ABIDE_fs-6.0.0/0051009/scripts/recon-all.log

Sat Oct  7 17:18:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051009 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051009/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051009
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-576 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    10485760 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked 64 kbytes
maxproc      1024 

             total       used       free     shared    buffers     cached
Mem:      65993848   27219312   38774536    1761332          0   24467628
-/+ buffers/cache:    2751684   63242164
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-15:18:08-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-576  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-6.0.0/0051009

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051009/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051009/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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/NYU/0051009/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-6.0.0/0051009/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 17:18:10 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/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-6.0.0/0051009/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 17:18:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/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-576 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:18:18 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.24067
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24067/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24067/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.24067/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:18:21 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.24067/nu0.mnc ./tmp.mri_nu_correct.mni.24067/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24067/0/ -iterations 1000 -distance 50
[ntraut@tars-576:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/] [2017-10-07 17:18:21] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24067/0/ ./tmp.mri_nu_correct.mni.24067/nu0.mnc ./tmp.mri_nu_correct.mni.24067/nu1.imp

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Number of iterations: 45 
CV of field change: 0.00099054
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.24067/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.24067/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.24067/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 17:19:30 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 17:19:30 CEST 2017
Ended   at Sat Oct  7 17:20:01 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 17:20:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6706, pval=0.3663 >= 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-6.0.0/0051009/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/transforms/talairach_avi.log 

TalAviQA: 0.97759
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 17:20:03 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-6.0.0/0051009/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-576 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:20:03 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.24903
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24903/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24903/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.24903/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:20:06 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.24903/nu0.mnc ./tmp.mri_nu_correct.mni.24903/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24903/0/
[ntraut@tars-576:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/] [2017-10-07 17:20:06] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24903/0/ ./tmp.mri_nu_correct.mni.24903/nu0.mnc ./tmp.mri_nu_correct.mni.24903/nu1.imp

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Number of iterations: 47 
CV of field change: 0.000955822
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 17:20:56 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.24903/nu1.mnc ./tmp.mri_nu_correct.mni.24903/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24903/1/
[ntraut@tars-576:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/] [2017-10-07 17:20:56] 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.24903/1/ ./tmp.mri_nu_correct.mni.24903/nu1.mnc ./tmp.mri_nu_correct.mni.24903/nu2.imp

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Number of iterations: 24 
CV of field change: 0.000999878
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.24903/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24903/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-6.0.0/0051009/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.24903/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24903/ones.mgz 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.24903/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.24903/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.24903/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24903/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24903/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.24903/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24903/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24903/input.mean.dat 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.24903/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.24903/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24903/ones.mgz --i ./tmp.mri_nu_correct.mni.24903/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24903/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24903/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.24903/ones.mgz --i ./tmp.mri_nu_correct.mni.24903/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24903/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24903/output.mean.dat 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.24903/ones.mgz
Loading ./tmp.mri_nu_correct.mni.24903/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.24903/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.24903/nu2.mnc ./tmp.mri_nu_correct.mni.24903/nu2.mnc mul .98875573269641965975
Saving result to './tmp.mri_nu_correct.mni.24903/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.24903/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.24903/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.24903/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (12, 133) to ( 3, 110)
 
 
Sat Oct  7 17:22:06 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 17:22:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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
 1.00311   0.08923  -0.12622  -1.33858;
-0.02183   1.00299   0.31136  -5.71952;
 0.12724  -0.20994   1.08905  -14.60684;
 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 54 (54), valley at 24 (24)
csf peak at 27, setting threshold to 45
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 56 (56), valley at 24 (24)
csf peak at 29, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 0 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 17:24:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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=5.0
skull bounding box = (43, 38, 16) --> (211, 188, 212)
using (99, 88, 114) as brain centroid...
mean wm in atlas = 108, using box (78,70,90) --> (119, 106,138) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 6.1
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.239
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.244763 @ (0.000, 0.000, 0.000)
max log p =    -4.150237 @ (-4.545, 4.545, -4.545)
max log p =    -4.107472 @ (2.273, 2.273, -2.273)
max log p =    -4.101546 @ (1.136, -1.136, -1.136)
max log p =    -4.088421 @ (-1.705, -0.568, 0.568)
max log p =    -4.088421 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, 5.1, -7.4): log p = -4.088
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.807, old_max_log_p =-4.088 (thresh=-4.1)
 0.99144  -0.14499  -0.03885   20.76262;
 0.14032   1.18391   0.31723  -67.05776;
 0.00000  -0.27532   1.02750   27.09505;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.802, old_max_log_p =-3.807 (thresh=-3.8)
 0.99144  -0.14499  -0.03885   20.76262;
 0.12979   1.09512   0.29344  -51.36538;
 0.00000  -0.27532   1.02750   27.09505;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.802, old_max_log_p =-3.802 (thresh=-3.8)
 0.99144  -0.14499  -0.03885   20.76262;
 0.12979   1.09512   0.29344  -51.36538;
 0.00000  -0.27532   1.02750   27.09505;
 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=-3.710, old_max_log_p =-3.802 (thresh=-3.8)
 0.98932  -0.12667  -0.10597   24.59315;
 0.13006   1.12307   0.26697  -51.95737;
 0.06804  -0.24066   1.01248   17.45434;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.700, old_max_log_p =-3.710 (thresh=-3.7)
 0.98932  -0.12667  -0.10597   24.59315;
 0.13470   1.13549   0.30557  -58.60698;
 0.06494  -0.28248   1.02201   20.34869;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.700, old_max_log_p =-3.700 (thresh=-3.7)
 0.98932  -0.12667  -0.10597   24.59315;
 0.13470   1.13549   0.30557  -58.60698;
 0.06494  -0.28248   1.02201   20.34869;
 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=-3.680, old_max_log_p =-3.700 (thresh=-3.7)
 0.98864  -0.14771  -0.10271   26.58647;
 0.15105   1.13455   0.30429  -60.93713;
 0.05691  -0.28176   1.02404   21.06721;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.676, old_max_log_p =-3.680 (thresh=-3.7)
 0.99332  -0.13896  -0.10058   24.58423;
 0.14258   1.13307   0.30441  -59.17956;
 0.05698  -0.28209   1.02524   21.43091;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.675, old_max_log_p =-3.676 (thresh=-3.7)
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 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
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.675 (old=-4.239)
transform before final EM align:
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 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
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 013: -log(p) =    4.1  tol 0.000000
final transform:
 0.99712  -0.12285  -0.08730   20.92098;
 0.12630   1.13523   0.30588  -57.03100;
 0.04879  -0.28062   1.02482   22.35830;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1491.652234
mri_em_register stimesec    1.248810
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   157606
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    154
mri_em_register ru_nivcsw   4177
registration took 12 minutes and 50 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=128 y=103 z=112 r=68
      first estimation of the main basin volume: 1375675 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=146, y=86, z=80, Imax=255
      CSF=14, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=9580903367 voxels, voxel volume =1.000 
                     = 9580903367 mmm3 = 9580903.424 cm3
done.
PostAnalyze...Basin Prior
 397 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=111, z=104, r=9655 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=42 , nb = 44648
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = -1035419957
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = -1044783673
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = 1088052609
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=45 , nb = 1075754914
    OTHER      CSF_MIN=0, CSF_intensity=15, CSF_MAX=37 , nb = 1071810950
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    42,      36,        34,   50
  after  analyzing :    27,      36,        36,   39
   RIGHT_CER   
  before analyzing :    23,      26,        31,   54
  after  analyzing :    23,      29,        31,   35
   LEFT_CER    
  before analyzing :    21,      27,        34,   54
  after  analyzing :    21,      31,        34,   36
  RIGHT_BRAIN  
  before analyzing :    40,      35,        33,   50
  after  analyzing :    28,      35,        35,   38
  LEFT_BRAIN   
  before analyzing :    45,      36,        33,   51
  after  analyzing :    27,      36,        36,   39
     OTHER     
  before analyzing :    37,      52,        70,   95
  after  analyzing :    37,      64,        70,   71
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...60 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 71.825, std = 7.336

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.53, sigma = 5.32
      after  rotation: sse = 3.53, sigma = 5.32
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  3.70, its var is  4.70   
      before Erosion-Dilatation  0.78% 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...41 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1795510 voxels, voxel volume = 1.000 mm3
           = 1795510 mmm3 = 1795.510 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    22.985505
mri_watershed stimesec    0.435933
mri_watershed ru_maxrss   823824
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213297
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2920
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    2707
mri_watershed ru_nivcsw   59
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 17:37:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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=22.9
skull bounding box = (56, 52, 30) --> (201, 182, 196)
using (104, 95, 113) as brain centroid...
