ABIDE_fs-6.0.0/0050111/scripts/recon-all.log

Sat Oct  7 18:03:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050111 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Olin/0050111/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050111
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-935 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   52224384   13850424    1758200          0   48827936
-/+ buffers/cache:    3396448   62678360
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:03:54-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-935  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-6.0.0/0050111

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Olin/0050111/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Olin/0050111/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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/Olin/0050111/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-6.0.0/0050111/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 18:03:57 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/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-6.0.0/0050111/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 18:04:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/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-935 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:04:07 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.26980
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26980/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.26980/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.26980/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:04:09 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.26980/nu0.mnc ./tmp.mri_nu_correct.mni.26980/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.26980/0/ -iterations 1000 -distance 50
[ntraut@tars-935:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/] [2017-10-07 18:04:10] 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.26980/0/ ./tmp.mri_nu_correct.mni.26980/nu0.mnc ./tmp.mri_nu_correct.mni.26980/nu1.imp

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Number of iterations: 47 
CV of field change: 0.000979377
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.26980/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.26980/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.26980/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 18:05:25 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 18:05:25 CEST 2017
Ended   at Sat Oct  7 18:06:06 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 18:06:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7171, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/transforms/talairach_avi.log 

TalAviQA: 0.98149
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 18:06:08 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-6.0.0/0050111/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-935 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:06:08 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.28849
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28849/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28849/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.28849/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:06:11 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.28849/nu0.mnc ./tmp.mri_nu_correct.mni.28849/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28849/0/
[ntraut@tars-935:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/] [2017-10-07 18:06:11] 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.28849/0/ ./tmp.mri_nu_correct.mni.28849/nu0.mnc ./tmp.mri_nu_correct.mni.28849/nu1.imp

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Number of iterations: 46 
CV of field change: 0.000964605
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 18:07:05 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.28849/nu1.mnc ./tmp.mri_nu_correct.mni.28849/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.28849/1/
[ntraut@tars-935:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/] [2017-10-07 18:07:05] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.28849/1/ ./tmp.mri_nu_correct.mni.28849/nu1.mnc ./tmp.mri_nu_correct.mni.28849/nu2.imp

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Number of iterations: 20 
CV of field change: 0.000962035
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.28849/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28849/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-6.0.0/0050111/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.28849/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28849/ones.mgz 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.28849/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.28849/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.28849/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28849/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28849/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.28849/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28849/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28849/input.mean.dat 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.28849/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.28849/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28849/ones.mgz --i ./tmp.mri_nu_correct.mni.28849/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28849/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28849/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.28849/ones.mgz --i ./tmp.mri_nu_correct.mni.28849/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28849/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28849/output.mean.dat 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.28849/ones.mgz
Loading ./tmp.mri_nu_correct.mni.28849/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.28849/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.28849/nu2.mnc ./tmp.mri_nu_correct.mni.28849/nu2.mnc mul 1.00410744024731221129
Saving result to './tmp.mri_nu_correct.mni.28849/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.28849/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.28849/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.28849/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 9 seconds.
mapping ( 7, 128) to ( 3, 110)
 
 
Sat Oct  7 18:08:30 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 18:08:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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
 1.02554  -0.08522   0.01626   1.00961;
 0.03247   1.01648   0.32758  -8.78342;
-0.04034  -0.29445   1.14311  -25.66072;
 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 = 20
Starting OpenSpline(): npoints = 20
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 68 (68), valley at 29 (29)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 67 (67), valley at 24 (24)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 4 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 18:10:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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=8.0
skull bounding box = (44, 39, 21) --> (211, 198, 220)
using (100, 92, 121) as brain centroid...
mean wm in atlas = 108, using box (79,72,96) --> (120, 111,145) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 6.8
after smoothing, mri peak at 106, scaling input intensities by 1.019
scaling channel 0 by 1.01887
initial log_p = -4.231
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.249402 @ (0.000, 0.000, 0.000)
max log p =    -4.249402 @ (0.000, 0.000, 0.000)
max log p =    -4.168948 @ (-2.273, -2.273, -6.818)
max log p =    -4.168948 @ (0.000, 0.000, 0.000)
max log p =    -4.164805 @ (-0.568, -2.841, -0.568)
max log p =    -4.163926 @ (0.852, 0.852, -0.852)
Found translation: (-2.0, -4.3, -8.2): log p = -4.164
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.952, old_max_log_p =-4.164 (thresh=-4.2)
 0.99144  -0.03885   0.14499  -12.49159;
 0.00000   1.19413   0.31997  -63.31590;
-0.12074  -0.27296   1.01871   44.82016;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.931, old_max_log_p =-3.952 (thresh=-3.9)
 0.99872  -0.00289   0.01078  -2.68823;
 0.00000   1.19413   0.31997  -63.31590;
 0.00971  -0.27570   1.02892   27.45570;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.931, old_max_log_p =-3.931 (thresh=-3.9)
 0.99872  -0.00289   0.01078  -2.68823;
 0.00000   1.19413   0.31997  -63.31590;
 0.00971  -0.27570   1.02892   27.45570;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.862, old_max_log_p =-3.931 (thresh=-3.9)
 1.01362   0.05764   0.10297  -22.06068;
-0.06836   1.20517   0.35530  -60.47473;
-0.05661  -0.31807   1.03370   39.46045;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.856, old_max_log_p =-3.862 (thresh=-3.9)
 1.01531   0.01818   0.09129  -17.22652;
-0.03582   1.22903   0.36520  -69.06159;
-0.05661  -0.31807   1.03370   39.46045;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.852, old_max_log_p =-3.856 (thresh=-3.9)
 0.99229   0.05025   0.13288  -21.88663;
-0.06517   1.24619   0.29254  -60.96199;
-0.09374  -0.24193   1.07154   27.10993;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.827, old_max_log_p =-3.852 (thresh=-3.8)
 0.99600   0.05467   0.11568  -21.82857;
-0.06669   1.24207   0.31003  -62.30613;
-0.07615  -0.26051   1.06489   29.28183;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.827, old_max_log_p =-3.827 (thresh=-3.8)
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 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
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.827 (old=-4.231)
transform before final EM align:
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 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
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.3  tol 0.000000
final transform:
 0.99717   0.05473   0.11582  -22.00048;
-0.06607   1.24416   0.30131  -62.10013;
-0.07660  -0.25004   1.06614   27.70930;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1529.284513
mri_em_register stimesec    1.827722
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   157057
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    2792
mri_em_register ru_nivcsw   3362
registration took 13 minutes and 19 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=127 y=120 z=113 r=68
      first estimation of the main basin volume: 1365944 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        16 found in the rest of the brain 
      global maximum in x=109, y=111, z=81, Imax=255
      CSF=17, 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=8397810156 voxels, voxel volume =1.000 
                     = 8397810156 mmm3 = 8397810.176 cm3
done.
PostAnalyze...Basin Prior
 141 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=127,y=124, z=110, r=10065 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=23, CSF_MAX=69 , nb = 41789
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=69 , nb = -1036594145
  LEFT_CER     CSF_MIN=0, CSF_intensity=25, CSF_MAX=61 , nb = -1047797344
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=23, CSF_MAX=69 , nb = -1068256090
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=23, CSF_MAX=75 , nb = 1078404872
    OTHER      CSF_MIN=9, CSF_intensity=23, CSF_MAX=54 , nb = 1076288774
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    69,      49,        40,   62
  after  analyzing :    42,      49,        49,   52
   RIGHT_CER   
  before analyzing :    69,      45,        35,   67
  after  analyzing :    24,      45,        45,   50
   LEFT_CER    
  before analyzing :    61,      49,        41,   69
  after  analyzing :    42,      49,        49,   54
  RIGHT_BRAIN  
  before analyzing :    69,      49,        39,   62
  after  analyzing :    42,      49,        49,   52
  LEFT_BRAIN   
  before analyzing :    75,      51,        43,   62
  after  analyzing :    43,      51,        51,   53
     OTHER     
  before analyzing :    54,      70,        79,   95
  after  analyzing :    54,      76,        79,   80
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...70 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 69.060, std = 8.081

