=3.175 (1.853%)
rms = 3.16, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1431027.0, rms=3.157 (0.562%)
positioning took 1.2 minutes
mean border=57.9, 7025 (7) missing vertices, mean dist 0.1 [0.2 (%46.2)->0.3 (%53.8))]
%41 local maxima, %15 large gradients and %37 min vals, 176 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-6.0.0/0051359/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1453645.2, rms=3.262
rms = 3.53, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1435664.1, rms=3.174 (2.679%)
rms = 3.13, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1422767.9, rms=3.131 (1.363%)
064: dt: 0.1250, sse=1412767.6, rms=3.077 (1.730%)
rms = 3.05, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1406357.2, rms=3.051 (0.846%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.area.pial
vertex spacing 0.99 +- 0.45 (0.05-->6.63) (max @ vno 110091 --> 110077)
face area 0.39 +- 0.32 (0.00-->6.16)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 169870 vertices processed
25000 of 169870 vertices processed
50000 of 169870 vertices processed
75000 of 169870 vertices processed
100000 of 169870 vertices processed
125000 of 169870 vertices processed
150000 of 169870 vertices processed
0 of 169870 vertices processed
25000 of 169870 vertices processed
50000 of 169870 vertices processed
75000 of 169870 vertices processed
100000 of 169870 vertices processed
125000 of 169870 vertices processed
150000 of 169870 vertices processed
thickness calculation complete, 637:1214 truncations.
30490 vertices at 0 distance
105693 vertices at 1 distance
107193 vertices at 2 distance
53835 vertices at 3 distance
19965 vertices at 4 distance
6584 vertices at 5 distance
2137 vertices at 6 distance
722 vertices at 7 distance
267 vertices at 8 distance
145 vertices at 9 distance
62 vertices at 10 distance
52 vertices at 11 distance
46 vertices at 12 distance
52 vertices at 13 distance
48 vertices at 14 distance
40 vertices at 15 distance
27 vertices at 16 distance
22 vertices at 17 distance
18 vertices at 18 distance
19 vertices at 19 distance
17 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.thickness
positioning took 21.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051359 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-6.0.0/0051359/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
41371 bright wm thresholded.
694 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.orig...
computing class statistics...
border white:    322490 voxels (1.92%)
border gray      366609 voxels (2.19%)
WM (96.0): 96.9 +- 8.5 [70.0 --> 110.0]
GM (74.0) : 72.8 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.0 (was 70)
setting MAX_BORDER_WHITE to 110.5 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 53.0 (was 40)
setting MAX_GRAY to 93.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-8.7,    GM=73+-6.1
mean inside = 93.0, mean outside = 76.8
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 0.87 +- 0.26 (0.02-->7.33) (max @ vno 67814 --> 67823)
face area 0.32 +- 0.16 (0.00-->8.75)
mean absolute distance = 0.63 +- 0.84
3858 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 3 with 9 points - only 0.00% unknown
deleting segment 4 with 5 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 171 points - only 0.00% unknown
deleting segment 7 with 44 points - only 0.00% unknown
deleting segment 8 with 51 points - only 0.00% unknown
deleting segment 9 with 10 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
mean border=82.4, 210 (210) missing vertices, mean dist 0.4 [1.0 (%13.1)->0.6 (%86.9))]
%70 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.26 (0.09-->6.97) (max @ vno 67823 --> 69241)
face area 0.32 +- 0.16 (0.00-->8.19)
mean absolute distance = 0.37 +- 0.58
4941 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2354657.2, rms=6.924
001: dt: 0.5000, sse=1343149.2, rms=4.112 (40.621%)
002: dt: 0.5000, sse=1099269.0, rms=3.112 (24.310%)
003: dt: 0.5000, sse=1066426.2, rms=2.990 (3.938%)
004: dt: 0.5000, sse=1042295.4, rms=2.839 (5.024%)
rms = 2.96, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=935685.2, rms=2.167 (23.674%)
006: dt: 0.2500, sse=899204.2, rms=1.851 (14.609%)
007: dt: 0.2500, sse=890074.1, rms=1.772 (4.224%)
rms = 1.75, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=887483.1, rms=1.748 (1.367%)
rms = 1.71, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=883995.1, rms=1.713 (2.038%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 2 with 23 points - only 0.00% unknown
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 47 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 20 points - only 0.00% unknown
deleting segment 8 with 55 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
mean border=85.4, 166 (64) missing vertices, mean dist -0.2 [0.4 (%73.5)->0.2 (%26.5))]
%83 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.26 (0.06-->6.81) (max @ vno 67823 --> 69241)
face area 0.34 +- 0.17 (0.00-->9.27)
mean absolute distance = 0.28 +- 0.41
4997 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1349273.1, rms=3.998
010: dt: 0.5000, sse=1057464.6, rms=2.608 (34.768%)
rms = 2.62, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=969546.5, rms=2.060 (21.027%)
012: dt: 0.2500, sse=921988.8, rms=1.675 (18.668%)
013: dt: 0.2500, sse=909684.9, rms=1.536 (8.325%)
rms = 1.49, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=908687.6, rms=1.492 (2.837%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=900928.6, rms=1.452 (2.700%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 2 with 47 points - only 0.00% unknown
deleting segment 3 with 68 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
deleting segment 7 with 61 points - only 0.00% unknown
deleting segment 8 with 19 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 11 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
mean border=87.1, 188 (40) missing vertices, mean dist -0.1 [0.3 (%65.5)->0.2 (%34.5))]
%89 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.87 +- 0.26 (0.07-->6.69) (max @ vno 67823 --> 69241)
face area 0.33 +- 0.17 (0.00-->8.63)
mean absolute distance = 0.25 +- 0.34
4836 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1028161.9, rms=2.612
016: dt: 0.5000, sse=998807.6, rms=2.304 (11.799%)
rms = 2.50, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=907261.7, rms=1.714 (25.581%)
018: dt: 0.2500, sse=882382.2, rms=1.441 (15.928%)
019: dt: 0.2500, sse=871386.1, rms=1.389 (3.597%)
rms = 1.38, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=872317.1, rms=1.380 (0.689%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=869361.5, rms=1.341 (2.818%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 3 with 47 points - only 0.00% unknown
deleting segment 4 with 57 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 27 points - only 0.00% unknown
deleting segment 8 with 61 points - only 0.00% unknown
deleting segment 9 with 22 points - only 0.00% unknown
deleting segment 10 with 28 points - only 0.00% unknown
deleting segment 11 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
mean border=87.8, 221 (26) missing vertices, mean dist -0.0 [0.3 (%54.3)->0.2 (%45.7))]
%91 local maxima, % 5 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-6.0.0/0051359/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=883252.1, rms=1.589
022: dt: 0.5000, sse=895923.7, rms=1.466 (7.741%)
rms = 2.18, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=836880.4, rms=1.099 (24.995%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
rms = 1.07, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=833550.0, rms=1.071 (2.617%)
positioning took 0.7 minutes
generating cortex label...
14 non-cortical segments detected
only using segment with 7130 vertices
erasing segment 0 (vno[0] = 38506)
erasing segment 2 (vno[0] = 100446)
erasing segment 3 (vno[0] = 105987)
erasing segment 4 (vno[0] = 114404)
erasing segment 5 (vno[0] = 115459)
erasing segment 6 (vno[0] = 116658)
erasing segment 7 (vno[0] = 117465)
erasing segment 8 (vno[0] = 117782)
erasing segment 9 (vno[0] = 120255)
erasing segment 10 (vno[0] = 121471)
erasing segment 11 (vno[0] = 122625)
erasing segment 12 (vno[0] = 122641)