mean wm in atlas = 107, using box (86,79,93) --> (121, 110,133) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 5.8
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -3.949
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.923429 @ (-9.091, 9.091, -9.091)
max log p =    -3.739565 @ (4.545, -4.545, 4.545)
max log p =    -3.638911 @ (2.273, 2.273, 2.273)
max log p =    -3.638911 @ (0.000, 0.000, 0.000)
max log p =    -3.638911 @ (0.000, 0.000, 0.000)
max log p =    -3.629850 @ (0.284, 0.852, 0.284)
Found translation: (-2.0, 7.7, -2.0): log p = -3.630
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.422, old_max_log_p =-3.630 (thresh=-3.6)
 0.99618  -0.10460  -0.04567   15.08448;
 0.16649   1.12081   0.16635  -45.11710;
 0.03885  -0.11655   0.99519   6.53708;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.406, old_max_log_p =-3.422 (thresh=-3.4)
 0.99618  -0.10460  -0.04567   15.08448;
 0.17014   1.09601   0.29482  -56.62057;
 0.01679  -0.26185   0.96496   28.84268;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.406, old_max_log_p =-3.406 (thresh=-3.4)
 0.99618  -0.10460  -0.04567   15.08448;
 0.17014   1.09601   0.29482  -56.62057;
 0.01679  -0.26185   0.96496   28.84268;
 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=-3.286, old_max_log_p =-3.406 (thresh=-3.4)
 0.96678  -0.12716  -0.11531   28.87020;
 0.19609   1.08653   0.22323  -49.33714;
 0.09646  -0.20340   1.01373   8.69781;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.282, old_max_log_p =-3.286 (thresh=-3.3)
 0.98015  -0.06403  -0.06540   14.92530;
 0.13786   1.10617   0.26601  -48.54110;
 0.05722  -0.23015   0.99020   19.16649;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.282, old_max_log_p =-3.282 (thresh=-3.3)
 0.98015  -0.06403  -0.06540   14.92530;
 0.13786   1.10617   0.26601  -48.54110;
 0.05722  -0.23015   0.99020   19.16649;
 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=-3.268, old_max_log_p =-3.282 (thresh=-3.3)
 0.97611  -0.08007  -0.07790   18.53134;
 0.15412   1.10179   0.27255  -51.30165;
 0.06409  -0.23971   0.98742   19.63266;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.249, old_max_log_p =-3.268 (thresh=-3.3)
 0.97397  -0.10001  -0.07412   20.14695;
 0.16954   1.10223   0.26328  -52.82195;
 0.05742  -0.23029   0.99138   18.55816;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.247, old_max_log_p =-3.249 (thresh=-3.2)
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 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
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.247 (old=-3.949)
transform before final EM align:
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 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
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 0.97283  -0.09989  -0.07403   20.27186;
 0.16915   1.09965   0.26267  -52.41856;
 0.05742  -0.23029   0.99138   18.55816;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 012: -log(p) = 3.8
after pass:transform: ( 0.97, -0.10, -0.07, 20.27)
                      ( 0.17, 1.10, 0.26, -52.42)
                      ( 0.06, -0.23, 0.99, 18.56)
dfp_em_step_func: 013: -log(p) = 3.8
after pass:transform: ( 0.97, -0.10, -0.07, 20.27)
                      ( 0.17, 1.10, 0.26, -52.42)
                      ( 0.06, -0.23, 0.99, 18.56)
dfp_em_step_func: 014: -log(p) = 3.8
after pass:transform: ( 0.97, -0.10, -0.07, 20.27)
                      ( 0.17, 1.10, 0.26, -52.42)
                      ( 0.06, -0.23, 0.99, 18.56)
pass 2 through quasi-newton minimization...
outof QuasiNewtonEMA: 016: -log(p) =    3.8  tol 0.000000
final transform:
 0.97292  -0.09981  -0.07396   20.27186;
 0.16912   1.09963   0.26263  -52.41856;
 0.05747  -0.23025   0.99142   18.55816;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1388.077980
mri_em_register stimesec    1.415784
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   158989
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    155
mri_em_register ru_nivcsw   2381
registration took 11 minutes and 59 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 17:49:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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=22.9
skull bounding box = (56, 52, 30) --> (201, 182, 196)
using (104, 95, 113) as brain centroid...
mean wm in atlas = 107, using box (86,79,93) --> (121, 110,133) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 5.8
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 0.97292  -0.09981  -0.07396   20.27186;
 0.16912   1.09963   0.26263  -52.41856;
 0.05747  -0.23025   0.99142   18.55816;
 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 (125, 51, 30) --> (197, 155, 191)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 78 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (61, 54, 32) --> (132, 157, 194)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 62 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 134, 57) --> (182, 168, 110)
Left_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0
0 of 8 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 134, 58) --> (131, 174, 114)
Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0
5 of 10 (50.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (114, 120, 93) --> (151, 183, 123)
Brain_Stem: limiting intensities to 91.0 --> 132.0
6 of 14 (42.9%) samples deleted
using 172 total control points for intensity normalization...
bias field = 0.940 +- 0.079
0 of 161 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (125, 51, 30) --> (197, 155, 191)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
0 of 153 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (61, 54, 32) --> (132, 157, 194)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 143 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 134, 57) --> (182, 168, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
16 of 72 (22.2%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 134, 58) --> (131, 174, 114)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
26 of 59 (44.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (114, 120, 93) --> (151, 183, 123)
Brain_Stem: limiting intensities to 88.0 --> 132.0
60 of 94 (63.8%) samples deleted
using 521 total control points for intensity normalization...
bias field = 0.999 +- 0.071
0 of 416 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (125, 51, 30) --> (197, 155, 191)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 262 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (61, 54, 32) --> (132, 157, 194)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 312 (1.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 134, 57) --> (182, 168, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
28 of 75 (37.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 134, 58) --> (131, 174, 114)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
69 of 85 (81.2%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (114, 120, 93) --> (151, 183, 123)
Brain_Stem: limiting intensities to 88.0 --> 132.0
147 of 176 (83.5%) samples deleted
using 910 total control points for intensity normalization...
bias field = 1.003 +- 0.053
0 of 653 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 48 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 17:51:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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) = 1.14 (predicted orig area = 7.0)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.818, neg=0, invalid=762
0001: dt=208.956522, rms=0.759 (7.251%), neg=0, invalid=762
0002: dt=259.439011, rms=0.742 (2.204%), neg=0, invalid=762
0003: dt=205.333333, rms=0.734 (1.154%), neg=0, invalid=762
0004: dt=295.936000, rms=0.729 (0.681%), neg=0, invalid=762
0005: dt=129.472000, rms=0.725 (0.477%), neg=0, invalid=762
0006: dt=1775.616000, rms=0.713 (1.648%), neg=0, invalid=762
0007: dt=369.920000, rms=0.711 (0.332%), neg=0, invalid=762
0008: dt=129.472000, rms=0.710 (0.153%), neg=0, invalid=762
0009: dt=129.472000, rms=0.709 (0.087%), neg=0, invalid=762
0010: dt=129.472000, rms=0.708 (0.147%), neg=0, invalid=762
0011: dt=129.472000, rms=0.707 (0.183%), neg=0, invalid=762
0012: dt=129.472000, rms=0.706 (0.202%), neg=0, invalid=762
0013: dt=129.472000, rms=0.704 (0.218%), neg=0, invalid=762
0014: dt=129.472000, rms=0.703 (0.214%), neg=0, invalid=762
0015: dt=129.472000, rms=0.701 (0.209%), neg=0, invalid=762
0016: dt=129.472000, rms=0.700 (0.208%), neg=0, invalid=762
0017: dt=129.472000, rms=0.698 (0.197%), neg=0, invalid=762
0018: dt=129.472000, rms=0.697 (0.194%), neg=0, invalid=762
0019: dt=129.472000, rms=0.696 (0.188%), neg=0, invalid=762
0020: dt=129.472000, rms=0.694 (0.182%), neg=0, invalid=762
0021: dt=129.472000, rms=0.693 (0.162%), neg=0, invalid=762
0022: dt=129.472000, rms=0.692 (0.151%), neg=0, invalid=762