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.40, sigma = 5.53
      after  rotation: sse = 3.40, sigma = 5.53
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  3.58, its var is  4.78   
      before Erosion-Dilatation  0.59% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1614882 voxels, voxel volume = 1.000 mm3
           = 1614882 mmm3 = 1614.882 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    27.380837
mri_watershed stimesec    0.412937
mri_watershed ru_maxrss   827332
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   214158
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2648
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1211
mri_watershed ru_nivcsw   782
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:24:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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=29.1
skull bounding box = (56, 65, 39) --> (197, 197, 201)
using (103, 109, 120) as brain centroid...
mean wm in atlas = 107, using box (86,93,100) --> (120, 125,139) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 6.5
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -3.915
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.927553 @ (0.000, 0.000, 0.000)
max log p =    -3.859186 @ (-4.545, -4.545, -13.636)
max log p =    -3.768482 @ (2.273, 2.273, 6.818)
max log p =    -3.738747 @ (1.136, -1.136, 1.136)
max log p =    -3.735733 @ (-0.568, 0.568, -1.705)
max log p =    -3.735733 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -2.8, -7.4): log p = -3.736
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.513, old_max_log_p =-3.736 (thresh=-3.7)
 1.00000   0.00000   0.00000  -1.70455;
 0.00000   1.11081   0.29764  -49.95796;
 0.00000  -0.25882   0.96593   35.56806;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.513, old_max_log_p =-3.513 (thresh=-3.5)
 1.00000   0.00000   0.00000  -1.70455;
 0.00000   1.11081   0.29764  -49.95796;
 0.00000  -0.25882   0.96593   35.56806;
 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=-3.334, old_max_log_p =-3.513 (thresh=-3.5)
 0.99732   0.01943   0.07288  -11.46624;
-0.03204   1.08995   0.28988  -44.30904;
-0.06786  -0.26795   1.00000   38.06842;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.334, old_max_log_p =-3.334 (thresh=-3.3)
 0.99732   0.01943   0.07288  -11.46624;
-0.03204   1.08995   0.28988  -44.30904;
-0.06786  -0.26795   1.00000   38.06842;
 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=-3.302, old_max_log_p =-3.334 (thresh=-3.3)
 0.99376   0.01498   0.08894  -13.16503;
-0.03205   1.09002   0.28960  -43.36435;
-0.08435  -0.26826   0.99991   40.68341;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.296, old_max_log_p =-3.302 (thresh=-3.3)
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.296, old_max_log_p =-3.296 (thresh=-3.3)
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 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
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.296 (old=-3.915)
transform before final EM align:
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 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
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.8  tol 0.000000
final transform:
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1172.411766
mri_em_register stimesec    1.728737
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   158955
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    3497
mri_em_register ru_nivcsw   3230
registration took 10 minutes and 9 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:34:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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=29.1
skull bounding box = (56, 65, 39) --> (197, 197, 201)
using (103, 109, 120) as brain centroid...
mean wm in atlas = 107, using box (86,93,100) --> (120, 125,139) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 6.5
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
 0.99608   0.01502   0.08914  -13.49293;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 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 (126, 65, 38) --> (195, 171, 195)
Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0
0 of 10 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 64, 34) --> (132, 165, 194)
Right_Cerebral_White_Matter: limiting intensities to 105.0 --> 132.0
0 of 9 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 148, 67) --> (179, 186, 118)
Left_Cerebellum_White_Matter: limiting intensities to 109.0 --> 132.0
6 of 8 (75.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 148, 61) --> (131, 184, 115)
Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0
8 of 17 (47.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 134, 98) --> (146, 197, 128)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 26 (0.0%) samples deleted
using 70 total control points for intensity normalization...
bias field = 0.857 +- 0.083
0 of 56 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 65, 38) --> (195, 171, 195)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 110 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 64, 34) --> (132, 165, 194)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 118 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 148, 67) --> (179, 186, 118)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
11 of 57 (19.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 148, 61) --> (131, 184, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
36 of 73 (49.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 134, 98) --> (146, 197, 128)
Brain_Stem: limiting intensities to 88.0 --> 132.0
42 of 106 (39.6%) samples deleted
using 464 total control points for intensity normalization...
bias field = 0.985 +- 0.097
0 of 367 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 65, 38) --> (195, 171, 195)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 235 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 64, 34) --> (132, 165, 194)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
0 of 219 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 148, 67) --> (179, 186, 118)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
50 of 79 (63.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 148, 61) --> (131, 184, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
47 of 56 (83.9%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 134, 98) --> (146, 197, 128)
Brain_Stem: limiting intensities to 88.0 --> 132.0
154 of 189 (81.5%) samples deleted
using 778 total control points for intensity normalization...
bias field = 0.998 +- 0.058
0 of 523 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 49 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:36:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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) = 1.17 (predicted orig area = 6.8)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.779, neg=0, invalid=762
0001: dt=186.187440, rms=0.715 (8.175%), neg=0, invalid=762
0002: dt=202.088670, rms=0.699 (2.227%), neg=0, invalid=762
0003: dt=169.967213, rms=0.692 (1.083%), neg=0, invalid=762
0004: dt=295.936000, rms=0.686 (0.777%), neg=0, invalid=762
0005: dt=133.565217, rms=0.683 (0.527%), neg=0, invalid=762
0006: dt=517.888000, rms=0.679 (0.534%), neg=0, invalid=762
0007: dt=129.472000, rms=0.677 (0.377%), neg=0, invalid=762
0008: dt=517.888000, rms=0.675 (0.243%), neg=0, invalid=762
0009: dt=517.888000, rms=0.675 (-1.739%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.676, neg=0, invalid=762
0010: dt=129.472000, rms=0.673 (0.441%), neg=0, invalid=762
0011: dt=517.888000, rms=0.670 (0.319%), neg=0, invalid=762
0012: dt=517.888000, rms=0.669 (0.243%), neg=0, invalid=762
0013: dt=517.888000, rms=0.669 (-0.279%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.671, neg=0, invalid=762
0014: dt=207.877238, rms=0.655 (2.389%), neg=0, invalid=762
0015: dt=99.059618, rms=0.646 (1.391%), neg=0, invalid=762
0016: dt=90.594595, rms=0.641 (0.760%), neg=0, invalid=762
0017: dt=85.134884, rms=0.638 (0.511%), neg=0, invalid=762
0018: dt=103.680000, rms=0.635 (0.467%), neg=0, invalid=762
0019: dt=69.706024, rms=0.632 (0.375%), neg=0, invalid=762
0020: dt=145.152000, rms=0.630 (0.405%), neg=0, invalid=762
0021: dt=36.288000, rms=0.628 (0.254%), neg=0, invalid=762
0022: dt=331.776000, rms=0.625 (0.559%), neg=0, invalid=762
0023: dt=72.000000, rms=0.622 (0.418%), neg=0, invalid=762
0024: dt=36.288000, rms=0.621 (0.140%), neg=0, invalid=762
0025: dt=36.288000, rms=0.621 (0.074%), neg=0, invalid=762
0026: dt=36.288000, rms=0.620 (0.110%), neg=0, invalid=762
0027: dt=36.288000, rms=0.619 (0.160%), neg=0, invalid=762
0028: dt=36.288000, rms=0.618 (0.186%), neg=0, invalid=762
0029: dt=36.288000, rms=0.617 (0.217%), neg=0, invalid=762
0030: dt=36.288000, rms=0.615 (0.231%), neg=0, invalid=762
0031: dt=36.288000, rms=0.614 (0.244%), neg=0, invalid=762
0032: dt=36.288000, rms=0.612 (0.254%), neg=0, invalid=762
0033: dt=36.288000, rms=0.611 (0.241%), neg=0, invalid=762
0034: dt=36.288000, rms=0.609 (0.234%), neg=0, invalid=762
0035: dt=36.288000, rms=0.608 (0.222%), neg=0, invalid=762
0036: dt=36.288000, rms=0.607 (0.200%), neg=0, invalid=762
0037: dt=36.288000, rms=0.606 (0.176%), neg=0, invalid=762
0038: dt=36.288000, rms=0.605 (0.155%), neg=0, invalid=762
0039: dt=36.288000, rms=0.604 (0.150%), neg=0, invalid=762
0040: dt=36.288000, rms=0.603 (0.136%), neg=0, invalid=762
0041: dt=36.288000, rms=0.602 (0.123%), neg=0, invalid=762
0042: dt=36.288000, rms=0.601 (0.107%), neg=0, invalid=762
0043: dt=82.944000, rms=0.601 (0.004%), neg=0, invalid=762
0044: dt=82.944000, rms=0.601 (0.027%), neg=0, invalid=762
0045: dt=82.944000, rms=0.601 (0.017%), neg=0, invalid=762
0046: dt=82.944000, rms=0.601 (0.014%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.602, neg=0, invalid=762
0047: dt=99.555556, rms=0.599 (0.421%), neg=0, invalid=762
0048: dt=82.944000, rms=0.599 (0.100%), neg=0, invalid=762
0049: dt=82.944000, rms=0.598 (0.073%), neg=0, invalid=762
0050: dt=82.944000, rms=0.598 (0.061%), neg=0, invalid=762
0051: dt=82.944000, rms=0.598 (0.024%), neg=0, invalid=762
0052: dt=82.944000, rms=0.597 (0.053%), neg=0, invalid=762
0053: dt=25.920000, rms=0.597 (0.005%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.616, neg=0, invalid=762
0054: dt=6.400000, rms=0.616 (0.134%), neg=0, invalid=762
0055: dt=2.000000, rms=0.616 (0.001%), neg=0, invalid=762
0056: dt=2.000000, rms=0.616 (0.001%), neg=0, invalid=762
0057: dt=2.000000, rms=0.616 (-0.015%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.616, neg=0, invalid=762
0058: dt=0.000000, rms=0.616 (0.095%), neg=0, invalid=762
0059: dt=0.000000, rms=0.616 (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=0.666, neg=0, invalid=762
0060: dt=5.630901, rms=0.651 (2.222%), neg=0, invalid=762
0061: dt=2.628571, rms=0.651 (0.068%), neg=0, invalid=762
0062: dt=2.628571, rms=0.651 (-0.026%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.652, neg=0, invalid=762
0063: dt=0.000000, rms=0.651 (0.081%), neg=0, invalid=762
0064: dt=0.000000, rms=0.651 (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=0.701, neg=0, invalid=762
0065: dt=1.024000, rms=0.698 (0.404%), neg=0, invalid=762
0066: dt=1.853448, rms=0.695 (0.553%), neg=0, invalid=762
0067: dt=1.024000, rms=0.694 (0.078%), neg=0, invalid=762
0068: dt=1.024000, rms=0.693 (0.144%), neg=0, invalid=762
0069: dt=1.024000, rms=0.693 (0.045%), neg=0, invalid=762
0070: dt=1.024000, rms=0.693 (-0.197%), neg=0, invalid=762
0071: dt=0.000000, rms=0.693 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.693, neg=0, invalid=762
0072: dt=1.280000, rms=0.692 (0.167%), neg=0, invalid=762
0073: dt=0.448000, rms=0.692 (0.017%), neg=0, invalid=762
0074: dt=0.448000, rms=0.692 (0.007%), neg=0, invalid=762
0075: dt=0.448000, rms=0.692 (0.000%), neg=0, invalid=762
0076: dt=0.448000, rms=0.692 (-0.013%), 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=0.663, neg=0, invalid=762
0077: dt=0.803319, rms=0.647 (2.433%), neg=0, invalid=762
0078: dt=0.080000, rms=0.646 (0.141%), neg=0, invalid=762
0079: dt=0.080000, rms=0.646 (-0.084%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.647, neg=0, invalid=762
0080: dt=0.028000, rms=0.646 (0.099%), neg=0, invalid=762
0081: dt=0.016000, rms=0.646 (0.002%), neg=0, invalid=762
0082: dt=0.016000, rms=0.646 (-0.002%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.06718 (21)
Left_Lateral_Ventricle (4): linear fit = 1.24 x + 0.0 (887 voxels, overlap=0.713)
Left_Lateral_Ventricle (4): linear fit = 1.24 x + 0.0 (887 voxels, peak = 25), gca=24.7
gca peak = 0.15565 (16)
mri peak = 0.06668 (47)
Right_Lateral_Ventricle (43): linear fit = 2.39 x + 0.0 (434 voxels, overlap=0.212)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (434 voxels, peak = 38), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.08386 (93)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (834 voxels, overlap=0.999)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (834 voxels, peak = 93), gca=92.6
gca peak = 0.20183 (93)
mri peak = 0.07848 (83)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (654 voxels, overlap=0.236)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (654 voxels, peak = 82), gca=82.3
gca peak = 0.21683 (55)
mri peak = 0.06776 (71)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (634 voxels, overlap=0.358)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (634 voxels, peak = 64), gca=63.5
gca peak = 0.30730 (58)
mri peak = 0.08067 (67)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (830 voxels, overlap=0.589)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (830 voxels, peak = 65), gca=64.7
gca peak = 0.11430 (101)
mri peak = 0.06724 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (56094 voxels, overlap=0.748)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (56094 voxels, peak = 106), gca=105.5
gca peak = 0.12076 (102)
mri peak = 0.06824 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54569 voxels, overlap=0.719)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54569 voxels, peak = 107), gca=106.6
gca peak = 0.14995 (59)
mri peak = 0.04521 (63)
Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (18849 voxels, overlap=0.946)
Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (18849 voxels, peak = 63), gca=63.4
gca peak = 0.15082 (58)
mri peak = 0.04622 (60)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (18639 voxels, overlap=0.979)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (18639 voxels, peak = 59), gca=59.4
gca peak = 0.14161 (67)
mri peak = 0.08533 (76)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (812 voxels, overlap=0.420)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (812 voxels, peak = 76), gca=76.0
gca peak = 0.15243 (71)
mri peak = 0.07072 (80)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (778 voxels, overlap=0.579)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (778 voxels, peak = 77), gca=77.0
gca peak = 0.13336 (57)
mri peak = 0.04041 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19426 voxels, overlap=0.960)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19426 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.04219 (59)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (23297 voxels, overlap=0.964)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (23297 voxels, peak = 59), gca=58.5
gca peak = 0.18181 (84)
mri peak = 0.06280 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7574 voxels, overlap=0.928)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7574 voxels, peak = 85), gca=85.3
gca peak = 0.20573 (83)
mri peak = 0.06744 (79)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6879 voxels, overlap=0.981)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6879 voxels, peak = 82), gca=81.8
gca peak = 0.21969 (57)
mri peak = 0.09222 (66)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (401 voxels, overlap=0.288)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (401 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.07611 (67)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (468 voxels, overlap=0.799)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (468 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.05236 (92)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5487 voxels, overlap=0.852)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5487 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.06474 (84)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4200 voxels, overlap=0.928)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4200 voxels, peak = 85), gca=85.1
gca peak = 0.13399 (79)
mri peak = 0.06670 (80)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1847 voxels, overlap=0.921)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1847 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.07132 (82)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2183 voxels, overlap=0.913)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2183 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.13049 (82)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (11432 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (11432 voxels, peak = 85), gca=85.2
gca peak = 0.13281 (86)
mri peak = 0.07883 (88)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1061 voxels, overlap=0.724)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1061 voxels, peak = 89), gca=89.0
gca peak = 0.12801 (89)
mri peak = 0.07091 (91)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1183 voxels, overlap=0.850)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1183 voxels, peak = 91), gca=91.2
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.13926 (19)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (317 voxels, overlap=0.684)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (317 voxels, peak = 20), gca=20.5
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 1.10 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 1.24 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=0.652, neg=0, invalid=762
0083: dt=129.472000, rms=0.646 (0.918%), neg=0, invalid=762
0084: dt=295.936000, rms=0.642 (0.586%), neg=0, invalid=762
0085: dt=110.976000, rms=0.641 (0.182%), neg=0, invalid=762
0086: dt=369.920000, rms=0.639 (0.325%), neg=0, invalid=762
0087: dt=92.480000, rms=0.638 (0.139%), neg=0, invalid=762
0088: dt=1183.744000, rms=0.636 (0.370%), neg=0, invalid=762
0089: dt=92.480000, rms=0.634 (0.212%), neg=0, invalid=762
0090: dt=517.888000, rms=0.633 (0.130%), neg=0, invalid=762
0091: dt=73.984000, rms=0.633 (0.069%), neg=0, invalid=762
0092: dt=887.808000, rms=0.632 (0.129%), neg=0, invalid=762
0093: dt=129.472000, rms=0.632 (0.103%), neg=0, invalid=762
0094: dt=129.472000, rms=0.631 (0.033%), neg=0, invalid=762
0095: dt=129.472000, rms=0.631 (0.036%), neg=0, invalid=762
0096: dt=129.472000, rms=0.631 (0.055%), neg=0, invalid=762
0097: dt=129.472000, rms=0.630 (0.066%), neg=0, invalid=762
0098: dt=129.472000, rms=0.630 (0.079%), neg=0, invalid=762
0099: dt=129.472000, rms=0.629 (0.099%), neg=0, invalid=762
0100: dt=129.472000, rms=0.629 (0.091%), neg=0, invalid=762
0101: dt=129.472000, rms=0.628 (0.088%), neg=0, invalid=762
0102: dt=129.472000, rms=0.628 (0.083%), neg=0, invalid=762
0103: dt=129.472000, rms=0.627 (0.083%), neg=0, invalid=762
0104: dt=129.472000, rms=0.627 (0.081%), neg=0, invalid=762
0105: dt=129.472000, rms=0.626 (0.069%), neg=0, invalid=762
0106: dt=129.472000, rms=0.626 (0.060%), neg=0, invalid=762
0107: dt=129.472000, rms=0.625 (0.057%), neg=0, invalid=762
0108: dt=129.472000, rms=0.625 (0.059%), neg=0, invalid=762
0109: dt=129.472000, rms=0.625 (0.054%), neg=0, invalid=762
0110: dt=129.472000, rms=0.624 (0.051%), neg=0, invalid=762
0111: dt=129.472000, rms=0.624 (0.051%), neg=0, invalid=762
0112: dt=129.472000, rms=0.624 (0.059%), neg=0, invalid=762
0113: dt=129.472000, rms=0.623 (0.060%), neg=0, invalid=762
0114: dt=129.472000, rms=0.623 (0.055%), neg=0, invalid=762
0115: dt=129.472000, rms=0.623 (0.053%), neg=0, invalid=762
0116: dt=129.472000, rms=0.622 (0.056%), neg=0, invalid=762
0117: dt=129.472000, rms=0.622 (0.058%), neg=0, invalid=762
0118: dt=129.472000, rms=0.622 (0.053%), neg=0, invalid=762
0119: dt=129.472000, rms=0.621 (0.048%), neg=0, invalid=762
0120: dt=129.472000, rms=0.621 (0.048%), neg=0, invalid=762
0121: dt=129.472000, rms=0.621 (0.051%), neg=0, invalid=762
0122: dt=129.472000, rms=0.620 (0.051%), neg=0, invalid=762
0123: dt=129.472000, rms=0.620 (0.045%), neg=0, invalid=762
0124: dt=129.472000, rms=0.620 (0.037%), neg=0, invalid=762
0125: dt=129.472000, rms=0.620 (0.040%), neg=0, invalid=762
0126: dt=129.472000, rms=0.619 (0.042%), neg=0, invalid=762
0127: dt=129.472000, rms=0.619 (0.039%), neg=0, invalid=762
0128: dt=129.472000, rms=0.619 (0.033%), neg=0, invalid=762
0129: dt=129.472000, rms=0.619 (0.034%), neg=0, invalid=762
0130: dt=129.472000, rms=0.618 (0.034%), neg=0, invalid=762
0131: dt=129.472000, rms=0.618 (0.030%), neg=0, invalid=762
0132: dt=129.472000, rms=0.618 (0.023%), neg=0, invalid=762
0133: dt=129.472000, rms=0.618 (0.022%), neg=0, invalid=762
0134: dt=1183.744000, rms=0.618 (0.030%), neg=0, invalid=762
0135: dt=32.368000, rms=0.618 (0.007%), neg=0, invalid=762
0136: dt=32.368000, rms=0.618 (0.001%), neg=0, invalid=762
0137: dt=32.368000, rms=0.618 (-0.006%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.618, neg=0, invalid=762
0138: dt=129.472000, rms=0.617 (0.155%), neg=0, invalid=762
0139: dt=517.888000, rms=0.617 (0.099%), neg=0, invalid=762
0140: dt=369.920000, rms=0.616 (0.089%), neg=0, invalid=762
0141: dt=129.472000, rms=0.616 (0.022%), neg=0, invalid=762
0142: dt=129.472000, rms=0.616 (0.001%), neg=0, invalid=762
0143: dt=129.472000, rms=0.616 (0.009%), neg=0, invalid=762
0144: dt=129.472000, rms=0.616 (0.027%), neg=0, invalid=762
0145: dt=129.472000, rms=0.615 (0.039%), neg=0, invalid=762
0146: dt=129.472000, rms=0.615 (0.040%), neg=0, invalid=762
0147: dt=129.472000, rms=0.615 (0.033%), neg=0, invalid=762
0148: dt=129.472000, rms=0.615 (0.034%), neg=0, invalid=762
0149: dt=129.472000, rms=0.615 (0.033%), neg=0, invalid=762
0150: dt=129.472000, rms=0.614 (0.027%), neg=0, invalid=762
0151: dt=129.472000, rms=0.614 (0.019%), neg=0, invalid=762
0152: dt=129.472000, rms=0.614 (0.022%), neg=0, invalid=762
0153: dt=129.472000, rms=0.614 (0.030%), neg=0, invalid=762
0154: dt=129.472000, rms=0.614 (0.030%), neg=0, invalid=762
0155: dt=129.472000, rms=0.614 (0.020%), neg=0, invalid=762
0156: dt=129.472000, rms=0.614 (0.014%), neg=0, invalid=762
0157: dt=517.888000, rms=0.614 (0.015%), neg=0, invalid=762
0158: dt=0.017340, rms=0.614 (0.001%), neg=0, invalid=762
0159: dt=0.017340, rms=0.614 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.615, neg=0, invalid=762
0160: dt=102.082645, rms=0.612 (0.472%), neg=0, invalid=762
0161: dt=179.764706, rms=0.608 (0.664%), neg=0, invalid=762
0162: dt=68.266667, rms=0.605 (0.413%), neg=0, invalid=762
0163: dt=82.944000, rms=0.603 (0.328%), neg=0, invalid=762
0164: dt=69.647059, rms=0.602 (0.266%), neg=0, invalid=762
0165: dt=98.868966, rms=0.600 (0.258%), neg=0, invalid=762
0166: dt=36.288000, rms=0.599 (0.192%), neg=0, invalid=762
0167: dt=580.608000, rms=0.593 (1.059%), neg=0, invalid=762
0168: dt=36.288000, rms=0.591 (0.265%), neg=0, invalid=762
0169: dt=145.152000, rms=0.590 (0.220%), neg=0, invalid=762
0170: dt=36.288000, rms=0.589 (0.108%), neg=0, invalid=762
0171: dt=580.608000, rms=0.586 (0.492%), neg=0, invalid=762
0172: dt=62.208000, rms=0.585 (0.319%), neg=0, invalid=762
0173: dt=124.416000, rms=0.584 (0.128%), neg=0, invalid=762
0174: dt=36.288000, rms=0.583 (0.066%), neg=0, invalid=762
0175: dt=580.608000, rms=0.581 (0.392%), neg=0, invalid=762
0176: dt=36.288000, rms=0.580 (0.166%), neg=0, invalid=762
0177: dt=145.152000, rms=0.579 (0.128%), neg=0, invalid=762
0178: dt=82.944000, rms=0.579 (0.053%), neg=0, invalid=762
0179: dt=82.944000, rms=0.579 (0.066%), neg=0, invalid=762
0180: dt=82.944000, rms=0.578 (0.063%), neg=0, invalid=762
0181: dt=62.208000, rms=0.578 (0.050%), neg=0, invalid=762
0182: dt=145.152000, rms=0.578 (0.076%), neg=0, invalid=762
0183: dt=36.288000, rms=0.577 (0.056%), neg=0, invalid=762
0184: dt=1327.104000, rms=0.575 (0.425%), neg=0, invalid=762
0185: dt=63.255814, rms=0.573 (0.353%), neg=0, invalid=762
0186: dt=36.288000, rms=0.572 (0.090%), neg=0, invalid=762
0187: dt=497.664000, rms=0.572 (0.140%), neg=0, invalid=762
0188: dt=36.288000, rms=0.571 (0.099%), neg=0, invalid=762
0189: dt=103.680000, rms=0.571 (0.037%), neg=0, invalid=762
0190: dt=103.680000, rms=0.570 (0.061%), neg=0, invalid=762
0191: dt=103.680000, rms=0.570 (0.087%), neg=0, invalid=762
0192: dt=103.680000, rms=0.569 (0.081%), neg=0, invalid=762
0193: dt=103.680000, rms=0.569 (0.145%), neg=0, invalid=762
0194: dt=103.680000, rms=0.568 (0.171%), neg=0, invalid=762
0195: dt=103.680000, rms=0.567 (0.175%), neg=0, invalid=762
0196: dt=103.680000, rms=0.567 (0.021%), neg=0, invalid=762
0197: dt=103.680000, rms=0.566 (0.066%), neg=0, invalid=762
0198: dt=103.680000, rms=0.566 (0.048%), neg=0, invalid=762
0199: dt=103.680000, rms=0.566 (0.062%), neg=0, invalid=762
0200: dt=25.920000, rms=0.565 (0.006%), neg=0, invalid=762
0201: dt=12.960000, rms=0.565 (0.005%), neg=0, invalid=762
0202: dt=2.268000, rms=0.565 (0.000%), neg=0, invalid=762
0203: dt=1.134000, rms=0.565 (0.000%), neg=0, invalid=762
0204: dt=0.004430, rms=0.565 (0.000%), neg=0, invalid=762
0205: dt=0.002215, rms=0.565 (0.000%), neg=0, invalid=762
0206: dt=0.000138, rms=0.565 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.566, neg=0, invalid=762
0207: dt=118.153846, rms=0.563 (0.486%), neg=0, invalid=762
0208: dt=103.680000, rms=0.562 (0.203%), neg=0, invalid=762
0209: dt=82.944000, rms=0.562 (0.105%), neg=0, invalid=762
0210: dt=145.152000, rms=0.561 (0.135%), neg=0, invalid=762
0211: dt=62.208000, rms=0.560 (0.069%), neg=0, invalid=762
0212: dt=145.152000, rms=0.560 (0.102%), neg=0, invalid=762
0213: dt=62.208000, rms=0.560 (0.036%), neg=0, invalid=762
0214: dt=62.208000, rms=0.559 (0.049%), neg=0, invalid=762
0215: dt=62.208000, rms=0.559 (0.060%), neg=0, invalid=762
0216: dt=62.208000, rms=0.559 (0.084%), neg=0, invalid=762
0217: dt=62.208000, rms=0.558 (0.095%), neg=0, invalid=762
0218: dt=62.208000, rms=0.557 (0.102%), neg=0, invalid=762
0219: dt=62.208000, rms=0.557 (0.091%), neg=0, invalid=762
0220: dt=62.208000, rms=0.556 (0.094%), neg=0, invalid=762
0221: dt=62.208000, rms=0.556 (0.100%), neg=0, invalid=762
0222: dt=62.208000, rms=0.555 (0.098%), neg=0, invalid=762
0223: dt=62.208000, rms=0.555 (0.095%), neg=0, invalid=762
0224: dt=62.208000, rms=0.554 (0.091%), neg=0, invalid=762
0225: dt=62.208000, rms=0.554 (0.089%), neg=0, invalid=762
0226: dt=62.208000, rms=0.553 (0.099%), neg=0, invalid=762
0227: dt=62.208000, rms=0.553 (0.094%), neg=0, invalid=762
0228: dt=62.208000, rms=0.552 (0.099%), neg=0, invalid=762
0229: dt=31.104000, rms=0.552 (0.013%), neg=0, invalid=762
0230: dt=15.552000, rms=0.552 (0.003%), neg=0, invalid=762
0231: dt=2.268000, rms=0.552 (0.001%), neg=0, invalid=762
0232: dt=0.283500, rms=0.552 (0.000%), neg=0, invalid=762
0233: dt=0.141750, rms=0.552 (0.000%), neg=0, invalid=762
0234: dt=0.035437, rms=0.552 (0.000%), neg=0, invalid=762
0235: dt=0.017719, rms=0.552 (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=0.560, neg=0, invalid=762
0236: dt=0.175000, rms=0.559 (0.108%), neg=0, invalid=762
0237: dt=0.043750, rms=0.559 (0.001%), neg=0, invalid=762
0238: dt=0.043750, rms=0.559 (0.001%), neg=0, invalid=762
0239: dt=0.021875, rms=0.559 (0.001%), neg=0, invalid=762
0240: dt=0.010937, rms=0.559 (0.000%), neg=0, invalid=762
0241: dt=0.001250, rms=0.559 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.560, neg=0, invalid=762
0242: dt=0.000000, rms=0.559 (0.102%), neg=0, invalid=762
0243: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=762
0244: dt=0.000977, rms=0.559 (0.000%), neg=0, invalid=762
0245: dt=0.000122, rms=0.559 (0.000%), neg=0, invalid=762
0246: dt=0.000015, rms=0.559 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.582, neg=0, invalid=762
0247: dt=0.000000, rms=0.581 (0.095%), neg=0, invalid=762
0248: dt=0.000000, rms=0.581 (0.000%), neg=0, invalid=762
0249: dt=0.000001, rms=0.581 (0.000%), neg=0, invalid=762
0250: dt=0.000000, rms=0.581 (0.000%), neg=0, invalid=762
0251: dt=0.000000, rms=0.581 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.582, neg=0, invalid=762
0252: dt=0.000000, rms=0.581 (0.095%), neg=0, invalid=762
0253: dt=0.000000, rms=0.581 (0.000%), neg=0, invalid=762
0254: dt=0.000000, rms=0.581 (-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=0.626, neg=0, invalid=762
0255: dt=1.792000, rms=0.608 (2.751%), neg=0, invalid=762
0256: dt=7.800995, rms=0.585 (3.908%), neg=0, invalid=762
0257: dt=0.000000, rms=0.585 (0.004%), neg=0, invalid=762
0258: dt=0.100000, rms=0.585 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.585, neg=0, invalid=762
0259: dt=1.792000, rms=0.583 (0.361%), neg=0, invalid=762
0260: dt=4.096000, rms=0.581 (0.305%), neg=0, invalid=762
0261: dt=7.168000, rms=0.578 (0.535%), neg=0, invalid=762
0262: dt=1.792000, rms=0.578 (0.018%), neg=0, invalid=762
0263: dt=1.792000, rms=0.578 (0.034%), neg=0, invalid=762
0264: dt=1.792000, rms=0.577 (0.049%), neg=0, invalid=762
0265: dt=1.792000, rms=0.577 (0.061%), neg=0, invalid=762
0266: dt=1.792000, rms=0.577 (0.019%), neg=0, invalid=762
0267: dt=1.792000, rms=0.577 (-0.050%), neg=0, invalid=762
0268: dt=6.144000, rms=0.577 (0.030%), neg=0, invalid=762
0269: dt=5.120000, rms=0.577 (0.047%), neg=0, invalid=762
0270: dt=1.792000, rms=0.576 (0.041%), 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=0.563, neg=0, invalid=762
0271: dt=0.448000, rms=0.548 (2.754%), neg=0, invalid=762
0272: dt=1.536000, rms=0.533 (2.629%), neg=0, invalid=762
0273: dt=0.000000, rms=0.533 (-0.004%), neg=0, invalid=762
0274: dt=0.050000, rms=0.533 (-0.018%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.534, neg=0, invalid=762
0275: dt=0.448000, rms=0.528 (1.013%), neg=0, invalid=762
0276: dt=0.448000, rms=0.528 (0.087%), neg=0, invalid=762
0277: dt=0.448000, rms=0.527 (0.105%), neg=0, invalid=762
0278: dt=0.448000, rms=0.527 (0.060%), neg=0, invalid=762
0279: dt=0.448000, rms=0.527 (0.062%), neg=0, invalid=762
0280: dt=0.448000, rms=0.527 (0.047%), neg=0, invalid=762
0281: dt=0.448000, rms=0.526 (0.052%), neg=0, invalid=762
0282: dt=0.448000, rms=0.526 (0.088%), neg=0, invalid=762
0283: dt=0.448000, rms=0.525 (0.110%), neg=0, invalid=762
0284: dt=0.448000, rms=0.525 (0.131%), neg=0, invalid=762
0285: dt=0.448000, rms=0.524 (0.138%), neg=0, invalid=762
0286: dt=0.448000, rms=0.523 (0.127%), neg=0, invalid=762
0287: dt=0.448000, rms=0.523 (0.110%), neg=0, invalid=762
0288: dt=0.448000, rms=0.522 (0.098%), neg=0, invalid=762
0289: dt=0.448000, rms=0.522 (-0.008%), neg=0, invalid=762
0290: dt=0.000000, rms=0.522 (0.000%), 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=0.520, neg=0, invalid=762
0291: dt=32.368000, rms=0.519 (0.120%), neg=0, invalid=762
0292: dt=8.092000, rms=0.519 (0.000%), neg=0, invalid=762
0293: dt=8.092000, rms=0.519 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0294: dt=129.472000, rms=0.519 (0.144%), neg=0, invalid=762
0295: dt=129.472000, rms=0.519 (0.036%), neg=0, invalid=762
0296: dt=129.472000, rms=0.519 (0.026%), neg=0, invalid=762
0297: dt=129.472000, rms=0.518 (0.028%), neg=0, invalid=762
0298: dt=129.472000, rms=0.518 (0.037%), neg=0, invalid=762
0299: dt=129.472000, rms=0.518 (0.027%), neg=0, invalid=762
0300: dt=129.472000, rms=0.518 (0.013%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.518, neg=0, invalid=762
0301: dt=31.104000, rms=0.517 (0.229%), neg=0, invalid=762
0302: dt=20.736000, rms=0.517 (0.021%), neg=0, invalid=762
0303: dt=20.736000, rms=0.517 (0.004%), neg=0, invalid=762
0304: dt=20.736000, rms=0.517 (-0.049%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.518, neg=0, invalid=762
0305: dt=68.440816, rms=0.515 (0.526%), neg=0, invalid=762
0306: dt=69.966102, rms=0.514 (0.263%), neg=0, invalid=762
0307: dt=36.288000, rms=0.513 (0.127%), neg=0, invalid=762
0308: dt=36.288000, rms=0.513 (0.077%), neg=0, invalid=762
0309: dt=36.288000, rms=0.512 (0.126%), neg=0, invalid=762
0310: dt=36.288000, rms=0.511 (0.156%), neg=0, invalid=762
0311: dt=36.288000, rms=0.510 (0.155%), neg=0, invalid=762
0312: dt=36.288000, rms=0.510 (0.147%), neg=0, invalid=762
0313: dt=36.288000, rms=0.509 (0.130%), neg=0, invalid=762
0314: dt=36.288000, rms=0.508 (0.107%), neg=0, invalid=762
0315: dt=36.288000, rms=0.508 (0.101%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0316: dt=497.664000, rms=0.507 (0.183%), neg=0, invalid=762
0317: dt=36.288000, rms=0.506 (0.083%), neg=0, invalid=762
0318: dt=36.288000, rms=0.506 (0.020%), neg=0, invalid=762
0319: dt=36.288000, rms=0.506 (0.015%), neg=0, invalid=762
0320: dt=36.288000, rms=0.506 (0.035%), neg=0, invalid=762
0321: dt=36.288000, rms=0.506 (0.037%), neg=0, invalid=762
0322: dt=36.288000, rms=0.506 (0.049%), neg=0, invalid=762
0323: dt=36.288000, rms=0.505 (0.052%), neg=0, invalid=762
0324: dt=36.288000, rms=0.505 (0.052%), neg=0, invalid=762
0325: dt=36.288000, rms=0.505 (0.056%), neg=0, invalid=762
0326: dt=36.288000, rms=0.505 (0.053%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.506, neg=0, invalid=762
0327: dt=11.200000, rms=0.504 (0.317%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0328: dt=11.200000, rms=0.504 (0.115%), neg=0, invalid=762
0329: dt=11.200000, rms=0.503 (0.091%), neg=0, invalid=762
0330: dt=11.200000, rms=0.503 (0.083%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 2 iterations, nbhd size=0, neg = 0
0331: dt=11.200000, rms=0.503 (0.041%), neg=0, invalid=762
iter 0, gcam->neg = 52
after 3 iterations, nbhd size=0, neg = 0
0332: dt=148.268503, rms=0.497 (1.156%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0333: dt=11.200000, rms=0.496 (0.103%), neg=0, invalid=762
0334: dt=11.200000, rms=0.496 (0.034%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0335: dt=11.200000, rms=0.496 (-0.035%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.497, neg=0, invalid=762
0336: dt=57.483283, rms=0.489 (1.569%), neg=0, invalid=762
0337: dt=30.720000, rms=0.486 (0.628%), neg=0, invalid=762
0338: dt=32.000000, rms=0.485 (0.213%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0339: dt=32.000000, rms=0.484 (0.231%), neg=0, invalid=762
0340: dt=32.000000, rms=0.482 (0.290%), neg=0, invalid=762
0341: dt=32.000000, rms=0.481 (0.227%), neg=0, invalid=762
0342: dt=32.000000, rms=0.480 (0.255%), neg=0, invalid=762
0343: dt=32.000000, rms=0.479 (0.237%), neg=0, invalid=762
0344: dt=32.000000, rms=0.478 (0.215%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0345: dt=32.000000, rms=0.476 (0.306%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0346: dt=32.000000, rms=0.475 (0.294%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0347: dt=32.000000, rms=0.473 (0.349%), neg=0, invalid=762
0348: dt=32.000000, rms=0.472 (0.244%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0349: dt=32.000000, rms=0.471 (0.249%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0350: dt=32.000000, rms=0.470 (0.181%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0351: dt=32.000000, rms=0.469 (0.151%), neg=0, invalid=762
0352: dt=32.000000, rms=0.469 (0.144%), neg=0, invalid=762
0353: dt=32.000000, rms=0.468 (0.104%), neg=0, invalid=762
0354: dt=32.000000, rms=0.468 (0.084%), neg=0, invalid=762
0355: dt=19.200000, rms=0.468 (0.060%), neg=0, invalid=762
0356: dt=19.200000, rms=0.467 (0.022%), neg=0, invalid=762
0357: dt=19.200000, rms=0.467 (0.019%), neg=0, invalid=762
0358: dt=19.200000, rms=0.467 (0.017%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0359: dt=0.000000, rms=0.476 (0.117%), neg=0, invalid=762
0360: dt=0.000000, rms=0.476 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0361: dt=0.000000, rms=0.476 (0.117%), neg=0, invalid=762
0362: dt=0.000000, rms=0.476 (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=0.495, neg=0, invalid=762
0363: dt=1.024000, rms=0.493 (0.387%), neg=0, invalid=762
0364: dt=0.192000, rms=0.493 (0.010%), neg=0, invalid=762
0365: dt=0.192000, rms=0.493 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.494, neg=0, invalid=762
0366: dt=1.024000, rms=0.492 (0.289%), neg=0, invalid=762
0367: dt=0.448000, rms=0.492 (0.019%), neg=0, invalid=762
0368: dt=0.448000, rms=0.492 (-0.007%), 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=0.475, neg=0, invalid=762
iter 0, gcam->neg = 547
after 12 iterations, nbhd size=1, neg = 0
0369: dt=2.166864, rms=0.447 (5.909%), neg=0, invalid=762
0370: dt=0.096000, rms=0.446 (0.063%), neg=0, invalid=762
0371: dt=0.096000, rms=0.446 (-0.078%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.447, neg=0, invalid=762
0372: dt=0.112000, rms=0.446 (0.219%), neg=0, invalid=762
0373: dt=0.000438, rms=0.446 (0.002%), neg=0, invalid=762
0374: dt=0.000438, rms=0.446 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0375: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0376: dt=32.368000, rms=0.433 (0.008%), neg=0, invalid=762
0377: dt=32.368000, rms=0.433 (0.002%), neg=0, invalid=762
0378: dt=32.368000, rms=0.433 (0.000%), neg=0, invalid=762
0379: dt=32.368000, rms=0.433 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0380: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0381: dt=82.944000, rms=0.433 (0.066%), neg=0, invalid=762
0382: dt=103.680000, rms=0.433 (0.076%), neg=0, invalid=762
0383: dt=36.288000, rms=0.433 (0.022%), neg=0, invalid=762
0384: dt=36.288000, rms=0.433 (0.013%), neg=0, invalid=762
0385: dt=36.288000, rms=0.433 (0.022%), neg=0, invalid=762
0386: dt=36.288000, rms=0.433 (0.026%), neg=0, invalid=762
0387: dt=36.288000, rms=0.433 (0.025%), neg=0, invalid=762
0388: dt=36.288000, rms=0.432 (0.021%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0389: dt=2.800000, rms=0.433 (0.012%), neg=0, invalid=762
0390: dt=0.700000, rms=0.433 (0.001%), neg=0, invalid=762
0391: dt=0.700000, rms=0.433 (0.000%), neg=0, invalid=762
0392: dt=0.700000, rms=0.433 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0393: dt=99.341067, rms=0.429 (0.915%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0394: dt=24.146520, rms=0.428 (0.276%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0395: dt=44.800000, rms=0.427 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0396: dt=44.800000, rms=0.427 (0.127%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0397: dt=44.800000, rms=0.426 (0.255%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 9 iterations, nbhd size=1, neg = 0
0398: dt=44.800000, rms=0.425 (0.186%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0399: dt=44.800000, rms=0.424 (0.261%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 5 iterations, nbhd size=0, neg = 0
0400: dt=44.800000, rms=0.423 (0.211%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0401: dt=44.800000, rms=0.422 (0.153%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0402: dt=44.800000, rms=0.422 (0.181%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 8 iterations, nbhd size=1, neg = 0
0403: dt=44.800000, rms=0.421 (0.108%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0404: dt=44.800000, rms=0.421 (0.097%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0405: dt=32.000000, rms=0.421 (0.033%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0406: dt=32.000000, rms=0.420 (0.012%), neg=0, invalid=762
0407: dt=32.000000, rms=0.420 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 4 iterations, nbhd size=0, neg = 0
0408: dt=32.000000, rms=0.420 (0.030%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0409: dt=32.000000, rms=0.420 (0.017%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 7 iterations, nbhd size=0, neg = 0
0410: dt=32.000000, rms=0.420 (0.008%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.425, neg=0, invalid=762
0411: dt=0.000135, rms=0.425 (0.000%), neg=0, invalid=762
0412: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.425, neg=0, invalid=762
0413: dt=2.833333, rms=0.425 (0.015%), neg=0, invalid=762
0414: dt=1.500000, rms=0.425 (0.004%), neg=0, invalid=762
0415: dt=1.500000, rms=0.425 (0.001%), neg=0, invalid=762
0416: dt=1.500000, rms=0.425 (-0.009%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0417: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0418: dt=0.000000, rms=0.433 (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=0.419, neg=0, invalid=762
iter 0, gcam->neg = 395
after 13 iterations, nbhd size=1, neg = 0
0419: dt=1.205231, rms=0.410 (2.193%), neg=0, invalid=762
0420: dt=0.000023, rms=0.410 (0.000%), neg=0, invalid=762
0421: dt=0.000023, rms=0.410 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.410, neg=0, invalid=762
0422: dt=0.112000, rms=0.409 (0.120%), neg=0, invalid=762
0423: dt=0.112000, rms=0.409 (0.069%), neg=0, invalid=762
0424: dt=0.112000, rms=0.409 (0.057%), neg=0, invalid=762
0425: dt=0.112000, rms=0.409 (0.042%), neg=0, invalid=762
0426: dt=0.112000, rms=0.409 (-0.029%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 16 minutes and 58 seconds.
mri_ca_register utimesec    9141.559271
mri_ca_register stimesec    7.124916
mri_ca_register ru_maxrss   1339624
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   3519340
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63720
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    6378
mri_ca_register ru_nivcsw   22259
FSRUNTIME@ mri_ca_register  2.2827 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 20:53:18 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-935
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-6.0.0/0050111/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.83
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 = 0.08355 (24)
Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (384 voxels, overlap=0.958)
Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (384 voxels, peak = 22), gca=21.7
gca peak = 0.17677 (13)
mri peak = 0.07194 (36)
Right_Lateral_Ventricle (43): linear fit = 1.38 x + 0.0 (144 voxels, overlap=0.363)
Right_Lateral_Ventricle (43): linear fit = 1.38 x + 0.0 (144 voxels, peak = 18), gca=18.0
gca peak = 0.28129 (95)
mri peak = 0.09913 (93)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (743 voxels, overlap=1.013)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (743 voxels, peak = 92), gca=91.7
gca peak = 0.16930 (96)
mri peak = 0.08872 (94)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (789 voxels, overlap=1.014)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (789 voxels, peak = 93), gca=92.6
gca peak = 0.24553 (55)
mri peak = 0.08541 (66)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1063 voxels, overlap=0.361)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1063 voxels, peak = 62), gca=62.4
gca peak = 0.30264 (59)
mri peak = 0.08255 (62)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (849 voxels, overlap=0.561)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (849 voxels, peak = 67), gca=67.0
gca peak = 0.07580 (103)
mri peak = 0.07170 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (42565 voxels, overlap=0.693)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (42565 voxels, peak = 107), gca=106.6
gca peak = 0.07714 (104)
mri peak = 0.06842 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43468 voxels, overlap=0.659)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43468 voxels, peak = 109), gca=108.7
gca peak = 0.09712 (58)
mri peak = 0.04874 (63)
Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (25250 voxels, overlap=0.913)
Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (25250 voxels, peak = 62), gca=61.8
gca peak = 0.11620 (58)
mri peak = 0.05009 (60)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24793 voxels, overlap=0.960)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24793 voxels, peak = 59), gca=59.4
gca peak = 0.30970 (66)
mri peak = 0.09114 (79)
Right_Caudate (50): linear fit = 1.17 x + 0.0 (800 voxels, overlap=0.033)
Right_Caudate (50): linear fit = 1.17 x + 0.0 (800 voxels, peak = 78), gca=77.5
gca peak = 0.15280 (69)
mri peak = 0.08696 (76)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (845 voxels, overlap=0.680)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (845 voxels, peak = 73), gca=73.5
gca peak = 0.13902 (56)
mri peak = 0.04931 (59)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (23214 voxels, overlap=0.978)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (23214 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.04993 (59)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (22688 voxels, overlap=0.993)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (22688 voxels, peak = 59), gca=58.6
gca peak = 0.16765 (84)
mri peak = 0.09963 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6008 voxels, overlap=0.959)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6008 voxels, peak = 84), gca=84.0
gca peak = 0.18739 (84)
mri peak = 0.08418 (80)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (5511 voxels, overlap=0.988)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (5511 voxels, peak = 82), gca=81.9
gca peak = 0.29869 (57)
mri peak = 0.09455 (64)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (485 voxels, overlap=0.204)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (485 voxels, peak = 64), gca=63.6
gca peak = 0.33601 (57)
mri peak = 0.09207 (66)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (581 voxels, overlap=0.296)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (581 voxels, peak = 65), gca=64.7
gca peak = 0.11131 (90)
mri peak = 0.06527 (87)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4757 voxels, overlap=0.997)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4757 voxels, peak = 89), gca=88.7
gca peak = 0.11793 (83)
mri peak = 0.07118 (84)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4486 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4486 voxels, peak = 85), gca=85.1
gca peak = 0.08324 (81)
mri peak = 0.08092 (86)
Left_Putamen (12): linear fit = 1.05 x + 0.0 (2084 voxels, overlap=0.759)
Left_Putamen (12): linear fit = 1.05 x + 0.0 (2084 voxels, peak = 85), gca=85.5
gca peak = 0.10360 (77)
mri peak = 0.07512 (82)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (2436 voxels, overlap=0.750)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (2436 voxels, peak = 81), gca=81.2
gca peak = 0.08424 (78)
mri peak = 0.12683 (82)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11480 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11480 voxels, peak = 81), gca=80.7
gca peak = 0.12631 (89)
mri peak = 0.07293 (90)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1442 voxels, overlap=0.824)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1442 voxels, peak = 92), gca=92.1
gca peak = 0.14500 (87)
mri peak = 0.07306 (91)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1489 voxels, overlap=0.893)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1489 voxels, peak = 89), gca=89.2
gca peak = 0.14975 (24)
mri peak = 0.12153 (25)
gca peak = 0.19357 (14)
mri peak = 0.11311 (19)
Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (383 voxels, overlap=0.874)
Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (383 voxels, peak = 17), gca=17.4
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 1.10 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 1.24 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.17231 (22)
mri peak = 0.08355 (24)
Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (384 voxels, overlap=0.959)
Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (384 voxels, peak = 25), gca=24.8
gca peak = 0.13018 (17)
mri peak = 0.07194 (36)
Right_Lateral_Ventricle (43): linear fit = 0.99 x + 0.0 (144 voxels, overlap=0.624)
Right_Lateral_Ventricle (43): linear fit = 0.99 x + 0.0 (144 voxels, peak = 17), gca=16.7
gca peak = 0.24945 (90)
mri peak = 0.09913 (93)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (743 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (743 voxels, peak = 91), gca=91.3
gca peak = 0.18582 (93)
mri peak = 0.08872 (94)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (789 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (789 voxels, peak = 93), gca=92.5
gca peak = 0.26348 (63)
mri peak = 0.08541 (66)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1063 voxels, overlap=1.002)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1063 voxels, peak = 63), gca=63.0
gca peak = 0.27634 (64)
mri peak = 0.08255 (62)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (849 voxels, overlap=1.006)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (849 voxels, peak = 61), gca=61.1
gca peak = 0.07501 (106)
mri peak = 0.07170 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42565 voxels, overlap=0.825)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42565 voxels, peak = 105), gca=105.5
gca peak = 0.07788 (109)
mri peak = 0.06842 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43468 voxels, overlap=0.827)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43468 voxels, peak = 108), gca=108.5
gca peak = 0.09118 (62)
mri peak = 0.04874 (63)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25250 voxels, overlap=0.978)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25250 voxels, peak = 64), gca=63.5
gca peak = 0.11329 (59)
mri peak = 0.05009 (60)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24793 voxels, overlap=0.972)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24793 voxels, peak = 60), gca=60.5
gca peak = 0.22963 (78)
mri peak = 0.09114 (79)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (800 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (800 voxels, peak = 77), gca=76.8
gca peak = 0.12687 (73)
mri peak = 0.08696 (76)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (845 voxels, overlap=1.000)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (845 voxels, peak = 72), gca=71.9
gca peak = 0.13187 (57)
mri peak = 0.04931 (59)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (23214 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (23214 voxels, peak = 58), gca=58.4
gca peak = 0.13841 (58)
mri peak = 0.04993 (59)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22688 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22688 voxels, peak = 57), gca=57.1
gca peak = 0.16815 (84)
mri peak = 0.09963 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6008 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6008 voxels, peak = 84), gca=84.0
gca peak = 0.18568 (82)
mri peak = 0.08418 (80)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5511 voxels, overlap=0.970)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5511 voxels, peak = 82), gca=82.0
gca peak = 0.29602 (65)
mri peak = 0.09455 (64)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (485 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (485 voxels, peak = 66), gca=66.0
gca peak = 0.31151 (65)
mri peak = 0.09207 (66)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (581 voxels, overlap=1.012)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (581 voxels, peak = 67), gca=66.6
gca peak = 0.10102 (87)
mri peak = 0.06527 (87)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4757 voxels, overlap=0.971)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4757 voxels, peak = 88), gca=88.3
gca peak = 0.11184 (85)
mri peak = 0.07118 (84)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4486 voxels, overlap=0.995)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4486 voxels, peak = 85), gca=84.6
gca peak = 0.09278 (87)
mri peak = 0.08092 (86)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2084 voxels, overlap=0.905)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2084 voxels, peak = 86), gca=85.7
gca peak = 0.08162 (81)
mri peak = 0.07512 (82)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2436 voxels, overlap=0.932)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2436 voxels, peak = 81), gca=81.0
gca peak = 0.08410 (81)
mri peak = 0.12683 (82)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11480 voxels, overlap=0.622)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11480 voxels, peak = 82), gca=82.2
gca peak = 0.12072 (92)
mri peak = 0.07293 (90)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1442 voxels, overlap=0.869)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1442 voxels, peak = 92), gca=91.5
gca peak = 0.14407 (89)
mri peak = 0.07306 (91)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1489 voxels, overlap=0.932)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1489 voxels, peak = 89), gca=88.6
gca peak = 0.16783 (32)
mri peak = 0.12153 (25)
gca peak = 0.16542 (20)
mri peak = 0.11311 (19)
Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (383 voxels, overlap=0.782)
Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (383 voxels, peak = 20), gca=19.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15127 (30)
gca peak Left_Thalamus = 0.72551 (104)
gca peak Third_Ventricle = 0.16783 (32)
gca peak CSF = 0.19161 (45)
gca peak Left_Accumbens_area = 0.64433 (66)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.11035 (35)
gca peak Right_Inf_Lat_Vent = 0.21972 (26)
gca peak Right_Accumbens_area = 0.29771 (76)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14507 (37)
gca peak Fifth_Ventricle = 0.51764 (39)
gca peak WM_hypointensities = 0.07683 (79)
gca peak non_WM_hypointensities = 0.09744 (45)
gca peak Optic_Chiasm = 0.70923 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.03 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
83817 voxels changed in iteration 0 of unlikely voxel relabeling
170 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
43325 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
474 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 81262 changed. image ll: -2.123, PF=0.500
pass 2: 21364 changed. image ll: -2.123, PF=0.500
pass 3: 6016 changed.
pass 4: 2091 changed.
44317 voxels changed in iteration 0 of unlikely voxel relabeling
201 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
6328 voxels changed in iteration 0 of unlikely voxel relabeling
148 voxels changed in iteration 1 of unlikely voxel relabeling
23 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5679 voxels changed in iteration 0 of unlikely voxel relabeling
101 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4770 voxels changed in iteration 0 of unlikely voxel relabeling
38 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3666.402622
mri_ca_label stimesec    1.577760
mri_ca_label ru_maxrss   2091468
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   731955
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63712
mri_ca_label ru_oublock  480
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    292
mri_ca_label ru_nivcsw   4687
auto-labeling took 60 minutes and 22 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/transforms/cc_up.lta 0050111 