erasing segment 13 (vno[0] = 123788)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.area
vertex spacing 0.88 +- 0.27 (0.03-->6.54) (max @ vno 71974 --> 79477)
face area 0.32 +- 0.17 (0.00-->8.37)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 0 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 46 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=61.5, 225 (225) missing vertices, mean dist 1.7 [0.2 (%0.0)->3.2 (%100.0))]
%14 local maxima, %37 large gradients and %46 min vals, 382 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=24873856.0, rms=27.166
001: dt: 0.0500, sse=21908246.0, rms=25.439 (6.359%)
002: dt: 0.0500, sse=19813326.0, rms=24.144 (5.090%)
003: dt: 0.0500, sse=18231888.0, rms=23.118 (4.248%)
004: dt: 0.0500, sse=16974232.0, rms=22.269 (3.675%)
005: dt: 0.0500, sse=15935074.0, rms=21.541 (3.266%)
006: dt: 0.0500, sse=15049102.0, rms=20.901 (2.972%)
007: dt: 0.0500, sse=14277008.0, rms=20.327 (2.748%)
008: dt: 0.0500, sse=13592083.0, rms=19.803 (2.576%)
009: dt: 0.0500, sse=12977380.0, rms=19.321 (2.434%)
010: dt: 0.0500, sse=12419496.0, rms=18.873 (2.319%)
positioning took 1.4 minutes
mean border=61.4, 179 (123) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.6 (%100.0))]
%15 local maxima, %37 large gradients and %44 min vals, 335 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=13333522.0, rms=19.608
011: dt: 0.0500, sse=12818799.0, rms=19.201 (2.074%)
012: dt: 0.0500, sse=12345543.0, rms=18.819 (1.988%)
013: dt: 0.0500, sse=11908372.0, rms=18.460 (1.911%)
014: dt: 0.0500, sse=11503478.0, rms=18.120 (1.839%)
015: dt: 0.0500, sse=11126503.0, rms=17.798 (1.777%)
016: dt: 0.0500, sse=10774959.0, rms=17.492 (1.718%)
017: dt: 0.0500, sse=10446967.0, rms=17.202 (1.659%)
018: dt: 0.0500, sse=10140556.0, rms=16.927 (1.602%)
019: dt: 0.0500, sse=9853512.0, rms=16.664 (1.550%)
020: dt: 0.0500, sse=9583905.0, rms=16.414 (1.502%)
positioning took 1.4 minutes
mean border=61.2, 213 (106) missing vertices, mean dist 1.2 [0.1 (%0.5)->2.3 (%99.5))]
%15 local maxima, %37 large gradients and %44 min vals, 334 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=9716796.0, rms=16.546
021: dt: 0.0500, sse=9459202.0, rms=16.305 (1.456%)
022: dt: 0.0500, sse=9217034.0, rms=16.075 (1.410%)
023: dt: 0.0500, sse=8987888.0, rms=15.854 (1.373%)
024: dt: 0.0500, sse=8771307.0, rms=15.643 (1.334%)
025: dt: 0.0500, sse=8566311.0, rms=15.440 (1.297%)
026: dt: 0.0500, sse=8371508.5, rms=15.244 (1.265%)
027: dt: 0.0500, sse=8185648.5, rms=15.056 (1.239%)
028: dt: 0.0500, sse=8006998.5, rms=14.872 (1.221%)
029: dt: 0.0500, sse=7834560.0, rms=14.692 (1.208%)
030: dt: 0.0500, sse=7668379.5, rms=14.517 (1.194%)
positioning took 1.4 minutes
mean border=61.2, 251 (89) missing vertices, mean dist 1.1 [0.1 (%3.6)->2.0 (%96.4))]
%16 local maxima, %37 large gradients and %43 min vals, 287 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=7758687.5, rms=14.613
031: dt: 0.5000, sse=6519264.5, rms=13.243 (9.378%)
032: dt: 0.5000, sse=5577810.5, rms=12.093 (8.686%)
033: dt: 0.5000, sse=4815378.5, rms=11.074 (8.427%)
034: dt: 0.5000, sse=4194502.5, rms=10.164 (8.216%)
035: dt: 0.5000, sse=3664523.2, rms=9.319 (8.317%)
036: dt: 0.5000, sse=3208809.8, rms=8.523 (8.542%)
037: dt: 0.5000, sse=2795943.5, rms=7.735 (9.238%)
038: dt: 0.5000, sse=2454715.2, rms=7.016 (9.304%)
039: dt: 0.5000, sse=2181591.2, rms=6.385 (8.990%)
040: dt: 0.5000, sse=1990495.4, rms=5.900 (7.589%)
041: dt: 0.5000, sse=1851719.1, rms=5.524 (6.370%)
042: dt: 0.5000, sse=1769361.6, rms=5.286 (4.317%)
043: dt: 0.5000, sse=1708502.1, rms=5.105 (3.424%)
044: dt: 0.5000, sse=1675706.1, rms=5.001 (2.031%)
045: dt: 0.5000, sse=1646207.6, rms=4.909 (1.841%)
046: dt: 0.5000, sse=1630949.0, rms=4.857 (1.069%)
rms = 4.81, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1616889.4, rms=4.812 (0.926%)
048: dt: 0.2500, sse=1498863.1, rms=4.363 (9.333%)
049: dt: 0.2500, sse=1460549.2, rms=4.225 (3.157%)
rms = 4.22, time step reduction 2 of 3 to 0.125...
050: dt: 0.2500, sse=1461784.1, rms=4.224 (0.020%)
051: dt: 0.1250, sse=1437536.6, rms=4.128 (2.284%)
rms = 4.11, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1433130.2, rms=4.111 (0.401%)
positioning took 4.2 minutes
mean border=60.1, 3416 (21) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.6 (%55.3))]
%28 local maxima, %28 large gradients and %38 min vals, 133 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=1745616.0, rms=4.448
053: dt: 0.5000, sse=1687540.6, rms=4.260 (4.236%)
054: dt: 0.5000, sse=1623117.1, rms=4.054 (4.816%)
rms = 4.21, time step reduction 1 of 3 to 0.250...
055: dt: 0.2500, sse=1505338.9, rms=3.526 (13.039%)
056: dt: 0.2500, sse=1474929.8, rms=3.368 (4.481%)
rms = 3.36, time step reduction 2 of 3 to 0.125...
057: dt: 0.2500, sse=1472728.2, rms=3.357 (0.326%)
058: dt: 0.1250, sse=1444024.4, rms=3.210 (4.378%)
rms = 3.18, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1438193.8, rms=3.182 (0.859%)
positioning took 1.8 minutes
mean border=59.5, 3794 (14) missing vertices, mean dist 0.1 [0.2 (%45.0)->0.4 (%55.0))]
%39 local maxima, %18 large gradients and %37 min vals, 190 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=1486325.2, rms=3.405
rms = 3.78, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1454999.8, rms=3.253 (4.459%)
rms = 3.22, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1446562.0, rms=3.219 (1.047%)
062: dt: 0.1250, sse=1434561.0, rms=3.156 (1.967%)
rms = 3.13, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1429378.6, rms=3.134 (0.706%)
positioning took 1.2 minutes
mean border=59.0, 7139 (13) missing vertices, mean dist 0.1 [0.2 (%46.6)->0.3 (%53.4))]
%41 local maxima, %15 large gradients and %36 min vals, 173 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-6.0.0/0051359/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1447795.1, rms=3.216
rms = 3.47, time step reduction 1 of 3 to 0.250...
064: dt: 0.2500, sse=1430139.8, rms=3.129 (2.704%)
065: dt: 0.2500, sse=1415656.9, rms=3.077 (1.643%)
rms = 3.07, time step reduction 2 of 3 to 0.125...
066: dt: 0.2500, sse=1412822.6, rms=3.073 (0.149%)
067: dt: 0.1250, sse=1393998.4, rms=2.973 (3.255%)
rms = 2.95, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1388544.4, rms=2.949 (0.789%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.area.pial
vertex spacing 0.99 +- 0.45 (0.06-->7.51) (max @ vno 62212 --> 66561)
face area 0.39 +- 0.32 (0.00-->11.62)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 169093 vertices processed
25000 of 169093 vertices processed
50000 of 169093 vertices processed
75000 of 169093 vertices processed
100000 of 169093 vertices processed
125000 of 169093 vertices processed
150000 of 169093 vertices processed
0 of 169093 vertices processed
25000 of 169093 vertices processed
50000 of 169093 vertices processed
75000 of 169093 vertices processed
100000 of 169093 vertices processed
125000 of 169093 vertices processed
150000 of 169093 vertices processed
thickness calculation complete, 662:1371 truncations.
30065 vertices at 0 distance
103503 vertices at 1 distance
106491 vertices at 2 distance
55126 vertices at 3 distance
20816 vertices at 4 distance
6798 vertices at 5 distance
2326 vertices at 6 distance
794 vertices at 7 distance
306 vertices at 8 distance
169 vertices at 9 distance
103 vertices at 10 distance
66 vertices at 11 distance
44 vertices at 12 distance
30 vertices at 13 distance
27 vertices at 14 distance
42 vertices at 15 distance
37 vertices at 16 distance
26 vertices at 17 distance
27 vertices at 18 distance
12 vertices at 19 distance
16 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.thickness
positioning took 22.4 minutes
PIDs (6152 6155) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 05:30:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label
Total face volume 317227
Total vertex volume 313307 (mask=0)
#@# 0051359 lh 313307
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 05:30:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label
Total face volume 317093
Total vertex volume 313472 (mask=0)
#@# 0051359 rh 313472
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 05:30:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 