0023: dt=129.472000, rms=0.691 (0.143%), neg=0, invalid=762
0024: dt=129.472000, rms=0.690 (0.131%), neg=0, invalid=762
0025: dt=129.472000, rms=0.689 (0.126%), neg=0, invalid=762
0026: dt=129.472000, rms=0.689 (0.117%), neg=0, invalid=762
0027: dt=129.472000, rms=0.688 (0.108%), neg=0, invalid=762
0028: dt=887.808000, rms=0.687 (0.049%), neg=0, invalid=762
0029: dt=887.808000, rms=0.687 (-0.864%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.688, neg=0, invalid=762
0030: dt=295.936000, rms=0.687 (0.208%), neg=0, invalid=762
0031: dt=295.936000, rms=0.686 (0.095%), neg=0, invalid=762
0032: dt=295.936000, rms=0.685 (0.066%), neg=0, invalid=762
0033: dt=295.936000, rms=0.685 (0.081%), neg=0, invalid=762
0034: dt=295.936000, rms=0.684 (0.056%), neg=0, invalid=762
0035: dt=295.936000, rms=0.684 (0.142%), neg=0, invalid=762
0036: dt=295.936000, rms=0.683 (0.064%), neg=0, invalid=762
0037: dt=295.936000, rms=0.683 (0.064%), neg=0, invalid=762
0038: dt=295.936000, rms=0.682 (0.029%), neg=0, invalid=762
0039: dt=295.936000, rms=0.682 (-0.022%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.687, neg=0, invalid=762
0040: dt=167.031390, rms=0.681 (0.939%), neg=0, invalid=762
0041: dt=145.152000, rms=0.673 (1.074%), neg=0, invalid=762
0042: dt=77.632520, rms=0.669 (0.633%), neg=0, invalid=762
0043: dt=248.832000, rms=0.664 (0.800%), neg=0, invalid=762
0044: dt=62.208000, rms=0.660 (0.550%), neg=0, invalid=762
0045: dt=580.608000, rms=0.650 (1.475%), neg=0, invalid=762
0046: dt=60.081633, rms=0.648 (0.331%), neg=0, invalid=762
0047: dt=331.776000, rms=0.646 (0.337%), neg=0, invalid=762
0048: dt=36.288000, rms=0.645 (0.177%), neg=0, invalid=762
0049: dt=36.288000, rms=0.644 (0.068%), neg=0, invalid=762
0050: dt=36.288000, rms=0.644 (0.073%), neg=0, invalid=762
0051: dt=36.288000, rms=0.643 (0.112%), neg=0, invalid=762
0052: dt=36.288000, rms=0.642 (0.162%), neg=0, invalid=762
0053: dt=36.288000, rms=0.641 (0.186%), neg=0, invalid=762
0054: dt=36.288000, rms=0.640 (0.182%), neg=0, invalid=762
0055: dt=36.288000, rms=0.639 (0.181%), neg=0, invalid=762
0056: dt=36.288000, rms=0.637 (0.178%), neg=0, invalid=762
0057: dt=36.288000, rms=0.636 (0.182%), neg=0, invalid=762
0058: dt=36.288000, rms=0.635 (0.199%), neg=0, invalid=762
0059: dt=36.288000, rms=0.634 (0.210%), neg=0, invalid=762
0060: dt=36.288000, rms=0.632 (0.213%), neg=0, invalid=762
0061: dt=36.288000, rms=0.631 (0.204%), neg=0, invalid=762
0062: dt=36.288000, rms=0.630 (0.188%), neg=0, invalid=762
0063: dt=36.288000, rms=0.629 (0.160%), neg=0, invalid=762
0064: dt=36.288000, rms=0.628 (0.143%), neg=0, invalid=762
0065: dt=36.288000, rms=0.627 (0.138%), neg=0, invalid=762
0066: dt=36.288000, rms=0.626 (0.133%), neg=0, invalid=762
0067: dt=36.288000, rms=0.625 (0.127%), neg=0, invalid=762
0068: dt=36.288000, rms=0.625 (0.116%), neg=0, invalid=762
0069: dt=36.288000, rms=0.624 (0.113%), neg=0, invalid=762
0070: dt=145.152000, rms=0.624 (0.015%), neg=0, invalid=762
0071: dt=145.152000, rms=0.624 (0.019%), neg=0, invalid=762
0072: dt=145.152000, rms=0.624 (0.027%), neg=0, invalid=762
0073: dt=145.152000, rms=0.623 (0.061%), neg=0, invalid=762
0074: dt=145.152000, rms=0.623 (0.072%), neg=0, invalid=762
0075: dt=145.152000, rms=0.622 (0.071%), neg=0, invalid=762
0076: dt=145.152000, rms=0.622 (0.118%), neg=0, invalid=762
0077: dt=145.152000, rms=0.621 (0.122%), neg=0, invalid=762
0078: dt=145.152000, rms=0.620 (0.131%), neg=0, invalid=762
0079: dt=145.152000, rms=0.619 (0.159%), neg=0, invalid=762
0080: dt=145.152000, rms=0.618 (0.153%), neg=0, invalid=762
0081: dt=145.152000, rms=0.617 (0.135%), neg=0, invalid=762
0082: dt=145.152000, rms=0.616 (0.155%), neg=0, invalid=762
0083: dt=145.152000, rms=0.615 (0.148%), neg=0, invalid=762
0084: dt=145.152000, rms=0.615 (0.111%), neg=0, invalid=762
0085: dt=145.152000, rms=0.614 (0.112%), neg=0, invalid=762
0086: dt=145.152000, rms=0.613 (0.117%), neg=0, invalid=762
0087: dt=145.152000, rms=0.613 (0.094%), neg=0, invalid=762
0088: dt=82.944000, rms=0.613 (0.019%), neg=0, invalid=762
0089: dt=82.944000, rms=0.613 (-0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0090: dt=78.328358, rms=0.612 (0.259%), neg=0, invalid=762
0091: dt=145.152000, rms=0.611 (0.121%), neg=0, invalid=762
0092: dt=145.152000, rms=0.611 (-0.098%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.636, neg=0, invalid=762
0093: dt=0.000000, rms=0.635 (0.115%), neg=0, invalid=762
0094: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.636, neg=0, invalid=762
0095: dt=0.000000, rms=0.635 (0.115%), neg=0, invalid=762
0096: dt=0.000000, rms=0.635 (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=0.709, neg=0, invalid=762
0097: dt=5.300699, rms=0.685 (3.330%), neg=0, invalid=762
0098: dt=2.492754, rms=0.684 (0.117%), neg=0, invalid=762
0099: dt=2.492754, rms=0.684 (-0.039%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.685, neg=0, invalid=762
0100: dt=0.000000, rms=0.684 (0.077%), neg=0, invalid=762
0101: dt=0.000000, rms=0.684 (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=0.748, neg=0, invalid=762
0102: dt=1.792000, rms=0.740 (0.994%), neg=0, invalid=762
0103: dt=2.120603, rms=0.732 (1.063%), neg=0, invalid=762
0104: dt=0.448000, rms=0.732 (0.067%), neg=0, invalid=762
0105: dt=0.448000, rms=0.732 (0.010%), neg=0, invalid=762
0106: dt=0.448000, rms=0.732 (-0.024%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.732, neg=0, invalid=762
0107: dt=1.280000, rms=0.730 (0.243%), neg=0, invalid=762
0108: dt=1.792000, rms=0.729 (0.144%), neg=0, invalid=762
0109: dt=1.792000, rms=0.729 (-0.048%), 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=0.692, neg=0, invalid=762
0110: dt=0.857973, rms=0.673 (2.789%), neg=0, invalid=762
0111: dt=0.080000, rms=0.672 (0.148%), neg=0, invalid=762
0112: dt=0.080000, rms=0.672 (-0.077%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.672, neg=0, invalid=762
0113: dt=0.028000, rms=0.671 (0.098%), neg=0, invalid=762
0114: dt=0.016000, rms=0.671 (0.004%), neg=0, invalid=762
0115: dt=0.016000, rms=0.671 (-0.003%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.07011 (54)
Left_Lateral_Ventricle (4): linear fit = 1.91 x + 0.0 (893 voxels, overlap=0.129)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (893 voxels, peak = 38), gca=30.0
gca peak = 0.15565 (16)
mri peak = 0.08024 ( 6)
Right_Lateral_Ventricle (43): linear fit = 3.29 x + 0.0 (1113 voxels, overlap=0.003)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1113 voxels, peak = 53), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.07200 (85)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (842 voxels, overlap=0.105)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (842 voxels, peak = 85), gca=85.0
gca peak = 0.20183 (93)
mri peak = 0.08008 (75)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (809 voxels, overlap=0.032)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (809 voxels, peak = 81), gca=81.4
gca peak = 0.21683 (55)
mri peak = 0.08236 (50)
Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (727 voxels, overlap=0.986)
Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (727 voxels, peak = 50), gca=50.3
gca peak = 0.30730 (58)
mri peak = 0.10582 (53)
Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (711 voxels, overlap=0.963)
Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (711 voxels, peak = 52), gca=51.9
gca peak = 0.11430 (101)
mri peak = 0.07553 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (57807 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (57807 voxels, peak = 107), gca=106.6
gca peak = 0.12076 (102)
mri peak = 0.07992 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (59124 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (59124 voxels, peak = 107), gca=106.6
gca peak = 0.14995 (59)
mri peak = 0.05146 (54)
Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (20833 voxels, overlap=0.715)
Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (20833 voxels, peak = 53), gca=52.8
gca peak = 0.15082 (58)
mri peak = 0.05200 (53)
Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (21173 voxels, overlap=0.755)
Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (21173 voxels, peak = 52), gca=51.9
gca peak = 0.14161 (67)
mri peak = 0.09038 (63)
Right_Caudate (50): linear fit = 0.93 x + 0.0 (578 voxels, overlap=0.667)
Right_Caudate (50): linear fit = 0.93 x + 0.0 (578 voxels, peak = 62), gca=62.0
gca peak = 0.15243 (71)
mri peak = 0.08247 (63)
Left_Caudate (11): linear fit = 0.87 x + 0.0 (974 voxels, overlap=0.200)
Left_Caudate (11): linear fit = 0.87 x + 0.0 (974 voxels, peak = 61), gca=61.4
gca peak = 0.13336 (57)
mri peak = 0.04184 (50)
Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (22981 voxels, overlap=0.557)
Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (22981 voxels, peak = 51), gca=51.0