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-6.0.0/0050111/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/norm.mgz
67035 voxels in left wm, 63042 in right wm, xrange [122, 136]
searching rotation angles z=[-7  7], y=[-2 12]

searching scale 1 Z rot -7.3  
searching scale 1 Z rot -7.1  
searching scale 1 Z rot -6.8  
searching scale 1 Z rot -6.6  
searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.4  global minimum found at slice 128.6, rotations (5.29, -0.35)
final transformation (x=128.6, yr=5.294, zr=-0.349):
 0.99572   0.00610   0.09227  -10.88897;
-0.00607   0.99998  -0.00056   22.84516;
-0.09227   0.00000   0.99573   30.33935;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [124, 130] in xformed coordinates
best xformed slice 126
cc center is found at 126 106 110
eigenvectors:
-0.00042  -0.00306   1.00000;
-0.11897  -0.99289  -0.00309;
 0.99290  -0.11897   0.00005;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.4 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 21:55:03 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 21:55:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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...
1449 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 107
gm peak at 68 (68), valley at  0 (-1)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 66 (66), valley at  0 (-1)
csf peak at 33, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 14 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 21:58:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1599282 voxels in mask (pct=  9.53)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 21:58:22 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (105.0): 105.5 +- 5.8 [79.0 --> 125.0]
GM (70.0) : 67.9 +- 9.5 [30.0 --> 95.0]
setting bottom of white matter range to 77.4
setting top of gray matter range to 86.9
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...
15542 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4868 filled
2713 bright non-wm voxels segmented.
6476 diagonally connected voxels added...
white matter segmentation took 1.8 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 0.54 minutes
reading wm segmentation from wm.seg.mgz...
133 voxels added to wm to prevent paths from MTL structures to cortex
2679 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 31240 voxels turned on, 32627 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 112   new 112
115,126,128 old 112   new 112
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  20 found -  20 modified     |    TOTAL:  20
pass   2 (xy+):   0 found -  20 modified     |    TOTAL:  20
pass   1 (xy-):  22 found -  22 modified     |    TOTAL:  42
pass   2 (xy-):   0 found -  22 modified     |    TOTAL:  42
pass   1 (yz+):  48 found -  48 modified     |    TOTAL:  90
pass   2 (yz+):   0 found -  48 modified     |    TOTAL:  90
pass   1 (yz-):  23 found -  23 modified     |    TOTAL: 113
pass   2 (yz-):   0 found -  23 modified     |    TOTAL: 113
pass   1 (xz+):  34 found -  34 modified     |    TOTAL: 147
pass   2 (xz+):   0 found -  34 modified     |    TOTAL: 147
pass   1 (xz-):  37 found -  37 modified     |    TOTAL: 184
pass   2 (xz-):   0 found -  37 modified     |    TOTAL: 184
Iteration Number : 1
pass   1 (+++):  45 found -  45 modified     |    TOTAL:  45
pass   2 (+++):   0 found -  45 modified     |    TOTAL:  45
pass   1 (+++):  50 found -  50 modified     |    TOTAL:  95
pass   2 (+++):   0 found -  50 modified     |    TOTAL:  95
pass   1 (+++):  45 found -  45 modified     |    TOTAL: 140
pass   2 (+++):   0 found -  45 modified     |    TOTAL: 140
pass   1 (+++):  46 found -  46 modified     |    TOTAL: 186
pass   2 (+++):   0 found -  46 modified     |    TOTAL: 186
Iteration Number : 1
pass   1 (++): 172 found - 172 modified     |    TOTAL: 172
pass   2 (++):   0 found - 172 modified     |    TOTAL: 172
pass   1 (+-): 230 found - 230 modified     |    TOTAL: 402
pass   2 (+-):   1 found - 231 modified     |    TOTAL: 403
pass   3 (+-):   0 found - 231 modified     |    TOTAL: 403
pass   1 (--): 182 found - 182 modified     |    TOTAL: 585
pass   2 (--):   0 found - 182 modified     |    TOTAL: 585
pass   1 (-+): 220 found - 220 modified     |    TOTAL: 805
pass   2 (-+):   0 found - 220 modified     |    TOTAL: 805
Iteration Number : 2
pass   1 (xy+):  10 found -  10 modified     |    TOTAL:  10
pass   2 (xy+):   0 found -  10 modified     |    TOTAL:  10
pass   1 (xy-):  13 found -  13 modified     |    TOTAL:  23
pass   2 (xy-):   0 found -  13 modified     |    TOTAL:  23
pass   1 (yz+):  13 found -  13 modified     |    TOTAL:  36
pass   2 (yz+):   0 found -  13 modified     |    TOTAL:  36
pass   1 (yz-):  14 found -  14 modified     |    TOTAL:  50
pass   2 (yz-):   0 found -  14 modified     |    TOTAL:  50
pass   1 (xz+):   9 found -   9 modified     |    TOTAL:  59
pass   2 (xz+):   0 found -   9 modified     |    TOTAL:  59
pass   1 (xz-):  13 found -  13 modified     |    TOTAL:  72
pass   2 (xz-):   0 found -  13 modified     |    TOTAL:  72
Iteration Number : 2
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  10
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  10
pass   1 (+++):   0 found -   0 modified     |    TOTAL:  10
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  16
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  16
Iteration Number : 2
pass   1 (++):   7 found -   7 modified     |    TOTAL:   7
pass   2 (++):   0 found -   7 modified     |    TOTAL:   7
pass   1 (+-):   4 found -   4 modified     |    TOTAL:  11
pass   2 (+-):   0 found -   4 modified     |    TOTAL:  11
pass   1 (--):   2 found -   2 modified     |    TOTAL:  13
pass   2 (--):   0 found -   2 modified     |    TOTAL:  13
pass   1 (-+):   8 found -   8 modified     |    TOTAL:  21
pass   2 (-+):   0 found -   8 modified     |    TOTAL:  21
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   7
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   9
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   9
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  12
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  12
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   0 found -   0 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-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1301 (out of 569586: 0.228412)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 22:00:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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
 0.99608   0.01502   0.08914  -13.49292;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 0.99608   0.01502   0.08914  -13.49292;
-0.03205   1.09002   0.28960  -43.36435;
-0.08425  -0.26794   0.99874   40.75948;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1131 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75)
no need to search
using seed (125, 121, 149), TAL = (3.0, 21.0, 7.0)
talairach voxel to voxel transform
 0.99616  -0.03321  -0.07928   15.23245;
 0.00650   0.85616  -0.24884   47.35710;
 0.08578   0.22689   0.92782  -26.82109;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (125,  121,  149) --> (3.0, 21.0, 7.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (3.00, 21.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, 21.00, 7.00) SRC: (105.99, 114.57, 148.06)
search lh wm seed point around talairach space (-15.00, 21.00, 7.00), SRC: (141.85, 114.80, 151.14)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 22:01:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   3
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   7
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 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (--):   0 found -   0 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 11 (out of 274566: 0.004006)
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: 1094 vertices, 1218 faces
slice 50: 8844 vertices, 9159 faces
slice 60: 20323 vertices, 20795 faces
slice 70: 32962 vertices, 33427 faces
slice 80: 45532 vertices, 46010 faces
slice 90: 57732 vertices, 58210 faces
slice 100: 71027 vertices, 71542 faces
slice 110: 83812 vertices, 84306 faces
slice 120: 95662 vertices, 96139 faces
slice 130: 107325 vertices, 107843 faces
slice 140: 118792 vertices, 119289 faces
slice 150: 129064 vertices, 129532 faces
slice 160: 138744 vertices, 139191 faces
slice 170: 145292 vertices, 145673 faces
slice 180: 151553 vertices, 151887 faces
slice 190: 155830 vertices, 156071 faces
slice 200: 157034 vertices, 157180 faces
slice 210: 157034 vertices, 157180 faces
slice 220: 157034 vertices, 157180 faces
slice 230: 157034 vertices, 157180 faces
slice 240: 157034 vertices, 157180 faces
slice 250: 157034 vertices, 157180 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...
   157034 voxel in cpt #1: X=-146 [v=157034,e=471540,f=314360] located at (-30.065832, -20.862698, 7.984577)
For the whole surface: X=-146 [v=157034,e=471540,f=314360]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 22:01:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   6
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   9
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   2 found -   2 modified     |    TOTAL:   2
pass   2 (--):   0 found -   2 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
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 = 12 (out of 274883: 0.004365)
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: 888 vertices, 998 faces
slice 50: 9275 vertices, 9682 faces
slice 60: 21549 vertices, 22078 faces
slice 70: 35804 vertices, 36333 faces
slice 80: 49278 vertices, 49795 faces
slice 90: 62927 vertices, 63412 faces
slice 100: 76705 vertices, 77196 faces
slice 110: 89070 vertices, 89564 faces
slice 120: 101026 vertices, 101516 faces
slice 130: 112401 vertices, 112924 faces
slice 140: 124347 vertices, 124867 faces
slice 150: 134266 vertices, 134746 faces
slice 160: 142908 vertices, 143307 faces
slice 170: 149677 vertices, 150053 faces
slice 180: 155303 vertices, 155647 faces
slice 190: 159139 vertices, 159418 faces
slice 200: 160236 vertices, 160408 faces
slice 210: 160236 vertices, 160408 faces
slice 220: 160236 vertices, 160408 faces
slice 230: 160236 vertices, 160408 faces
slice 240: 160236 vertices, 160408 faces
slice 250: 160236 vertices, 160408 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...
   160236 voxel in cpt #1: X=-172 [v=160236,e=481224,f=320816] located at (29.103266, -22.921366, 10.698414)
For the whole surface: X=-172 [v=160236,e=481224,f=320816]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 22:01:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 22:01:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

Waiting for PID 10108 of (10108 10111) to complete...
Waiting for PID 10111 of (10108 10111) 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 (10108 10111) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 22:02:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 22:02:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

Waiting for PID 10152 of (10152 10155) to complete...
Waiting for PID 10155 of (10152 10155) 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 = 47.8 mm, total surface area = 80489 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 1.1 minutes

step 000: RMS=0.163 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.085 (target=0.015)   
step 020: RMS=0.077 (target=0.015)   
step 025: RMS=0.070 (target=0.015)   
step 030: RMS=0.066 (target=0.015)   
step 035: RMS=0.063 (target=0.015)   
step 040: RMS=0.060 (target=0.015)   
step 045: RMS=0.058 (target=0.015)   
step 050: RMS=0.058 (target=0.015)   
step 055: RMS=0.058 (target=0.015)   
step 060: RMS=0.058 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    58.154159
mris_inflate stimesec    0.092985
mris_inflate ru_maxrss   230024
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32914
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11072
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1755
mris_inflate ru_nivcsw   4538

 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 = 81585 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.1 minutes

step 000: RMS=0.166 (target=0.015)   
step 005: RMS=0.126 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.076 (target=0.015)   
step 025: RMS=0.069 (target=0.015)   
step 030: RMS=0.065 (target=0.015)   
step 035: RMS=0.060 (target=0.015)   
step 040: RMS=0.057 (target=0.015)   
step 045: RMS=0.056 (target=0.015)   
step 050: RMS=0.055 (target=0.015)   
step 055: RMS=0.055 (target=0.015)   
step 060: RMS=0.055 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.652451
mris_inflate stimesec    0.119981
mris_inflate ru_maxrss   234756
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33585
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11296
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2114
mris_inflate ru_nivcsw   4630
PIDs (10152 10155) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 22:03:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 22:03:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

Waiting for PID 10225 of (10225 10229) to complete...
Waiting for PID 10229 of (10225 10229) 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 0.93 +- 0.57 (0.00-->7.73) (max @ vno 74751 --> 74781)
face area 0.02 +- 0.03 (-0.58-->0.78)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.304...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.051, avgs=0
005/300: dt: 0.9000, rms radial error=175.796, avgs=0
010/300: dt: 0.9000, rms radial error=175.241, avgs=0
015/300: dt: 0.9000, rms radial error=174.508, avgs=0
020/300: dt: 0.9000, rms radial error=173.669, avgs=0
025/300: dt: 0.9000, rms radial error=172.772, avgs=0
030/300: dt: 0.9000, rms radial error=171.842, avgs=0
035/300: dt: 0.9000, rms radial error=170.896, avgs=0
040/300: dt: 0.9000, rms radial error=169.949, avgs=0
045/300: dt: 0.9000, rms radial error=169.003, avgs=0
050/300: dt: 0.9000, rms radial error=168.056, avgs=0
055/300: dt: 0.9000, rms radial error=167.113, avgs=0
060/300: dt: 0.9000, rms radial error=166.173, avgs=0
065/300: dt: 0.9000, rms radial error=165.237, avgs=0
070/300: dt: 0.9000, rms radial error=164.306, avgs=0
075/300: dt: 0.9000, rms radial error=163.381, avgs=0
080/300: dt: 0.9000, rms radial error=162.466, avgs=0
085/300: dt: 0.9000, rms radial error=161.555, avgs=0
090/300: dt: 0.9000, rms radial error=160.649, avgs=0
095/300: dt: 0.9000, rms radial error=159.748, avgs=0
100/300: dt: 0.9000, rms radial error=158.852, avgs=0
105/300: dt: 0.9000, rms radial error=157.960, avgs=0
110/300: dt: 0.9000, rms radial error=157.074, avgs=0
115/300: dt: 0.9000, rms radial error=156.192, avgs=0
120/300: dt: 0.9000, rms radial error=155.315, avgs=0
125/300: dt: 0.9000, rms radial error=154.443, avgs=0
130/300: dt: 0.9000, rms radial error=153.576, avgs=0
135/300: dt: 0.9000, rms radial error=152.714, avgs=0
140/300: dt: 0.9000, rms radial error=151.856, avgs=0
145/300: dt: 0.9000, rms radial error=151.004, avgs=0
150/300: dt: 0.9000, rms radial error=150.156, avgs=0
155/300: dt: 0.9000, rms radial error=149.313, avgs=0
160/300: dt: 0.9000, rms radial error=148.474, avgs=0
165/300: dt: 0.9000, rms radial error=147.640, avgs=0
170/300: dt: 0.9000, rms radial error=146.810, avgs=0
175/300: dt: 0.9000, rms radial error=145.985, avgs=0
180/300: dt: 0.9000, rms radial error=145.165, avgs=0
185/300: dt: 0.9000, rms radial error=144.349, avgs=0
190/300: dt: 0.9000, rms radial error=143.537, avgs=0
195/300: dt: 0.9000, rms radial error=142.730, avgs=0
200/300: dt: 0.9000, rms radial error=141.927, avgs=0
205/300: dt: 0.9000, rms radial error=141.129, avgs=0
210/300: dt: 0.9000, rms radial error=140.335, avgs=0
215/300: dt: 0.9000, rms radial error=139.545, avgs=0
220/300: dt: 0.9000, rms radial error=138.760, avgs=0
225/300: dt: 0.9000, rms radial error=137.979, avgs=0
230/300: dt: 0.9000, rms radial error=137.203, avgs=0
235/300: dt: 0.9000, rms radial error=136.431, avgs=0
240/300: dt: 0.9000, rms radial error=135.663, avgs=0
245/300: dt: 0.9000, rms radial error=134.899, avgs=0
250/300: dt: 0.9000, rms radial error=134.140, avgs=0
255/300: dt: 0.9000, rms radial error=133.384, avgs=0
260/300: dt: 0.9000, rms radial error=132.634, avgs=0
265/300: dt: 0.9000, rms radial error=131.887, avgs=0
270/300: dt: 0.9000, rms radial error=131.145, avgs=0
275/300: dt: 0.9000, rms radial error=130.406, avgs=0
280/300: dt: 0.9000, rms radial error=129.672, avgs=0
285/300: dt: 0.9000, rms radial error=128.942, avgs=0
290/300: dt: 0.9000, rms radial error=128.215, avgs=0
295/300: dt: 0.9000, rms radial error=127.493, avgs=0
300/300: dt: 0.9000, rms radial error=126.775, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18620.62
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 3219.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
epoch 3 (K=160.0), pass 1, starting sse = 371.52
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00527
epoch 4 (K=640.0), pass 1, starting sse = 35.07
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/12 = 0.00718
final distance error %27.40
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    361.074108
mris_sphere stimesec    0.215967
mris_sphere ru_maxrss   230208
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33471
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11056
mris_sphere ru_oublock  11096
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    7374
mris_sphere ru_nivcsw   21477
FSRUNTIME@ mris_sphere  0.0951 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 0.92 +- 0.58 (0.00-->7.68) (max @ vno 121640 --> 121641)
face area 0.02 +- 0.03 (-0.25-->0.71)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.306...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.706, avgs=0
005/300: dt: 0.9000, rms radial error=175.447, avgs=0
010/300: dt: 0.9000, rms radial error=174.889, avgs=0
015/300: dt: 0.9000, rms radial error=174.157, avgs=0
020/300: dt: 0.9000, rms radial error=173.331, avgs=0
025/300: dt: 0.9000, rms radial error=172.453, avgs=0
030/300: dt: 0.9000, rms radial error=171.542, avgs=0
035/300: dt: 0.9000, rms radial error=170.616, avgs=0
040/300: dt: 0.9000, rms radial error=169.681, avgs=0
045/300: dt: 0.9000, rms radial error=168.744, avgs=0
050/300: dt: 0.9000, rms radial error=167.807, avgs=0
055/300: dt: 0.9000, rms radial error=166.872, avgs=0
060/300: dt: 0.9000, rms radial error=165.940, avgs=0
065/300: dt: 0.9000, rms radial error=165.013, avgs=0
070/300: dt: 0.9000, rms radial error=164.089, avgs=0
075/300: dt: 0.9000, rms radial error=163.170, avgs=0
080/300: dt: 0.9000, rms radial error=162.255, avgs=0
085/300: dt: 0.9000, rms radial error=161.345, avgs=0
090/300: dt: 0.9000, rms radial error=160.439, avgs=0
095/300: dt: 0.9000, rms radial error=159.539, avgs=0
100/300: dt: 0.9000, rms radial error=158.642, avgs=0
105/300: dt: 0.9000, rms radial error=157.750, avgs=0
110/300: dt: 0.9000, rms radial error=156.863, avgs=0
115/300: dt: 0.9000, rms radial error=155.980, avgs=0
120/300: dt: 0.9000, rms radial error=155.102, avgs=0
125/300: dt: 0.9000, rms radial error=154.229, avgs=0
130/300: dt: 0.9000, rms radial error=153.361, avgs=0
135/300: dt: 0.9000, rms radial error=152.497, avgs=0
140/300: dt: 0.9000, rms radial error=151.638, avgs=0
145/300: dt: 0.9000, rms radial error=150.785, avgs=0
150/300: dt: 0.9000, rms radial error=149.936, avgs=0
155/300: dt: 0.9000, rms radial error=149.091, avgs=0
160/300: dt: 0.9000, rms radial error=148.251, avgs=0
165/300: dt: 0.9000, rms radial error=147.415, avgs=0
170/300: dt: 0.9000, rms radial error=146.584, avgs=0
175/300: dt: 0.9000, rms radial error=145.757, avgs=0
180/300: dt: 0.9000, rms radial error=144.935, avgs=0
185/300: dt: 0.9000, rms radial error=144.116, avgs=0
190/300: dt: 0.9000, rms radial error=143.303, avgs=0
195/300: dt: 0.9000, rms radial error=142.493, avgs=0
200/300: dt: 0.9000, rms radial error=141.688, avgs=0
205/300: dt: 0.9000, rms radial error=140.888, avgs=0
210/300: dt: 0.9000, rms radial error=140.092, avgs=0
215/300: dt: 0.9000, rms radial error=139.303, avgs=0
220/300: dt: 0.9000, rms radial error=138.517, avgs=0
225/300: dt: 0.9000, rms radial error=137.736, avgs=0
230/300: dt: 0.9000, rms radial error=136.959, avgs=0
235/300: dt: 0.9000, rms radial error=136.186, avgs=0
240/300: dt: 0.9000, rms radial error=135.418, avgs=0
245/300: dt: 0.9000, rms radial error=134.654, avgs=0
250/300: dt: 0.9000, rms radial error=133.894, avgs=0
255/300: dt: 0.9000, rms radial error=133.138, avgs=0
260/300: dt: 0.9000, rms radial error=132.387, avgs=0
265/300: dt: 0.9000, rms radial error=131.640, avgs=0
270/300: dt: 0.9000, rms radial error=130.897, avgs=0
275/300: dt: 0.9000, rms radial error=130.158, avgs=0
280/300: dt: 0.9000, rms radial error=129.424, avgs=0
285/300: dt: 0.9000, rms radial error=128.694, avgs=0
290/300: dt: 0.9000, rms radial error=127.967, avgs=0
295/300: dt: 0.9000, rms radial error=127.245, avgs=0
300/300: dt: 0.9000, rms radial error=126.526, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18982.92
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 2 (K=40.0), pass 1, starting sse = 3282.66
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 3 (K=160.0), pass 1, starting sse = 385.95
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00581
epoch 4 (K=640.0), pass 1, starting sse = 38.25
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00529
final distance error %27.42
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    291.441694
mris_sphere stimesec    0.211967
mris_sphere ru_maxrss   234960
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   34146
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11320
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8427
mris_sphere ru_nivcsw   21032
FSRUNTIME@ mris_sphere  0.0830 hours 1 threads
PIDs (10225 10229) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 22:08:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 22:08:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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


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

#@# Fix Topology lh Sat Oct  7 22:08:50 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050111 lh 

#@# Fix Topology rh Sat Oct  7 22:08:50 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050111 rh 

Waiting for PID 10506 of (10506 10509) to complete...
Waiting for PID 10509 of (10506 10509) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050111 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=-146 (nv=157034, nf=314360, ne=471540, g=74)
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...
16021 ambiguous faces found in tessellation
segmenting defects...
72 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 62 into 38
      -merging segment 43 into 42
70 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4560  (-4.7280)
      -vertex     loglikelihood: -6.2960  (-3.1480)
      -normal dot loglikelihood: -3.6157  (-3.6157)
      -quad curv  loglikelihood: -6.2977  (-3.1489)
      Total Loglikelihood : -25.6655

CORRECTING DEFECT 0 (vertices=1660, convex hull=706, v0=253)
XL defect detected...
After retessellation of defect 0 (v0=253), euler #=-64 (148188,442190,293938) : difference with theory (-67) = -3 

CORRECTING DEFECT 1 (vertices=118, convex hull=37, v0=323)
After retessellation of defect 1 (v0=323), euler #=-63 (148193,442217,293961) : difference with theory (-66) = -3 

CORRECTING DEFECT 2 (vertices=61, convex hull=83, v0=626)
After retessellation of defect 2 (v0=626), euler #=-62 (148213,442309,294034) : difference with theory (-65) = -3 

CORRECTING DEFECT 3 (vertices=2260, convex hull=240, v0=1130)
After retessellation of defect 3 (v0=1130), euler #=-62 (148302,442697,294333) : difference with theory (-64) = -2 

CORRECTING DEFECT 4 (vertices=57, convex hull=107, v0=1559)
After retessellation of defect 4 (v0=1559), euler #=-61 (148331,442834,294442) : difference with theory (-63) = -2 