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 = 119
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/ribbon.mgz
mris_volmask took 39.67 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 06:10:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 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 0051359 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 06:10:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 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 0051359 rh pial 

Waiting for PID 8726 of (8726 8729 8732 8738) to complete...
Waiting for PID 8729 of (8726 8729 8732 8738) to complete...
Waiting for PID 8732 of (8726 8729 8732 8738) to complete...
Waiting for PID 8738 of (8726 8729 8732 8738) 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 0051359 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317227
Total vertex volume 313307 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 2453   1663   4865  2.638 0.486     0.113     0.027       26     2.5  bankssts
 1320    851   2444  2.504 0.646     0.138     0.046       26     2.2  caudalanteriorcingulate
 4722   2993   9231  2.832 0.550     0.115     0.034       52     6.3  caudalmiddlefrontal
 3126   1968   4032  1.962 0.425     0.142     0.038       44     5.1  cuneus
  651    419   1697  3.152 0.806     0.132     0.059       10     1.5  entorhinal
 4609   3146   9997  2.817 0.665     0.142     0.043      121     8.3  fusiform
 7358   4706  13900  2.684 0.593     0.125     0.034      100    10.0  inferiorparietal
 5317   3521  13241  3.074 0.730     0.132     0.042       81     9.1  inferiortemporal
 1963   1249   3473  2.522 0.885     0.120     0.038       24     2.6  isthmuscingulate
 9667   5823  14291  2.262 0.576     0.128     0.036      123    13.4  lateraloccipital
 5235   3423  10453  2.844 0.599     0.137     0.043       77     9.2  lateralorbitofrontal
 5454   3425   7897  2.171 0.609     0.136     0.043       80     9.1  lingual
 3467   2292   7495  2.889 0.838     0.140     0.042       66     6.2  medialorbitofrontal
 5367   3533  13670  3.105 0.692     0.136     0.045       85     9.9  middletemporal
 1115    703   2730  3.208 0.634     0.124     0.047       14     2.0  parahippocampal
 2608   1559   4051  2.514 0.579     0.116     0.044       33     5.1  paracentral
 3306   2130   6573  2.815 0.515     0.122     0.032       43     4.3  parsopercularis
 1612   1050   3921  2.949 0.515     0.149     0.050       31     3.1  parsorbitalis
 2978   1960   5861  2.671 0.508     0.129     0.037       43     4.4  parstriangularis
 2470   1736   2605  1.700 0.377     0.148     0.038       33     3.8  pericalcarine
 9412   5783  15507  2.391 0.648     0.126     0.042      128    16.7  postcentral
 2312   1514   4511  2.725 0.845     0.133     0.035       39     3.0  posteriorcingulate
10151   6186  18235  2.762 0.570     0.116     0.038      120    16.3  precentral
 6583   4429  12032  2.557 0.568     0.132     0.033       77     8.9  precuneus
 1270    808   2662  2.931 0.689     0.140     0.046       25     2.5  rostralanteriorcingulate
11555   7579  23750  2.697 0.498     0.136     0.041      196    19.5  rostralmiddlefrontal
12799   8431  29300  3.054 0.595     0.124     0.039      185    20.4  superiorfrontal
10002   6128  16945  2.397 0.542     0.116     0.030      116    11.4  superiorparietal
 8811   5703  19181  2.908 0.629     0.117     0.033      100    11.3  superiortemporal
 6771   4472  13624  2.801 0.576     0.126     0.035       86     9.1  supramarginal
  419    281   1340  3.377 0.507     0.174     0.048       11     0.8  frontalpole
  812    586   2926  3.568 0.824     0.162     0.053       14     2.0  temporalpole
 1291    728   1979  2.402 0.512     0.133     0.061       22     3.2  transversetemporal
 4459   2865   8812  3.050 0.741     0.133     0.053       61     8.7  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 0051359 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317227
Total vertex volume 313307 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 2453   1999   4865  2.638 0.486     0.144     0.035       45     3.8  bankssts
 1320   1030   2444  2.504 0.646     0.160     0.058       30     3.1  caudalanteriorcingulate
 4722   3482   9231  2.832 0.550     0.128     0.032       85     6.6  caudalmiddlefrontal
 3126   2297   4032  1.962 0.425     0.131     0.033       38     4.7  cuneus
  651    663   1697  3.152 0.806     0.170     0.052       13     1.5  entorhinal
 4609   3854   9997  2.817 0.665     0.161     0.047      103     9.3  fusiform
 7358   5524  13900  2.684 0.593     0.136     0.035      120    10.8  inferiorparietal
 5317   4975  13241  3.074 0.730     0.168     0.044       97    10.6  inferiortemporal
 1963   1482   3473  2.522 0.885     0.149     0.046       35     3.6  isthmuscingulate
 9667   6718  14291  2.262 0.576     0.120     0.029      154    12.2  lateraloccipital
 5235   3871  10453  2.844 0.599     0.147     0.045      122    10.7  lateralorbitofrontal
 5454   4083   7897  2.171 0.609     0.142     0.036       74     9.2  lingual
 3467   2941   7495  2.889 0.838     0.157     0.043       57     6.5  medialorbitofrontal
 5367   4977  13670  3.105 0.692     0.157     0.041       90    10.0  middletemporal
 1115   1039   2730  3.208 0.634     0.180     0.053       15     2.7  parahippocampal
 2608   1683   4051  2.514 0.579     0.112     0.041       32     5.8  paracentral
 3306   2479   6573  2.815 0.515     0.134     0.033       37     4.6  parsopercularis
 1612   1554   3921  2.949 0.515     0.185     0.047       26     3.7  parsorbitalis
 2978   2331   5861  2.671 0.508     0.150     0.038       48     4.7  parstriangularis
 2470   1412   2605  1.700 0.377     0.116     0.031       34     3.4  pericalcarine
 9412   7086  15507  2.391 0.648     0.128     0.032      103    12.9  postcentral
 2312   1761   4511  2.725 0.845     0.151     0.042       64     4.3  posteriorcingulate
10151   6826  18235  2.762 0.570     0.112     0.028      117    11.9  precentral
 6583   4893  12032  2.557 0.568     0.139     0.036      116    10.3  precuneus
 1270   1006   2662  2.931 0.689     0.181     0.057       36     3.3  rostralanteriorcingulate
11555   9672  23750  2.697 0.498     0.158     0.037      230    20.2  rostralmiddlefrontal
12799  10404  29300  3.054 0.595     0.137     0.037      206    19.7  superiorfrontal
10002   7728  16945  2.397 0.542     0.132     0.030      116    13.3  superiorparietal
 8811   7144  19181  2.908 0.629     0.146     0.040      142    15.2  superiortemporal
 6771   5193  13624  2.801 0.576     0.141     0.037      105    10.9  supramarginal
  419    512   1340  3.377 0.507     0.213     0.051        6     1.0  frontalpole
  812   1041   2926  3.568 0.824     0.214     0.051       13     2.1  temporalpole
 1291    942   1979  2.402 0.512     0.132     0.037       14     2.1  transversetemporal
 4459   2729   8812  3.050 0.741     0.139     0.049      101     9.6  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 0051359 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317093
Total vertex volume 313472 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1718   1154   2912  2.779 0.430     0.113     0.023       15     1.5  bankssts
 1455    916   2579  2.557 0.670     0.126     0.034       27     1.8  caudalanteriorcingulate
 5180   3362  10749  2.785 0.600     0.120     0.033       58     6.8  caudalmiddlefrontal
 3136   1952   4532  2.116 0.560     0.137     0.040       44     4.9  cuneus
  836    524   2463  3.508 0.823     0.146     0.080       17     2.7  entorhinal
 5708   3798  13188  2.904 0.598     0.136     0.043       87     9.5  fusiform
 9739   6301  19353  2.647 0.580     0.119     0.033      123    13.1  inferiorparietal
 6568   4172  15945  3.186 0.723     0.127     0.041       94    11.0  inferiortemporal
 1967   1261   3620  2.557 0.891     0.133     0.039       36     2.8  isthmuscingulate
 9766   5984  15435  2.363 0.564     0.134     0.039      132    15.2  lateraloccipital
 4399   2930   9481  2.920 0.720     0.141     0.043       69     8.0  lateralorbitofrontal
 5228   3309   7518  2.078 0.596     0.137     0.049       85    10.0  lingual
 3274   2265   7561  2.821 0.709     0.145     0.051       90     7.4  medialorbitofrontal
 7459   4814  17711  3.007 0.682     0.130     0.040      131    11.6  middletemporal
 1129    702   2164  2.729 0.674     0.112     0.036       12     1.4  parahippocampal
 2823   1715   4701  2.602 0.562     0.127     0.045       37     5.2  paracentral
 2160   1418   4316  2.765 0.447     0.119     0.029       23     2.5  parsopercularis
 1810   1171   4547  3.197 0.702     0.154     0.049       34     3.3  parsorbitalis
 2803   1878   5356  2.627 0.501     0.134     0.037       42     4.5  parstriangularis
 2639   1854   3002  1.834 0.502     0.149     0.040       34     4.5  pericalcarine
 8469   5026  13128  2.352 0.625     0.119     0.039      103    13.9  postcentral
 2228   1497   4341  2.740 0.889     0.153     0.042       44     3.8  posteriorcingulate
 9216   5708  16033  2.632 0.551     0.119     0.041      129    16.6  precentral
 6723   4439  11998  2.631 0.571     0.130     0.034       87     8.9  precuneus
 1063    677   2477  3.117 0.588     0.136     0.040       20     1.7  rostralanteriorcingulate
11384   7462  22876  2.666 0.549     0.135     0.037      182    17.3  rostralmiddlefrontal
12547   8294  28081  3.002 0.569     0.123     0.036      153    16.7  superiorfrontal
 8467   5281  13182  2.288 0.530     0.125     0.037      118    12.4  superiorparietal
 6700   4225  14071  2.907 0.602     0.114     0.035       78     9.4  superiortemporal
 7518   4826  14296  2.657 0.546     0.121     0.037       97    10.9  supramarginal
  567    376   1799  3.139 0.774     0.172     0.055       19     1.6  frontalpole
  747    496   2710  3.492 0.794     0.154     0.056       15     1.8  temporalpole
  846    415   1268  2.509 0.542     0.125     0.055       15     2.3  transversetemporal
 5148   3310  10023  2.984 0.769     0.134     0.053       77    11.5  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051359 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317093
Total vertex volume 313472 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1718    958   2912  2.779 0.430     0.121     0.042       63     2.8  bankssts
 1455   1077   2579  2.557 0.670     0.159     0.053       42     2.8  caudalanteriorcingulate
 5180   4144  10749  2.785 0.600     0.136     0.034       79     8.1  caudalmiddlefrontal
 3136   2327   4532  2.116 0.560     0.135     0.035       56     4.9  cuneus
  836    793   2463  3.508 0.823     0.162     0.053       29     2.0  entorhinal
 5708   5081  13188  2.904 0.598     0.162     0.041      110    10.4  fusiform
 9739   7939  19353  2.647 0.580     0.142     0.034      130    16.0  inferiorparietal
 6568   5601  15945  3.186 0.723     0.153     0.042      118    12.8  inferiortemporal
 1967   1502   3620  2.557 0.891     0.164     0.053       64     4.3  isthmuscingulate
 9766   6947  15435  2.363 0.564     0.123     0.032      207    14.0  lateraloccipital
 4399   3468   9481  2.920 0.720     0.158     0.047       92     8.5  lateralorbitofrontal
 5228   3929   7518  2.078 0.596     0.135     0.035       99     8.0  lingual
 3274   2970   7561  2.821 0.709     0.165     0.044       59     6.6  medialorbitofrontal
 7459   6660  17711  3.007 0.682     0.160     0.039      129    13.9  middletemporal
 1129    899   2164  2.729 0.674     0.147     0.044       25     2.0  parahippocampal
 2823   1877   4701  2.602 0.562     0.126     0.036       43     4.4  paracentral
 2160   1657   4316  2.765 0.447     0.136     0.033       27     3.2  parsopercularis
 1810   1661   4547  3.197 0.702     0.169     0.042       27     3.3  parsorbitalis
 2803   2204   5356  2.627 0.501     0.156     0.037       43     4.9  parstriangularis
 2639   1586   3002  1.834 0.502     0.115     0.028       33     3.1  pericalcarine
 8469   6136  13128  2.352 0.625     0.117     0.028       80    10.1  postcentral
 2228   1761   4341  2.740 0.889     0.170     0.047       51     4.3  posteriorcingulate
 9216   6294  16033  2.632 0.551     0.116     0.031      108    12.5  precentral
 6723   4663  11998  2.631 0.571     0.132     0.035      222    10.2  precuneus
 1063    911   2477  3.117 0.588     0.159     0.043       24     1.8  rostralanteriorcingulate
11384   9577  22876  2.666 0.549     0.159     0.037      172    19.4  rostralmiddlefrontal
12547  10078  28081  3.002 0.569     0.142     0.037      178    20.4  superiorfrontal
 8467   6208  13182  2.288 0.530     0.132     0.032      111    11.4  superiorparietal
 6700   5332  14071  2.907 0.602     0.135     0.033       91     9.8  superiortemporal
 7518   5654  14296  2.657 0.546     0.130     0.034      106    11.0  supramarginal
  567    704   1799  3.139 0.774     0.207     0.043        9     1.0  frontalpole
  747    971   2710  3.492 0.794     0.239     0.059       13     2.0  temporalpole
  846    568   1268  2.509 0.542     0.105     0.039        8     1.3  transversetemporal
 5148   3192  10023  2.984 0.769     0.146     0.052      142    12.3  insula
PIDs (8726 8729 8732 8738) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 06:12:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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 06:12:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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 8892 of (8892 8895) to complete...
Waiting for PID 8895 of (8892 8895) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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...
33 labels changed using aseg
relabeling using gibbs priors...
000:  11066 changed, 169870 examined...
001:   2647 changed, 43025 examined...
002:    758 changed, 13703 examined...
003:    311 changed, 4260 examined...
004:    138 changed, 1779 examined...
005:     60 changed, 794 examined...
006:     27 changed, 340 examined...
007:     17 changed, 152 examined...
008:     10 changed, 96 examined...
009:      2 changed, 51 examined...
010:      4 changed, 14 examined...
011:      2 changed, 21 examined...
012:      0 changed, 10 examined...
15 labels changed using aseg
000: 325 total segments, 236 labels (2893 vertices) changed
001: 98 total segments, 9 labels (27 vertices) changed
002: 89 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 49 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1389 vertices marked for relabeling...
1389 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 37 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 719 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1 labels changed using aseg
relabeling using gibbs priors...
000:  10949 changed, 169093 examined...
001:   2550 changed, 42958 examined...
002:    738 changed, 13151 examined...
003:    336 changed, 4172 examined...
004:    157 changed, 1906 examined...
005:     84 changed, 921 examined...
006:     38 changed, 477 examined...
007:     25 changed, 226 examined...
008:     12 changed, 138 examined...
009:      9 changed, 74 examined...
010:      4 changed, 51 examined...
011:      4 changed, 18 examined...
012:      0 changed, 19 examined...
0 labels changed using aseg
000: 332 total segments, 242 labels (3062 vertices) changed
001: 96 total segments, 8 labels (48 vertices) changed
002: 88 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 65 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1563 vertices marked for relabeling...
1563 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 29 seconds.
PIDs (8892 8895) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 06:13:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 06:13:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 rh white 