gca peak = 0.13252 (56)
mri peak = 0.04107 (50)
Right_Cerebellum_Cortex (47): linear fit = 0.93 x + 0.0 (23374 voxels, overlap=0.817)
Right_Cerebellum_Cortex (47): linear fit = 0.93 x + 0.0 (23374 voxels, peak = 52), gca=51.8
gca peak = 0.18181 (84)
mri peak = 0.05202 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7393 voxels, overlap=0.929)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7393 voxels, peak = 85), gca=85.3
gca peak = 0.20573 (83)
mri peak = 0.05329 (81)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6810 voxels, overlap=0.978)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6810 voxels, peak = 83), gca=82.6
gca peak = 0.21969 (57)
mri peak = 0.15126 (52)
Left_Amygdala (18): linear fit = 0.89 x + 0.0 (318 voxels, overlap=0.992)
Left_Amygdala (18): linear fit = 0.89 x + 0.0 (318 voxels, peak = 51), gca=51.0
gca peak = 0.39313 (56)
mri peak = 0.09375 (54)
Right_Amygdala (54): linear fit = 0.94 x + 0.0 (325 voxels, overlap=1.003)
Right_Amygdala (54): linear fit = 0.94 x + 0.0 (325 voxels, peak = 53), gca=52.9
gca peak = 0.14181 (85)
mri peak = 0.05132 (77)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5523 voxels, overlap=0.995)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5523 voxels, peak = 81), gca=81.2
gca peak = 0.11978 (83)
mri peak = 0.07183 (76)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4408 voxels, overlap=0.928)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4408 voxels, peak = 83), gca=82.6
gca peak = 0.13399 (79)
mri peak = 0.07035 (68)
Left_Putamen (12): linear fit = 0.88 x + 0.0 (2402 voxels, overlap=0.752)
Left_Putamen (12): linear fit = 0.88 x + 0.0 (2402 voxels, peak = 69), gca=69.1
gca peak = 0.14159 (79)
mri peak = 0.07659 (72)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (2295 voxels, overlap=0.811)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (2295 voxels, peak = 74), gca=73.9
gca peak = 0.10025 (80)
mri peak = 0.11949 (80)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (12375 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (12375 voxels, peak = 85), gca=85.2
gca peak = 0.13281 (86)
mri peak = 0.08451 (83)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (975 voxels, overlap=0.719)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (975 voxels, peak = 87), gca=87.3
gca peak = 0.12801 (89)
mri peak = 0.07703 (91)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1222 voxels, overlap=0.849)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1222 voxels, peak = 90), gca=90.3
gca peak = 0.20494 (23)
mri peak = 0.05969 (44)
gca peak = 0.15061 (21)
mri peak = 0.09586 ( 9)
Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (154 voxels, overlap=0.018)
Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (154 voxels, peak =  8), gca=8.1
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 0.91 x + 0.0
estimating mean wm scale to be 1.05 x + 0.0
estimating mean csf scale to be 1.50 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=0.700, neg=0, invalid=762
0116: dt=146.285714, rms=0.695 (0.667%), neg=0, invalid=762
0117: dt=443.904000, rms=0.691 (0.565%), neg=0, invalid=762
0118: dt=110.976000, rms=0.690 (0.205%), neg=0, invalid=762
0119: dt=369.920000, rms=0.689 (0.154%), neg=0, invalid=762
0120: dt=110.976000, rms=0.688 (0.139%), neg=0, invalid=762
0121: dt=295.936000, rms=0.687 (0.078%), neg=0, invalid=762
0122: dt=110.976000, rms=0.687 (0.095%), neg=0, invalid=762
0123: dt=221.952000, rms=0.686 (0.058%), neg=0, invalid=762
0124: dt=129.472000, rms=0.686 (0.067%), neg=0, invalid=762
0125: dt=129.472000, rms=0.686 (0.040%), neg=0, invalid=762
0126: dt=129.472000, rms=0.685 (0.046%), neg=0, invalid=762
0127: dt=129.472000, rms=0.685 (0.074%), neg=0, invalid=762
0128: dt=129.472000, rms=0.684 (0.093%), neg=0, invalid=762
0129: dt=129.472000, rms=0.683 (0.100%), neg=0, invalid=762
0130: dt=129.472000, rms=0.683 (0.119%), neg=0, invalid=762
0131: dt=129.472000, rms=0.682 (0.118%), neg=0, invalid=762
0132: dt=129.472000, rms=0.681 (0.107%), neg=0, invalid=762
0133: dt=129.472000, rms=0.680 (0.087%), neg=0, invalid=762
0134: dt=129.472000, rms=0.680 (0.083%), neg=0, invalid=762
0135: dt=129.472000, rms=0.679 (0.085%), neg=0, invalid=762
0136: dt=129.472000, rms=0.679 (0.080%), neg=0, invalid=762
0137: dt=129.472000, rms=0.678 (0.072%), neg=0, invalid=762
0138: dt=129.472000, rms=0.678 (0.068%), neg=0, invalid=762
0139: dt=129.472000, rms=0.677 (0.072%), neg=0, invalid=762
0140: dt=129.472000, rms=0.677 (0.073%), neg=0, invalid=762
0141: dt=129.472000, rms=0.676 (0.063%), neg=0, invalid=762
0142: dt=129.472000, rms=0.676 (0.061%), neg=0, invalid=762
0143: dt=129.472000, rms=0.676 (0.058%), neg=0, invalid=762
0144: dt=129.472000, rms=0.675 (0.062%), neg=0, invalid=762
0145: dt=129.472000, rms=0.675 (0.056%), neg=0, invalid=762
0146: dt=129.472000, rms=0.674 (0.053%), neg=0, invalid=762
0147: dt=129.472000, rms=0.674 (0.056%), neg=0, invalid=762
0148: dt=129.472000, rms=0.674 (0.056%), neg=0, invalid=762
0149: dt=129.472000, rms=0.673 (0.055%), neg=0, invalid=762
0150: dt=129.472000, rms=0.673 (0.047%), neg=0, invalid=762
0151: dt=129.472000, rms=0.673 (0.043%), neg=0, invalid=762
0152: dt=129.472000, rms=0.672 (0.046%), neg=0, invalid=762
0153: dt=129.472000, rms=0.672 (0.047%), neg=0, invalid=762
0154: dt=129.472000, rms=0.672 (0.045%), neg=0, invalid=762
0155: dt=129.472000, rms=0.672 (0.039%), neg=0, invalid=762
0156: dt=129.472000, rms=0.671 (0.039%), neg=0, invalid=762
0157: dt=129.472000, rms=0.671 (0.033%), neg=0, invalid=762
0158: dt=129.472000, rms=0.671 (0.030%), neg=0, invalid=762
0159: dt=129.472000, rms=0.671 (0.033%), neg=0, invalid=762
0160: dt=129.472000, rms=0.670 (0.035%), neg=0, invalid=762
0161: dt=129.472000, rms=0.670 (0.036%), neg=0, invalid=762
0162: dt=129.472000, rms=0.670 (0.034%), neg=0, invalid=762
0163: dt=129.472000, rms=0.670 (0.031%), neg=0, invalid=762
0164: dt=129.472000, rms=0.669 (0.030%), neg=0, invalid=762
0165: dt=129.472000, rms=0.669 (0.030%), neg=0, invalid=762
0166: dt=129.472000, rms=0.669 (0.028%), neg=0, invalid=762
0167: dt=129.472000, rms=0.669 (0.026%), neg=0, invalid=762
0168: dt=129.472000, rms=0.669 (0.026%), neg=0, invalid=762
0169: dt=129.472000, rms=0.669 (0.030%), neg=0, invalid=762
0170: dt=129.472000, rms=0.668 (0.031%), neg=0, invalid=762
0171: dt=129.472000, rms=0.668 (0.030%), neg=0, invalid=762
0172: dt=129.472000, rms=0.668 (0.027%), neg=0, invalid=762
0173: dt=129.472000, rms=0.668 (0.025%), neg=0, invalid=762
0174: dt=129.472000, rms=0.668 (0.024%), neg=0, invalid=762
0175: dt=129.472000, rms=0.667 (0.024%), neg=0, invalid=762
0176: dt=2071.552000, rms=0.667 (0.042%), neg=0, invalid=762
0177: dt=32.368000, rms=0.667 (0.003%), neg=0, invalid=762
0178: dt=32.368000, rms=0.667 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.668, neg=0, invalid=762
0179: dt=295.936000, rms=0.666 (0.248%), neg=0, invalid=762
0180: dt=129.472000, rms=0.666 (0.049%), neg=0, invalid=762
0181: dt=129.472000, rms=0.666 (0.019%), neg=0, invalid=762
0182: dt=129.472000, rms=0.666 (0.030%), neg=0, invalid=762
0183: dt=129.472000, rms=0.665 (0.034%), neg=0, invalid=762
0184: dt=129.472000, rms=0.665 (0.034%), neg=0, invalid=762
0185: dt=129.472000, rms=0.665 (0.034%), neg=0, invalid=762
0186: dt=129.472000, rms=0.665 (0.036%), neg=0, invalid=762
0187: dt=129.472000, rms=0.665 (0.033%), neg=0, invalid=762
0188: dt=129.472000, rms=0.664 (0.027%), neg=0, invalid=762
0189: dt=129.472000, rms=0.664 (0.023%), neg=0, invalid=762
0190: dt=129.472000, rms=0.664 (0.022%), neg=0, invalid=762
0191: dt=221.952000, rms=0.664 (0.003%), neg=0, invalid=762
0192: dt=221.952000, rms=0.664 (0.007%), neg=0, invalid=762
0193: dt=221.952000, rms=0.664 (0.003%), neg=0, invalid=762
0194: dt=221.952000, rms=0.664 (0.006%), neg=0, invalid=762
0195: dt=221.952000, rms=0.664 (0.013%), neg=0, invalid=762
0196: dt=221.952000, rms=0.664 (0.013%), neg=0, invalid=762
0197: dt=221.952000, rms=0.664 (0.014%), neg=0, invalid=762
0198: dt=221.952000, rms=0.664 (0.018%), neg=0, invalid=762
0199: dt=221.952000, rms=0.663 (0.021%), neg=0, invalid=762
0200: dt=221.952000, rms=0.663 (0.022%), neg=0, invalid=762
0201: dt=221.952000, rms=0.663 (0.026%), neg=0, invalid=762
0202: dt=221.952000, rms=0.663 (0.027%), neg=0, invalid=762
0203: dt=221.952000, rms=0.663 (0.023%), neg=0, invalid=762
0204: dt=221.952000, rms=0.663 (0.024%), neg=0, invalid=762
0205: dt=221.952000, rms=0.662 (0.024%), neg=0, invalid=762
0206: dt=221.952000, rms=0.662 (0.021%), neg=0, invalid=762
0207: dt=517.888000, rms=0.662 (0.006%), neg=0, invalid=762
0208: dt=517.888000, rms=0.662 (-0.121%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.664, neg=0, invalid=762
0209: dt=124.416000, rms=0.660 (0.607%), neg=0, invalid=762
0210: dt=172.765027, rms=0.655 (0.778%), neg=0, invalid=762