CORRECTING DEFECT 5 (vertices=16, convex hull=14, v0=1597)
After retessellation of defect 5 (v0=1597), euler #=-60 (148331,442837,294446) : difference with theory (-62) = -2 

CORRECTING DEFECT 6 (vertices=32, convex hull=61, v0=7040)
After retessellation of defect 6 (v0=7040), euler #=-59 (148345,442900,294496) : difference with theory (-61) = -2 

CORRECTING DEFECT 7 (vertices=61, convex hull=97, v0=11884)
After retessellation of defect 7 (v0=11884), euler #=-58 (148377,443037,294602) : difference with theory (-60) = -2 

CORRECTING DEFECT 8 (vertices=35, convex hull=95, v0=19311)
After retessellation of defect 8 (v0=19311), euler #=-57 (148386,443107,294664) : difference with theory (-59) = -2 

CORRECTING DEFECT 9 (vertices=67, convex hull=83, v0=20342)
After retessellation of defect 9 (v0=20342), euler #=-56 (148426,443262,294780) : difference with theory (-58) = -2 

CORRECTING DEFECT 10 (vertices=52, convex hull=61, v0=26246)
After retessellation of defect 10 (v0=26246), euler #=-55 (148436,443319,294828) : difference with theory (-57) = -2 

CORRECTING DEFECT 11 (vertices=36, convex hull=58, v0=29238)
After retessellation of defect 11 (v0=29238), euler #=-54 (148454,443397,294889) : difference with theory (-56) = -2 

CORRECTING DEFECT 12 (vertices=32, convex hull=34, v0=34370)
After retessellation of defect 12 (v0=34370), euler #=-53 (148456,443415,294906) : difference with theory (-55) = -2 

CORRECTING DEFECT 13 (vertices=28, convex hull=73, v0=41248)
After retessellation of defect 13 (v0=41248), euler #=-52 (148471,443489,294966) : difference with theory (-54) = -2 

CORRECTING DEFECT 14 (vertices=57, convex hull=96, v0=46310)
After retessellation of defect 14 (v0=46310), euler #=-51 (148486,443574,295037) : difference with theory (-53) = -2 

CORRECTING DEFECT 15 (vertices=35, convex hull=91, v0=48187)
After retessellation of defect 15 (v0=48187), euler #=-50 (148497,443651,295104) : difference with theory (-52) = -2 

CORRECTING DEFECT 16 (vertices=249, convex hull=230, v0=61342)
After retessellation of defect 16 (v0=61342), euler #=-49 (148524,443838,295265) : difference with theory (-51) = -2 

CORRECTING DEFECT 17 (vertices=23, convex hull=55, v0=66477)
After retessellation of defect 17 (v0=66477), euler #=-48 (148536,443896,295312) : difference with theory (-50) = -2 

CORRECTING DEFECT 18 (vertices=19, convex hull=24, v0=66509)
After retessellation of defect 18 (v0=66509), euler #=-47 (148540,443914,295327) : difference with theory (-49) = -2 

CORRECTING DEFECT 19 (vertices=5, convex hull=20, v0=66597)
After retessellation of defect 19 (v0=66597), euler #=-46 (148541,443923,295336) : difference with theory (-48) = -2 

CORRECTING DEFECT 20 (vertices=36, convex hull=51, v0=68349)
After retessellation of defect 20 (v0=68349), euler #=-45 (148562,444008,295401) : difference with theory (-47) = -2 

CORRECTING DEFECT 21 (vertices=45, convex hull=66, v0=70404)
After retessellation of defect 21 (v0=70404), euler #=-44 (148585,444101,295472) : difference with theory (-46) = -2 

CORRECTING DEFECT 22 (vertices=17, convex hull=22, v0=71815)
After retessellation of defect 22 (v0=71815), euler #=-43 (148587,444113,295483) : difference with theory (-45) = -2 

CORRECTING DEFECT 23 (vertices=10, convex hull=20, v0=77075)
After retessellation of defect 23 (v0=77075), euler #=-42 (148590,444127,295495) : difference with theory (-44) = -2 

CORRECTING DEFECT 24 (vertices=17, convex hull=28, v0=80891)
After retessellation of defect 24 (v0=80891), euler #=-41 (148593,444143,295509) : difference with theory (-43) = -2 

CORRECTING DEFECT 25 (vertices=51, convex hull=37, v0=82143)
After retessellation of defect 25 (v0=82143), euler #=-40 (148605,444192,295547) : difference with theory (-42) = -2 

CORRECTING DEFECT 26 (vertices=35, convex hull=63, v0=83072)
After retessellation of defect 26 (v0=83072), euler #=-39 (148628,444282,295615) : difference with theory (-41) = -2 

CORRECTING DEFECT 27 (vertices=297, convex hull=158, v0=87128)
After retessellation of defect 27 (v0=87128), euler #=-40 (148722,444665,295903) : difference with theory (-40) = 0 

CORRECTING DEFECT 28 (vertices=32, convex hull=35, v0=89234)
After retessellation of defect 28 (v0=89234), euler #=-39 (148730,444700,295931) : difference with theory (-39) = 0 

CORRECTING DEFECT 29 (vertices=68, convex hull=57, v0=96331)
After retessellation of defect 29 (v0=96331), euler #=-38 (148745,444767,295984) : difference with theory (-38) = 0 

CORRECTING DEFECT 30 (vertices=30, convex hull=70, v0=97936)
After retessellation of defect 30 (v0=97936), euler #=-37 (148759,444841,296045) : difference with theory (-37) = 0 

CORRECTING DEFECT 31 (vertices=544, convex hull=323, v0=99850)
After retessellation of defect 31 (v0=99850), euler #=-36 (148935,445530,296559) : difference with theory (-36) = 0 

CORRECTING DEFECT 32 (vertices=21, convex hull=50, v0=102235)
After retessellation of defect 32 (v0=102235), euler #=-35 (148947,445584,296602) : difference with theory (-35) = 0 

CORRECTING DEFECT 33 (vertices=9, convex hull=22, v0=104613)
After retessellation of defect 33 (v0=104613), euler #=-34 (148949,445596,296613) : difference with theory (-34) = 0 

CORRECTING DEFECT 34 (vertices=282, convex hull=67, v0=105818)
After retessellation of defect 34 (v0=105818), euler #=-33 (148972,445696,296691) : difference with theory (-33) = 0 

CORRECTING DEFECT 35 (vertices=26, convex hull=73, v0=107314)
After retessellation of defect 35 (v0=107314), euler #=-32 (148989,445772,296751) : difference with theory (-32) = 0 

CORRECTING DEFECT 36 (vertices=16, convex hull=59, v0=109426)
After retessellation of defect 36 (v0=109426), euler #=-31 (148999,445823,296793) : difference with theory (-31) = 0 

CORRECTING DEFECT 37 (vertices=10, convex hull=27, v0=109547)
After retessellation of defect 37 (v0=109547), euler #=-30 (149003,445847,296814) : difference with theory (-30) = 0 

CORRECTING DEFECT 38 (vertices=826, convex hull=472, v0=113853)
L defect detected...
After retessellation of defect 38 (v0=113853), euler #=-29 (149076,446312,297207) : difference with theory (-29) = 0 

CORRECTING DEFECT 39 (vertices=67, convex hull=104, v0=113952)
After retessellation of defect 39 (v0=113952), euler #=-29 (149111,446467,297327) : difference with theory (-28) = 1 

CORRECTING DEFECT 40 (vertices=168, convex hull=47, v0=114057)
After retessellation of defect 40 (v0=114057), euler #=-28 (149121,446509,297360) : difference with theory (-27) = 1 

CORRECTING DEFECT 41 (vertices=26, convex hull=33, v0=114066)
After retessellation of defect 41 (v0=114066), euler #=-27 (149130,446545,297388) : difference with theory (-26) = 1 

CORRECTING DEFECT 42 (vertices=68, convex hull=107, v0=114298)
After retessellation of defect 42 (v0=114298), euler #=-25 (149156,446671,297490) : difference with theory (-25) = 0 

CORRECTING DEFECT 43 (vertices=23, convex hull=33, v0=114892)
After retessellation of defect 43 (v0=114892), euler #=-24 (149163,446702,297515) : difference with theory (-24) = 0 

CORRECTING DEFECT 44 (vertices=117, convex hull=97, v0=115077)
After retessellation of defect 44 (v0=115077), euler #=-23 (149182,446800,297595) : difference with theory (-23) = 0 

CORRECTING DEFECT 45 (vertices=13, convex hull=29, v0=118614)
After retessellation of defect 45 (v0=118614), euler #=-22 (149187,446826,297617) : difference with theory (-22) = 0 

CORRECTING DEFECT 46 (vertices=58, convex hull=68, v0=119406)
After retessellation of defect 46 (v0=119406), euler #=-21 (149196,446879,297662) : difference with theory (-21) = 0 

CORRECTING DEFECT 47 (vertices=87, convex hull=97, v0=123089)
After retessellation of defect 47 (v0=123089), euler #=-20 (149222,447003,297761) : difference with theory (-20) = 0 

CORRECTING DEFECT 48 (vertices=11, convex hull=21, v0=123337)
After retessellation of defect 48 (v0=123337), euler #=-19 (149224,447015,297772) : difference with theory (-19) = 0 

CORRECTING DEFECT 49 (vertices=72, convex hull=43, v0=125002)
After retessellation of defect 49 (v0=125002), euler #=-18 (149236,447069,297815) : difference with theory (-18) = 0 

CORRECTING DEFECT 50 (vertices=153, convex hull=139, v0=125257)
After retessellation of defect 50 (v0=125257), euler #=-17 (149287,447290,297986) : difference with theory (-17) = 0 

CORRECTING DEFECT 51 (vertices=64, convex hull=138, v0=125311)
After retessellation of defect 51 (v0=125311), euler #=-16 (149329,447472,298127) : difference with theory (-16) = 0 

CORRECTING DEFECT 52 (vertices=170, convex hull=60, v0=126810)
After retessellation of defect 52 (v0=126810), euler #=-15 (149338,447524,298171) : difference with theory (-15) = 0 

CORRECTING DEFECT 53 (vertices=22, convex hull=30, v0=126857)
After retessellation of defect 53 (v0=126857), euler #=-14 (149339,447535,298182) : difference with theory (-14) = 0 

CORRECTING DEFECT 54 (vertices=137, convex hull=205, v0=126988)
After retessellation of defect 54 (v0=126988), euler #=-13 (149415,447865,298437) : difference with theory (-13) = 0 

CORRECTING DEFECT 55 (vertices=47, convex hull=53, v0=127097)
After retessellation of defect 55 (v0=127097), euler #=-12 (149426,447923,298485) : difference with theory (-12) = 0 

CORRECTING DEFECT 56 (vertices=22, convex hull=56, v0=128580)
After retessellation of defect 56 (v0=128580), euler #=-11 (149435,447972,298526) : difference with theory (-11) = 0 

CORRECTING DEFECT 57 (vertices=121, convex hull=162, v0=128821)
After retessellation of defect 57 (v0=128821), euler #=-10 (149480,448180,298690) : difference with theory (-10) = 0 

CORRECTING DEFECT 58 (vertices=27, convex hull=54, v0=132353)
After retessellation of defect 58 (v0=132353), euler #=-9 (149495,448242,298738) : difference with theory (-9) = 0 

CORRECTING DEFECT 59 (vertices=103, convex hull=36, v0=133557)
After retessellation of defect 59 (v0=133557), euler #=-8 (149505,448286,298773) : difference with theory (-8) = 0 

CORRECTING DEFECT 60 (vertices=129, convex hull=107, v0=133740)
After retessellation of defect 60 (v0=133740), euler #=-7 (149538,448432,298887) : difference with theory (-7) = 0 

CORRECTING DEFECT 61 (vertices=9, convex hull=27, v0=135137)
After retessellation of defect 61 (v0=135137), euler #=-6 (149540,448450,298904) : difference with theory (-6) = 0 

CORRECTING DEFECT 62 (vertices=20, convex hull=56, v0=138413)
After retessellation of defect 62 (v0=138413), euler #=-5 (149549,448498,298944) : difference with theory (-5) = 0 

CORRECTING DEFECT 63 (vertices=13, convex hull=21, v0=140267)
After retessellation of defect 63 (v0=140267), euler #=-4 (149551,448512,298957) : difference with theory (-4) = 0 

CORRECTING DEFECT 64 (vertices=71, convex hull=90, v0=143688)
After retessellation of defect 64 (v0=143688), euler #=-3 (149577,448626,299046) : difference with theory (-3) = 0 

CORRECTING DEFECT 65 (vertices=14, convex hull=27, v0=144639)
After retessellation of defect 65 (v0=144639), euler #=-2 (149578,448639,299059) : difference with theory (-2) = 0 

CORRECTING DEFECT 66 (vertices=63, convex hull=41, v0=149787)
After retessellation of defect 66 (v0=149787), euler #=-1 (149582,448666,299083) : difference with theory (-1) = 0 

CORRECTING DEFECT 67 (vertices=36, convex hull=56, v0=150757)
After retessellation of defect 67 (v0=150757), euler #=0 (149599,448741,299142) : difference with theory (0) = 0 

CORRECTING DEFECT 68 (vertices=30, convex hull=48, v0=154421)
After retessellation of defect 68 (v0=154421), euler #=1 (149607,448786,299180) : difference with theory (1) = 0 

CORRECTING DEFECT 69 (vertices=35, convex hull=73, v0=155590)
After retessellation of defect 69 (v0=155590), euler #=2 (149622,448860,299240) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.27 (0.06-->15.14) (max @ vno 10720 --> 151584)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.27 (0.06-->15.14) (max @ vno 10720 --> 151584)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
234 mutations (34.1%), 452 crossovers (65.9%), 622 vertices were eliminated
building final representation...
7412 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=149622, nf=299240, ne=448860, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 54.9 minutes
0 defective edges
removing intersecting faces
000: 939 intersecting
001: 105 intersecting
002: 46 intersecting
003: 29 intersecting
004: 6 intersecting
005: 2 intersecting
mris_fix_topology utimesec    3291.116674
mris_fix_topology stimesec    0.229965
mris_fix_topology ru_maxrss   497972
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56484
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22112
mris_fix_topology ru_oublock  14616
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    523
mris_fix_topology ru_nivcsw   8160
FSRUNTIME@ mris_fix_topology lh  0.9145 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050111 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=-172 (nv=160236, nf=320816, ne=481224, 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 8 iterations
marking ambiguous vertices...
18748 ambiguous faces found in tessellation
segmenting defects...
72 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 50 into 43
      -merging segment 52 into 51
70 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5203  (-4.7602)
      -vertex     loglikelihood: -6.3564  (-3.1782)
      -normal dot loglikelihood: -3.4649  (-3.4649)
      -quad curv  loglikelihood: -6.1904  (-3.0952)
      Total Loglikelihood : -25.5320

CORRECTING DEFECT 0 (vertices=1665, convex hull=378, v0=574)
After retessellation of defect 0 (v0=574), euler #=-67 (149683,446448,296698) : difference with theory (-67) = 0 

CORRECTING DEFECT 1 (vertices=12, convex hull=20, v0=1071)
After retessellation of defect 1 (v0=1071), euler #=-66 (149684,446455,296705) : difference with theory (-66) = 0 

CORRECTING DEFECT 2 (vertices=19, convex hull=49, v0=1285)
After retessellation of defect 2 (v0=1285), euler #=-65 (149693,446498,296740) : difference with theory (-65) = 0 

CORRECTING DEFECT 3 (vertices=37, convex hull=32, v0=1943)
After retessellation of defect 3 (v0=1943), euler #=-64 (149695,446516,296757) : difference with theory (-64) = 0 

CORRECTING DEFECT 4 (vertices=28, convex hull=54, v0=2347)
After retessellation of defect 4 (v0=2347), euler #=-63 (149703,446558,296792) : difference with theory (-63) = 0 

CORRECTING DEFECT 5 (vertices=3446, convex hull=707, v0=2778)
XL defect detected...
After retessellation of defect 5 (v0=2778), euler #=-63 (149788,447171,297320) : difference with theory (-62) = 1 

CORRECTING DEFECT 6 (vertices=65, convex hull=71, v0=3998)
After retessellation of defect 6 (v0=3998), euler #=-62 (149814,447283,297407) : difference with theory (-61) = 1 

CORRECTING DEFECT 7 (vertices=23, convex hull=61, v0=6730)
After retessellation of defect 7 (v0=6730), euler #=-61 (149823,447338,297454) : difference with theory (-60) = 1 

CORRECTING DEFECT 8 (vertices=23, convex hull=67, v0=9061)
After retessellation of defect 8 (v0=9061), euler #=-60 (149831,447386,297495) : difference with theory (-59) = 1 

CORRECTING DEFECT 9 (vertices=70, convex hull=81, v0=13927)
After retessellation of defect 9 (v0=13927), euler #=-59 (149852,447484,297573) : difference with theory (-58) = 1 

CORRECTING DEFECT 10 (vertices=5, convex hull=24, v0=26857)
After retessellation of defect 10 (v0=26857), euler #=-58 (149853,447494,297583) : difference with theory (-57) = 1 

CORRECTING DEFECT 11 (vertices=38, convex hull=74, v0=30976)
After retessellation of defect 11 (v0=30976), euler #=-57 (149873,447584,297654) : difference with theory (-56) = 1 

CORRECTING DEFECT 12 (vertices=26, convex hull=43, v0=31482)
After retessellation of defect 12 (v0=31482), euler #=-56 (149883,447630,297691) : difference with theory (-55) = 1 

CORRECTING DEFECT 13 (vertices=29, convex hull=50, v0=32692)
After retessellation of defect 13 (v0=32692), euler #=-55 (149900,447703,297748) : difference with theory (-54) = 1 

CORRECTING DEFECT 14 (vertices=54, convex hull=85, v0=44028)
After retessellation of defect 14 (v0=44028), euler #=-54 (149910,447765,297801) : difference with theory (-53) = 1 

CORRECTING DEFECT 15 (vertices=29, convex hull=87, v0=44355)
After retessellation of defect 15 (v0=44355), euler #=-53 (149931,447863,297879) : difference with theory (-52) = 1 

CORRECTING DEFECT 16 (vertices=22, convex hull=33, v0=54784)
After retessellation of defect 16 (v0=54784), euler #=-52 (149932,447881,297897) : difference with theory (-51) = 1 

CORRECTING DEFECT 17 (vertices=63, convex hull=82, v0=60575)
After retessellation of defect 17 (v0=60575), euler #=-51 (149970,448031,298010) : difference with theory (-50) = 1 

CORRECTING DEFECT 18 (vertices=484, convex hull=244, v0=63877)
normal vector of length zero at vertex 155685 with 3 faces
After retessellation of defect 18 (v0=63877), euler #=-50 (150006,448259,298203) : difference with theory (-49) = 1 

CORRECTING DEFECT 19 (vertices=24, convex hull=45, v0=67304)
After retessellation of defect 19 (v0=67304), euler #=-49 (150015,448301,298237) : difference with theory (-48) = 1 

CORRECTING DEFECT 20 (vertices=30, convex hull=55, v0=67330)
After retessellation of defect 20 (v0=67330), euler #=-48 (150030,448370,298292) : difference with theory (-47) = 1 

CORRECTING DEFECT 21 (vertices=69, convex hull=88, v0=68625)
After retessellation of defect 21 (v0=68625), euler #=-47 (150064,448513,298402) : difference with theory (-46) = 1 

CORRECTING DEFECT 22 (vertices=15, convex hull=24, v0=69356)
After retessellation of defect 22 (v0=69356), euler #=-46 (150068,448532,298418) : difference with theory (-45) = 1 

CORRECTING DEFECT 23 (vertices=31, convex hull=57, v0=70079)
After retessellation of defect 23 (v0=70079), euler #=-45 (150083,448601,298473) : difference with theory (-44) = 1 

CORRECTING DEFECT 24 (vertices=27, convex hull=25, v0=76171)
After retessellation of defect 24 (v0=76171), euler #=-44 (150089,448626,298493) : difference with theory (-43) = 1 

CORRECTING DEFECT 25 (vertices=308, convex hull=201, v0=80987)
After retessellation of defect 25 (v0=80987), euler #=-43 (150152,448911,298716) : difference with theory (-42) = 1 

CORRECTING DEFECT 26 (vertices=22, convex hull=42, v0=83896)
After retessellation of defect 26 (v0=83896), euler #=-42 (150165,448964,298757) : difference with theory (-41) = 1 

CORRECTING DEFECT 27 (vertices=134, convex hull=43, v0=87445)
After retessellation of defect 27 (v0=87445), euler #=-41 (150177,449016,298798) : difference with theory (-40) = 1 

CORRECTING DEFECT 28 (vertices=682, convex hull=402, v0=88765)
normal vector of length zero at vertex 156526 with 4 faces
After retessellation of defect 28 (v0=88765), euler #=-40 (150361,449765,299364) : difference with theory (-39) = 1 

CORRECTING DEFECT 29 (vertices=22, convex hull=54, v0=91671)
After retessellation of defect 29 (v0=91671), euler #=-39 (150373,449823,299411) : difference with theory (-38) = 1 

CORRECTING DEFECT 30 (vertices=43, convex hull=24, v0=91958)
After retessellation of defect 30 (v0=91958), euler #=-38 (150375,449839,299426) : difference with theory (-37) = 1 

CORRECTING DEFECT 31 (vertices=67, convex hull=109, v0=97193)
After retessellation of defect 31 (v0=97193), euler #=-37 (150421,450025,299567) : difference with theory (-36) = 1 

CORRECTING DEFECT 32 (vertices=359, convex hull=183, v0=99375)
After retessellation of defect 32 (v0=99375), euler #=-36 (150482,450289,299771) : difference with theory (-35) = 1 

CORRECTING DEFECT 33 (vertices=10, convex hull=37, v0=100613)
After retessellation of defect 33 (v0=100613), euler #=-35 (150485,450309,299789) : difference with theory (-34) = 1 

CORRECTING DEFECT 34 (vertices=11, convex hull=23, v0=105495)
After retessellation of defect 34 (v0=105495), euler #=-34 (150487,450324,299803) : difference with theory (-33) = 1 

CORRECTING DEFECT 35 (vertices=64, convex hull=113, v0=106265)
After retessellation of defect 35 (v0=106265), euler #=-33 (150534,450521,299954) : difference with theory (-32) = 1 

CORRECTING DEFECT 36 (vertices=39, convex hull=74, v0=110737)
After retessellation of defect 36 (v0=110737), euler #=-32 (150551,450601,300018) : difference with theory (-31) = 1 

CORRECTING DEFECT 37 (vertices=66, convex hull=79, v0=110911)
After retessellation of defect 37 (v0=110911), euler #=-31 (150578,450718,300109) : difference with theory (-30) = 1 

CORRECTING DEFECT 38 (vertices=35, convex hull=56, v0=113884)
After retessellation of defect 38 (v0=113884), euler #=-30 (150593,450785,300162) : difference with theory (-29) = 1 

CORRECTING DEFECT 39 (vertices=159, convex hull=49, v0=114497)
After retessellation of defect 39 (v0=114497), euler #=-29 (150611,450859,300219) : difference with theory (-28) = 1 

CORRECTING DEFECT 40 (vertices=262, convex hull=54, v0=114985)
After retessellation of defect 40 (v0=114985), euler #=-28 (150629,450937,300280) : difference with theory (-27) = 1 

CORRECTING DEFECT 41 (vertices=7, convex hull=33, v0=115694)
After retessellation of defect 41 (v0=115694), euler #=-27 (150632,450955,300296) : difference with theory (-26) = 1 

CORRECTING DEFECT 42 (vertices=12, convex hull=23, v0=119277)
After retessellation of defect 42 (v0=119277), euler #=-26 (150637,450975,300312) : difference with theory (-25) = 1 

CORRECTING DEFECT 43 (vertices=539, convex hull=217, v0=120409)
After retessellation of defect 43 (v0=120409), euler #=-24 (150679,451224,300521) : difference with theory (-24) = 0 

CORRECTING DEFECT 44 (vertices=318, convex hull=210, v0=120421)
After retessellation of defect 44 (v0=120421), euler #=-23 (150738,451503,300742) : difference with theory (-23) = 0 

CORRECTING DEFECT 45 (vertices=29, convex hull=75, v0=121800)
After retessellation of defect 45 (v0=121800), euler #=-22 (150750,451570,300798) : difference with theory (-22) = 0 

CORRECTING DEFECT 46 (vertices=54, convex hull=99, v0=123039)
After retessellation of defect 46 (v0=123039), euler #=-21 (150783,451709,300905) : difference with theory (-21) = 0 

CORRECTING DEFECT 47 (vertices=7, convex hull=15, v0=123091)
After retessellation of defect 47 (v0=123091), euler #=-20 (150787,451724,300917) : difference with theory (-20) = 0 

CORRECTING DEFECT 48 (vertices=5, convex hull=23, v0=123633)
After retessellation of defect 48 (v0=123633), euler #=-19 (150788,451733,300926) : difference with theory (-19) = 0 

CORRECTING DEFECT 49 (vertices=19, convex hull=56, v0=125629)
After retessellation of defect 49 (v0=125629), euler #=-18 (150797,451780,300965) : difference with theory (-18) = 0 

CORRECTING DEFECT 50 (vertices=114, convex hull=175, v0=126406)
After retessellation of defect 50 (v0=126406), euler #=-16 (150846,452006,301144) : difference with theory (-17) = -1 

CORRECTING DEFECT 51 (vertices=97, convex hull=52, v0=129411)
After retessellation of defect 51 (v0=129411), euler #=-15 (150867,452088,301206) : difference with theory (-16) = -1 

CORRECTING DEFECT 52 (vertices=41, convex hull=85, v0=129506)
After retessellation of defect 52 (v0=129506), euler #=-14 (150891,452194,301289) : difference with theory (-15) = -1 

CORRECTING DEFECT 53 (vertices=24, convex hull=37, v0=130099)
After retessellation of defect 53 (v0=130099), euler #=-13 (150897,452224,301314) : difference with theory (-14) = -1 

CORRECTING DEFECT 54 (vertices=111, convex hull=134, v0=133137)
After retessellation of defect 54 (v0=133137), euler #=-12 (150951,452447,301484) : difference with theory (-13) = -1 

CORRECTING DEFECT 55 (vertices=9, convex hull=25, v0=133798)
After retessellation of defect 55 (v0=133798), euler #=-11 (150953,452459,301495) : difference with theory (-12) = -1 

CORRECTING DEFECT 56 (vertices=19, convex hull=24, v0=134629)
After retessellation of defect 56 (v0=134629), euler #=-10 (150954,452467,301503) : difference with theory (-11) = -1 

CORRECTING DEFECT 57 (vertices=17, convex hull=48, v0=136438)
After retessellation of defect 57 (v0=136438), euler #=-9 (150965,452519,301545) : difference with theory (-10) = -1 

CORRECTING DEFECT 58 (vertices=22, convex hull=60, v0=137124)
After retessellation of defect 58 (v0=137124), euler #=-8 (150974,452565,301583) : difference with theory (-9) = -1 

CORRECTING DEFECT 59 (vertices=23, convex hull=28, v0=139443)
After retessellation of defect 59 (v0=139443), euler #=-7 (150978,452585,301600) : difference with theory (-8) = -1 

CORRECTING DEFECT 60 (vertices=167, convex hull=177, v0=139519)
normal vector of length zero at vertex 159856 with 4 faces
After retessellation of defect 60 (v0=139519), euler #=-6 (151055,452897,301836) : difference with theory (-7) = -1 

CORRECTING DEFECT 61 (vertices=45, convex hull=72, v0=149197)
After retessellation of defect 61 (v0=149197), euler #=-5 (151078,452994,301911) : difference with theory (-6) = -1 

CORRECTING DEFECT 62 (vertices=34, convex hull=67, v0=149748)
After retessellation of defect 62 (v0=149748), euler #=-4 (151087,453047,301956) : difference with theory (-5) = -1 

CORRECTING DEFECT 63 (vertices=30, convex hull=21, v0=151558)
After retessellation of defect 63 (v0=151558), euler #=-3 (151089,453061,301969) : difference with theory (-4) = -1 

CORRECTING DEFECT 64 (vertices=36, convex hull=57, v0=151619)
After retessellation of defect 64 (v0=151619), euler #=-2 (151107,453139,302030) : difference with theory (-3) = -1 

CORRECTING DEFECT 65 (vertices=35, convex hull=64, v0=152163)
After retessellation of defect 65 (v0=152163), euler #=-1 (151126,453225,302098) : difference with theory (-2) = -1 