Waiting for PID 8965 of (8965 8968) to complete...
Waiting for PID 8968 of (8965 8968) 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 0051359 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317227
Total vertex volume 313307 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1492   1035   3126  2.625 0.546     0.148     0.037       36     2.4  G&S_frontomargin
 2060   1381   3945  2.505 0.541     0.128     0.030       25     2.5  G&S_occipital_inf
 2094   1166   3249  2.380 0.571     0.122     0.055       38     5.2  G&S_paracentral
 2600   1607   5071  2.861 0.527     0.131     0.045       37     4.1  G&S_subcentral
 1075    707   3095  3.271 0.564     0.177     0.062       31     3.0  G&S_transv_frontopol
 2763   1840   5918  2.945 0.582     0.128     0.039       40     4.1  G&S_cingul-Ant
 1565   1030   3191  2.881 0.547     0.125     0.041       22     2.5  G&S_cingul-Mid-Ant
 1726   1143   3415  2.913 0.541     0.119     0.034       21     2.2  G&S_cingul-Mid-Post
  830    533   2295  3.179 0.637     0.147     0.053       17     1.6  G_cingul-Post-dorsal
  455    281    870  2.808 0.681     0.136     0.048        8     0.7  G_cingul-Post-ventral
 3014   1859   4065  1.950 0.468     0.138     0.038       44     4.7  G_cuneus
 1923   1218   4634  3.024 0.474     0.127     0.041       32     2.9  G_front_inf-Opercular
  653    431   1998  3.039 0.421     0.162     0.054       20     1.4  G_front_inf-Orbital
 1593   1031   3872  2.887 0.488     0.140     0.045       31     2.8  G_front_inf-Triangul
 7107   4428  16539  2.857 0.559     0.140     0.047      131    13.1  G_front_middle
 8987   5721  22450  3.124 0.646     0.136     0.049      175    18.3  G_front_sup
  932    592   1929  2.973 0.790     0.158     0.069       19     2.4  G_Ins_lg&S_cent_ins
 1089    657   3230  3.640 0.763     0.143     0.072       20     2.6  G_insular_short
 3129   1717   6159  2.658 0.608     0.131     0.045       55     5.7  G_occipital_middle
 2452   1238   3548  2.376 0.621     0.113     0.033       28     3.5  G_occipital_sup
 1525   1038   3649  3.008 0.575     0.154     0.050       79     3.1  G_oc-temp_lat-fusifor
 3839   2296   5653  2.167 0.677     0.148     0.053       69     7.7  G_oc-temp_med-Lingual
 1642   1064   4396  3.211 0.623     0.139     0.054       27     3.6  G_oc-temp_med-Parahip
 3417   2203   8514  2.925 0.649     0.152     0.054       74     7.2  G_orbital
 3017   1851   6857  2.852 0.682     0.134     0.042       54     4.8  G_pariet_inf-Angular
 3779   2420   9039  2.922 0.578     0.138     0.042       67     5.9  G_pariet_inf-Supramar
 3216   1980   6481  2.442 0.654     0.127     0.036       49     4.2  G_parietal_sup
 3585   2017   6771  2.531 0.672     0.127     0.049       59     7.8  G_postcentral
 3693   1997   7575  2.929 0.576     0.113     0.043       54     6.6  G_precentral
 3337   2176   7359  2.624 0.579     0.144     0.042       57     5.3  G_precuneus
  892    586   2362  2.948 0.771     0.174     0.058       32     2.5  G_rectus
  916    592   1831  3.104 1.014     0.147     0.064       15     2.6  G_subcallosal
  990    530   1622  2.379 0.555     0.132     0.068       19     2.7  G_temp_sup-G_T_transv
 2942   1916   8114  3.049 0.672     0.144     0.050       58     5.2  G_temp_sup-Lateral
  881    581   2672  3.606 0.762     0.095     0.029        5     1.2  G_temp_sup-Plan_polar
 1734   1120   3562  2.837 0.590     0.107     0.027       17     1.7  G_temp_sup-Plan_tempo
 2979   1877   8316  3.297 0.720     0.147     0.052       62     6.3  G_temporal_inf
 2989   1901   9202  3.356 0.678     0.146     0.054       63     6.6  G_temporal_middle
  383    261    526  2.194 0.398     0.097     0.016        2     0.3  Lat_Fis-ant-Horizont
  562    374    733  2.664 0.417     0.109     0.022        4     0.5  Lat_Fis-ant-Vertical
 1666   1098   2276  2.715 0.404     0.126     0.037       15     2.5  Lat_Fis-post
 2700   1531   2940  1.854 0.493     0.133     0.041       39     4.3  Pole_occipital
 1902   1351   6390  3.199 0.772     0.157     0.050       34     4.1  Pole_temporal
 3235   2303   3890  1.961 0.600     0.138     0.033       36     4.5  S_calcarine
 3978   2670   4792  2.101 0.516     0.127     0.035       36     5.9  S_central
 1232    854   1800  2.453 0.653     0.112     0.025        8     1.3  S_cingul-Marginalis
  697    472   1151  2.964 0.408     0.117     0.027        4     0.9  S_circular_insula_ant
 1630   1065   2555  2.934 0.613     0.105     0.028       10     1.9  S_circular_insula_inf
 2179   1427   3232  2.731 0.459     0.105     0.030       14     2.5  S_circular_insula_sup
 1286    878   1979  2.577 0.597     0.104     0.024        8     1.3  S_collat_transv_ant
  602    399    835  2.126 0.406     0.116     0.022        5     0.6  S_collat_transv_post
 3182   2095   5216  2.558 0.402     0.121     0.030       37     4.1  S_front_inf
 1518   1065   2400  2.535 0.406     0.109     0.022        8     1.4  S_front_middle
 3506   2385   6132  2.721 0.424     0.096     0.023       21     3.1  S_front_sup
   49     33     48  2.291 0.235     0.171     0.023        1     0.1  S_interm_prim-Jensen
 3188   2221   4487  2.309 0.396     0.105     0.021       21     2.6  S_intrapariet&P_trans
  915    632   1196  2.327 0.496     0.129     0.027        8     1.0  S_oc_middle&Lunatus
 1888   1197   2441  2.358 0.487     0.127     0.028       17     2.2  S_oc_sup&transversal
  922    632   1367  2.380 0.375     0.108     0.028        6     0.8  S_occipital_ant
  946    664   1712  2.515 0.467     0.140     0.038       14     1.5  S_oc-temp_lat
 2122   1442   3790  2.592 0.679     0.120     0.030       19     2.5  S_oc-temp_med&Lingual
  764    522   1135  2.506 0.368     0.128     0.035        6     1.0  S_orbital_lateral
  785    550   1067  2.464 0.390     0.122     0.030        6     1.0  S_orbital_med-olfact
 2036   1323   3718  2.866 0.547     0.135     0.037       23     3.2  S_orbital-H_Shaped
 2349   1546   3459  2.526 0.498     0.119     0.028       21     2.7  S_parieto_occipital
 1604    997   1353  1.724 0.596     0.124     0.025       24     1.4  S_pericallosal
 4082   2718   6303  2.437 0.472     0.117     0.027       35     4.5  S_postcentral
 3132   2054   5227  2.681 0.429     0.105     0.025       21     3.3  S_precentral-inf-part
 1408    956   2257  2.758 0.497     0.107     0.020        8     1.4  S_precentral-sup-part
  876    589   1357  2.690 0.828     0.124     0.023        7     1.0  S_suborbital
 1269    897   1950  2.432 0.448     0.120     0.025        8     1.4  S_subparietal
 1307    908   2237  2.797 0.618     0.111     0.032       10     1.8  S_temporal_inf
 7946   5343  13864  2.630 0.486     0.109     0.025       65     8.0  S_temporal_sup
  731    477    918  2.450 0.426     0.111     0.026        4     0.9  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 0051359 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317093
Total vertex volume 313472 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1351    920   3204  2.738 0.699     0.151     0.044       30     2.9  G&S_frontomargin
 1500   1011   2625  2.474 0.524     0.141     0.039       22     2.2  G&S_occipital_inf
 1709    980   2738  2.428 0.522     0.140     0.053       25     4.1  G&S_paracentral
 1975   1270   4439  3.024 0.506     0.131     0.038       26     2.9  G&S_subcentral
 1607   1031   3960  2.799 0.622     0.154     0.054       39     3.8  G&S_transv_frontopol
 3724   2508   7826  2.938 0.493     0.128     0.038       60     5.8  G&S_cingul-Ant
 1720   1179   3582  2.914 0.502     0.128     0.031       22     2.1  G&S_cingul-Mid-Ant
 1633   1102   3177  2.908 0.564     0.136     0.036       20     2.4  G&S_cingul-Mid-Post
  804    504   2291  3.485 0.801     0.160     0.053       21     1.3  G_cingul-Post-dorsal
  537    316   1248  2.879 0.761     0.145     0.052       15     1.1  G_cingul-Post-ventral
 2925   1821   4222  2.026 0.576     0.138     0.041       42     4.8  G_cuneus