0211: dt=63.030303, rms=0.651 (0.494%), neg=0, invalid=762
0212: dt=94.857143, rms=0.649 (0.334%), neg=0, invalid=762
0213: dt=36.288000, rms=0.647 (0.271%), neg=0, invalid=762
0214: dt=580.608000, rms=0.637 (1.582%), neg=0, invalid=762
0215: dt=86.626263, rms=0.636 (0.265%), neg=0, invalid=762
0216: dt=70.564103, rms=0.635 (0.145%), neg=0, invalid=762
0217: dt=124.416000, rms=0.634 (0.159%), neg=0, invalid=762
0218: dt=36.288000, rms=0.633 (0.151%), neg=0, invalid=762
0219: dt=1658.880000, rms=0.625 (1.271%), neg=0, invalid=762
0220: dt=65.873466, rms=0.620 (0.698%), neg=0, invalid=762
0221: dt=36.288000, rms=0.620 (0.064%), neg=0, invalid=762
0222: dt=414.720000, rms=0.619 (0.168%), neg=0, invalid=762
0223: dt=82.944000, rms=0.618 (0.147%), neg=0, invalid=762
0224: dt=36.288000, rms=0.618 (0.029%), neg=0, invalid=762
0225: dt=36.288000, rms=0.618 (0.016%), neg=0, invalid=762
0226: dt=36.288000, rms=0.617 (0.035%), neg=0, invalid=762
0227: dt=36.288000, rms=0.617 (0.052%), neg=0, invalid=762
0228: dt=36.288000, rms=0.617 (0.067%), neg=0, invalid=762
0229: dt=36.288000, rms=0.616 (0.079%), neg=0, invalid=762
0230: dt=36.288000, rms=0.616 (0.091%), neg=0, invalid=762
0231: dt=36.288000, rms=0.615 (0.100%), neg=0, invalid=762
0232: dt=36.288000, rms=0.614 (0.102%), neg=0, invalid=762
0233: dt=36.288000, rms=0.614 (0.097%), neg=0, invalid=762
0234: dt=36.288000, rms=0.613 (0.094%), neg=0, invalid=762
0235: dt=36.288000, rms=0.613 (0.100%), neg=0, invalid=762
0236: dt=36.288000, rms=0.612 (0.105%), neg=0, invalid=762
0237: dt=36.288000, rms=0.611 (0.107%), neg=0, invalid=762
0238: dt=36.288000, rms=0.611 (0.105%), neg=0, invalid=762
0239: dt=36.288000, rms=0.610 (0.102%), neg=0, invalid=762
0240: dt=36.288000, rms=0.610 (0.010%), neg=0, invalid=762
0241: dt=36.288000, rms=0.610 (0.022%), neg=0, invalid=762
0242: dt=36.288000, rms=0.610 (0.032%), neg=0, invalid=762
0243: dt=36.288000, rms=0.609 (0.043%), neg=0, invalid=762
0244: dt=36.288000, rms=0.609 (0.012%), neg=0, invalid=762
0245: dt=36.288000, rms=0.609 (0.022%), neg=0, invalid=762
0246: dt=9.072000, rms=0.609 (0.003%), neg=0, invalid=762
0247: dt=7.776000, rms=0.609 (0.002%), neg=0, invalid=762
0248: dt=0.486000, rms=0.609 (0.000%), neg=0, invalid=762
0249: dt=0.243000, rms=0.609 (0.000%), neg=0, invalid=762
0250: dt=0.121500, rms=0.609 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.610, neg=0, invalid=762
0251: dt=0.030375, rms=0.609 (0.179%), neg=0, invalid=762
0252: dt=0.002215, rms=0.609 (0.000%), neg=0, invalid=762
0253: dt=0.000554, rms=0.609 (0.000%), neg=0, invalid=762
0254: dt=0.000138, rms=0.609 (0.000%), neg=0, invalid=762
0255: dt=0.000069, rms=0.609 (0.000%), neg=0, invalid=762
0256: dt=0.000000, rms=0.609 (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=0.616, neg=0, invalid=762
0257: dt=44.800000, rms=0.604 (2.012%), neg=0, invalid=762
0258: dt=44.800000, rms=0.596 (1.350%), neg=0, invalid=762
0259: dt=11.200000, rms=0.594 (0.273%), neg=0, invalid=762
0260: dt=0.700000, rms=0.594 (0.015%), neg=0, invalid=762
0261: dt=0.700000, rms=0.594 (0.016%), neg=0, invalid=762
0262: dt=0.350000, rms=0.594 (0.008%), neg=0, invalid=762
0263: dt=0.010937, rms=0.594 (0.000%), neg=0, invalid=762
0264: dt=0.001953, rms=0.594 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.595, neg=0, invalid=762
0265: dt=71.744292, rms=0.587 (1.435%), neg=0, invalid=762
0266: dt=38.400000, rms=0.581 (0.988%), neg=0, invalid=762
0267: dt=25.600000, rms=0.579 (0.350%), neg=0, invalid=762
0268: dt=44.800000, rms=0.576 (0.542%), neg=0, invalid=762
0269: dt=32.000000, rms=0.574 (0.281%), neg=0, invalid=762
0270: dt=11.200000, rms=0.573 (0.195%), neg=0, invalid=762
0271: dt=11.200000, rms=0.572 (0.123%), neg=0, invalid=762
0272: dt=2.800000, rms=0.572 (0.022%), neg=0, invalid=762
0273: dt=1.400000, rms=0.572 (0.013%), neg=0, invalid=762
0274: dt=0.087500, rms=0.572 (0.001%), neg=0, invalid=762
0275: dt=0.021875, rms=0.572 (0.000%), neg=0, invalid=762
0276: dt=0.010937, rms=0.572 (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=0.588, neg=0, invalid=762
0277: dt=10.579439, rms=0.584 (0.649%), neg=0, invalid=762
0278: dt=11.520000, rms=0.581 (0.463%), neg=0, invalid=762
0279: dt=1.008000, rms=0.581 (0.032%), neg=0, invalid=762
0280: dt=0.252000, rms=0.581 (0.008%), neg=0, invalid=762
0281: dt=0.063000, rms=0.581 (0.002%), neg=0, invalid=762
0282: dt=0.031500, rms=0.581 (0.001%), neg=0, invalid=762
0283: dt=0.015750, rms=0.581 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.582, neg=0, invalid=762
0284: dt=9.856540, rms=0.580 (0.351%), neg=0, invalid=762
0285: dt=19.622642, rms=0.578 (0.204%), neg=0, invalid=762
0286: dt=20.528302, rms=0.577 (0.230%), neg=0, invalid=762
0287: dt=12.537313, rms=0.576 (0.212%), neg=0, invalid=762
0288: dt=12.923077, rms=0.575 (0.136%), neg=0, invalid=762
0289: dt=14.376812, rms=0.574 (0.146%), neg=0, invalid=762
0290: dt=10.061856, rms=0.574 (0.107%), neg=0, invalid=762
0291: dt=16.128000, rms=0.573 (0.125%), neg=0, invalid=762
0292: dt=9.846154, rms=0.572 (0.083%), neg=0, invalid=762
0293: dt=16.128000, rms=0.572 (0.112%), neg=0, invalid=762
0294: dt=9.216000, rms=0.571 (0.067%), neg=0, invalid=762
0295: dt=16.128000, rms=0.571 (0.102%), neg=0, invalid=762
0296: dt=9.216000, rms=0.571 (0.058%), neg=0, invalid=762
0297: dt=16.128000, rms=0.570 (0.068%), neg=0, invalid=762
0298: dt=9.216000, rms=0.570 (0.062%), neg=0, invalid=762
0299: dt=16.128000, rms=0.569 (0.057%), neg=0, invalid=762
0300: dt=9.216000, rms=0.569 (0.053%), neg=0, invalid=762
0301: dt=13.824000, rms=0.569 (0.047%), neg=0, invalid=762
0302: dt=13.824000, rms=0.569 (0.028%), neg=0, invalid=762
0303: dt=13.824000, rms=0.568 (0.128%), neg=0, invalid=762
0304: dt=13.824000, rms=0.567 (0.096%), neg=0, invalid=762
0305: dt=13.824000, rms=0.567 (0.169%), neg=0, invalid=762
0306: dt=13.824000, rms=0.566 (0.073%), neg=0, invalid=762
0307: dt=13.824000, rms=0.566 (0.051%), neg=0, invalid=762
0308: dt=13.824000, rms=0.566 (0.010%), neg=0, invalid=762
0309: dt=13.824000, rms=0.566 (0.041%), neg=0, invalid=762
0310: dt=1.728000, rms=0.565 (0.009%), neg=0, invalid=762
0311: dt=1.728000, rms=0.565 (0.008%), neg=0, invalid=762
0312: dt=1.008000, rms=0.565 (0.004%), neg=0, invalid=762
0313: dt=0.504000, rms=0.565 (0.001%), neg=0, invalid=762
0314: dt=0.504000, rms=0.565 (0.002%), neg=0, invalid=762
0315: dt=0.504000, rms=0.565 (0.005%), neg=0, invalid=762
0316: dt=0.504000, rms=0.565 (0.002%), neg=0, invalid=762
0317: dt=0.504000, rms=0.565 (0.004%), neg=0, invalid=762
0318: dt=0.504000, rms=0.565 (0.004%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.580, neg=0, invalid=762
0319: dt=0.000000, rms=0.580 (0.145%), neg=0, invalid=762
0320: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0321: dt=0.100000, rms=0.580 (-0.147%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.580, neg=0, invalid=762
0322: dt=0.000000, rms=0.580 (0.145%), neg=0, invalid=762
0323: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0324: dt=0.100000, rms=0.580 (-0.130%), 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=0.557, neg=0, invalid=762
0325: dt=0.448000, rms=0.539 (3.089%), neg=0, invalid=762
0326: dt=0.448000, rms=0.535 (0.791%), neg=0, invalid=762
0327: dt=0.448000, rms=0.533 (0.411%), neg=0, invalid=762
0328: dt=0.448000, rms=0.532 (0.247%), neg=0, invalid=762
0329: dt=0.448000, rms=0.531 (0.193%), neg=0, invalid=762
0330: dt=0.448000, rms=0.530 (0.136%), neg=0, invalid=762
0331: dt=0.448000, rms=0.529 (0.114%), neg=0, invalid=762
0332: dt=0.448000, rms=0.529 (0.089%), neg=0, invalid=762
0333: dt=0.448000, rms=0.528 (0.079%), neg=0, invalid=762
0334: dt=0.448000, rms=0.528 (0.059%), neg=0, invalid=762
0335: dt=0.448000, rms=0.528 (0.057%), neg=0, invalid=762
0336: dt=0.448000, rms=0.528 (0.042%), neg=0, invalid=762
0337: dt=0.448000, rms=0.527 (0.042%), neg=0, invalid=762
0338: dt=0.448000, rms=0.527 (0.072%), neg=0, invalid=762
0339: dt=0.448000, rms=0.527 (0.025%), neg=0, invalid=762
0340: dt=0.448000, rms=0.527 (0.045%), neg=0, invalid=762
0341: dt=0.448000, rms=0.526 (0.020%), neg=0, invalid=762
0342: dt=0.448000, rms=0.526 (0.032%), neg=0, invalid=762
0343: dt=0.448000, rms=0.526 (0.014%), neg=0, invalid=762
0344: dt=0.448000, rms=0.526 (0.020%), neg=0, invalid=762
0345: dt=0.448000, rms=0.526 (0.031%), neg=0, invalid=762
0346: dt=0.448000, rms=0.526 (0.008%), neg=0, invalid=762
0347: dt=0.448000, rms=0.526 (0.003%), neg=0, invalid=762
0348: dt=0.448000, rms=0.526 (0.006%), neg=0, invalid=762
0349: dt=0.384000, rms=0.526 (0.007%), neg=0, invalid=762
0350: dt=0.384000, rms=0.526 (0.004%), neg=0, invalid=762
0351: dt=0.384000, rms=0.526 (0.001%), neg=0, invalid=762
0352: dt=0.384000, rms=0.526 (0.013%), neg=0, invalid=762
0353: dt=0.384000, rms=0.526 (0.008%), neg=0, invalid=762