CORRECTING DEFECT 66 (vertices=26, convex hull=71, v0=152473)
After retessellation of defect 66 (v0=152473), euler #=0 (151138,453287,302149) : difference with theory (-1) = -1 

CORRECTING DEFECT 67 (vertices=61, convex hull=83, v0=155464)
After retessellation of defect 67 (v0=155464), euler #=1 (151151,453360,302210) : difference with theory (0) = -1 

CORRECTING DEFECT 68 (vertices=26, convex hull=72, v0=156981)
After retessellation of defect 68 (v0=156981), euler #=2 (151160,453416,302258) : difference with theory (1) = -1 

CORRECTING DEFECT 69 (vertices=62, convex hull=98, v0=158197)
After retessellation of defect 69 (v0=158197), euler #=2 (151182,453540,302360) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.27 (0.06-->13.15) (max @ vno 2505 --> 11710)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.27 (0.06-->13.15) (max @ vno 2505 --> 11710)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
217 mutations (33.9%), 423 crossovers (66.1%), 1201 vertices were eliminated
building final representation...
9054 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=151182, nf=302360, ne=453540, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 69.2 minutes
0 defective edges
removing intersecting faces
000: 783 intersecting
001: 18 intersecting
mris_fix_topology utimesec    4152.541717
mris_fix_topology stimesec    0.225965
mris_fix_topology ru_maxrss   521700
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   61315
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  14776
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    559
mris_fix_topology ru_nivcsw   5441
FSRUNTIME@ mris_fix_topology rh  1.1538 hours 1 threads
PIDs (10506 10509) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 149622 - 448860 + 299240 = 2 --> 0 holes
      F =2V-4:          299240 = 299244-4 (0)
      2E=3F:            897720 = 897720 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 151182 - 453540 + 302360 = 2 --> 0 holes
      F =2V-4:          302360 = 302364-4 (0)
      2E=3F:            907080 = 907080 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 323 intersecting
001: 81 intersecting
002: 46 intersecting
003: 29 intersecting
004: 8 intersecting
005: 6 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 167 intersecting
001: 12 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 23:18:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050111 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 23:18:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050111 rh 

Waiting for PID 13648 of (13648 13651) to complete...
Waiting for PID 13651 of (13648 13651) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050111 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-6.0.0/0050111/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
35615 bright wm thresholded.
2923 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.orig...
computing class statistics...
border white:    285738 voxels (1.70%)
border gray      337026 voxels (2.01%)
WM (96.0): 96.4 +- 8.9 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 58.8 (was 70)
setting MAX_BORDER_WHITE to 109.9 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 48.5 (was 40)
setting MAX_GRAY to 92.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 58.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.23 (0.01-->4.72) (max @ vno 62032 --> 68449)
face area 0.27 +- 0.13 (0.00-->5.43)
mean absolute distance = 0.62 +- 0.79
3050 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=69+-7.0
mean inside = 92.2, mean outside = 73.8
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.6, 110 (110) missing vertices, mean dist 0.2 [0.6 (%39.1)->0.6 (%60.9))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.26 (0.09-->6.11) (max @ vno 87872 --> 89028)
face area 0.27 +- 0.13 (0.00-->4.42)
mean absolute distance = 0.33 +- 0.53
3426 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3052683.5, rms=9.178
001: dt: 0.5000, sse=1692665.8, rms=6.212 (32.316%)
002: dt: 0.5000, sse=1216314.0, rms=4.711 (24.159%)
003: dt: 0.5000, sse=1040627.7, rms=4.028 (14.508%)
004: dt: 0.5000, sse=977300.9, rms=3.728 (7.442%)
005: dt: 0.5000, sse=950391.7, rms=3.616 (3.016%)
006: dt: 0.5000, sse=938116.8, rms=3.551 (1.798%)
rms = 3.53, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=933157.0, rms=3.528 (0.637%)
008: dt: 0.2500, sse=749623.5, rms=2.356 (33.211%)
009: dt: 0.2500, sse=706605.5, rms=2.011 (14.659%)
010: dt: 0.2500, sse=702436.3, rms=1.939 (3.554%)
011: dt: 0.2500, sse=694763.0, rms=1.885 (2.827%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=693181.3, rms=1.868 (0.904%)
013: dt: 0.1250, sse=686257.1, rms=1.799 (3.696%)
rms = 1.79, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=685079.8, rms=1.790 (0.485%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=82.8, 159 (43) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.2 (%26.6))]
%79 local maxima, %16 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 0.89 +- 0.25 (0.10-->5.38) (max @ vno 68449 --> 148523)
face area 0.33 +- 0.16 (0.00-->5.90)
mean absolute distance = 0.24 +- 0.37
3084 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1281237.5, rms=4.416
015: dt: 0.5000, sse=987069.5, rms=2.964 (32.866%)
rms = 3.19, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=868941.7, rms=2.212 (25.374%)
017: dt: 0.2500, sse=816934.2, rms=1.792 (18.984%)
018: dt: 0.2500, sse=801171.5, rms=1.637 (8.640%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=798223.9, rms=1.599 (2.361%)
020: dt: 0.1250, sse=791388.2, rms=1.529 (4.375%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=790522.6, rms=1.525 (0.273%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=84.5, 129 (15) missing vertices, mean dist -0.1 [0.3 (%63.9)->0.2 (%36.1))]
%85 local maxima, %10 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 0.88 +- 0.25 (0.03-->5.42) (max @ vno 68449 --> 148523)
face area 0.33 +- 0.16 (0.00-->5.96)
mean absolute distance = 0.22 +- 0.32
2974 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=903414.3, rms=2.590
rms = 2.70, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=817586.6, rms=1.917 (25.963%)
023: dt: 0.2500, sse=780150.0, rms=1.525 (20.466%)
024: dt: 0.2500, sse=775793.5, rms=1.463 (4.085%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=774103.4, rms=1.462 (0.041%)
026: dt: 0.1250, sse=768196.9, rms=1.398 (4.394%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=768512.7, rms=1.400 (-0.195%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=85.2, 136 (12) missing vertices, mean dist -0.0 [0.2 (%53.2)->0.2 (%46.8))]
%87 local maxima, % 8 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-6.0.0/0050111/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=783816.9, rms=1.636
rms = 1.79, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=750334.9, rms=1.224 (25.160%)
029: dt: 0.2500, sse=739157.7, rms=1.050 (14.212%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
rms = 1.05, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=737486.4, rms=1.046 (0.440%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7415 vertices
erasing segment 1 (vno[0] = 91089)
erasing segment 2 (vno[0] = 105452)
erasing segment 3 (vno[0] = 106407)
erasing segment 4 (vno[0] = 106460)
erasing segment 5 (vno[0] = 107419)
erasing segment 6 (vno[0] = 114851)
erasing segment 7 (vno[0] = 149014)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.area
vertex spacing 0.88 +- 0.26 (0.03-->6.11) (max @ vno 87872 --> 89028)
face area 0.33 +- 0.16 (0.00-->5.98)
refinement took 5.9 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050111 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-6.0.0/0050111/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
35615 bright wm thresholded.
2923 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.orig...
computing class statistics...
border white:    285738 voxels (1.70%)
border gray      337026 voxels (2.01%)
WM (96.0): 96.4 +- 8.9 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70)
setting MAX_BORDER_WHITE to 108.9 (was 105)
setting MIN_BORDER_WHITE to 68.0 (was 85)
setting MAX_CSF to 47.5 (was 40)
setting MAX_GRAY to 91.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 57.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.24 (0.05-->5.71) (max @ vno 149976 --> 149980)
face area 0.27 +- 0.13 (0.00-->5.89)
mean absolute distance = 0.60 +- 0.76
3338 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-7.0,    GM=68+-7.0
mean inside = 92.0, mean outside = 73.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.1, 80 (80) missing vertices, mean dist 0.2 [0.5 (%39.7)->0.7 (%60.3))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.26 (0.10-->6.69) (max @ vno 64061 --> 64070)
face area 0.27 +- 0.13 (0.00-->5.83)
mean absolute distance = 0.32 +- 0.53
3430 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3193274.8, rms=9.375
001: dt: 0.5000, sse=1795154.5, rms=6.440 (31.300%)
002: dt: 0.5000, sse=1302257.9, rms=4.982 (22.644%)
003: dt: 0.5000, sse=1108779.2, rms=4.271 (14.264%)
004: dt: 0.5000, sse=1032370.0, rms=3.914 (8.368%)
005: dt: 0.5000, sse=990090.2, rms=3.753 (4.126%)
006: dt: 0.5000, sse=971098.2, rms=3.667 (2.275%)
rms = 3.64, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=966308.4, rms=3.641 (0.722%)
008: dt: 0.2500, sse=771488.6, rms=2.456 (32.546%)
009: dt: 0.2500, sse=723517.6, rms=2.089 (14.952%)
010: dt: 0.2500, sse=717243.9, rms=2.007 (3.901%)
011: dt: 0.2500, sse=708256.1, rms=1.949 (2.920%)
rms = 1.93, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=706848.0, rms=1.932 (0.848%)
013: dt: 0.1250, sse=700147.5, rms=1.863 (3.592%)
rms = 1.85, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=698903.2, rms=1.854 (0.441%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=82.2, 112 (11) missing vertices, mean dist -0.2 [0.3 (%73.2)->0.2 (%26.8))]
%81 local maxima, %15 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 0.89 +- 0.26 (0.03-->7.77) (max @ vno 64051 --> 64050)
face area 0.34 +- 0.17 (0.00-->7.37)
mean absolute distance = 0.24 +- 0.36
3156 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1276901.6, rms=4.326
015: dt: 0.5000, sse=1005334.7, rms=3.049 (29.518%)
rms = 3.33, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=882324.3, rms=2.250 (26.217%)
017: dt: 0.2500, sse=835284.2, rms=1.842 (18.136%)
018: dt: 0.2500, sse=817829.6, rms=1.689 (8.285%)
rms = 1.65, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=816100.4, rms=1.653 (2.154%)
020: dt: 0.1250, sse=807686.2, rms=1.581 (4.364%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=807650.7, rms=1.576 (0.319%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=83.9, 106 (5) missing vertices, mean dist -0.1 [0.3 (%63.5)->0.2 (%36.5))]
%86 local maxima, %10 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 0.88 +- 0.26 (0.07-->8.54) (max @ vno 64051 --> 64050)
face area 0.33 +- 0.17 (0.00-->7.11)
mean absolute distance = 0.23 +- 0.32
2981 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=919616.1, rms=2.599
rms = 2.80, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=833900.7, rms=1.932 (25.671%)
023: dt: 0.2500, sse=800671.4, rms=1.572 (18.647%)
024: dt: 0.2500, sse=790960.4, rms=1.509 (3.971%)
rms = 1.51, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=790141.8, rms=1.506 (0.237%)
026: dt: 0.1250, sse=786894.2, rms=1.433 (4.826%)
rms = 1.43, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=784327.4, rms=1.435 (-0.111%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=84.5, 124 (3) missing vertices, mean dist -0.0 [0.2 (%53.0)->0.2 (%47.0))]
%88 local maxima, % 8 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-6.0.0/0050111/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=801526.2, rms=1.650
rms = 1.85, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=762544.6, rms=1.224 (25.790%)
029: dt: 0.2500, sse=754327.0, rms=1.052 (14.104%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
rms = 1.05, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=750134.6, rms=1.046 (0.498%)
positioning took 0.5 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7646 vertices
erasing segment 1 (vno[0] = 68791)
erasing segment 2 (vno[0] = 106578)
erasing segment 3 (vno[0] = 107727)
erasing segment 4 (vno[0] = 109717)
erasing segment 5 (vno[0] = 113032)
erasing segment 6 (vno[0] = 115207)
erasing segment 7 (vno[0] = 116192)
erasing segment 8 (vno[0] = 117211)
erasing segment 9 (vno[0] = 150631)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.area
vertex spacing 0.88 +- 0.26 (0.04-->8.70) (max @ vno 64050 --> 64051)
face area 0.33 +- 0.16 (0.00-->7.04)
refinement took 5.6 minutes
PIDs (13648 13651) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 23:24:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 23:24:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

Waiting for PID 13916 of (13916 13919) to complete...
Waiting for PID 13919 of (13916 13919) 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 (13916 13919) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 23:24:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 23:24:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 13962 of (13962 13965) to complete...
Waiting for PID 13965 of (13962 13965) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 47.4 mm, total surface area = 88164 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.179 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.046 (target=0.015)   
step 035: RMS=0.038 (target=0.015)   
step 040: RMS=0.033 (target=0.015)   
step 045: RMS=0.029 (target=0.015)   
step 050: RMS=0.027 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    47.249816
mris_inflate stimesec    0.114982
mris_inflate ru_maxrss   219528
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31951
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10528
mris_inflate ru_oublock  11720
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2374
mris_inflate ru_nivcsw   3472

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 47.9 mm, total surface area = 89341 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.183 (target=0.015)   
step 005: RMS=0.127 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.079 (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=0.033 (target=0.015)   
step 045: RMS=0.029 (target=0.015)   
step 050: RMS=0.027 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    54.410728
mris_inflate stimesec    0.154976
mris_inflate ru_maxrss   221728
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31989
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11840
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2188
mris_inflate ru_nivcsw   3926
PIDs (13962 13965) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 23:25:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 23:25:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 14103 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14106 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14109 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14112 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14115 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14118 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14121 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14124 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14127 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14130 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14133 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...
Waiting for PID 14136 of (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = -11.386*4pi (-143.078) --> 12 handles
ICI = 207.5, FI = 1971.2, variation=32064.772
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
176 vertices thresholded to be in k1 ~ [-0.20 0.35], k2 ~ [-0.09 0.06]
total integrated curvature = 0.493*4pi (6.197) --> 1 handles
ICI = 1.6, FI = 10.4, variation=176.389
126 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
153 vertices thresholded to be in [-0.12 0.18]
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 = -13.801*4pi (-173.424) --> 15 handles
ICI = 214.6, FI = 1998.5, variation=32679.549
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
209 vertices thresholded to be in k1 ~ [-0.17 1.25], k2 ~ [-0.09 0.06]
total integrated curvature = 0.500*4pi (6.289) --> 0 handles
ICI = 1.6, FI = 10.4, variation=177.782
117 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
121 vertices thresholded to be in [-0.11 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023
done.
PIDs (14103 14106 14109 14112 14115 14118 14121 14124 14127 14130 14133 14136) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 23:26:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050111 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      [ 0050111/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                      [ 304 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.205353
WARN:    S explicit min:                          0.000000	vertex = 41

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 23:27:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050111 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      [ 0050111/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                      [ 311 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.100011
WARN:    S explicit min:                          0.000000	vertex = 34
#--------------------------------------------
#@# Sphere lh Sat Oct  7 23:27:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 23:27:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 14304 of (14304 14308) to complete...
Waiting for PID 14308 of (14304 14308) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0.286...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.53
pass 1: epoch 2 of 3 starting distance error %20.45
unfolding complete - removing small folds...
starting distance error %20.43
removing remaining folds...
final distance error %20.44
MRISunfold() return, current seed 1234
-01: dt=0.0000, 257 negative triangles
177: dt=0.9900, 257 negative triangles
178: dt=0.9900, 127 negative triangles
179: dt=0.9900, 96 negative triangles
180: dt=0.9900, 93 negative triangles
181: dt=0.9900, 76 negative triangles
182: dt=0.9900, 60 negative triangles
183: dt=0.9900, 57 negative triangles
184: dt=0.9900, 66 negative triangles
185: dt=0.9900, 47 negative triangles
186: dt=0.9900, 40 negative triangles
187: dt=0.9900, 44 negative triangles
188: dt=0.9900, 44 negative triangles
189: dt=0.9900, 34 negative triangles
190: dt=0.9900, 35 negative triangles
191: dt=0.9900, 31 negative triangles
192: dt=0.9900, 30 negative triangles
193: dt=0.9900, 32 negative triangles
194: dt=0.9900, 27 negative triangles
195: dt=0.9900, 26 negative triangles
196: dt=0.9900, 25 negative triangles
197: dt=0.9900, 22 negative triangles
198: dt=0.9900, 21 negative triangles
199: dt=0.9900, 23 negative triangles
200: dt=0.9900, 16 negative triangles
201: dt=0.9900, 19 negative triangles
202: dt=0.9900, 16 negative triangles
203: dt=0.9900, 13 negative triangles
204: dt=0.9900, 14 negative triangles
205: dt=0.9900, 11 negative triangles
206: dt=0.9900, 12 negative triangles
207: dt=0.9900, 6 negative triangles
208: dt=0.9900, 8 negative triangles
209: dt=0.9900, 2 negative triangles
210: dt=0.9900, 1 negative triangles
211: dt=0.9900, 3 negative triangles
212: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.30 hours
mris_sphere utimesec    4634.646426
mris_sphere stimesec    1.964701
mris_sphere ru_maxrss   307792
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   54165
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10592
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    132518
mris_sphere ru_nivcsw   393081
FSRUNTIME@ mris_sphere  1.2993 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0.288...
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 %19.75
pass 1: epoch 2 of 3 starting distance error %19.70
unfolding complete - removing small folds...
starting distance error %19.59
removing remaining folds...
final distance error %19.61
MRISunfold() return, current seed 1234
-01: dt=0.0000, 246 negative triangles
195: dt=0.9900, 246 negative triangles
196: dt=0.9900, 86 negative triangles
197: dt=0.9900, 59 negative triangles
198: dt=0.9900, 42 negative triangles
199: dt=0.9900, 48 negative triangles
200: dt=0.9900, 33 negative triangles
201: dt=0.9900, 31 negative triangles
202: dt=0.9900, 32 negative triangles
203: dt=0.9900, 26 negative triangles
204: dt=0.9900, 28 negative triangles
205: dt=0.9900, 27 negative triangles
206: dt=0.9900, 26 negative triangles
207: dt=0.9900, 28 negative triangles
208: dt=0.9900, 31 negative triangles
209: dt=0.9900, 29 negative triangles
210: dt=0.9900, 32 negative triangles
211: dt=0.9900, 27 negative triangles
212: dt=0.9900, 31 negative triangles
213: dt=0.9405, 27 negative triangles
214: dt=0.9405, 29 negative triangles
215: dt=0.9405, 28 negative triangles
216: dt=0.9405, 27 negative triangles
217: dt=0.9405, 28 negative triangles
218: dt=0.9405, 28 negative triangles
219: dt=0.9405, 26 negative triangles
220: dt=0.9405, 28 negative triangles
221: dt=0.9405, 26 negative triangles
222: dt=0.9405, 35 negative triangles
223: dt=0.8935, 26 negative triangles
224: dt=0.8935, 29 negative triangles
225: dt=0.8935, 31 negative triangles
226: dt=0.8935, 26 negative triangles
227: dt=0.8935, 25 negative triangles
228: dt=0.8935, 29 negative triangles
229: dt=0.8935, 26 negative triangles
230: dt=0.8935, 26 negative triangles
231: dt=0.8935, 26 negative triangles
232: dt=0.8935, 25 negative triangles
233: dt=0.8935, 25 negative triangles
234: dt=0.8935, 23 negative triangles
235: dt=0.8935, 26 negative triangles
236: dt=0.8935, 26 negative triangles
237: dt=0.8935, 26 negative triangles
238: dt=0.8935, 27 negative triangles
239: dt=0.8935, 20 negative triangles
240: dt=0.8935, 25 negative triangles
241: dt=0.8935, 21 negative triangles
242: dt=0.8935, 23 negative triangles
243: dt=0.8935, 20 negative triangles
244: dt=0.8935, 21 negative triangles
245: dt=0.8935, 19 negative triangles
246: dt=0.8935, 21 negative triangles
247: dt=0.8935, 24 negative triangles
248: dt=0.8935, 24 negative triangles
249: dt=0.8935, 20 negative triangles
250: dt=0.8935, 21 negative triangles
251: dt=0.8935, 20 negative triangles
252: dt=0.8935, 18 negative triangles
253: dt=0.8935, 16 negative triangles
254: dt=0.8935, 14 negative triangles
255: dt=0.8935, 13 negative triangles
256: dt=0.8935, 11 negative triangles
257: dt=0.8935, 14 negative triangles
258: dt=0.8935, 10 negative triangles
259: dt=0.8935, 15 negative triangles
260: dt=0.8935, 13 negative triangles
261: dt=0.8935, 9 negative triangles
262: dt=0.8935, 10 negative triangles
263: dt=0.8935, 14 negative triangles
264: dt=0.8935, 11 negative triangles
265: dt=0.8935, 9 negative triangles
266: dt=0.8935, 11 negative triangles
267: dt=0.8935, 10 negative triangles
268: dt=0.8935, 6 negative triangles
269: dt=0.8935, 3 negative triangles
270: dt=0.8935, 4 negative triangles
271: dt=0.8935, 1 negative triangles
272: dt=0.8935, 4 negative triangles
273: dt=0.8935, 4 negative triangles
274: dt=0.8935, 2 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.32 hours
mris_sphere utimesec    4812.849335
mris_sphere stimesec    2.022692
mris_sphere ru_maxrss   311176
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   54489
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10720
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    122717
mris_sphere ru_nivcsw   388762
FSRUNTIME@ mris_sphere  1.3248 hours 1 threads
PIDs (14304 14308) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 00:46:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 00:46:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 18063 of (18063 18131) to complete...
Waiting for PID 18131 of (18063 18131) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 5.605
curvature mean = 0.011, std = 0.817
curvature mean = 0.023, std = 0.860
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, -8.00) sse = 293259.0, tmin=2.8448
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 260942.0, tmin=4.0014
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 257141.3, tmin=5.1833
  d=4.00 min @ (1.00, 1.00, 0.00) sse = 255696.2, tmin=6.3730
  d=2.00 min @ (-0.50, -0.50, 0.50) sse = 255108.5, tmin=7.5608
  d=1.00 min @ (0.25, 0.00, -0.25) sse = 254919.5, tmin=8.7407
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 254916.3, tmin=9.9444
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.94 min
curvature mean = -0.017, std = 0.822
curvature mean = 0.010, std = 0.945
curvature mean = -0.021, std = 0.831
curvature mean = 0.004, std = 0.978
curvature mean = -0.023, std = 0.832
curvature mean = 0.001, std = 0.992
2 Reading smoothwm
curvature mean = -0.031, std = 0.318
curvature mean = 0.034, std = 0.247
curvature mean = 0.075, std = 0.298
curvature mean = 0.029, std = 0.306
curvature mean = 0.045, std = 0.467
curvature mean = 0.028, std = 0.334
curvature mean = 0.026, std = 0.604
curvature mean = 0.027, std = 0.346
curvature mean = 0.011, std = 0.720
MRISregister() return, current seed 0
-01: dt=0.0000, 32 negative triangles
118: dt=0.9900, 32 negative triangles
expanding nbhd size to 1
119: dt=0.9900, 51 negative triangles
120: dt=0.9405, 34 negative triangles
121: dt=0.9405, 35 negative triangles
122: dt=0.9405, 33 negative triangles
123: dt=0.9405, 36 negative triangles
124: dt=0.9405, 29 negative triangles
125: dt=0.9405, 30 negative triangles
126: dt=0.9405, 24 negative triangles
127: dt=0.9405, 26 negative triangles
128: dt=0.9405, 16 negative triangles
129: dt=0.9405, 17 negative triangles
130: dt=0.9405, 13 negative triangles
131: dt=0.9405, 14 negative triangles
132: dt=0.9405, 8 negative triangles
133: dt=0.9405, 8 negative triangles
134: dt=0.9405, 6 negative triangles
135: dt=0.9405, 7 negative triangles
136: dt=0.9405, 6 negative triangles
137: dt=0.9405, 6 negative triangles
138: dt=0.9405, 3 negative triangles
139: dt=0.9405, 5 negative triangles
140: dt=0.9405, 5 negative triangles
141: dt=0.9405, 2 negative triangles
142: dt=0.9405, 2 negative triangles
143: dt=0.9405, 5 negative triangles
144: dt=0.9405, 3 negative triangles
145: dt=0.9405, 3 negative triangles
146: dt=0.9405, 3 negative triangles
147: dt=0.9405, 2 negative triangles
148: dt=0.9405, 3 negative triangles
149: dt=0.9405, 2 negative triangles
150: dt=0.9405, 2 negative triangles
151: dt=0.8935, 3 negative triangles
152: dt=0.8935, 2 negative triangles
153: dt=0.8935, 2 negative triangles
154: dt=0.8935, 3 negative triangles
155: dt=0.8935, 4 negative triangles
156: dt=0.8935, 3 negative triangles
157: dt=0.8935, 2 negative triangles
158: dt=0.8935, 2 negative triangles
159: dt=0.8935, 2 negative triangles
160: dt=0.8935, 2 negative triangles
161: dt=0.8488, 5 negative triangles
162: dt=0.8488, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.45 hours
mris_register utimesec    5124.181006
mris_register stimesec    4.145369
mris_register ru_maxrss   273436
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38762
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  10528
mris_register ru_oublock  10624
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    394094
mris_register ru_nivcsw   272529
FSRUNTIME@ mris_register  1.4506 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 5.539
curvature mean = 0.017, std = 0.820
curvature mean = 0.022, std = 0.858
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 356643.4, tmin=1.8084
  d=32.00 min @ (0.00, 8.00, 0.00) sse = 313599.2, tmin=3.1711
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 293868.2, tmin=4.5508
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 292641.0, tmin=5.9459
  d=4.00 min @ (0.00, 1.00, 0.00) sse = 291455.5, tmin=7.3371
  d=1.00 min @ (-0.25, 0.00, 0.00) sse = 291354.5, tmin=10.1410
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 291330.0, tmin=11.5704
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  11.57 min
curvature mean = -0.010, std = 0.819
curvature mean = 0.009, std = 0.945
curvature mean = -0.016, std = 0.826
curvature mean = 0.003, std = 0.978
curvature mean = -0.019, std = 0.825
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.031, std = 0.316
curvature mean = 0.033, std = 0.243
curvature mean = 0.075, std = 0.304
curvature mean = 0.027, std = 0.302
curvature mean = 0.044, std = 0.481
curvature mean = 0.025, std = 0.329
curvature mean = 0.025, std = 0.621
curvature mean = 0.025, std = 0.341
curvature mean = 0.009, std = 0.738
MRISregister() return, current seed 0
-01: dt=0.0000, 75 negative triangles
123: dt=0.9900, 75 negative triangles
expanding nbhd size to 1
124: dt=0.9900, 111 negative triangles
125: dt=0.9900, 66 negative triangles
126: dt=0.9900, 58 negative triangles
127: dt=0.9900, 55 negative triangles
128: dt=0.9900, 44 negative triangles
129: dt=0.9900, 44 negative triangles
130: dt=0.9900, 32 negative triangles
131: dt=0.9900, 24 negative triangles
132: dt=0.9900, 25 negative triangles
133: dt=0.9900, 21 negative triangles
134: dt=0.9900, 22 negative triangles
135: dt=0.9900, 19 negative triangles
136: dt=0.9900, 15 negative triangles
137: dt=0.9900, 16 negative triangles
138: dt=0.9900, 13 negative triangles
139: dt=0.9900, 10 negative triangles
140: dt=0.9900, 15 negative triangles
141: dt=0.9900, 10 negative triangles
142: dt=0.9900, 9 negative triangles
143: dt=0.9900, 11 negative triangles
144: dt=0.9900, 7 negative triangles
145: dt=0.9900, 7 negative triangles
146: dt=0.9900, 5 negative triangles
147: dt=0.9900, 6 negative triangles
148: dt=0.9900, 3 negative triangles
149: dt=0.9900, 3 negative triangles
150: dt=0.9900, 2 negative triangles
151: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.57 hours
mris_register utimesec    5814.303091
mris_register stimesec    3.865412
mris_register ru_maxrss   275508
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   40833
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  10640
mris_register ru_oublock  10728
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    301597
mris_register ru_nivcsw   242695
FSRUNTIME@ mris_register  1.5674 hours 1 threads
PIDs (18063 18131) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 02:20:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 02:20:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