 1428    919   3653  2.967 0.371     0.142     0.042       27     2.2  G_front_inf-Opercular
  445    274   1115  3.107 0.474     0.156     0.044       10     0.8  G_front_inf-Orbital
 1122    738   2173  2.612 0.468     0.146     0.043       20     2.0  G_front_inf-Triangul
 5465   3335  13607  2.908 0.594     0.142     0.045      110     9.4  G_front_middle
 7537   4813  18979  3.139 0.595     0.132     0.046      129    13.0  G_front_sup
  850    552   1980  3.215 0.677     0.133     0.064       14     1.9  G_Ins_lg&S_cent_ins
  825    523   2551  3.372 0.992     0.168     0.078       25     3.0  G_insular_short
 3087   1883   6876  2.736 0.528     0.143     0.042       56     5.2  G_occipital_middle
 1759   1032   2605  2.124 0.520     0.131     0.049       28     3.3  G_occipital_sup
 2571   1674   6639  3.005 0.568     0.151     0.052       53     4.8  G_oc-temp_lat-fusifor
 3612   2161   5283  2.096 0.632     0.149     0.059       76     8.3  G_oc-temp_med-Lingual
 2382   1438   5575  3.123 0.840     0.148     0.074       47     7.0  G_oc-temp_med-Parahip
 3587   2314  10087  3.236 0.741     0.154     0.052       77     7.2  G_orbital
 3710   2268   9217  2.846 0.667     0.130     0.044       65     6.5  G_pariet_inf-Angular
 3475   2155   7887  2.759 0.597     0.128     0.048       63     6.9  G_pariet_inf-Supramar
 2876   1716   5269  2.369 0.606     0.140     0.052       58     6.0  G_parietal_sup
 3409   1687   5220  2.413 0.568     0.124     0.051       57     7.1  G_postcentral
 3686   2002   7345  2.782 0.554     0.117     0.058       81     9.3  G_precentral
 2454   1555   5081  2.627 0.559     0.134     0.038       43     3.2  G_precuneus
  895    637   2781  2.977 0.839     0.190     0.074       43     3.0  G_rectus
  495    316    911  2.565 0.763     0.084     0.029        3     0.4  G_subcallosal
  663    313   1144  2.549 0.581     0.135     0.068       14     2.2  G_temp_sup-G_T_transv
 2294   1393   6010  3.082 0.657     0.133     0.052       42     4.6  G_temp_sup-Lateral
  934    613   2212  3.126 0.686     0.097     0.031        7     1.1  G_temp_sup-Plan_polar
 1423    896   2871  2.847 0.504     0.117     0.030       16     1.7  G_temp_sup-Plan_tempo
 3395   2085  10047  3.369 0.757     0.142     0.052       67     7.2  G_temporal_inf
 4534   2820  12521  3.163 0.722     0.142     0.054      109     9.3  G_temporal_middle
  650    440   1249  2.714 0.414     0.125     0.036       10     1.1  Lat_Fis-ant-Horizont
  319    234    458  2.217 0.354     0.116     0.017        2     0.3  Lat_Fis-ant-Vertical
 1920   1233   2570  2.543 0.467     0.110     0.029       16     2.4  Lat_Fis-post
 3992   2272   5543  2.171 0.624     0.129     0.042       53     6.3  Pole_occipital
 2137   1460   6990  3.334 0.793     0.151     0.051       40     4.8  Pole_temporal
 3018   2154   3811  2.034 0.659     0.141     0.038       36     4.9  S_calcarine
 3651   2418   4183  1.987 0.477     0.115     0.029       25     4.6  S_central
 1498   1046   2488  2.544 0.428     0.130     0.031       16     2.0  S_cingul-Marginalis
  852    585   1395  3.003 0.490     0.112     0.026        5     0.9  S_circular_insula_ant
 1397    929   1996  2.812 0.572     0.106     0.026        9     1.6  S_circular_insula_inf
 2133   1414   3305  2.797 0.505     0.119     0.029       15     2.8  S_circular_insula_sup
 1629   1064   2780  2.895 0.462     0.089     0.020        6     1.4  S_collat_transv_ant
  461    328    581  2.134 0.372     0.132     0.025        3     0.6  S_collat_transv_post
 2310   1549   3953  2.531 0.408     0.120     0.027       23     2.8  S_front_inf
 3394   2298   5345  2.520 0.485     0.121     0.028       30     3.9  S_front_middle
 4016   2768   6849  2.617 0.474     0.106     0.023       29     3.6  S_front_sup
  436    298    630  2.126 0.403     0.082     0.016        2     0.3  S_interm_prim-Jensen
 3675   2411   5488  2.299 0.459     0.105     0.021       28     3.2  S_intrapariet&P_trans
 1340    919   1823  2.423 0.410     0.134     0.032       11     1.8  S_oc_middle&Lunatus
 1312    878   1877  2.294 0.578     0.110     0.020       10     1.0  S_oc_sup&transversal
 1141    769   1607  2.271 0.454     0.108     0.030        9     1.0  S_occipital_ant
 1609   1076   2498  2.747 0.469     0.119     0.027       12     1.9  S_oc-temp_lat
 1879   1293   2996  2.403 0.471     0.111     0.024       14     1.7  S_oc-temp_med&Lingual
  655    452   1030  2.453 0.702     0.120     0.027        5     0.8  S_orbital_lateral
  767    556   1120  2.321 0.431     0.116     0.026        5     0.9  S_orbital_med-olfact
 1713   1159   3299  2.867 0.714     0.136     0.040       21     2.9  S_orbital-H_Shaped
 3016   1990   4332  2.505 0.554     0.125     0.031       32     3.8  S_parieto_occipital
 2013   1251   2244  2.076 0.819     0.136     0.034       39     2.4  S_pericallosal
 3337   2268   4644  2.410 0.449     0.116     0.027       28     3.8  S_postcentral
 2808   1872   4486  2.590 0.438     0.103     0.021       17     2.6  S_precentral-inf-part
 1483   1034   2335  2.545 0.405     0.115     0.027        9     1.7  S_precentral-sup-part
  473    313    872  2.770 0.581     0.145     0.040        8     0.8  S_suborbital
 1729   1160   3253  2.758 0.564     0.127     0.031       18     2.2  S_subparietal
 1670   1148   2694  2.864 0.544     0.112     0.023        9     1.7  S_temporal_inf
 8218   5495  13197  2.609 0.455     0.109     0.023       66     7.9  S_temporal_sup
  413    268    596  2.985 0.327     0.118     0.028        2     0.5  S_temporal_transverse
PIDs (8965 8968) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 06:14:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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 06:14:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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 9058 of (9058 9061) to complete...
Waiting for PID 9061 of (9058 9061) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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...
1452 labels changed using aseg
relabeling using gibbs priors...
000:   2449 changed, 169870 examined...
001:    600 changed, 11257 examined...
002:    177 changed, 3429 examined...
003:     73 changed, 1114 examined...
004:     35 changed, 422 examined...
005:     17 changed, 193 examined...
006:      9 changed, 93 examined...
007:      8 changed, 57 examined...
008:     10 changed, 46 examined...
009:      6 changed, 58 examined...
010:      7 changed, 34 examined...
011:      5 changed, 40 examined...
012:      3 changed, 35 examined...
013:      6 changed, 18 examined...
014:      6 changed, 32 examined...
015:      3 changed, 30 examined...
016:      3 changed, 23 examined...
017:      2 changed, 19 examined...
018:      2 changed, 15 examined...
019:      0 changed, 11 examined...
277 labels changed using aseg
000: 81 total segments, 48 labels (394 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
891 vertices marked for relabeling...
891 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051359 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...
1279 labels changed using aseg
relabeling using gibbs priors...
000:   2493 changed, 169093 examined...
001:    605 changed, 11445 examined...
002:    153 changed, 3516 examined...
003:     57 changed, 959 examined...
004:     13 changed, 351 examined...
005:      7 changed, 79 examined...
006:      5 changed, 46 examined...
007:      6 changed, 32 examined...
008:      1 changed, 29 examined...
009:      1 changed, 7 examined...
010:      0 changed, 7 examined...
178 labels changed using aseg
000: 62 total segments, 29 labels (277 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1153 vertices marked for relabeling...
1153 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 32 seconds.
PIDs (9058 9061) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 06:15:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 06:15:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 rh white 