0354: dt=0.384000, rms=0.526 (0.008%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.527, neg=0, invalid=762
0355: dt=0.448000, rms=0.519 (1.518%), neg=0, invalid=762
0356: dt=0.448000, rms=0.518 (0.200%), neg=0, invalid=762
0357: dt=0.448000, rms=0.517 (0.076%), neg=0, invalid=762
0358: dt=0.448000, rms=0.517 (0.014%), neg=0, invalid=762
0359: dt=0.448000, rms=0.517 (0.002%), neg=0, invalid=762
0360: dt=0.448000, rms=0.517 (-0.006%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.515, neg=0, invalid=762
0361: dt=0.000000, rms=0.514 (0.195%), neg=0, invalid=762
0362: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.515, neg=0, invalid=762
0363: dt=92.480000, rms=0.514 (0.213%), neg=0, invalid=762
0364: dt=129.472000, rms=0.514 (0.023%), neg=0, invalid=762
0365: dt=129.472000, rms=0.514 (-0.019%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.515, neg=0, invalid=762
0366: dt=25.920000, rms=0.514 (0.261%), neg=0, invalid=762
0367: dt=20.736000, rms=0.514 (0.016%), neg=0, invalid=762
0368: dt=20.736000, rms=0.514 (0.005%), neg=0, invalid=762
0369: dt=20.736000, rms=0.514 (-0.033%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.515, neg=0, invalid=762
0370: dt=69.614035, rms=0.512 (0.483%), neg=0, invalid=762
0371: dt=36.288000, rms=0.512 (0.113%), neg=0, invalid=762
0372: dt=36.288000, rms=0.511 (0.069%), neg=0, invalid=762
0373: dt=36.288000, rms=0.511 (0.094%), neg=0, invalid=762
0374: dt=36.288000, rms=0.510 (0.115%), neg=0, invalid=762
0375: dt=36.288000, rms=0.510 (0.106%), neg=0, invalid=762
0376: dt=36.288000, rms=0.509 (0.103%), neg=0, invalid=762
0377: dt=145.152000, rms=0.509 (0.072%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.510, neg=0, invalid=762
iter 0, gcam->neg = 10
after 8 iterations, nbhd size=1, neg = 0
0378: dt=25.600000, rms=0.507 (0.629%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 4 iterations, nbhd size=0, neg = 0
0379: dt=25.600000, rms=0.506 (0.248%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 2 iterations, nbhd size=0, neg = 0
0380: dt=25.600000, rms=0.505 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 11 iterations, nbhd size=1, neg = 0
0381: dt=25.600000, rms=0.504 (0.144%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 11 iterations, nbhd size=1, neg = 0
0382: dt=25.600000, rms=0.504 (-0.010%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0383: dt=25.600000, rms=0.504 (0.149%), neg=0, invalid=762
0384: dt=11.200000, rms=0.503 (0.072%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.504, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0385: dt=43.069583, rms=0.497 (1.458%), neg=0, invalid=762
0386: dt=25.600000, rms=0.494 (0.525%), neg=0, invalid=762
0387: dt=25.355932, rms=0.493 (0.206%), neg=0, invalid=762
0388: dt=25.355932, rms=0.492 (0.185%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0389: dt=25.355932, rms=0.491 (0.298%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0390: dt=25.355932, rms=0.490 (0.226%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0391: dt=25.355932, rms=0.488 (0.311%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0392: dt=25.355932, rms=0.487 (0.259%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=1, neg = 0
0393: dt=25.355932, rms=0.486 (0.300%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 4 iterations, nbhd size=0, neg = 0
0394: dt=25.355932, rms=0.484 (0.243%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 4 iterations, nbhd size=0, neg = 0
0395: dt=25.355932, rms=0.483 (0.281%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 3 iterations, nbhd size=0, neg = 0
0396: dt=25.355932, rms=0.482 (0.259%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 2 iterations, nbhd size=0, neg = 0
0397: dt=25.355932, rms=0.481 (0.164%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 11 iterations, nbhd size=1, neg = 0
0398: dt=25.355932, rms=0.480 (0.188%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0399: dt=25.355932, rms=0.480 (0.111%), neg=0, invalid=762
0400: dt=25.355932, rms=0.479 (0.137%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0401: dt=25.355932, rms=0.478 (0.100%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0402: dt=25.355932, rms=0.478 (0.131%), neg=0, invalid=762
0403: dt=25.355932, rms=0.478 (0.064%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0404: dt=25.355932, rms=0.477 (0.042%), neg=0, invalid=762
0405: dt=11.200000, rms=0.477 (0.082%), neg=0, invalid=762
0406: dt=38.400000, rms=0.477 (0.030%), neg=0, invalid=762
0407: dt=38.400000, rms=0.477 (-0.034%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
0408: dt=0.000000, rms=0.482 (0.212%), neg=0, invalid=762
0409: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
0410: dt=0.252000, rms=0.482 (0.213%), neg=0, invalid=762
0411: dt=0.216000, rms=0.482 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.495, neg=0, invalid=762
0412: dt=1.024000, rms=0.493 (0.409%), neg=0, invalid=762
0413: dt=0.256000, rms=0.493 (0.010%), neg=0, invalid=762
0414: dt=0.256000, rms=0.493 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.494, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0415: dt=1.536000, rms=0.492 (0.449%), neg=0, invalid=762
0416: dt=0.448000, rms=0.492 (0.017%), neg=0, invalid=762
0417: dt=0.448000, rms=0.492 (0.006%), neg=0, invalid=762
0418: dt=0.448000, rms=0.492 (-0.018%), 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=0.483, neg=0, invalid=762
iter 0, gcam->neg = 721
after 13 iterations, nbhd size=1, neg = 0
0419: dt=2.252610, rms=0.448 (7.216%), neg=0, invalid=762
0420: dt=0.096000, rms=0.448 (0.077%), neg=0, invalid=762
0421: dt=0.096000, rms=0.448 (-0.072%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.449, neg=0, invalid=762
0422: dt=0.112000, rms=0.448 (0.363%), neg=0, invalid=762
0423: dt=0.001250, rms=0.448 (0.001%), neg=0, invalid=762
0424: dt=0.001250, rms=0.448 (0.000%), neg=0, invalid=762
0425: dt=0.001250, rms=0.448 (0.000%), neg=0, invalid=762
0426: dt=0.001250, rms=0.448 (-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
0427: 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
0428: dt=23.120000, rms=0.434 (0.002%), neg=0, invalid=762
0429: dt=8.092000, rms=0.434 (0.000%), neg=0, invalid=762
0430: dt=8.092000, rms=0.434 (0.000%), neg=0, invalid=762
0431: dt=8.092000, rms=0.434 (-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=0.434, neg=0, invalid=762
0432: 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
0433: dt=36.288000, rms=0.434 (0.029%), neg=0, invalid=762
0434: dt=103.680000, rms=0.434 (0.036%), neg=0, invalid=762
0435: dt=145.152000, rms=0.433 (0.047%), neg=0, invalid=762
0436: dt=36.288000, rms=0.433 (0.008%), neg=0, invalid=762
0437: dt=36.288000, rms=0.433 (0.006%), neg=0, invalid=762
0438: dt=36.288000, rms=0.433 (0.010%), neg=0, invalid=762
0439: dt=36.288000, rms=0.433 (0.013%), neg=0, invalid=762
0440: dt=36.288000, rms=0.433 (0.015%), neg=0, invalid=762
0441: dt=36.288000, rms=0.433 (0.014%), neg=0, invalid=762
0442: dt=36.288000, rms=0.433 (0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0443: dt=2.800000, rms=0.434 (0.013%), neg=0, invalid=762
0444: dt=2.400000, rms=0.434 (0.004%), neg=0, invalid=762
0445: dt=2.400000, rms=0.434 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0446: dt=95.292818, rms=0.431 (0.672%), neg=0, invalid=762
0447: dt=25.600000, rms=0.430 (0.271%), neg=0, invalid=762
0448: dt=38.400000, rms=0.429 (0.082%), neg=0, invalid=762
0449: dt=38.400000, rms=0.429 (0.128%), neg=0, invalid=762
0450: dt=38.400000, rms=0.428 (0.183%), neg=0, invalid=762
0451: dt=38.400000, rms=0.427 (0.149%), neg=0, invalid=762
0452: dt=38.400000, rms=0.426 (0.263%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0453: dt=38.400000, rms=0.425 (0.194%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0454: dt=38.400000, rms=0.425 (0.184%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0455: dt=38.400000, rms=0.424 (0.117%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0456: dt=38.400000, rms=0.423 (0.180%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
0457: dt=38.400000, rms=0.423 (0.096%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0458: dt=38.400000, rms=0.423 (0.083%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0459: dt=44.800000, rms=0.422 (0.035%), neg=0, invalid=762
0460: dt=44.800000, rms=0.422 (-0.045%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.427, neg=0, invalid=762
0461: dt=0.000135, rms=0.427 (0.000%), neg=0, invalid=762
0462: dt=0.000000, rms=0.427 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.427, neg=0, invalid=762
0463: dt=4.032000, rms=0.427 (0.045%), neg=0, invalid=762
0464: dt=2.880000, rms=0.427 (0.012%), neg=0, invalid=762
0465: dt=2.880000, rms=0.427 (0.003%), neg=0, invalid=762
0466: dt=2.880000, rms=0.427 (-0.025%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0467: 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