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

Waiting for PID 25953 of (25953 25956) to complete...
Waiting for PID 25956 of (25953 25956) 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 (25953 25956) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 02:20:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 02:20:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 25998 of (25998 26001) to complete...
Waiting for PID 26001 of (25998 26001) 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 (25998 26001) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 02:20:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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 02:20:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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 26044 of (26044 26047) to complete...
Waiting for PID 26047 of (26044 26047) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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...
2065 labels changed using aseg
relabeling using gibbs priors...
000:   3470 changed, 149622 examined...
001:    853 changed, 14256 examined...
002:    229 changed, 4708 examined...
003:     73 changed, 1370 examined...
004:     29 changed, 444 examined...
005:     11 changed, 172 examined...
006:      6 changed, 67 examined...
007:      2 changed, 37 examined...
008:      1 changed, 14 examined...
009:      2 changed, 7 examined...
010:      1 changed, 12 examined...
011:      0 changed, 7 examined...
279 labels changed using aseg
000: 153 total segments, 104 labels (458 vertices) changed
001: 48 total segments, 3 labels (11 vertices) changed
002: 45 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2432 vertices marked for relabeling...
2432 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 18 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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...
1402 labels changed using aseg
relabeling using gibbs priors...
000:   3013 changed, 151182 examined...
001:    710 changed, 12952 examined...
002:    152 changed, 3910 examined...
003:     58 changed, 951 examined...
004:     28 changed, 340 examined...
005:      5 changed, 145 examined...
006:      3 changed, 37 examined...
007:      2 changed, 18 examined...
008:      0 changed, 12 examined...
130 labels changed using aseg
000: 112 total segments, 71 labels (372 vertices) changed
001: 43 total segments, 2 labels (3 vertices) changed
002: 41 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...
1816 vertices marked for relabeling...
1816 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 19 seconds.
PIDs (26044 26047) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 02:21:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050111 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 02:21:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050111 rh 

Waiting for PID 26104 of (26104 26107) to complete...
Waiting for PID 26107 of (26104 26107) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050111 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-6.0.0/0050111/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
35615 bright wm thresholded.
2923 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.orig...
computing class statistics...
border white:    285738 voxels (1.70%)
border gray      337026 voxels (2.01%)
WM (96.0): 96.4 +- 8.9 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 58.8 (was 70)
setting MAX_BORDER_WHITE to 109.9 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 48.5 (was 40)
setting MAX_GRAY to 92.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 58.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.8,    GM=69+-7.0
mean inside = 92.2, mean outside = 73.8
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 0.88 +- 0.26 (0.03-->6.11) (max @ vno 87872 --> 89028)
face area 0.33 +- 0.16 (0.00-->5.97)
mean absolute distance = 0.53 +- 0.76
2669 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 points - only 0.00% unknown
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 228 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 7 with 98 points - only 0.00% unknown
deleting segment 8 with 26 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
mean border=79.4, 116 (116) missing vertices, mean dist 0.3 [0.8 (%13.8)->0.5 (%86.2))]
%67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.26 (0.11-->5.67) (max @ vno 68449 --> 148523)
face area 0.33 +- 0.16 (0.00-->6.09)
mean absolute distance = 0.32 +- 0.52
2997 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2121323.8, rms=7.019
001: dt: 0.5000, sse=1171086.1, rms=4.026 (42.649%)
002: dt: 0.5000, sse=1018829.7, rms=3.318 (17.580%)
rms = 3.43, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=887399.6, rms=2.539 (23.470%)
004: dt: 0.2500, sse=833637.8, rms=2.134 (15.962%)
005: dt: 0.2500, sse=814894.4, rms=1.970 (7.679%)
006: dt: 0.2500, sse=808873.2, rms=1.911 (3.013%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=805191.6, rms=1.870 (2.134%)
008: dt: 0.1250, sse=798946.2, rms=1.812 (3.097%)
rms = 1.80, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=798275.0, rms=1.801 (0.601%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 3 with 87 points - only 0.00% unknown
deleting segment 4 with 66 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 86 points - only 0.00% unknown
deleting segment 7 with 21 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
mean border=82.8, 91 (37) missing vertices, mean dist -0.2 [0.4 (%74.0)->0.2 (%26.0))]
%79 local maxima, %16 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 0.89 +- 0.26 (0.08-->5.81) (max @ vno 60816 --> 62011)
face area 0.34 +- 0.17 (0.00-->6.57)
mean absolute distance = 0.24 +- 0.37
2968 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1273868.8, rms=4.352
010: dt: 0.5000, sse=969950.9, rms=2.869 (34.075%)
rms = 3.11, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=861102.8, rms=2.116 (26.247%)
012: dt: 0.2500, sse=815402.9, rms=1.698 (19.766%)
013: dt: 0.2500, sse=804740.9, rms=1.562 (8.017%)
rms = 1.54, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=801819.6, rms=1.536 (1.628%)
015: dt: 0.1250, sse=795341.6, rms=1.474 (4.041%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=795106.4, rms=1.472 (0.120%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 87 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 72 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 85 points - only 0.00% unknown
deleting segment 9 with 20 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
mean border=84.5, 112 (24) missing vertices, mean dist -0.1 [0.3 (%64.2)->0.2 (%35.8))]
%85 local maxima, %11 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 0.88 +- 0.26 (0.05-->5.88) (max @ vno 60816 --> 62011)
face area 0.33 +- 0.17 (0.00-->6.47)
mean absolute distance = 0.23 +- 0.33
3044 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=906365.6, rms=2.571
rms = 2.68, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=820242.9, rms=1.889 (26.501%)
018: dt: 0.2500, sse=785165.0, rms=1.487 (21.298%)
019: dt: 0.2500, sse=779650.1, rms=1.425 (4.183%)
rms = 1.43, time step reduction 2 of 3 to 0.125...
rms = 1.39, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=774416.1, rms=1.392 (2.304%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 8 points - only 0.00% unknown
deleting segment 3 with 83 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 72 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 76 points - only 0.00% unknown
deleting segment 9 with 20 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 33.33% unknown
deleting segment 13 with 11 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 15 with 4 points - only 0.00% unknown
mean border=85.1, 129 (19) missing vertices, mean dist -0.0 [0.3 (%53.6)->0.2 (%46.4))]
%88 local maxima, % 8 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-6.0.0/0050111/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=794555.4, rms=1.664
rms = 1.97, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=757706.8, rms=1.218 (26.783%)
022: dt: 0.2500, sse=746095.1, rms=1.039 (14.699%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
rms = 1.03, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=744713.9, rms=1.032 (0.674%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 7511 vertices
erasing segment 1 (vno[0] = 89986)
erasing segment 2 (vno[0] = 105452)
erasing segment 3 (vno[0] = 106407)
erasing segment 4 (vno[0] = 106521)
erasing segment 5 (vno[0] = 107419)
erasing segment 6 (vno[0] = 114851)
erasing segment 7 (vno[0] = 149014)
erasing segment 8 (vno[0] = 149087)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.area
vertex spacing 0.88 +- 0.26 (0.03-->6.11) (max @ vno 87872 --> 89028)
face area 0.33 +- 0.17 (0.00-->6.48)
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...
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=56.7, 210 (210) missing vertices, mean dist 1.7 [0.9 (%0.0)->2.9 (%100.0))]
%13 local maxima, %45 large gradients and %39 min vals, 386 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=24802340.0, rms=28.972
001: dt: 0.0500, sse=21505454.0, rms=26.917 (7.093%)
002: dt: 0.0500, sse=19190652.0, rms=25.375 (5.730%)
003: dt: 0.0500, sse=17450250.0, rms=24.150 (4.826%)
004: dt: 0.0500, sse=16069850.0, rms=23.133 (4.213%)
005: dt: 0.0500, sse=14930276.0, rms=22.258 (3.783%)
006: dt: 0.0500, sse=13961437.0, rms=21.486 (3.469%)
007: dt: 0.0500, sse=13119396.0, rms=20.791 (3.232%)
008: dt: 0.0500, sse=12376192.0, rms=20.158 (3.043%)
009: dt: 0.0500, sse=11712162.0, rms=19.576 (2.891%)
010: dt: 0.0500, sse=11113874.0, rms=19.035 (2.760%)
positioning took 1.1 minutes
mean border=56.5, 146 (97) missing vertices, mean dist 1.4 [0.4 (%0.0)->2.4 (%100.0))]
%13 local maxima, %45 large gradients and %38 min vals, 345 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=11916668.0, rms=19.759
011: dt: 0.0500, sse=11365210.0, rms=19.266 (2.492%)
012: dt: 0.0500, sse=10861479.0, rms=18.805 (2.394%)
013: dt: 0.0500, sse=10399974.0, rms=18.372 (2.301%)
014: dt: 0.0500, sse=9976740.0, rms=17.966 (2.210%)
015: dt: 0.0500, sse=9587693.0, rms=17.585 (2.124%)
016: dt: 0.0500, sse=9229987.0, rms=17.226 (2.038%)
017: dt: 0.0500, sse=8899918.0, rms=16.889 (1.959%)
018: dt: 0.0500, sse=8595213.0, rms=16.571 (1.881%)
019: dt: 0.0500, sse=8313332.0, rms=16.272 (1.808%)
020: dt: 0.0500, sse=8051949.5, rms=15.989 (1.738%)
positioning took 1.1 minutes
mean border=56.3, 153 (84) missing vertices, mean dist 1.2 [0.1 (%1.2)->2.1 (%98.8))]
%14 local maxima, %45 large gradients and %38 min vals, 320 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=8158857.0, rms=16.113
021: dt: 0.0500, sse=7909502.0, rms=15.840 (1.691%)
022: dt: 0.0500, sse=7678241.0, rms=15.583 (1.623%)
023: dt: 0.0500, sse=7461632.5, rms=15.338 (1.570%)
024: dt: 0.0500, sse=7259797.0, rms=15.107 (1.510%)
025: dt: 0.0500, sse=7071108.0, rms=14.887 (1.456%)
026: dt: 0.0500, sse=6894041.5, rms=14.677 (1.407%)
027: dt: 0.0500, sse=6726775.5, rms=14.477 (1.368%)
028: dt: 0.0500, sse=6567363.0, rms=14.283 (1.340%)
029: dt: 0.0500, sse=6414874.0, rms=14.095 (1.317%)
030: dt: 0.0500, sse=6268799.5, rms=13.912 (1.296%)
positioning took 1.1 minutes
mean border=56.3, 192 (70) missing vertices, mean dist 1.1 [0.1 (%6.5)->1.9 (%93.5))]
%14 local maxima, %44 large gradients and %37 min vals, 275 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=6362931.5, rms=14.029
031: dt: 0.5000, sse=5281866.0, rms=12.610 (10.113%)
032: dt: 0.5000, sse=4501653.5, rms=11.470 (9.044%)
033: dt: 0.5000, sse=3869531.5, rms=10.456 (8.837%)
034: dt: 0.5000, sse=3376645.0, rms=9.585 (8.329%)
035: dt: 0.5000, sse=2977642.0, rms=8.818 (8.002%)
036: dt: 0.5000, sse=2664190.0, rms=8.162 (7.440%)
037: dt: 0.5000, sse=2395038.8, rms=7.557 (7.417%)
038: dt: 0.5000, sse=2176349.5, rms=7.024 (7.051%)
039: dt: 0.5000, sse=1997817.8, rms=6.561 (6.590%)
040: dt: 0.5000, sse=1869374.1, rms=6.204 (5.448%)
041: dt: 0.5000, sse=1767808.5, rms=5.908 (4.768%)
042: dt: 0.5000, sse=1702966.0, rms=5.708 (3.377%)
043: dt: 0.5000, sse=1654606.0, rms=5.558 (2.635%)
044: dt: 0.5000, sse=1625656.6, rms=5.463 (1.709%)
045: dt: 0.5000, sse=1605054.0, rms=5.396 (1.226%)
rms = 5.35, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1591634.5, rms=5.349 (0.865%)
047: dt: 0.2500, sse=1497312.1, rms=4.987 (6.765%)
048: dt: 0.2500, sse=1462880.2, rms=4.865 (2.460%)
rms = 4.88, time step reduction 2 of 3 to 0.125...
rms = 4.83, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1453247.0, rms=4.827 (0.772%)
positioning took 2.8 minutes
mean border=55.3, 3108 (41) missing vertices, mean dist 0.2 [0.2 (%45.8)->0.6 (%54.2))]
%28 local maxima, %32 large gradients and %35 min vals, 162 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=1741666.6, rms=5.048
050: dt: 0.5000, sse=1656670.6, rms=4.747 (5.960%)
051: dt: 0.5000, sse=1611925.6, rms=4.608 (2.919%)
rms = 4.76, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1513274.5, rms=4.169 (9.522%)
053: dt: 0.2500, sse=1501575.1, rms=4.098 (1.716%)
rms = 4.12, time step reduction 2 of 3 to 0.125...
054: dt: 0.1250, sse=1488833.5, rms=4.038 (1.453%)
055: dt: 0.1250, sse=1473632.9, rms=3.965 (1.818%)
rms = 3.94, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1469154.8, rms=3.944 (0.540%)
positioning took 1.4 minutes
mean border=54.5, 3519 (29) missing vertices, mean dist 0.1 [0.2 (%45.4)->0.4 (%54.6))]
%41 local maxima, %19 large gradients and %34 min vals, 180 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=1529579.5, rms=4.220
rms = 4.63, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1494509.6, rms=4.065 (3.669%)
rms = 4.06, time step reduction 2 of 3 to 0.125...
058: dt: 0.2500, sse=1493588.2, rms=4.062 (0.055%)
059: dt: 0.1250, sse=1478433.0, rms=3.990 (1.784%)
rms = 3.96, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1471164.5, rms=3.961 (0.735%)
positioning took 0.9 minutes
mean border=53.9, 6533 (28) missing vertices, mean dist 0.1 [0.2 (%47.1)->0.3 (%52.9))]
%43 local maxima, %16 large gradients and %32 min vals, 159 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-6.0.0/0050111/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1503073.4, rms=4.095
rms = 4.34, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1473435.4, rms=3.966 (3.162%)
062: dt: 0.2500, sse=1446965.4, rms=3.866 (2.525%)
rms = 3.87, time step reduction 2 of 3 to 0.125...
063: dt: 0.1250, sse=1436414.6, rms=3.815 (1.311%)
064: dt: 0.1250, sse=1418822.6, rms=3.735 (2.110%)
065: dt: 0.1250, sse=1405406.8, rms=3.676 (1.582%)
rms = 3.64, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1395951.2, rms=3.635 (1.102%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.area.pial
vertex spacing 1.01 +- 0.46 (0.07-->8.06) (max @ vno 126267 --> 149471)
face area 0.41 +- 0.33 (0.00-->9.76)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 149622 vertices processed
25000 of 149622 vertices processed
50000 of 149622 vertices processed
75000 of 149622 vertices processed
100000 of 149622 vertices processed
125000 of 149622 vertices processed
0 of 149622 vertices processed
25000 of 149622 vertices processed
50000 of 149622 vertices processed
75000 of 149622 vertices processed
100000 of 149622 vertices processed
125000 of 149622 vertices processed
thickness calculation complete, 229:831 truncations.
28583 vertices at 0 distance
95603 vertices at 1 distance
96451 vertices at 2 distance
45204 vertices at 3 distance
14773 vertices at 4 distance
4372 vertices at 5 distance
1370 vertices at 6 distance
497 vertices at 7 distance
211 vertices at 8 distance
95 vertices at 9 distance
70 vertices at 10 distance
57 vertices at 11 distance
67 vertices at 12 distance
44 vertices at 13 distance
13 vertices at 14 distance
10 vertices at 15 distance
21 vertices at 16 distance
6 vertices at 17 distance
12 vertices at 18 distance
6 vertices at 19 distance
1 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.thickness
positioning took 17.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050111 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-6.0.0/0050111/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
35615 bright wm thresholded.
2923 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.orig...
computing class statistics...
border white:    285738 voxels (1.70%)
border gray      337026 voxels (2.01%)
WM (96.0): 96.4 +- 8.9 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70)
setting MAX_BORDER_WHITE to 108.9 (was 105)
setting MIN_BORDER_WHITE to 68.0 (was 85)
setting MAX_CSF to 47.5 (was 40)
setting MAX_GRAY to 91.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 57.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-7.0,    GM=68+-7.0
mean inside = 92.0, mean outside = 73.0
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.26 (0.04-->8.70) (max @ vno 64050 --> 64051)
face area 0.33 +- 0.16 (0.00-->7.03)
mean absolute distance = 0.51 +- 0.72
3097 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 3 with 117 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 86 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
deleting segment 9 with 46 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
mean border=78.9, 124 (124) missing vertices, mean dist 0.3 [0.7 (%13.9)->0.5 (%86.1))]
%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 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.26 (0.07-->9.30) (max @ vno 64051 --> 64050)
face area 0.33 +- 0.17 (0.00-->6.52)
mean absolute distance = 0.31 +- 0.52
3190 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2116562.8, rms=6.939
001: dt: 0.5000, sse=1195846.2, rms=4.062 (41.457%)
002: dt: 0.5000, sse=1050141.5, rms=3.416 (15.893%)
rms = 3.55, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=908980.2, rms=2.595 (24.048%)
004: dt: 0.2500, sse=853977.2, rms=2.190 (15.621%)
005: dt: 0.2500, sse=832612.4, rms=2.010 (8.216%)
006: dt: 0.2500, sse=827643.6, rms=1.953 (2.815%)
rms = 1.91, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=822112.5, rms=1.909 (2.251%)
008: dt: 0.1250, sse=815964.8, rms=1.847 (3.233%)
rms = 1.84, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=815306.5, rms=1.838 (0.492%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 50 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 6 with 69 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
deleting segment 9 with 22 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
mean border=82.1, 87 (24) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))]
%81 local maxima, %15 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 0.89 +- 0.26 (0.08-->9.41) (max @ vno 64051 --> 64050)
face area 0.34 +- 0.17 (0.00-->6.98)
mean absolute distance = 0.24 +- 0.37
3030 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1257818.2, rms=4.214
010: dt: 0.5000, sse=994146.7, rms=2.927 (30.543%)
rms = 3.24, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=879657.3, rms=2.114 (27.765%)
012: dt: 0.2500, sse=829029.1, rms=1.705 (19.344%)
013: dt: 0.2500, sse=819733.0, rms=1.576 (7.595%)
rms = 1.56, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=814941.1, rms=1.555 (1.311%)
015: dt: 0.1250, sse=827232.3, rms=1.490 (4.159%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=810151.7, rms=1.494 (-0.213%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 2 with 63 points - only 0.00% unknown
deleting segment 3 with 71 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 40 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 23 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
mean border=83.8, 76 (13) missing vertices, mean dist -0.1 [0.3 (%63.8)->0.2 (%36.2))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.26 (0.10-->9.41) (max @ vno 64051 --> 64050)
face area 0.33 +- 0.17 (0.00-->7.06)
mean absolute distance = 0.23 +- 0.33
3046 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=939259.9, rms=2.577
rms = 2.78, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=833952.8, rms=1.895 (26.469%)
018: dt: 0.2500, sse=804701.6, rms=1.522 (19.709%)
019: dt: 0.2500, sse=792634.9, rms=1.470 (3.381%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=792271.8, rms=1.464 (0.425%)
021: dt: 0.1250, sse=786261.5, rms=1.393 (4.816%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=786453.7, rms=1.397 (-0.229%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 12 points - only 0.00% unknown
deleting segment 3 with 65 points - only 0.00% unknown
deleting segment 4 with 88 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 50 points - only 0.00% unknown
deleting segment 7 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 23 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
mean border=84.5, 104 (9) missing vertices, mean dist -0.0 [0.2 (%53.1)->0.2 (%46.9))]
%88 local maxima, % 8 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-6.0.0/0050111/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=800478.0, rms=1.614
rms = 1.83, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=765686.4, rms=1.189 (26.370%)
024: dt: 0.2500, sse=755501.7, rms=1.028 (13.555%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
rms = 1.02, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=753234.9, rms=1.022 (0.502%)
positioning took 0.5 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7645 vertices
erasing segment 1 (vno[0] = 68791)
erasing segment 2 (vno[0] = 91522)
erasing segment 3 (vno[0] = 106578)
erasing segment 4 (vno[0] = 107727)
erasing segment 5 (vno[0] = 109717)
erasing segment 6 (vno[0] = 113032)
erasing segment 7 (vno[0] = 115207)
erasing segment 8 (vno[0] = 116192)
erasing segment 9 (vno[0] = 117211)
erasing segment 10 (vno[0] = 150631)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.area
vertex spacing 0.89 +- 0.27 (0.06-->9.41) (max @ vno 64050 --> 64051)
face area 0.33 +- 0.17 (0.00-->7.07)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 12 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=55.9, 150 (150) missing vertices, mean dist 1.7 [0.0 (%0.0)->3.0 (%100.0))]
%11 local maxima, %42 large gradients and %42 min vals, 367 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=25343970.0, rms=29.163
001: dt: 0.0500, sse=21999168.0, rms=27.110 (7.039%)
002: dt: 0.0500, sse=19631510.0, rms=25.557 (5.728%)
003: dt: 0.0500, sse=17848352.0, rms=24.322 (4.832%)
004: dt: 0.0500, sse=16431605.0, rms=23.294 (4.227%)
005: dt: 0.0500, sse=15260229.0, rms=22.409 (3.802%)
006: dt: 0.0500, sse=14265107.0, rms=21.628 (3.485%)
007: dt: 0.0500, sse=13400227.0, rms=20.925 (3.248%)
008: dt: 0.0500, sse=12637080.0, rms=20.285 (3.059%)
009: dt: 0.0500, sse=11955170.0, rms=19.696 (2.907%)
010: dt: 0.0500, sse=11339836.0, rms=19.148 (2.781%)
positioning took 1.1 minutes
mean border=55.7, 95 (63) missing vertices, mean dist 1.4 [0.3 (%0.0)->2.5 (%100.0))]
%12 local maxima, %43 large gradients and %41 min vals, 342 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=12173623.0, rms=19.891
011: dt: 0.0500, sse=11607666.0, rms=19.393 (2.503%)
012: dt: 0.0500, sse=11092162.0, rms=18.928 (2.397%)
013: dt: 0.0500, sse=10620172.0, rms=18.493 (2.303%)
014: dt: 0.0500, sse=10185761.0, rms=18.082 (2.220%)
015: dt: 0.0500, sse=9786432.0, rms=17.696 (2.134%)
016: dt: 0.0500, sse=9418816.0, rms=17.333 (2.051%)
017: dt: 0.0500, sse=9079397.0, rms=16.991 (1.973%)
018: dt: 0.0500, sse=8765895.0, rms=16.669 (1.897%)
019: dt: 0.0500, sse=8475679.0, rms=16.365 (1.824%)
020: dt: 0.0500, sse=8206780.5, rms=16.078 (1.753%)
positioning took 1.1 minutes
mean border=55.5, 116 (42) missing vertices, mean dist 1.2 [0.1 (%1.1)->2.2 (%98.9))]
%13 local maxima, %43 large gradients and %41 min vals, 357 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=8318422.5, rms=16.205
021: dt: 0.0500, sse=8061382.0, rms=15.928 (1.709%)
022: dt: 0.0500, sse=7823023.0, rms=15.667 (1.640%)
023: dt: 0.0500, sse=7600635.5, rms=15.419 (1.582%)
024: dt: 0.0500, sse=7393429.5, rms=15.185 (1.521%)
025: dt: 0.0500, sse=7199929.5, rms=14.962 (1.465%)
026: dt: 0.0500, sse=7018510.0, rms=14.750 (1.415%)
027: dt: 0.0500, sse=6846622.5, rms=14.547 (1.380%)
028: dt: 0.0500, sse=6683179.5, rms=14.351 (1.349%)
029: dt: 0.0500, sse=6527071.0, rms=14.161 (1.325%)
030: dt: 0.0500, sse=6377518.5, rms=13.976 (1.304%)
positioning took 1.1 minutes
mean border=55.5, 156 (37) missing vertices, mean dist 1.1 [0.1 (%6.2)->2.0 (%93.8))]
%13 local maxima, %43 large gradients and %40 min vals, 319 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=6462762.0, rms=14.082
031: dt: 0.5000, sse=5353178.5, rms=12.642 (10.223%)
032: dt: 0.5000, sse=4569867.0, rms=11.509 (8.961%)
033: dt: 0.5000, sse=3955635.8, rms=10.537 (8.451%)
034: dt: 0.5000, sse=3484170.0, rms=9.718 (7.770%)
035: dt: 0.5000, sse=3106150.2, rms=9.009 (7.296%)
036: dt: 0.5000, sse=2808316.0, rms=8.405 (6.705%)
037: dt: 0.5000, sse=2534788.5, rms=7.814 (7.031%)
038: dt: 0.5000, sse=2313783.2, rms=7.298 (6.598%)
039: dt: 0.5000, sse=2121373.8, rms=6.821 (6.536%)
040: dt: 0.5000, sse=1976984.5, rms=6.438 (5.616%)
041: dt: 0.5000, sse=1863494.0, rms=6.124 (4.884%)
042: dt: 0.5000, sse=1795167.2, rms=5.922 (3.300%)
043: dt: 0.5000, sse=1735261.6, rms=5.744 (3.001%)
044: dt: 0.5000, sse=1711227.1, rms=5.665 (1.371%)
045: dt: 0.5000, sse=1679603.2, rms=5.570 (1.686%)
rms = 5.54, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1670886.1, rms=5.538 (0.567%)
047: dt: 0.2500, sse=1572358.6, rms=5.179 (6.488%)
048: dt: 0.2500, sse=1546323.1, rms=5.089 (1.732%)
rms = 5.10, time step reduction 2 of 3 to 0.125...
rms = 5.04, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1533882.6, rms=5.044 (0.890%)
positioning took 2.8 minutes
mean border=54.6, 3391 (13) missing vertices, mean dist 0.2 [0.2 (%46.4)->0.7 (%53.6))]
%26 local maxima, %31 large gradients and %37 min vals, 168 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=1801547.4, rms=5.171
050: dt: 0.5000, sse=1730532.6, rms=4.934 (4.592%)
051: dt: 0.5000, sse=1674889.6, rms=4.761 (3.498%)
rms = 4.89, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1576765.1, rms=4.345 (8.741%)
053: dt: 0.2500, sse=1568428.8, rms=4.291 (1.241%)
rms = 4.32, time step reduction 2 of 3 to 0.125...
054: dt: 0.1250, sse=1553929.4, rms=4.228 (1.481%)
055: dt: 0.1250, sse=1535780.8, rms=4.146 (1.928%)
rms = 4.12, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1530509.8, rms=4.123 (0.563%)
positioning took 1.4 minutes
mean border=53.9, 3646 (9) missing vertices, mean dist 0.1 [0.2 (%46.2)->0.5 (%53.8))]
%38 local maxima, %19 large gradients and %36 min vals, 162 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=1589872.5, rms=4.361
rms = 4.75, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1555305.4, rms=4.216 (3.338%)
rms = 4.21, time step reduction 2 of 3 to 0.125...
058: dt: 0.2500, sse=1553206.1, rms=4.211 (0.105%)
059: dt: 0.1250, sse=1532794.0, rms=4.121 (2.148%)
rms = 4.08, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1522559.6, rms=4.080 (0.976%)
positioning took 0.9 minutes
mean border=53.4, 6724 (8) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))]
%41 local maxima, %16 large gradients and %35 min vals, 179 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-6.0.0/0050111/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1548178.6, rms=4.177
rms = 4.46, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1518570.1, rms=4.052 (2.989%)
062: dt: 0.2500, sse=1496197.2, rms=3.974 (1.917%)
rms = 3.99, time step reduction 2 of 3 to 0.125...
063: dt: 0.1250, sse=1483785.9, rms=3.917 (1.439%)
064: dt: 0.1250, sse=1464360.4, rms=3.831 (2.185%)
065: dt: 0.1250, sse=1451072.2, rms=3.775 (1.462%)
rms = 3.74, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1442603.0, rms=3.741 (0.905%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.area.pial
vertex spacing 1.02 +- 0.47 (0.06-->11.80) (max @ vno 64061 --> 64070)
face area 0.41 +- 0.34 (0.00-->13.47)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 151182 vertices processed
25000 of 151182 vertices processed
50000 of 151182 vertices processed
75000 of 151182 vertices processed
100000 of 151182 vertices processed
125000 of 151182 vertices processed
150000 of 151182 vertices processed
0 of 151182 vertices processed
25000 of 151182 vertices processed
50000 of 151182 vertices processed
75000 of 151182 vertices processed
100000 of 151182 vertices processed
125000 of 151182 vertices processed
150000 of 151182 vertices processed
thickness calculation complete, 160:1152 truncations.
27726 vertices at 0 distance
93801 vertices at 1 distance
97110 vertices at 2 distance
47918 vertices at 3 distance
16150 vertices at 4 distance
4674 vertices at 5 distance
1380 vertices at 6 distance
506 vertices at 7 distance
192 vertices at 8 distance
92 vertices at 9 distance
56 vertices at 10 distance
64 vertices at 11 distance
46 vertices at 12 distance
23 vertices at 13 distance
16 vertices at 14 distance
23 vertices at 15 distance
18 vertices at 16 distance
16 vertices at 17 distance
15 vertices at 18 distance
15 vertices at 19 distance
27 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.thickness
positioning took 17.5 minutes
PIDs (26104 26107) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 02:38:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label
Total face volume 292163
Total vertex volume 288372 (mask=0)
#@# 0050111 lh 288372
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 02:38:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label
Total face volume 295475
Total vertex volume 291711 (mask=0)
#@# 0050111 rh 291711
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 02:38:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 