Waiting for PID 9111 of (9111 9114) to complete...
Waiting for PID 9114 of (9111 9114) 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 0051359 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317227
Total vertex volume 313307 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 2026   1313   3813  2.623 0.644     0.134     0.042       35     3.2  caudalanteriorcingulate
 5080   3205   9918  2.834 0.548     0.115     0.034       56     6.7  caudalmiddlefrontal
 4035   2534   5556  2.082 0.489     0.133     0.034       52     5.7  cuneus
  651    414   1703  3.195 0.804     0.140     0.063       11     1.7  entorhinal
 4174   2854   8555  2.767 0.597     0.138     0.039      109     6.7  fusiform
 7107   4571  13397  2.693 0.597     0.123     0.033       90     9.3  inferiorparietal
 5363   3561  13730  3.084 0.757     0.139     0.045       92    10.0  inferiortemporal
 1936   1235   3471  2.548 0.859     0.124     0.039       25     2.7  isthmuscingulate
 9912   5906  14593  2.279 0.583     0.128     0.036      126    13.8  lateraloccipital
 5835   3842  12035  2.845 0.628     0.148     0.048      107    12.1  lateralorbitofrontal
 5514   3465   7890  2.157 0.607     0.136     0.043       77     9.1  lingual
 2858   1879   6229  2.921 0.842     0.140     0.043       57     5.2  medialorbitofrontal
 7160   4758  17437  3.014 0.685     0.127     0.039      100    11.6  middletemporal
 1223    769   2983  3.175 0.647     0.125     0.047       18     2.3  parahippocampal
 3081   1854   4899  2.567 0.593     0.115     0.042       36     5.7  paracentral
 3162   2019   6275  2.829 0.497     0.123     0.033       42     4.1  parsopercularis
 1385    911   3100  2.904 0.495     0.137     0.041       23     2.3  parsorbitalis
 3708   2448   7256  2.671 0.500     0.131     0.037       54     5.6  parstriangularis
 2453   1727   2577  1.697 0.374     0.147     0.038       33     3.7  pericalcarine
10631   6574  17634  2.405 0.639     0.125     0.042      141    18.3  postcentral
 2510   1660   4749  2.710 0.843     0.132     0.034       40     3.1  posteriorcingulate
10087   6145  18059  2.766 0.567     0.117     0.038      119    16.2  precentral
 6537   4353  12062  2.547 0.576     0.132     0.033       77     8.9  precuneus
 1775   1144   3767  2.978 0.677     0.136     0.045       30     3.2  rostralanteriorcingulate
 8706   5662  18024  2.705 0.499     0.133     0.041      140    14.2  rostralmiddlefrontal
13899   9217  32326  3.016 0.616     0.130     0.040      216    23.2  superiorfrontal
 7686   4764  13046  2.381 0.541     0.116     0.031       91     9.0  superiorparietal
11609   7608  25985  2.905 0.662     0.122     0.035      142    16.1  superiortemporal
 6262   4130  12478  2.798 0.577     0.128     0.035       82     8.5  supramarginal
 1261    710   1921  2.391 0.517     0.133     0.062       21     3.2  transversetemporal
 3863   2458   7842  3.077 0.730     0.125     0.049       49     6.8  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 0051359 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 317093
Total vertex volume 313472 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1709   1063   3165  2.613 0.691     0.128     0.034       33     2.2  caudalanteriorcingulate
 5336   3466  11013  2.789 0.596     0.121     0.033       61     7.0  caudalmiddlefrontal
 3737   2331   5410  2.148 0.558     0.136     0.042       52     6.2  cuneus
  789    490   2269  3.484 0.824     0.146     0.074       15     2.4  entorhinal
 5271   3477  11701  2.889 0.571     0.135     0.042       79     8.2  fusiform
 9546   6185  18824  2.641 0.583     0.120     0.033      120    12.9  inferiorparietal
 7075   4538  17364  3.146 0.742     0.128     0.043      107    13.1  inferiortemporal
 1943   1249   3560  2.541 0.876     0.131     0.039       34     2.7  isthmuscingulate
 9848   6021  15662  2.359 0.575     0.135     0.040      137    15.3  lateraloccipital
 5281   3509  11825  2.944 0.781     0.148     0.049       96    10.9  lateralorbitofrontal
 5133   3267   7373  2.070 0.596     0.137     0.049       84    10.0  lingual
 2478   1712   6048  2.828 0.780     0.149     0.054       70     5.8  medialorbitofrontal
 8918   5791  20508  2.989 0.648     0.127     0.036      138    12.2  middletemporal
 1172    727   2189  2.730 0.693     0.112     0.040       13     1.8  parahippocampal
 2972   1809   4966  2.603 0.565     0.127     0.046       41     5.5  paracentral
 2641   1729   5177  2.718 0.452     0.122     0.031       31     3.3  parsopercularis
 1500    964   3473  2.968 0.632     0.141     0.044       26     2.6  parsorbitalis
 2683   1786   5296  2.684 0.531     0.137     0.039       43     4.4  parstriangularis
 2654   1838   3012  1.854 0.501     0.148     0.040       34     4.5  pericalcarine
 9241   5539  14233  2.359 0.618     0.120     0.039      111    15.0  postcentral
 2264   1529   4417  2.777 0.897     0.155     0.043       45     3.9  posteriorcingulate
 8911   5499  15572  2.630 0.556     0.119     0.041      126    16.1  precentral
 6930   4559  12401  2.599 0.592     0.128     0.034       90     9.0  precuneus
 1397    895   2911  2.994 0.632     0.127     0.037       22     2.0  rostralanteriorcingulate
 7741   5080  15445  2.714 0.581     0.136     0.037      117    11.5  rostralmiddlefrontal
16745  11082  36856  2.909 0.576     0.126     0.037      234    24.0  superiorfrontal
 6878   4287  10747  2.296 0.520     0.125     0.038       99    10.1  superiorparietal
 8502   5433  18521  2.933 0.644     0.119     0.038      104    13.0  superiortemporal
 7185   4595  13814  2.660 0.546     0.120     0.037       94    10.5  supramarginal
  841    409   1273  2.518 0.540     0.124     0.056       15     2.3  transversetemporal
 4141   2693   8444  3.087 0.741     0.132     0.049       58     8.6  insula
PIDs (9111 9114) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 06:17:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 pctsurfcon --s 0051359 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 06:17:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts

 pctsurfcon --s 0051359 --rh-only 

Waiting for PID 9207 of (9207 9215) to complete...
Waiting for PID 9215 of (9207 9215) to complete...

 pctsurfcon --s 0051359 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts/pctsurfcon.log
Sun Oct  8 06:17:06 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-6.0.0/0051359/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-908 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-6.0.0/0051359/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9207/lh.wm.mgh --regheader 0051359 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00001;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 87867
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9207/lh.wm.mgh
Dim: 169870 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9207/lh.gm.mgh --projfrac 0.3 --regheader 0051359 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00001;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 108527
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9207/lh.gm.mgh
Dim: 169870 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9207/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9207/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.w-g.pct.mgh --annot 0051359 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/lh.w-g.pct.mgh --annot 0051359 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/lh.w-g.pct.mgh
Vertex Area is 0.642425 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 0051359 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/scripts/pctsurfcon.log
Sun Oct  8 06:17:06 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-6.0.0/0051359/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-908 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-6.0.0/0051359/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9215/rh.wm.mgh --regheader 0051359 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00001;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 87505
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9215/rh.wm.mgh
Dim: 169093 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9215/rh.gm.mgh --projfrac 0.3 --regheader 0051359 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00001;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 108306
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9215/rh.gm.mgh
Dim: 169093 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9215/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/tmp.pctsurfcon.9215/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.w-g.pct.mgh --annot 0051359 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.w-g.pct.mgh --annot 0051359 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.w-g.pct.mgh
Vertex Area is 0.642712 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 (9207 9215) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 06:17:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2235 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1975 voxels changed to hypointensity...
4167 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 06:18:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359

 mri_aparc2aseg --s 0051359 --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 06:18:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359

 mri_aparc2aseg --s 0051359 --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 06:18:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359

 mri_aparc2aseg --s 0051359 --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 9477 of (9477 9480 9483) to complete...
Waiting for PID 9480 of (9477 9480 9483) to complete...
Waiting for PID 9483 of (9477 9480 9483) to complete...

 mri_aparc2aseg --s 0051359 --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 0051359
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/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-6.0.0/0051359/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 7.62
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 26
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 82
rescaling Left_Cerebellum_Cortex from 60 --> 63
rescaling Left_Thalamus from 94 --> 103
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 83
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 36
rescaling Fourth_Ventricle from 22 --> 23
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 66
rescaling CSF from 32 --> 55
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 84
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 82
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 47
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 620702
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 140 changed.
pass 2: 6 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051359 --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 0051359
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/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-6.0.0/0051359/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 7.62
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 26
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 82
rescaling Left_Cerebellum_Cortex from 60 --> 63
rescaling Left_Thalamus from 94 --> 103
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 83
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 36
rescaling Fourth_Ventricle from 22 --> 23
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 66
rescaling CSF from 32 --> 55
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 84
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 82
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 47
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 620810
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 140 changed.
pass 2: 6 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051359 --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 0051359
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/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-6.0.0/0051359/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 7.62
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 26
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 82
rescaling Left_Cerebellum_Cortex from 60 --> 63
rescaling Left_Thalamus from 94 --> 103
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 83
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 36
rescaling Fourth_Ventricle from 22 --> 23
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 66
rescaling CSF from 32 --> 55
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 84
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 82
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 47
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 620810
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 140 changed.
pass 2: 6 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (9477 9480 9483) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 06:33:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri

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

Sun Oct  8 06:33:33 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-6.0.0/0051359/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-908 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-6.0.0/0051359/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-908
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 06:33:33 CEST 2017 
Ended   at Sun Oct  8 06:33:46 CEST 2017
Apas2aseg-Run-Time-Sec 13
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 06:33:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359

 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 0051359 


$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 0051359 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1693737 mm^3    (det: 1.150182 )
Computing euler number
orig.nofix lheno = -172, rheno = -196
orig.nofix lhholes =   87, rhholes = 99
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
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 06:39:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359

 mri_aparc2aseg --s 0051359 --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 0051359
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-6.0.0/0051359/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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-6.0.0/0051359/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8425 vertices from left hemi
Ripped 7673 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-6.0.0/0051359/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 = 1123995
Used brute-force search on 36 voxels
Fixing Parahip LH WM
  Found 11 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 2.000000
     4 k 1430.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1.000000
     9 k 2.000000
     10 k 1.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 9.000000
     1 k 10.000000
     2 k 1.000000
     3 k 1386.000000
     4 k 1.000000
     5 k 1.000000
     6 k 3.000000
     7 k 5.000000
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 0051359 --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 0051359 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-908
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1693737 mm^3    (det: 1.150182 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
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-6.0.0/0051359/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 07:01:10 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11214 of (11214 11220 11226 11232 11237) to complete...
Waiting for PID 11220 of (11214 11220 11226 11232 11237) to complete...
Waiting for PID 11226 of (11214 11220 11226 11232 11237) to complete...
Waiting for PID 11232 of (11214 11220 11226 11232 11237) to complete...
Waiting for PID 11237 of (11214 11220 11226 11232 11237) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 1226
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 5355
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 1921
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9830
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 437
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4514
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 1219
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 7202
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 985
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6769
mri_label2label: Done

PIDs (11214 11220 11226 11232 11237) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11308 of (11308 11314 11320 11326) to complete...
Waiting for PID 11314 of (11308 11314 11320 11326) to complete...
Waiting for PID 11320 of (11308 11314 11320 11326) to complete...
Waiting for PID 11326 of (11308 11314 11320 11326) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 542
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4612
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 2642
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16231
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 1286
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 5467
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 2155
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 5577
mri_label2label: Done

PIDs (11308 11314 11320 11326) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11407 of (11407 11413 11419 11425 11430) to complete...
Waiting for PID 11413 of (11407 11413 11419 11425 11430) to complete...
Waiting for PID 11419 of (11407 11413 11419 11425 11430) to complete...
Waiting for PID 11425 of (11407 11413 11419 11425 11430) to complete...
Waiting for PID 11430 of (11407 11413 11419 11425 11430) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 2399
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 7040
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 5288
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 13402
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 745
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2763
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 344
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1634
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 374
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1573
mri_label2label: Done

PIDs (11407 11413 11419 11425 11430) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11495 of (11495 11501 11507 11513 11519) to complete...
Waiting for PID 11501 of (11495 11501 11507 11513 11519) to complete...
Waiting for PID 11507 of (11495 11501 11507 11513 11519) to complete...
Waiting for PID 11513 of (11495 11501 11507 11513 11519) to complete...
Waiting for PID 11519 of (11495 11501 11507 11513 11519) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 269
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1283
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 626
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2718
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 100
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1604
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 432
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2428
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 487
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2806
mri_label2label: Done

PIDs (11495 11501 11507 11513 11519) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11580 of (11580 11586 11592 11598) to complete...
Waiting for PID 11586 of (11580 11586 11592 11598) to complete...
Waiting for PID 11592 of (11580 11586 11592 11598) to complete...
Waiting for PID 11598 of (11580 11586 11592 11598) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1723
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 860
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7895
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 498
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2410
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 763
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1914
mri_label2label: Done

PIDs (11580 11586 11592 11598) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11646 of (11646 11652 11658 11664 11669) to complete...
Waiting for PID 11652 of (11646 11652 11658 11664 11669) to complete...
Waiting for PID 11658 of (11646 11652 11658 11664 11669) to complete...
Waiting for PID 11664 of (11646 11652 11658 11664 11669) to complete...
Waiting for PID 11669 of (11646 11652 11658 11664 11669) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 1606
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 5011
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 2536
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5870
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 247
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 760
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 99
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 569
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169870
Number of reverse mapping hits = 201
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 651
mri_label2label: Done

PIDs (11646 11652 11658 11664 11669) completed and logs appended.

 mris_label2annot --s 0051359 --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-6.0.0/0051359/label
cmdline mris_label2annot --s 0051359 --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-908
machine  x86_64
user     ntraut

subject 0051359
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-6.0.0/0051359/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 114378 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051359 --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-6.0.0/0051359/label
cmdline mris_label2annot --s 0051359 --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-908
machine  x86_64
user     ntraut