0468: dt=0.000000, rms=0.434 (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=0.421, neg=0, invalid=762
iter 0, gcam->neg = 564
after 13 iterations, nbhd size=1, neg = 0
0469: dt=1.446970, rms=0.410 (2.740%), neg=0, invalid=762
0470: dt=0.000013, rms=0.410 (0.000%), neg=0, invalid=762
0471: dt=0.000013, 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
0472: dt=0.112000, rms=0.410 (0.089%), neg=0, invalid=762
0473: dt=0.064000, rms=0.410 (0.014%), neg=0, invalid=762
0474: dt=0.064000, rms=0.410 (-0.001%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 20 minutes and 56 seconds.
mri_ca_register utimesec    9360.561978
mri_ca_register stimesec    8.967636
mri_ca_register ru_maxrss   1349840
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4532698
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63448
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3933
mri_ca_register ru_nivcsw   12341
FSRUNTIME@ mri_ca_register  2.3488 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 20:12:03 CEST 2017

 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 

sysname  Linux
hostname tars-576
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-6.0.0/0051009/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.00
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 = 0.07380 ( 6)
Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (219 voxels, overlap=0.007)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (219 voxels, peak =  5), gca=8.0
gca peak = 0.17677 (13)
mri peak = 0.06796 ( 6)
Right_Lateral_Ventricle (43): linear fit = 0.38 x + 0.0 (184 voxels, overlap=0.088)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (184 voxels, peak =  5), gca=5.2
gca peak = 0.28129 (95)
mri peak = 0.08322 (86)
Right_Pallidum (52): linear fit = 0.89 x + 0.0 (725 voxels, overlap=0.271)
Right_Pallidum (52): linear fit = 0.89 x + 0.0 (725 voxels, peak = 85), gca=85.0
gca peak = 0.16930 (96)
mri peak = 0.09358 (84)
Left_Pallidum (13): linear fit = 0.90 x + 0.0 (769 voxels, overlap=0.412)
Left_Pallidum (13): linear fit = 0.90 x + 0.0 (769 voxels, peak = 87), gca=86.9
gca peak = 0.24553 (55)
mri peak = 0.08783 (55)
Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (844 voxels, overlap=1.006)
Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (844 voxels, peak = 52), gca=52.0
gca peak = 0.30264 (59)
mri peak = 0.11056 (51)
Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (817 voxels, overlap=1.009)
Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (817 voxels, peak = 53), gca=52.8
gca peak = 0.07580 (103)
mri peak = 0.07707 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44317 voxels, overlap=0.643)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44317 voxels, peak = 107), gca=106.6
gca peak = 0.07714 (104)
mri peak = 0.08230 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (45159 voxels, overlap=0.659)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (45159 voxels, peak = 107), gca=106.6
gca peak = 0.09712 (58)
mri peak = 0.05415 (54)
Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (33205 voxels, overlap=0.725)
Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (33205 voxels, peak = 52), gca=51.9
gca peak = 0.11620 (58)
mri peak = 0.05294 (52)
Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (29445 voxels, overlap=0.777)
Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (29445 voxels, peak = 52), gca=51.9
gca peak = 0.30970 (66)
mri peak = 0.10563 (66)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (994 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (994 voxels, peak = 65), gca=65.0
gca peak = 0.15280 (69)
mri peak = 0.08168 (64)
Left_Caudate (11): linear fit = 0.86 x + 0.0 (907 voxels, overlap=0.423)
Left_Caudate (11): linear fit = 0.86 x + 0.0 (907 voxels, peak = 59), gca=59.0
gca peak = 0.13902 (56)
mri peak = 0.04840 (51)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22354 voxels, overlap=0.925)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22354 voxels, peak = 53), gca=52.9
gca peak = 0.14777 (55)
mri peak = 0.04861 (51)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (22749 voxels, overlap=0.916)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (22749 voxels, peak = 52), gca=52.0
gca peak = 0.16765 (84)
mri peak = 0.06917 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5629 voxels, overlap=0.976)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5629 voxels, peak = 85), gca=85.3
gca peak = 0.18739 (84)
mri peak = 0.06615 (85)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5223 voxels, overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5223 voxels, peak = 84), gca=83.6
gca peak = 0.29869 (57)
mri peak = 0.12827 (52)
Left_Amygdala: unreasonable value (49.9/52.0), not in range [50, 90] - rejecting
gca peak = 0.33601 (57)
mri peak = 0.11699 (55)
Right_Amygdala (54): linear fit = 0.93 x + 0.0 (476 voxels, overlap=1.014)
Right_Amygdala (54): linear fit = 0.93 x + 0.0 (476 voxels, peak = 53), gca=52.7
gca peak = 0.11131 (90)
mri peak = 0.09246 (77)
Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (4217 voxels, overlap=0.633)
Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (4217 voxels, peak = 83), gca=83.2
gca peak = 0.11793 (83)
mri peak = 0.08306 (76)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4014 voxels, overlap=0.960)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4014 voxels, peak = 81), gca=80.9
gca peak = 0.08324 (81)
mri peak = 0.07998 (71)
Left_Putamen (12): linear fit = 0.92 x + 0.0 (2240 voxels, overlap=0.653)
Left_Putamen (12): linear fit = 0.92 x + 0.0 (2240 voxels, peak = 74), gca=74.1
gca peak = 0.10360 (77)
mri peak = 0.07317 (72)
Right_Putamen (51): linear fit = 0.93 x + 0.0 (2540 voxels, overlap=0.774)
Right_Putamen (51): linear fit = 0.93 x + 0.0 (2540 voxels, peak = 71), gca=71.2
gca peak = 0.08424 (78)
mri peak = 0.11860 (80)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (11533 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (11533 voxels, peak = 82), gca=82.3
gca peak = 0.12631 (89)
mri peak = 0.07169 (89)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1366 voxels, overlap=0.823)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1366 voxels, peak = 88), gca=87.7
gca peak = 0.14500 (87)
mri peak = 0.07802 (91)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1302 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1302 voxels, peak = 87), gca=86.6
gca peak = 0.14975 (24)
mri peak = 0.02438 ( 3)
gca peak = 0.19357 (14)
mri peak = 0.09624 ( 4)
Fourth_Ventricle (15): linear fit = 0.04 x + 0.0 (222 voxels, overlap=0.027)
Fourth_Ventricle (15): linear fit = 0.04 x + 0.0 (222 voxels, peak =  0), gca=0.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak Left_Amygdala = 0.29869 (57)
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
setting label Left_Amygdala based on Right_Amygdala = 0.93 x +  0: 53
estimating mean gm scale to be 0.91 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.30837 ( 7)
mri peak = 0.07380 ( 6)
Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (219 voxels, overlap=0.887)
Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (219 voxels, peak =  5), gca=5.4
gca peak = 0.30173 ( 5)
mri peak = 0.06796 ( 6)
Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (184 voxels, overlap=0.832)
Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (184 voxels, peak =  5), gca=5.5
gca peak = 0.28024 (85)
mri peak = 0.08322 (86)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (725 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (725 voxels, peak = 85), gca=85.0
gca peak = 0.16376 (88)
mri peak = 0.09358 (84)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (769 voxels, overlap=1.008)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (769 voxels, peak = 87), gca=86.7
gca peak = 0.28382 (52)
mri peak = 0.08783 (55)
Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (844 voxels, overlap=1.006)
Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (844 voxels, peak = 50), gca=50.2
gca peak = 0.29494 (53)
mri peak = 0.11056 (51)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (817 voxels, overlap=1.004)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (817 voxels, peak = 52), gca=51.7
gca peak = 0.07496 (106)
mri peak = 0.07707 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44317 voxels, overlap=0.793)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44317 voxels, peak = 105), gca=105.5
gca peak = 0.07686 (107)
mri peak = 0.08230 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45159 voxels, overlap=0.765)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45159 voxels, peak = 106), gca=106.5
gca peak = 0.10757 (52)