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 = 90
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/ribbon.mgz
mris_volmask took 21.16 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 03:00:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 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 0050111 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 03:00:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 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 0050111 rh pial 

Waiting for PID 29028 of (29028 29031 29034 29037) to complete...
Waiting for PID 29031 of (29028 29031 29034 29037) to complete...
Waiting for PID 29034 of (29028 29031 29034 29037) to complete...
Waiting for PID 29037 of (29028 29031 29034 29037) 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 0050111 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 292163
Total vertex volume 288372 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1959   1269   3630  3.061 0.497     0.108     0.024       14     1.8  bankssts
 1296    847   2653  2.643 0.719     0.136     0.033       24     1.6  caudalanteriorcingulate
 3375   2233   7105  2.847 0.513     0.115     0.028       31     3.8  caudalmiddlefrontal
 2305   1410   3180  2.039 0.473     0.139     0.039       36     3.6  cuneus
  622    428   1962  3.487 0.707     0.108     0.036        5     0.8  entorhinal
 4862   3285  11034  2.915 0.542     0.130     0.039       76     7.3  fusiform
 7619   4948  15119  2.754 0.511     0.117     0.029       90     8.2  inferiorparietal
 5414   3618  12200  2.827 0.612     0.117     0.032       67     6.9  inferiortemporal
 2013   1283   3608  2.447 0.905     0.113     0.034       27     2.3  isthmuscingulate
 8666   5514  14329  2.282 0.634     0.137     0.043      132    14.1  lateraloccipital
 4074   2675   9182  3.004 0.628     0.130     0.040       61     5.5  lateralorbitofrontal
 5435   3477   9127  2.353 0.718     0.141     0.041       92     8.6  lingual
 3181   2089   6118  2.527 0.776     0.109     0.034       42     4.0  medialorbitofrontal
 5631   3754  15885  3.312 0.666     0.127     0.036       77     7.6  middletemporal
  974    667   2468  3.300 0.573     0.116     0.030       12     1.2  parahippocampal
 2498   1500   4320  2.670 0.511     0.103     0.033       25     3.4  paracentral
 2374   1621   5574  2.930 0.479     0.103     0.026       22     2.1  parsopercularis
  970    643   2826  3.024 0.705     0.115     0.030       13     1.0  parsorbitalis
 2435   1627   5428  2.792 0.562     0.116     0.030       28     2.7  parstriangularis
 1993   1307   2115  1.808 0.437     0.123     0.034       21     2.5  pericalcarine
 6943   4356  10396  2.129 0.675     0.109     0.037       76     9.9  postcentral
 1998   1326   3785  2.613 0.917     0.133     0.032       32     2.3  posteriorcingulate
 8260   5207  15744  2.727 0.580     0.112     0.035       84    11.5  precentral
 5915   3938  12128  2.734 0.544     0.123     0.031       69     7.2  precuneus
 1298    864   3027  2.924 0.574     0.124     0.033       19     1.5  rostralanteriorcingulate
 9602   6322  20192  2.650 0.583     0.130     0.039      144    14.7  rostralmiddlefrontal
10355   6915  23507  2.832 0.625     0.128     0.036      139    14.4  superiorfrontal
10583   6908  19563  2.561 0.496     0.118     0.033      121    13.5  superiorparietal
 6322   4242  14716  2.984 0.602     0.109     0.029       63     7.2  superiortemporal
 7016   4614  15103  2.833 0.553     0.117     0.032       81     8.2  supramarginal
  444    268   1053  2.619 0.690     0.169     0.097       20     1.8  frontalpole
  666    477   2575  3.529 0.788     0.155     0.048       13     1.2  temporalpole
  742    466   1167  2.433 0.559     0.127     0.039       10     1.0  transversetemporal
 3992   2547   7544  3.045 0.698     0.135     0.050       69     8.2  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 0050111 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 292163
Total vertex volume 288372 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1959   1162   3630  3.061 0.497     0.127     0.039       34     3.3  bankssts
 1296   1137   2653  2.643 0.719     0.188     0.051       46     2.9  caudalanteriorcingulate
 3375   2661   7105  2.847 0.513     0.133     0.033       45     4.7  caudalmiddlefrontal
 2305   1723   3180  2.039 0.473     0.144     0.036       31     3.5  cuneus
  622    742   1962  3.487 0.707     0.211     0.049       12     1.5  entorhinal
 4862   4173  11034  2.915 0.542     0.157     0.043       77     9.5  fusiform
 7619   6023  15119  2.754 0.511     0.139     0.034      102    11.5  inferiorparietal
 5414   4691  12200  2.827 0.612     0.163     0.044       96    11.0  inferiortemporal
 2013   1690   3608  2.447 0.905     0.174     0.046       54     4.6  isthmuscingulate
 8666   6890  14329  2.282 0.634     0.147     0.039      138    15.5  lateraloccipital
 4074   3392   9182  3.004 0.628     0.161     0.045       81     8.1  lateralorbitofrontal
 5435   4381   9127  2.353 0.718     0.154     0.044       89    10.6  lingual
 3181   2716   6118  2.527 0.776     0.159     0.046       50     6.6  medialorbitofrontal
 5631   5611  15885  3.312 0.666     0.169     0.042       91    10.6  middletemporal
  974    867   2468  3.300 0.573     0.167     0.044       16     2.0  parahippocampal
 2498   1722   4320  2.670 0.511     0.119     0.032       27     3.5  paracentral
 2374   2106   5574  2.930 0.479     0.156     0.037       36     3.7  parsopercularis
  970   1136   2826  3.024 0.705     0.182     0.038       13     1.5  parsorbitalis
 2435   2156   5428  2.792 0.562     0.154     0.037       34     4.2  parstriangularis
 1993   1136   2115  1.808 0.437     0.123     0.035       27     3.1  pericalcarine
 6943   5367  10396  2.129 0.675     0.123     0.029       61     9.1  postcentral
 1998   1566   3785  2.613 0.917     0.157     0.047       49     4.2  posteriorcingulate
 8260   6056  15744  2.727 0.580     0.118     0.029       94    10.3  precentral
 5915   4741  12128  2.734 0.544     0.146     0.038       89     9.8  precuneus
 1298   1224   3027  2.924 0.574     0.188     0.050       37     3.0  rostralanteriorcingulate
 9602   8508  20192  2.650 0.583     0.166     0.041      138    17.5  rostralmiddlefrontal
10355   9081  23507  2.832 0.625     0.159     0.042      183    19.3  superiorfrontal
10583   8105  19563  2.561 0.496     0.136     0.034      147    15.9  superiorparietal
 6322   5393  14716  2.984 0.602     0.158     0.043       93    12.4  superiortemporal
 7016   5856  15103  2.833 0.553     0.143     0.039      101    11.1  supramarginal
  444    502   1053  2.619 0.690     0.234     0.066       15     1.3  frontalpole
  666    955   2575  3.529 0.788     0.241     0.058       13     1.8  temporalpole
  742    532   1167  2.433 0.559     0.140     0.039       10     1.3  transversetemporal
 3992   2355   7544  3.045 0.698     0.150     0.055       88     9.7  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 0050111 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 295475
Total vertex volume 291711 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1686   1155   3153  2.908 0.402     0.102     0.020       11     1.4  bankssts
  914    598   1826  2.493 0.838     0.139     0.027       18     0.9  caudalanteriorcingulate
 3239   2194   6871  2.734 0.581     0.123     0.033       38     4.1  caudalmiddlefrontal
 2616   1684   3966  2.098 0.480     0.140     0.047       51     4.4  cuneus
  559    375   1812  3.562 0.645     0.110     0.043        6     1.1  entorhinal
 4674   3123  10325  2.921 0.569     0.128     0.031       65     5.5  fusiform
 8526   5895  17562  2.675 0.487     0.123     0.033      109    10.6  inferiorparietal
 5986   3862  13738  2.905 0.713     0.125     0.041       84     9.6  inferiortemporal
 1739   1105   3550  2.574 0.943     0.126     0.036       25     2.0  isthmuscingulate
 8852   5494  14383  2.277 0.671     0.137     0.041      133    14.7  lateraloccipital
 4645   3101   9640  2.829 0.737     0.136     0.048       74     8.7  lateralorbitofrontal
 6244   4020  10565  2.366 0.689     0.141     0.044       98    10.4  lingual
 3034   2050   6588  2.743 0.593     0.122     0.034       44     4.3  medialorbitofrontal
 6058   4054  15930  3.098 0.665     0.123     0.032       80     7.3  middletemporal
 1074    708   2703  3.199 0.779     0.104     0.024        9     0.9  parahippocampal
 2486   1555   4540  2.677 0.446     0.109     0.036       26     3.3  paracentral
 1877   1250   4421  2.895 0.547     0.118     0.033       20     2.4  parsopercularis
 1440    959   3905  3.054 0.624     0.144     0.047       32     2.6  parsorbitalis
 2561   1722   5615  2.709 0.588     0.138     0.042       47     4.2  parstriangularis
 2922   1902   2954  1.760 0.479     0.128     0.039       34     4.7  pericalcarine
 7081   4556  11513  2.224 0.675     0.113     0.036       80     9.4  postcentral
 1940   1272   3961  2.684 0.752     0.131     0.031       28     2.4  posteriorcingulate
 8193   5306  15612  2.663 0.546     0.117     0.036       88    11.7  precentral
 6594   4404  13850  2.794 0.555     0.127     0.035       81     8.7  precuneus
  678    437   1317  2.907 0.474     0.115     0.029        8     0.7  rostralanteriorcingulate
 9125   6082  19665  2.623 0.646     0.135     0.044      158    16.4  rostralmiddlefrontal
10681   7076  24140  2.866 0.629     0.127     0.034      132    13.9  superiorfrontal
 9415   6086  17081  2.486 0.516     0.119     0.035      108    12.1  superiorparietal
 5890   3887  14079  3.101 0.591     0.103     0.028       52     5.5  superiortemporal
 6463   4216  13362  2.793 0.539     0.131     0.038       95     9.1  supramarginal
  508    303   1415  3.436 0.534     0.161     0.067       14     1.5  frontalpole
  701    476   2327  3.226 0.901     0.154     0.061       13     1.7  temporalpole
  622    369   1100  2.534 0.487     0.129     0.046       10     0.9  transversetemporal
 4164   2721   8238  3.072 0.614     0.132     0.046       56     7.7  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050111 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 295475
Total vertex volume 291711 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1686   1043   3153  2.908 0.402     0.124     0.039       26     2.6  bankssts
  914    779   1826  2.493 0.838     0.172     0.052       56     1.5  caudalanteriorcingulate
 3239   2734   6871  2.734 0.581     0.152     0.037       43     5.3  caudalmiddlefrontal
 2616   2133   3966  2.098 0.480     0.152     0.038       41     4.3  cuneus
  559    640   1812  3.562 0.645     0.156     0.035        5     0.9  entorhinal
 4674   3873  10325  2.921 0.569     0.159     0.043       89     9.2  fusiform
 8526   7307  17562  2.675 0.487     0.153     0.040      136    15.2  inferiorparietal
 5986   5228  13738  2.905 0.713     0.165     0.043      110    12.2  inferiortemporal
 1739   1455   3550  2.574 0.943     0.169     0.052       36     3.7  isthmuscingulate
 8852   6895  14383  2.277 0.671     0.147     0.041      160    16.6  lateraloccipital
 4645   3743   9640  2.829 0.737     0.166     0.056      170    11.0  lateralorbitofrontal
 6244   4945  10565  2.366 0.689     0.152     0.044      108    12.3  lingual
 3034   2751   6588  2.743 0.593     0.157     0.040       40     5.5  medialorbitofrontal
 6058   6024  15930  3.098 0.665     0.167     0.038       80    10.9  middletemporal
 1074    960   2703  3.199 0.779     0.153     0.037       17     1.8  parahippocampal
 2486   1771   4540  2.677 0.446     0.128     0.035       35     3.7  paracentral
 1877   1687   4421  2.895 0.547     0.150     0.040       27     3.0  parsopercularis
 1440   1567   3905  3.054 0.624     0.190     0.041       19     2.8  parsorbitalis
 2561   2349   5615  2.709 0.588     0.167     0.042       38     4.7  parstriangularis
 2922   1627   2954  1.760 0.479     0.118     0.033       58     4.2  pericalcarine
 7081   5669  11513  2.224 0.675     0.130     0.031       81     9.3  postcentral
 1940   1582   3961  2.684 0.752     0.154     0.038       41     3.4  posteriorcingulate
 8193   6061  15612  2.663 0.546     0.125     0.031      119    11.1  precentral
 6594   5283  13850  2.794 0.555     0.152     0.041      119    11.6  precuneus
  678    516   1317  2.907 0.474     0.166     0.049       20     1.6  rostralanteriorcingulate
 9125   8599  19665  2.623 0.646     0.180     0.046      151    18.9  rostralmiddlefrontal
10681   9218  24140  2.866 0.629     0.164     0.046      202    21.2  superiorfrontal
 9415   7360  17081  2.486 0.516     0.139     0.037      132    14.8  superiorparietal
 5890   5207  14079  3.101 0.591     0.161     0.041       82    11.5  superiortemporal
 6463   5144  13362  2.793 0.539     0.151     0.042       99    11.6  supramarginal
  508    535   1415  3.436 0.534     0.202     0.061        8     1.3  frontalpole
  701    837   2327  3.226 0.901     0.199     0.073       15     1.8  temporalpole
  622    499   1100  2.534 0.487     0.151     0.042        7     1.3  transversetemporal
 4164   2622   8238  3.072 0.614     0.155     0.056      114    11.1  insula
PIDs (29028 29031 29034 29037) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 03:01:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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 03:01:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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 29138 of (29138 29141) to complete...
Waiting for PID 29141 of (29138 29141) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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...
2 labels changed using aseg
relabeling using gibbs priors...
000:   9756 changed, 149622 examined...
001:   2340 changed, 37999 examined...
002:    693 changed, 12107 examined...
003:    298 changed, 3845 examined...
004:    136 changed, 1680 examined...
005:     62 changed, 823 examined...
006:     28 changed, 370 examined...
007:     21 changed, 169 examined...
008:     13 changed, 121 examined...
009:     10 changed, 75 examined...
010:      6 changed, 47 examined...
011:      3 changed, 34 examined...
012:      2 changed, 21 examined...
013:      2 changed, 13 examined...
014:      0 changed, 12 examined...
0 labels changed using aseg
000: 262 total segments, 175 labels (1844 vertices) changed
001: 94 total segments, 7 labels (10 vertices) changed
002: 87 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 37 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1729 vertices marked for relabeling...
1729 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 23 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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...
85 labels changed using aseg
relabeling using gibbs priors...
000:   9635 changed, 151182 examined...
001:   2245 changed, 37863 examined...
002:    657 changed, 11630 examined...
003:    260 changed, 3818 examined...
004:    147 changed, 1558 examined...
005:     72 changed, 793 examined...
006:     55 changed, 406 examined...
007:     25 changed, 261 examined...
008:     11 changed, 137 examined...
009:      2 changed, 52 examined...
010:      0 changed, 12 examined...
21 labels changed using aseg
000: 282 total segments, 198 labels (2192 vertices) changed
001: 93 total segments, 10 labels (22 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 46 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1275 vertices marked for relabeling...
1275 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 22 seconds.
PIDs (29138 29141) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 03:02:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 03:02:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 rh white 

Waiting for PID 29221 of (29221 29224) to complete...
Waiting for PID 29224 of (29221 29224) 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 0050111 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 292163
Total vertex volume 288372 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1179    783   2231  2.563 0.705     0.135     0.041       17     2.2  G&S_frontomargin
 2051   1323   4401  2.638 0.617     0.141     0.043       32     3.5  G&S_occipital_inf
 2165   1202   3725  2.453 0.644     0.114     0.051       33     4.2  G&S_paracentral
 1421    912   3210  3.049 0.543     0.129     0.039       16     2.0  G&S_subcentral
  884    583   2360  2.878 0.620     0.159     0.055       21     1.7  G&S_transv_frontopol
 2284   1569   4731  2.719 0.589     0.125     0.029       26     2.7  G&S_cingul-Ant
 1366    932   2833  2.826 0.516     0.122     0.031       18     1.6  G&S_cingul-Mid-Ant
 1373    927   2596  2.732 0.535     0.135     0.034       19     1.8  G&S_cingul-Mid-Post
  799    513   2219  3.263 0.690     0.144     0.048       15     1.5  G_cingul-Post-dorsal
  408    255   1011  2.893 0.977     0.121     0.049        7     0.6  G_cingul-Post-ventral
 2112   1274   2982  1.940 0.535     0.142     0.042       38     3.4  G_cuneus
 1342    897   3968  3.109 0.452     0.127     0.038       21     1.8  G_front_inf-Opercular
  442    280   1319  3.011 0.425     0.140     0.051       11     0.8  G_front_inf-Orbital
 1580   1024   4294  2.973 0.543     0.138     0.047       28     2.9  G_front_inf-Triangul
 4974   3195  13618  2.951 0.544     0.139     0.044       97     8.2  G_front_middle
 7414   4792  18859  2.954 0.640     0.136     0.043      130    12.4  G_front_sup
  960    602   1898  2.903 0.628     0.165     0.071       20     2.6  G_Ins_lg&S_cent_ins
  951    589   2593  3.355 0.905     0.145     0.062       19     2.3  G_insular_short
 2646   1614   5700  2.595 0.697     0.136     0.046       48     3.9  G_occipital_middle
 1501    949   2294  2.117 0.486     0.134     0.039       19     2.3  G_occipital_sup
 2048   1367   5331  2.966 0.545     0.137     0.039       40     2.7  G_oc-temp_lat-fusifor
 3838   2397   6822  2.267 0.763     0.147     0.046       78     6.5  G_oc-temp_med-Lingual
 1391    896   3908  3.332 0.744     0.119     0.041       20     2.2  G_oc-temp_med-Parahip
 2331   1485   6897  3.146 0.640     0.135     0.053       48     3.8  G_orbital
 3323   2135   8237  2.937 0.493     0.137     0.038       59     4.5  G_pariet_inf-Angular
 3309   2149   8329  2.984 0.558     0.132     0.041       53     4.9  G_pariet_inf-Supramar
 4286   2760   9611  2.733 0.503     0.126     0.041       67     6.5  G_parietal_sup
 2644   1577   4221  2.113 0.611     0.118     0.050       40     5.0  G_postcentral
 3236   1983   7632  2.897 0.570     0.120     0.046       46     5.6  G_precentral
 3204   2113   8554  2.898 0.563     0.138     0.041       55     4.8  G_precuneus
 1119    746   3113  2.822 0.727     0.138     0.054       31     2.4  G_rectus
  666    368    742  1.957 0.895     0.082     0.050        9     1.0  G_subcallosal
  599    357   1058  2.499 0.538     0.118     0.044        8     1.0  G_temp_sup-G_T_transv
 2176   1368   6773  3.317 0.610     0.132     0.042       38     3.4  G_temp_sup-Lateral
  754    532   2139  3.342 0.614     0.113     0.034        7     1.0  G_temp_sup-Plan_polar
 1010    673   2119  2.719 0.500     0.102     0.030        9     0.8  G_temp_sup-Plan_tempo
 2837   1830   7925  2.931 0.676     0.133     0.044       54     4.8  G_temporal_inf
 3239   2094  10732  3.542 0.633     0.140     0.044       58     5.2  G_temporal_middle
  467    308    640  2.365 0.383     0.087     0.015        2     0.3  Lat_Fis-ant-Horizont
  439    310    711  2.795 0.510     0.087     0.014        2     0.2  Lat_Fis-ant-Vertical
 1102    717   1580  2.642 0.525     0.105     0.026        7     1.1  Lat_Fis-post
 2149   1331   2552  1.819 0.507     0.161     0.058       50     4.9  Pole_occipital
 1651   1182   5525  3.190 0.787     0.155     0.054       36     3.8  Pole_temporal
 2769   1836   3284  2.103 0.575     0.119     0.030       26     3.3  S_calcarine
 3565   2351   4167  2.034 0.581     0.098     0.023       20     3.3  S_central
 1246    831   1968  2.683 0.413     0.082     0.013        4     0.7  S_cingul-Marginalis
  528    360    965  3.166 0.465     0.089     0.016        2     0.3  S_circular_insula_ant
 1664   1137   2861  2.997 0.546     0.098     0.019        8     1.4  S_circular_insula_inf
 1674   1132   2684  3.000 0.432     0.103     0.023        8     1.7  S_circular_insula_sup
 1188    821   2019  2.835 0.423     0.099     0.016        6     0.8  S_collat_transv_ant
  653    436    846  2.200 0.402     0.147     0.041        7     1.2  S_collat_transv_post
 2341   1610   3727  2.484 0.433     0.110     0.025       18     2.2  S_front_inf
 1915   1275   2802  2.414 0.416     0.102     0.023       11     1.8  S_front_middle
 3106   2109   5581  2.579 0.501     0.112     0.026       24     3.3  S_front_sup
  799    524   1133  2.567 0.361     0.091     0.017        4     0.6  S_interm_prim-Jensen
 4113   2721   6216  2.517 0.424     0.101     0.022       27     3.7  S_intrapariet&P_trans
  959    664   1368  2.202 0.544     0.121     0.027        7     1.1  S_oc_middle&Lunatus
 1498    984   2223  2.500 0.364     0.110     0.023       11     1.4  S_oc_sup&transversal
 1042    690   1454  2.427 0.377     0.099     0.019        6     0.7  S_occipital_ant
  946    651   1689  2.613 0.510     0.093     0.019        5     0.7  S_oc-temp_lat
 2015   1394   3475  2.918 0.506     0.118     0.028       14     2.3  S_oc-temp_med&Lingual
  493    335    664  2.240 0.363     0.108     0.022        3     0.5  S_orbital_lateral
  780    553   1152  2.532 0.492     0.113     0.023        5     0.7  S_orbital_med-olfact
 1516   1025   3068  2.947 0.692     0.124     0.028       15     1.7  S_orbital-H_Shaped
 1831   1195   2689  2.522 0.462     0.113     0.024       15     1.8  S_parieto_occipital
 1930   1191   1769  1.863 0.688     0.112     0.022       25     1.3  S_pericallosal
 3630   2428   5323  2.348 0.443     0.101     0.024       21     3.6  S_postcentral
 1476    993   2517  2.710 0.450     0.094     0.020        7     1.1  S_precentral-inf-part
 1610   1069   2449  2.666 0.451     0.094     0.019        7     1.3  S_precentral-sup-part
  640    438   1001  2.681 0.551     0.091     0.017        3     0.4  S_suborbital
 1229    844   1847  2.540 0.498     0.115     0.028       10     1.2  S_subparietal
 1964   1354   3370  2.906 0.508     0.105     0.022       10     1.8  S_temporal_inf
 6525   4422  11441  2.858 0.474     0.097     0.019       35     5.0  S_temporal_sup
  368    286    627  2.564 0.473     0.140     0.027        3     0.4  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 0050111 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 295475
Total vertex volume 291711 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
  941    621   1978  2.866 0.787     0.140     0.042       13     1.8  G&S_frontomargin
 1296    857   2978  2.827 0.686     0.133     0.033       19     1.5  G&S_occipital_inf
 1654    972   3030  2.496 0.602     0.128     0.061       28     3.9  G&S_paracentral
 1759   1150   3883  2.895 0.562     0.134     0.036       24     2.3  G&S_subcentral
 1169    771   3163  2.808 0.705     0.158     0.060       32     3.0  G&S_transv_frontopol
 3138   2088   6101  2.831 0.527     0.117     0.029       35     3.4  G&S_cingul-Ant
 1267    856   2651  2.800 0.567     0.119     0.025       14     1.2  G&S_cingul-Mid-Ant
 1493   1007   3094  2.757 0.497     0.123     0.033       17     1.9  G&S_cingul-Mid-Post
  723    451   1916  3.106 0.552     0.165     0.045       17     1.1  G_cingul-Post-dorsal
  382    236   1316  3.292 0.943     0.130     0.037        6     0.5  G_cingul-Post-ventral
 2511   1610   3811  2.024 0.550     0.144     0.047       49     4.4  G_cuneus
 1277    872   3893  3.143 0.528     0.146     0.045       22     2.2  G_front_inf-Opercular
  630    387   1717  3.096 0.525     0.158     0.054       15     1.2  G_front_inf-Orbital
 1120    749   2822  2.748 0.594     0.158     0.058       30     2.6  G_front_inf-Triangul
 4759   3083  13348  2.926 0.641     0.150     0.055      115    10.5  G_front_middle
 6921   4494  18173  3.003 0.628     0.136     0.041      110    10.9  G_front_sup
 1084    709   2061  2.899 0.612     0.149     0.056       20     2.5  G_Ins_lg&S_cent_ins
  994    646   2779  3.272 0.657     0.160     0.072       21     2.8  G_insular_short
 2841   1824   6182  2.486 0.625     0.151     0.050       59     5.5  G_occipital_middle
 1894   1123   3228  2.309 0.526     0.128     0.039       28     2.8  G_occipital_sup
 2357   1476   5943  2.977 0.611     0.150     0.042       49     3.5  G_oc-temp_lat-fusifor
 3896   2461   7426  2.362 0.753     0.148     0.049       74     7.0  G_oc-temp_med-Lingual
 1134    701   3506  3.448 0.787     0.104     0.032       11     1.3  G_oc-temp_med-Parahip
 2989   1952   8200  3.002 0.725     0.154     0.063       82     7.0  G_orbital
 3267   2144   8388  2.850 0.520     0.147     0.050       74     5.7  G_pariet_inf-Angular
 3069   1995   7876  2.990 0.538     0.139     0.041       55     4.7  G_pariet_inf-Supramar
 3216   2030   7153  2.651 0.582     0.132     0.050       53     5.1  G_parietal_sup
 2567   1576   4448  2.145 0.589     0.117     0.045       37     3.8  G_postcentral
 3180   1939   7704  2.832 0.604     0.127     0.052       52     6.2  G_precentral
 3124   2039   8059  2.929 0.609     0.139     0.043       55     4.9  G_precuneus
  934    616   2504  2.774 0.686     0.146     0.055       22     2.3  G_rectus
  439    290    793  2.739 1.115     0.102     0.041        5     0.5  G_subcallosal
  437    254    942  2.677 0.625     0.139     0.053        9     0.8  G_temp_sup-G_T_transv
 1924   1244   6183  3.382 0.639     0.128     0.037       27     2.6  G_temp_sup-Lateral
 1193    783   2621  2.967 0.684     0.105     0.049       10     2.0  G_temp_sup-Plan_polar
  889    581   1967  2.843 0.453     0.102     0.027        9     0.8  G_temp_sup-Plan_tempo
 3165   1958   8480  2.983 0.750     0.138     0.054       65     6.9  G_temporal_inf
 3591   2360  11594  3.352 0.642     0.137     0.040       64     5.3  G_temporal_middle
  412    291    667  2.522 0.582     0.111     0.019        2     0.4  Lat_Fis-ant-Horizont
  183    122    318  2.732 0.429     0.095     0.025        1     0.1  Lat_Fis-ant-Vertical
 1406    921   1965  2.533 0.467     0.103     0.023        8     1.3  Lat_Fis-post
 4005   2397   4451  1.770 0.478     0.142     0.051       70     8.0  Pole_occipital
 1887   1311   6658  3.359 0.859     0.147     0.051       32     3.6  Pole_temporal
 3247   2118   3871  2.112 0.533     0.122     0.033       33     4.5  S_calcarine
 3393   2270   4008  2.108 0.558     0.096     0.022       17     3.0  S_central
 1457    995   2443  2.576 0.453     0.102     0.022        9     1.5  S_cingul-Marginalis
  736    483   1324  3.308 0.657     0.114     0.032        5     0.9  S_circular_insula_ant
 1329    873   2134  2.965 0.509     0.087     0.022       10     1.0  S_circular_insula_inf
 1753   1191   2859  2.874 0.442     0.104     0.021        8     1.7  S_circular_insula_sup
 1006    713   1839  2.741 0.443     0.106     0.023        7     0.9  S_collat_transv_ant
  542    347    686  2.389 0.471     0.113     0.022        3     0.5  S_collat_transv_post
 2222   1535   3462  2.376 0.416     0.111     0.025       15     2.2  S_front_inf
 2382   1637   3481  2.318 0.497     0.112     0.024       17     2.3  S_front_middle
 2320   1608   3765  2.491 0.447     0.118     0.027       17     2.5  S_front_sup
  549    368    810  2.587 0.389     0.103     0.021        3     0.5  S_interm_prim-Jensen
 3725   2495   5555  2.432 0.423     0.100     0.022       21     3.5  S_intrapariet&P_trans
 1119    780   1459  2.163 0.415     0.140     0.036       10     1.8  S_oc_middle&Lunatus
 1888   1240   2812  2.502 0.401     0.109     0.023       14     1.6  S_oc_sup&transversal
  963    683   1775  2.605 0.458     0.116     0.025        7     1.0  S_occipital_ant
 1286    868   2028  2.706 0.384     0.103     0.021        7     1.0  S_oc-temp_lat
 2395   1702   3883  2.846 0.504     0.107     0.020       13     1.9  S_oc-temp_med&Lingual
  563    383    879  2.501 0.446     0.129     0.033        6     0.9  S_orbital_lateral
  839    582   1243  2.597 0.554     0.111     0.024        6     0.9  S_orbital_med-olfact
 1632   1099   3270  2.855 0.666     0.124     0.033       17     2.2  S_orbital-H_Shaped
 2251   1496   3364  2.536 0.449     0.113     0.029       18     2.5  S_parieto_occipital
 1377    838   1163  1.738 0.661     0.125     0.025       19     1.1  S_pericallosal
 2787   1857   3747  2.361 0.461     0.114     0.028       22     2.9  S_postcentral
 1427    960   2270  2.592 0.407     0.102     0.022        8     1.3  S_precentral-inf-part
 1739   1179   2571  2.526 0.472     0.097     0.019        8     1.4  S_precentral-sup-part
  342    242    636  2.778 0.647     0.089     0.012        1     0.2  S_suborbital
 1811   1237   3423  2.780 0.489     0.122     0.030       16     2.1  S_subparietal
 1861   1293   2689  2.563 0.423     0.104     0.017        9     1.5  S_temporal_inf
 6697   4666  11578  2.778 0.438     0.099     0.019       35     5.4  S_temporal_sup
  434    310    716  2.921 0.400     0.124     0.020        3     0.3  S_temporal_transverse
PIDs (29221 29224) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 03:02:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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 03:02:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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 29288 of (29288 29291) to complete...
Waiting for PID 29291 of (29288 29291) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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...
1449 labels changed using aseg
relabeling using gibbs priors...
000:   2018 changed, 149622 examined...
001:    441 changed, 9434 examined...
002:    112 changed, 2579 examined...
003:     41 changed, 666 examined...
004:     12 changed, 225 examined...
005:      7 changed, 79 examined...
006:      4 changed, 35 examined...
007:      2 changed, 20 examined...
008:      1 changed, 10 examined...
009:      0 changed, 9 examined...
109 labels changed using aseg
000: 54 total segments, 21 labels (206 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1331 vertices marked for relabeling...
1331 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050111 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...
1965 labels changed using aseg
relabeling using gibbs priors...
000:   2164 changed, 151182 examined...
001:    472 changed, 9897 examined...
002:    135 changed, 2729 examined...
003:     49 changed, 794 examined...
004:     23 changed, 293 examined...
005:     14 changed, 136 examined...
006:     10 changed, 96 examined...
007:      4 changed, 47 examined...
008:      2 changed, 26 examined...
009:      0 changed, 16 examined...
201 labels changed using aseg
000: 63 total segments, 30 labels (241 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, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
981 vertices marked for relabeling...
981 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.
PIDs (29288 29291) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 03:03:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 03:03:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 rh white 