subject 0051359
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-6.0.0/0051359/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 137954 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 317227
Total vertex volume 313307 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1688    947   3359  2.605 0.653     0.122     0.044       23     2.8  BA1_exvivo
 5694   3631   9934  2.547 0.520     0.125     0.034       67     8.0  BA2_exvivo
 1295    887   1362  1.975 0.445     0.141     0.040       13     2.1  BA3a_exvivo
 3451   2108   5180  2.235 0.677     0.123     0.044       49     7.0  BA3b_exvivo
 2207   1167   3499  2.676 0.592     0.121     0.060       43     6.2  BA4a_exvivo
 1626   1032   2409  2.510 0.470     0.125     0.039       15     2.8  BA4p_exvivo
11511   7170  24280  2.977 0.603     0.115     0.038      154    18.1  BA6_exvivo
 3382   2201   7188  2.889 0.468     0.118     0.032       40     4.4  BA44_exvivo
 4816   3143   9804  2.740 0.490     0.133     0.040       76     7.7  BA45_exvivo
 4409   2971   4971  1.716 0.438     0.140     0.038       57     6.8  V1_exvivo
11107   6580  14814  2.147 0.564     0.136     0.041      155    18.1  V2_exvivo
 2523   1657   4498  2.523 0.504     0.114     0.030       23     2.9  MT_exvivo
  751    487   1978  3.270 0.644     0.123     0.050       10     1.7  perirhinal_exvivo
 1032    659   2678  3.132 0.694     0.152     0.059       21     2.4  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051359 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 317227
Total vertex volume 313307 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1072    591   2031  2.597 0.624     0.128     0.053       16     2.6  BA1_exvivo
 2403   1493   4097  2.522 0.536     0.117     0.031       25     2.9  BA2_exvivo
 1049    733   1055  1.911 0.394     0.149     0.041       10     1.9  BA3a_exvivo
 1967   1231   2443  1.927 0.513     0.118     0.041       25     3.7  BA3b_exvivo
 2197   1169   3390  2.673 0.575     0.114     0.052       37     5.7  BA4a_exvivo
 1257    801   1734  2.388 0.409     0.126     0.041       13     2.1  BA4p_exvivo
 5874   3597  12411  2.970 0.586     0.113     0.035       64     8.3  BA6_exvivo
 2113   1362   4546  2.906 0.505     0.121     0.034       28     2.8  BA44_exvivo
 1853   1201   3942  2.844 0.529     0.137     0.044       31     3.1  BA45_exvivo
 4694   3147   5343  1.726 0.440     0.140     0.038       61     7.4  V1_exvivo
 5690   3312   6803  1.993 0.514     0.138     0.045       82    10.0  V2_exvivo
  732    470   1237  2.403 0.414     0.128     0.034        8     1.0  MT_exvivo
  411    271   1069  3.322 0.547     0.113     0.031        3     0.6  perirhinal_exvivo
  604    380   1526  3.057 0.751     0.155     0.063       11     1.6  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 07:07:04 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 11873 of (11873 11879 11885 11891 11895) to complete...
Waiting for PID 11879 of (11873 11879 11885 11891 11895) to complete...
Waiting for PID 11885 of (11873 11879 11885 11891 11895) to complete...
Waiting for PID 11891 of (11873 11879 11885 11891 11895) to complete...
Waiting for PID 11895 of (11873 11879 11885 11891 11895) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1104
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 5066
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1278
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7965
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 329
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4309
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 757
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5279
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 856
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6603
mri_label2label: Done

PIDs (11873 11879 11885 11891 11895) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 11950 of (11950 11956 11962 11968) to complete...
Waiting for PID 11956 of (11950 11956 11962 11968) to complete...
Waiting for PID 11962 of (11950 11956 11962 11968) to complete...
Waiting for PID 11968 of (11950 11956 11962 11968) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 406
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4879
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1866
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14122
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1255
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8167
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1628
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6983
mri_label2label: Done

PIDs (11950 11956 11962 11968) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 12057 of (12057 12063 12069 12075 12079) to complete...
Waiting for PID 12063 of (12057 12063 12069 12075 12079) to complete...
Waiting for PID 12069 of (12057 12063 12069 12075 12079) to complete...
Waiting for PID 12075 of (12057 12063 12069 12075 12079) to complete...
Waiting for PID 12079 of (12057 12063 12069 12075 12079) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 2479
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 7206
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 4461
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12477
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1170
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 3102
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 372
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1410
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 282
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 1034
mri_label2label: Done

PIDs (12057 12063 12069 12075 12079) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12267 of (12267 12273 12279 12284 12290) to complete...
Waiting for PID 12273 of (12267 12273 12279 12284 12290) to complete...
Waiting for PID 12279 of (12267 12273 12279 12284 12290) to complete...
Waiting for PID 12284 of (12267 12273 12279 12284 12290) to complete...
Waiting for PID 12290 of (12267 12273 12279 12284 12290) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 286
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1162
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 593
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3281
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 74
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1772
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 419
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2602
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 236
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1624
mri_label2label: Done

PIDs (12267 12273 12279 12284 12290) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12385 of (12385 12391 12394 12403) to complete...
Waiting for PID 12391 of (12385 12391 12394 12403) to complete...
Waiting for PID 12394 of (12385 12391 12394 12403) to complete...
Waiting for PID 12403 of (12385 12391 12394 12403) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 171
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1660
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 923
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7882
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 142
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1154
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 251
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1429
mri_label2label: Done

PIDs (12385 12391 12394 12403) 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 0051359 --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 0051359 --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 0051359 --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 0051359 --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 0051359 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12522 of (12522 12528 12534 12540 12544) to complete...
Waiting for PID 12528 of (12522 12528 12534 12540 12544) to complete...
Waiting for PID 12534 of (12522 12528 12534 12540 12544) to complete...
Waiting for PID 12540 of (12522 12528 12534 12540 12544) to complete...
Waiting for PID 12544 of (12522 12528 12534 12540 12544) 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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 1551
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4783
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 2139
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5576
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 181
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 449
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 298
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 992
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 0051359 --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 = 0051359
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-6.0.0/0051359/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 169093
Number of reverse mapping hits = 150
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 441
mri_label2label: Done

PIDs (12522 12528 12534 12540 12544) completed and logs appended.

 mris_label2annot --s 0051359 --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-6.0.0/0051359/label
cmdline mris_label2annot --s 0051359 --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-908
machine  x86_64
user     ntraut

subject 0051359
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-6.0.0/0051359/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 118478 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051359 --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-6.0.0/0051359/label
cmdline mris_label2annot --s 0051359 --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-908
machine  x86_64
user     ntraut

subject 0051359
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-6.0.0/0051359/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 140702 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/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 0051359 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 317093
Total vertex volume 313472 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1274    654   2254  2.531 0.588     0.137     0.059       23     3.2  BA1_exvivo
 4434   2707   6504  2.453 0.490     0.114     0.033       48     5.8  BA2_exvivo
 1201    827   1212  1.931 0.484     0.134     0.034       11     1.8  BA3a_exvivo
 2635   1590   3579  2.034 0.598     0.120     0.041       29     4.8  BA3b_exvivo
 1913   1066   2922  2.474 0.501     0.121     0.050       23     4.1  BA4a_exvivo
 1426    912   2041  2.370 0.443     0.112     0.032       11     1.9  BA4p_exvivo
 9264   5830  18863  2.870 0.590     0.118     0.043      137    16.2  BA6_exvivo
 4219   2785   8421  2.771 0.483     0.118     0.030       45     5.1  BA44_exvivo
 5112   3359  10844  2.760 0.564     0.139     0.039       84     8.2  BA45_exvivo
 4687   3078   6140  1.938 0.569     0.138     0.042       57     8.1  V1_exvivo
10105   6119  14097  2.141 0.591     0.138     0.045      157    17.8  V2_exvivo
 2988   1955   5200  2.548 0.544     0.134     0.035       37     4.2  MT_exvivo
  841    522   2355  3.352 0.736     0.144     0.074       17     2.3  perirhinal_exvivo
  516    346   1670  3.555 0.779     0.158     0.074       11     1.6  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051359 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051359/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 317093
Total vertex volume 313472 (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) = 1693737 mm^3    (det: 1.150182 )
lhCtxGM: 311606.038 310553.000  diff= 1053.0  pctdiff= 0.338
rhCtxGM: 311490.000 310365.000  diff= 1125.0  pctdiff= 0.361
lhCtxWM: 253765.125 254051.000  diff= -285.9  pctdiff=-0.113
rhCtxWM: 250461.244 251940.000  diff=-1478.8  pctdiff=-0.590
SubCortGMVol  64346.000
SupraTentVol  1208711.406 (1205497.000) diff=3214.406 pctdiff=0.266
SupraTentVolNotVent  1194596.406 (1191382.000) diff=3214.406 pctdiff=0.269
BrainSegVol  1355055.000 (1352758.000) diff=2297.000 pctdiff=0.170
BrainSegVolNotVent  1337554.000 (1337813.406) diff=-259.406 pctdiff=-0.019
BrainSegVolNotVent  1337554.000
CerebellumVol 146018.000
VentChorVol   14115.000
3rd4th5thCSF   3386.000
CSFVol  1089.000, OptChiasmVol   154.000
MaskVol 1773525.000
 1011    470   1483  2.338 0.488     0.131     0.062       18     2.7  BA1_exvivo
 2734   1614   4181  2.445 0.529     0.113     0.035       33     3.8  BA2_exvivo
 1049    743    975  1.859 0.374     0.142     0.035        9     1.6  BA3a_exvivo
 2116   1296   2462  1.842 0.430     0.111     0.035       19     3.4  BA3b_exvivo
 1221    657   1778  2.377 0.512     0.132     0.063       21     3.5  BA4a_exvivo
 1190    741   1676  2.385 0.432     0.111     0.034       11     1.6  BA4p_exvivo
 5767   3567  12061  2.904 0.578     0.120     0.046       98    10.8  BA6_exvivo
  908    615   2106  2.865 0.398     0.128     0.035       12     1.3  BA44_exvivo
 1203    820   2330  2.558 0.489     0.141     0.038       18     2.0  BA45_exvivo
 4474   2962   5753  1.922 0.566     0.139     0.042       55     7.7  V1_exvivo
 5332   3134   7011  2.021 0.596     0.142     0.049       91    10.6  V2_exvivo
  437    278   1054  2.660 0.542     0.150     0.038        8     0.8  MT_exvivo
  534    316   1389  3.328 0.697     0.156     0.084       13     1.9  perirhinal_exvivo
  415    272   1002  3.483 0.799     0.128     0.064        5     1.1  entorhinal_exvivo

Started at Sat Oct 7 17:06:05 CEST 2017 
Ended   at Sun Oct 8 07:12:47 CEST 2017
#@#%# recon-all-run-time-hours 14.112
recon-all -s 0051359 finished without error at Sun Oct  8 07:12:47 CEST 2017