Waiting for PID 29373 of (29373 29376) to complete...
Waiting for PID 29376 of (29373 29376) 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 0050111 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 292163
Total vertex volume 288372 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1776   1179   3367  2.658 0.673     0.133     0.032       28     2.1  caudalanteriorcingulate
 3631   2408   7610  2.831 0.508     0.115     0.028       34     4.0  caudalmiddlefrontal
 2927   1807   4117  2.090 0.490     0.132     0.036       42     4.2  cuneus
  576    393   1818  3.490 0.727     0.107     0.036        4     0.7  entorhinal
 4374   2953   9362  2.876 0.518     0.128     0.034       59     5.7  fusiform
 7991   5200  16025  2.765 0.515     0.118     0.029       94     8.6  inferiorparietal
 5498   3680  13189  2.862 0.622     0.123     0.037       83     8.5  inferiortemporal
 1993   1280   3600  2.472 0.895     0.113     0.034       27     2.2  isthmuscingulate
 8618   5484  14085  2.273 0.627     0.136     0.043      131    13.7  lateraloccipital
 4397   2839   9726  2.915 0.716     0.138     0.048       74     7.9  lateralorbitofrontal
 5495   3513   9246  2.343 0.720     0.141     0.042       93     8.7  lingual
 2614   1717   5380  2.559 0.785     0.108     0.039       45     3.6  medialorbitofrontal
 7569   5010  19286  3.220 0.658     0.120     0.033       89     9.3  middletemporal
 1045    713   2622  3.295 0.590     0.115     0.029       12     1.2  parahippocampal
 2916   1758   5314  2.745 0.540     0.104     0.033       29     3.8  paracentral
 2217   1502   5140  2.933 0.479     0.104     0.026       21     2.1  parsopercularis
 1048    693   2515  2.860 0.542     0.113     0.033       13     1.3  parsorbitalis
 2889   1949   6436  2.767 0.559     0.121     0.035       37     4.0  parstriangularis
 2004   1311   2132  1.809 0.440     0.124     0.034       22     2.5  pericalcarine
 7938   5009  12248  2.190 0.681     0.111     0.037       87    11.4  postcentral
 2138   1405   3965  2.600 0.901     0.133     0.033       34     2.6  posteriorcingulate
 8135   5123  15579  2.746 0.572     0.112     0.036       83    11.3  precentral
 5985   3974  12582  2.742 0.540     0.124     0.032       72     7.4  precuneus
 1857   1219   3705  2.811 0.555     0.123     0.033       25     2.1  rostralanteriorcingulate
 6635   4396  14191  2.651 0.598     0.125     0.035       90     8.7  rostralmiddlefrontal
12115   8038  27978  2.809 0.631     0.130     0.038      176    17.8  superiorfrontal
 8715   5707  16193  2.586 0.488     0.115     0.032       96    10.7  superiorparietal
 8356   5624  19919  3.022 0.626     0.115     0.032       92    10.3  superiortemporal
 6206   4066  13199  2.822 0.559     0.119     0.033       71     7.5  supramarginal
  718    447   1122  2.428 0.563     0.126     0.039        9     0.9  transversetemporal
 3307   2155   6722  3.134 0.637     0.129     0.041       42     5.2  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 0050111 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 295475
Total vertex volume 291711 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1016    670   2019  2.502 0.806     0.138     0.029       19     1.0  caudalanteriorcingulate
 3370   2270   7142  2.740 0.587     0.124     0.033       41     4.3  caudalmiddlefrontal
 3145   2033   4752  2.109 0.496     0.137     0.044       55     4.8  cuneus
  506    338   1647  3.567 0.655     0.104     0.041        5     0.9  entorhinal
 4306   2880   8930  2.876 0.523     0.127     0.030       58     4.9  fusiform
 8703   5986  17659  2.657 0.484     0.124     0.033      113    10.8  inferiorparietal
 6399   4147  15210  2.936 0.723     0.126     0.041       91    10.4  inferiortemporal
 1791   1137   3576  2.562 0.924     0.125     0.036       25     2.1  isthmuscingulate
 8830   5473  14367  2.262 0.667     0.137     0.041      132    14.5  lateraloccipital
 4967   3307  10600  2.855 0.720     0.145     0.054       93    11.1  lateralorbitofrontal
 6153   3941  10371  2.368 0.685     0.141     0.045       98    10.6  lingual
 2367   1589   5189  2.753 0.747     0.118     0.038       35     3.6  medialorbitofrontal
 7313   4912  18543  3.089 0.637     0.122     0.030       90     8.7  middletemporal
 1156    766   2910  3.195 0.783     0.106     0.025       10     1.0  parahippocampal
 2581   1612   4767  2.672 0.456     0.112     0.040       30     3.9  paracentral
 2221   1487   5092  2.830 0.542     0.121     0.034       26     2.9  parsopercularis
 1213    782   2814  3.001 0.639     0.137     0.045       21     1.9  parsorbitalis
 2515   1685   5391  2.699 0.587     0.138     0.043       46     4.4  parstriangularis
 2844   1858   2907  1.768 0.479     0.128     0.039       33     4.7  pericalcarine
 7725   4957  12425  2.242 0.662     0.113     0.036       85     9.9  postcentral
 1991   1306   4045  2.681 0.751     0.131     0.032       29     2.4  posteriorcingulate
 7857   5086  15237  2.676 0.546     0.116     0.036       84    11.1  precentral
 6806   4552  14374  2.785 0.557     0.128     0.035       85     9.0  precuneus
  925    596   1740  2.865 0.517     0.110     0.029       10     1.0  rostralanteriorcingulate
 6788   4538  14828  2.630 0.633     0.133     0.041      112    11.4  rostralmiddlefrontal
13836   9175  31230  2.832 0.634     0.131     0.037      194    20.1  superiorfrontal
 7843   5057  14433  2.510 0.520     0.118     0.035       91    10.0  superiorparietal
 7813   5185  18439  3.047 0.627     0.109     0.032       77     9.2  superiortemporal
 6018   3948  12523  2.796 0.545     0.131     0.038       87     8.6  supramarginal
  600    355   1077  2.535 0.502     0.128     0.046       10     0.9  transversetemporal
 3591   2368   7472  3.160 0.570     0.124     0.035       39     5.0  insula
PIDs (29373 29376) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 03:04:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 pctsurfcon --s 0050111 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 03:04:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts

 pctsurfcon --s 0050111 --rh-only 

Waiting for PID 29584 of (29584 29594) to complete...
Waiting for PID 29594 of (29584 29594) to complete...

 pctsurfcon --s 0050111 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts/pctsurfcon.log
Sun Oct  8 03:04:01 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-6.0.0/0050111/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-935 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-6.0.0/0050111/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29584/lh.wm.mgh --regheader 0050111 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 79119
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29584/lh.wm.mgh
Dim: 149622 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29584/lh.gm.mgh --projfrac 0.3 --regheader 0050111 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 97795
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29584/lh.gm.mgh
Dim: 149622 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29584/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29584/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.w-g.pct.mgh --annot 0050111 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/lh.w-g.pct.mgh --annot 0050111 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/lh.w-g.pct.mgh
Vertex Area is 0.653537 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 0050111 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/scripts/pctsurfcon.log
Sun Oct  8 03:04:01 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-6.0.0/0050111/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-935 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-6.0.0/0050111/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29594/rh.wm.mgh --regheader 0050111 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 80252
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29594/rh.wm.mgh
Dim: 151182 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29594/rh.gm.mgh --projfrac 0.3 --regheader 0050111 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 98780
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29594/rh.gm.mgh
Dim: 151182 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29594/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/tmp.pctsurfcon.29594/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.w-g.pct.mgh --annot 0050111 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.w-g.pct.mgh --annot 0050111 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.w-g.pct.mgh
Vertex Area is 0.657172 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 (29584 29594) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 03:04:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1304 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
993 voxels changed to hypointensity...
2369 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 03:04:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111

 mri_aparc2aseg --s 0050111 --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 03:04:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111

 mri_aparc2aseg --s 0050111 --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 03:04:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111

 mri_aparc2aseg --s 0050111 --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 29747 of (29747 29750 29753) to complete...
Waiting for PID 29750 of (29747 29750 29753) to complete...
Waiting for PID 29753 of (29747 29750 29753) to complete...

 mri_aparc2aseg --s 0050111 --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 0050111
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/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-6.0.0/0050111/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.83
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 108
rescaling Left_Cerebral_Cortex from 61 --> 64
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 84
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 88
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 86
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 66
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 17
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 82
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 85
rescaling Right_Caudate from 62 --> 77
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 63
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 75
rescaling Right_VentralDC from 86 --> 92
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 79
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 574974
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 129 changed.
pass 2: 4 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050111 --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 0050111
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/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-6.0.0/0050111/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.83
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 108
rescaling Left_Cerebral_Cortex from 61 --> 64
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 84
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 88
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 86
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 66
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 17
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 82
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 85
rescaling Right_Caudate from 62 --> 77
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 63
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 75
rescaling Right_VentralDC from 86 --> 92
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 79
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 574857
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 129 changed.
pass 2: 4 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050111 --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 0050111
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/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-6.0.0/0050111/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.83
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 108
rescaling Left_Cerebral_Cortex from 61 --> 64
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 84
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 88
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 86
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 66
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 17
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 82
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 85
rescaling Right_Caudate from 62 --> 77
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 63
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 75
rescaling Right_VentralDC from 86 --> 92
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 79
rescaling non_WM_hypointensities from 40 --> 45
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 574857
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 129 changed.
pass 2: 4 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (29747 29750 29753) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 03:12:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri

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

Sun Oct  8 03:12:58 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-6.0.0/0050111/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-935 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-6.0.0/0050111/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-935
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 03:12:58 CEST 2017 
Ended   at Sun Oct  8 03:13:06 CEST 2017
Apas2aseg-Run-Time-Sec 8
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 03:13:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111

 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 0050111 


$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 0050111 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1503924 mm^3    (det: 1.295348 )
Computing euler number
orig.nofix lheno = -146, rheno = -172
orig.nofix lhholes =   74, rhholes = 87
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
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 03:15:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111

 mri_aparc2aseg --s 0050111 --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 0050111
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-6.0.0/0050111/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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-6.0.0/0050111/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7790 vertices from left hemi
Ripped 7995 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-6.0.0/0050111/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 = 1037649
Used brute-force search on 127 voxels
Fixing Parahip LH WM
  Found 7 clusters
     0 k 1.000000
     1 k 1426.000000
     2 k 5.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1.000000
     6 k 2.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 7.000000
     1 k 1.000000
     2 k 2.000000
     3 k 1.000000
     4 k 1.000000
     5 k 2.000000
     6 k 1.000000
     7 k 1646.000000
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 0050111 --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 0050111 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-935
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1503924 mm^3    (det: 1.295348 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
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-6.0.0/0050111/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 03:26:17 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 31041 of (31041 31047 31053 31059 31065) to complete...
Waiting for PID 31047 of (31041 31047 31053 31059 31065) to complete...
Waiting for PID 31053 of (31041 31047 31053 31059 31065) to complete...
Waiting for PID 31059 of (31041 31047 31053 31059 31065) to complete...
Waiting for PID 31065 of (31041 31047 31053 31059 31065) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 551
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4680
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 926
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8835
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 249
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4326
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 569
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6552
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 722
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6506
mri_label2label: Done

PIDs (31041 31047 31053 31059 31065) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 31121 of (31121 31127 31133 31139) to complete...
Waiting for PID 31127 of (31121 31127 31133 31139) to complete...
Waiting for PID 31133 of (31121 31127 31133 31139) to complete...
Waiting for PID 31139 of (31121 31127 31133 31139) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 412
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4482
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 1473
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15062
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 317
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4498
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 965
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4387
mri_label2label: Done

PIDs (31121 31127 31133 31139) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 31184 of (31184 31190 31196 31200 31207) to complete...
Waiting for PID 31190 of (31184 31190 31196 31200 31207) to complete...
Waiting for PID 31196 of (31184 31190 31196 31200 31207) to complete...
Waiting for PID 31200 of (31184 31190 31196 31200 31207) to complete...
Waiting for PID 31207 of (31184 31190 31196 31200 31207) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 1572
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6213
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 3679
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11793
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 671
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2689
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 157
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1447
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 146
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1345
mri_label2label: Done

PIDs (31184 31190 31196 31200 31207) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 31265 of (31265 31271 31277 31283 31288) to complete...
Waiting for PID 31271 of (31265 31271 31277 31283 31288) to complete...
Waiting for PID 31277 of (31265 31271 31277 31283 31288) to complete...
Waiting for PID 31283 of (31265 31271 31277 31283 31288) to complete...
Waiting for PID 31288 of (31265 31271 31277 31283 31288) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 199
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1213
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 244
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2336
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 91
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1595
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 192
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2188
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 380
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2699
mri_label2label: Done

PIDs (31265 31271 31277 31283 31288) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 31339 of (31339 31345 31351 31356) to complete...
Waiting for PID 31345 of (31339 31345 31351 31356) to complete...
Waiting for PID 31351 of (31339 31345 31351 31356) to complete...
Waiting for PID 31356 of (31339 31345 31351 31356) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 166
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1715
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 740
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7775
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 146
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2058
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 448
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1599
mri_label2label: Done

PIDs (31339 31345 31351 31356) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 31401 of (31401 31407 31413 31419 31425) to complete...
Waiting for PID 31407 of (31401 31407 31413 31419 31425) to complete...
Waiting for PID 31413 of (31401 31407 31413 31419 31425) to complete...
Waiting for PID 31419 of (31401 31407 31413 31419 31425) to complete...
Waiting for PID 31425 of (31401 31407 31413 31419 31425) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 1067
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4472
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 1695
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5029
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 653
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 27
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 497
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 149622
Number of reverse mapping hits = 50
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 500
mri_label2label: Done

PIDs (31401 31407 31413 31419 31425) completed and logs appended.

 mris_label2annot --s 0050111 --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-6.0.0/0050111/label
cmdline mris_label2annot --s 0050111 --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-935
machine  x86_64
user     ntraut

subject 0050111
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-6.0.0/0050111/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 104457 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050111 --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-6.0.0/0050111/label
cmdline mris_label2annot --s 0050111 --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-935
machine  x86_64
user     ntraut

subject 0050111
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-6.0.0/0050111/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 122793 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 292163
Total vertex volume 288372 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1465    811   2438  2.181 0.679     0.139     0.075       35     4.3  BA1_exvivo
 4540   2949   7149  2.383 0.477     0.105     0.028       34     4.8  BA2_exvivo
 1170    789   1146  1.930 0.453     0.138     0.038       14     2.0  BA3a_exvivo
 2539   1626   3556  1.906 0.691     0.100     0.029       22     2.8  BA3b_exvivo
 2003   1133   3577  2.742 0.501     0.108     0.046       23     3.4  BA4a_exvivo
 1534    935   2199  2.510 0.541     0.100     0.031       11     2.0  BA4p_exvivo
 9614   6244  22088  2.877 0.573     0.122     0.035      116    13.1  BA6_exvivo
 2137   1441   4741  2.837 0.475     0.107     0.029       21     2.2  BA44_exvivo
 3497   2353   8032  2.781 0.567     0.122     0.035       45     4.7  BA45_exvivo
 3623   2318   4125  1.779 0.452     0.134     0.040       57     5.4  V1_exvivo
 9278   5842  13711  2.124 0.602     0.145     0.045      156    16.4  V2_exvivo
 2419   1581   4969  2.635 0.548     0.122     0.035       32     2.6  MT_exvivo
  587    382   1996  3.633 0.628     0.091     0.028        5     0.6  perirhinal_exvivo
  759    514   1878  3.159 0.748     0.135     0.051       15     1.5  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 0050111 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 292163
Total vertex volume 288372 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
  954    515   1588  2.222 0.650     0.138     0.069       20     2.3  BA1_exvivo
 1754   1138   2735  2.233 0.475     0.096     0.027       11     2.2  BA2_exvivo
  994    678    944  1.906 0.441     0.140     0.034       10     1.4  BA3a_exvivo
 1643   1079   1751  1.575 0.336     0.085     0.023       10     1.4  BA3b_exvivo
 2003   1125   3434  2.780 0.515     0.104     0.044       22     3.8  BA4a_exvivo
 1222    750   1667  2.380 0.516     0.106     0.038       13     2.0  BA4p_exvivo
 5504   3540  12260  2.820 0.580     0.121     0.038       65     7.6  BA6_exvivo
 1398    943   3319  2.875 0.470     0.112     0.032       16     1.5  BA44_exvivo
 1491    999   3993  2.953 0.539     0.131     0.042       24     2.6  BA45_exvivo
 3944   2498   4530  1.799 0.459     0.137     0.041       65     6.4  V1_exvivo
 4673   2938   6077  1.933 0.534     0.151     0.050       90     9.0  V2_exvivo
  597    416    918  2.401 0.369     0.107     0.021        4     0.5  MT_exvivo
  273    186   1047  3.764 0.535     0.077     0.017        1     0.1  perirhinal_exvivo
  379    268   1005  3.446 0.672     0.118     0.042        5     0.7  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 03:29:48 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 31584 of (31584 31590 31596 31602 31607) to complete...
Waiting for PID 31590 of (31584 31590 31596 31602 31607) to complete...
Waiting for PID 31596 of (31584 31590 31596 31602 31607) to complete...
Waiting for PID 31602 of (31584 31590 31596 31602 31607) to complete...
Waiting for PID 31607 of (31584 31590 31596 31602 31607) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 555
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4517
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 632
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7319
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 272
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4252
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 519
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5041
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 592
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6339
mri_label2label: Done

PIDs (31584 31590 31596 31602 31607) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 31665 of (31665 31671 31677 31683) to complete...
Waiting for PID 31671 of (31665 31671 31677 31683) to complete...
Waiting for PID 31677 of (31665 31671 31677 31683) to complete...
Waiting for PID 31683 of (31665 31671 31677 31683) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 510
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4983
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 1453
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13709
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 661
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7573
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 1240
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6595
mri_label2label: Done

PIDs (31665 31671 31677 31683) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 31733 of (31733 31739 31745 31750 31756) to complete...
Waiting for PID 31739 of (31733 31739 31745 31750 31756) to complete...
Waiting for PID 31745 of (31733 31739 31745 31750 31756) to complete...
Waiting for PID 31750 of (31733 31739 31745 31750 31756) to complete...
Waiting for PID 31756 of (31733 31739 31745 31750 31756) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 2677
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 7404
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 4346
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12362
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 835
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2767
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 106
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1144
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 76
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 828
mri_label2label: Done

PIDs (31733 31739 31745 31750 31756) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 31810 of (31810 31816 31821 31828 31834) to complete...
Waiting for PID 31816 of (31810 31816 31821 31828 31834) to complete...
Waiting for PID 31821 of (31810 31816 31821 31828 31834) to complete...
Waiting for PID 31828 of (31810 31816 31821 31828 31834) to complete...
Waiting for PID 31834 of (31810 31816 31821 31828 31834) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 193
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1069
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 176
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2864
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 76
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1774
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 221
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2404
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 159
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1547
mri_label2label: Done

PIDs (31810 31816 31821 31828 31834) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 31873 of (31873 31879 31885 31891) to complete...
Waiting for PID 31879 of (31873 31879 31885 31891) to complete...
Waiting for PID 31885 of (31873 31879 31885 31891) to complete...
Waiting for PID 31891 of (31873 31879 31885 31891) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1673
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 721
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7680
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 110
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1122
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 230
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1408
mri_label2label: Done

PIDs (31873 31879 31885 31891) 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 0050111 --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 0050111 --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 0050111 --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 0050111 --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 0050111 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 31948 of (31948 31954 31960 31966 31972) to complete...
Waiting for PID 31954 of (31948 31954 31960 31966 31972) to complete...
Waiting for PID 31960 of (31948 31954 31960 31966 31972) to complete...
Waiting for PID 31966 of (31948 31954 31960 31966 31972) to complete...
Waiting for PID 31972 of (31948 31954 31960 31966 31972) 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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 1835
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 5067
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 2125
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5562
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 110
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 378
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 74
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 768
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 0050111 --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 = 0050111
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-6.0.0/0050111/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 151182
Number of reverse mapping hits = 36
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 327
mri_label2label: Done

PIDs (31948 31954 31960 31966 31972) completed and logs appended.

 mris_label2annot --s 0050111 --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-6.0.0/0050111/label
cmdline mris_label2annot --s 0050111 --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-935
machine  x86_64
user     ntraut

subject 0050111
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-6.0.0/0050111/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 104516 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050111 --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-6.0.0/0050111/label
cmdline mris_label2annot --s 0050111 --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-935
machine  x86_64
user     ntraut

subject 0050111
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-6.0.0/0050111/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 124519 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/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 0050111 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 295475
Total vertex volume 291711 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
 1121    639   2272  2.421 0.587     0.141     0.070       26     2.7  BA1_exvivo
 3505   2276   5251  2.306 0.480     0.110     0.033       33     4.2  BA2_exvivo
 1206    811   1276  2.034 0.399     0.117     0.028        9     1.2  BA3a_exvivo
 2319   1519   3223  1.850 0.603     0.103     0.030       19     2.6  BA3b_exvivo
 1865   1078   3409  2.688 0.478     0.111     0.043       24     3.5  BA4a_exvivo
 1485    916   2279  2.541 0.482     0.113     0.047       20     2.9  BA4p_exvivo
 8780   5792  19340  2.755 0.586     0.123     0.036      102    11.7  BA6_exvivo
 3367   2286   7444  2.821 0.558     0.124     0.032       37     4.3  BA44_exvivo
 4591   3074  10148  2.734 0.604     0.137     0.043       79     7.7  BA45_exvivo
 5057   3153   5738  1.789 0.516     0.138     0.047       80     9.8  V1_exvivo
 9824   6159  14614  2.196 0.604     0.141     0.045      159    16.7  V2_exvivo
 2549   1746   5205  2.612 0.525     0.128     0.031       29     3.1  MT_exvivo
  611    378   1921  3.774 0.665     0.092     0.024        4     0.5  perirhinal_exvivo
  386    268   1097  3.384 0.526     0.106     0.044        4     0.8  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 0050111 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050111/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 295475
Total vertex volume 291711 (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) = 1503924 mm^3    (det: 1.295348 )
lhCtxGM: 285932.122 284964.000  diff=  968.1  pctdiff= 0.339
rhCtxGM: 289799.788 288994.000  diff=  805.8  pctdiff= 0.278
lhCtxWM: 230558.863 232032.500  diff=-1473.6  pctdiff=-0.639
rhCtxWM: 233818.232 234267.500  diff= -449.3  pctdiff=-0.192
SubCortGMVol  65855.000
SupraTentVol  1116759.004 (1113037.000) diff=3722.004 pctdiff=0.333
SupraTentVolNotVent  1109884.004 (1106162.000) diff=3722.004 pctdiff=0.335
BrainSegVol  1268144.000 (1265685.000) diff=2459.000 pctdiff=0.194
BrainSegVolNotVent  1257993.000 (1257754.004) diff=238.996 pctdiff=0.019
BrainSegVolNotVent  1257993.000
CerebellumVol 151741.000
VentChorVol    6875.000
3rd4th5thCSF   3276.000
CSFVol   817.000, OptChiasmVol    90.000
MaskVol 1609942.000
  808    458   1513  2.237 0.557     0.137     0.063       18     1.5  BA1_exvivo
 1988   1300   3135  2.286 0.471     0.100     0.026       14     1.9  BA2_exvivo
 1069    716   1027  2.038 0.367     0.120     0.029        8     1.1  BA3a_exvivo
 1792   1202   1984  1.645 0.385     0.086     0.018        8     1.4  BA3b_exvivo
 1110    640   1969  2.671 0.449     0.117     0.048       14     2.1  BA4a_exvivo
 1206    766   1831  2.573 0.488     0.106     0.037       13     1.9  BA4p_exvivo
 5587   3704  12376  2.765 0.575     0.125     0.036       64     7.3  BA6_exvivo
  857    589   2422  3.052 0.603     0.135     0.039       12     1.2  BA44_exvivo
 1102    741   2494  2.683 0.569     0.147     0.050       24     2.4  BA45_exvivo
 4825   3011   5423  1.794 0.500     0.134     0.046       73     9.0  V1_exvivo
 5332   3314   7511  2.069 0.620     0.146     0.047       86     9.6  V2_exvivo
  357    234    963  2.732 0.580     0.132     0.038        4     0.6  MT_exvivo
  364    230   1344  3.968 0.604     0.081     0.019        2     0.3  perirhinal_exvivo
  266    178    724  3.292 0.515     0.110     0.050        3     0.6  entorhinal_exvivo

Started at Sat Oct 7 18:03:54 CEST 2017 
Ended   at Sun Oct 8 03:33:20 CEST 2017
#@#%# recon-all-run-time-hours 9.491
recon-all -s 0050111 finished without error at Sun Oct  8 03:33:20 CEST 2017