mri peak = 0.05415 (54)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (33205 voxels, overlap=0.995)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (33205 voxels, peak = 52), gca=52.0
gca peak = 0.12860 (52)
mri peak = 0.05294 (52)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29445 voxels, overlap=0.986)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29445 voxels, peak = 52), gca=52.0
gca peak = 0.31023 (65)
mri peak = 0.10563 (66)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (994 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (994 voxels, peak = 65), gca=65.0
gca peak = 0.14240 (66)
mri peak = 0.08168 (64)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (907 voxels, overlap=0.994)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (907 voxels, peak = 68), gca=67.7
gca peak = 0.14745 (53)
mri peak = 0.04840 (51)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (22354 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (22354 voxels, peak = 51), gca=51.1
gca peak = 0.15520 (52)
mri peak = 0.04861 (51)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22749 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22749 voxels, peak = 50), gca=50.2
gca peak = 0.16137 (86)
mri peak = 0.06917 (85)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5629 voxels, overlap=0.986)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5629 voxels, peak = 85), gca=84.7
gca peak = 0.15690 (83)
mri peak = 0.06615 (85)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5223 voxels, overlap=0.980)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5223 voxels, peak = 84), gca=84.2
gca peak = 0.34115 (54)
mri peak = 0.12827 (52)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (476 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (476 voxels, peak = 54), gca=54.0
gca peak = 0.43038 (53)
mri peak = 0.11699 (55)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (476 voxels, overlap=1.018)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (476 voxels, peak = 54), gca=53.8
gca peak = 0.12186 (82)
mri peak = 0.09246 (77)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4217 voxels, overlap=0.874)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4217 voxels, peak = 82), gca=81.6
gca peak = 0.10970 (79)
mri peak = 0.08306 (76)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4014 voxels, overlap=0.920)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4014 voxels, peak = 79), gca=79.0
gca peak = 0.08998 (74)
mri peak = 0.07998 (71)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2240 voxels, overlap=0.984)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2240 voxels, peak = 74), gca=74.0
gca peak = 0.09183 (69)
mri peak = 0.07317 (72)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2540 voxels, overlap=0.999)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2540 voxels, peak = 69), gca=69.0
gca peak = 0.07740 (85)
mri peak = 0.11860 (80)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11533 voxels, overlap=0.683)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11533 voxels, peak = 85), gca=84.6
gca peak = 0.13552 (88)
mri peak = 0.07169 (89)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1366 voxels, overlap=0.802)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1366 voxels, peak = 88), gca=87.6
gca peak = 0.17063 (85)
mri peak = 0.07802 (91)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1302 voxels, overlap=0.915)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1302 voxels, peak = 86), gca=86.3
gca peak = 0.33708 (10)
mri peak = 0.02438 ( 3)
gca peak = 0.45928 ( 6)
mri peak = 0.09624 ( 4)
Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (222 voxels, overlap=0.913)
Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (222 voxels, peak =  8), gca=7.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.19080 (30)
gca peak Left_Thalamus = 1.00000 (86)
gca peak Third_Ventricle = 0.33708 (10)
gca peak CSF = 0.26605 (13)
gca peak Left_Accumbens_area = 0.78952 (53)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.73117 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24804 (22)
gca peak Right_Accumbens_area = 0.43065 (64)
gca peak Right_vessel = 0.81794 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65560 (13)
gca peak WM_hypointensities = 0.06955 (80)
gca peak non_WM_hypointensities = 0.11606 (56)
gca peak Optic_Chiasm = 0.71117 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.04 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
68158 voxels changed in iteration 0 of unlikely voxel relabeling
211 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
31751 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels)
585 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 74957 changed. image ll: -2.156, PF=0.500
pass 2: 20368 changed. image ll: -2.155, PF=0.500
pass 3: 6284 changed.
pass 4: 2366 changed.
36824 voxels changed in iteration 0 of unlikely voxel relabeling
266 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
6232 voxels changed in iteration 0 of unlikely voxel relabeling
32 voxels changed in iteration 1 of unlikely voxel relabeling
18 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5678 voxels changed in iteration 0 of unlikely voxel relabeling
50 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5069 voxels changed in iteration 0 of unlikely voxel relabeling
18 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    3645.368819
mri_ca_label stimesec    1.479775
mri_ca_label ru_maxrss   2116144
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   695488
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63440
mri_ca_label ru_oublock  496
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    290
mri_ca_label ru_nivcsw   4639
auto-labeling took 60 minutes and 4 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/transforms/cc_up.lta 0051009 

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-6.0.0/0051009/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/norm.mgz
98030 voxels in left wm, 82578 in right wm, xrange [118, 136]
searching rotation angles z=[-1 13], y=[-12  2]

searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.8  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.3  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.8  
searching scale 1 Z rot 9.1  
searching scale 1 Z rot 9.3  
searching scale 1 Z rot 9.6  
searching scale 1 Z rot 9.8  
searching scale 1 Z rot 10.1  
searching scale 1 Z rot 10.3  
searching scale 1 Z rot 10.6  
searching scale 1 Z rot 10.8  
searching scale 1 Z rot 11.1  
searching scale 1 Z rot 11.3  
searching scale 1 Z rot 11.6  
searching scale 1 Z rot 11.8  
searching scale 1 Z rot 12.1  
searching scale 1 Z rot 12.3  
searching scale 1 Z rot 12.6  
searching scale 1 Z rot 12.8  
searching scale 1 Z rot 13.1  
searching scale 1 Z rot 13.3  global minimum found at slice 126.0, rotations (-4.96, 6.55)
final transformation (x=126.0, yr=-4.964, zr=6.553):
 0.98974  -0.11412  -0.08597   23.73378;
 0.11370   0.99347  -0.00988   18.38444;
 0.08654   0.00000   0.99625   8.50529;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [123, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 97 109
eigenvectors:
 0.00053   0.01659   0.99986;
-0.05181  -0.99852   0.01659;
 0.99866  -0.05181   0.00033;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/aseg.auto.mgz...
corpus callosum segmentation took 2.2 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 21:14:21 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 21:14:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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...
1840 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 55 (55), valley at 20 (20)
csf peak at 28, setting threshold to 46
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 56 (56), valley at 19 (19)
csf peak at 29, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 5 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 21:17:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1752075 voxels in mask (pct= 10.44)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 21:17:29 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 (106.0): 106.8 +- 5.2 [79.0 --> 125.0]
GM (65.0) : 64.1 +- 10.4 [30.0 --> 95.0]
setting bottom of white matter range to 74.5
setting top of gray matter range to 85.0
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
11297 sparsely connected voxels removed...
thickening thin strands....
20 segments, 6894 filled
8036 bright non-wm voxels segmented.
4060 diagonally connected voxels added...
white matter segmentation took 1.4 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 0.48 minutes
reading wm segmentation from wm.seg.mgz...
301 voxels added to wm to prevent paths from MTL structures to cortex
2747 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 42044 voxels turned on, 32668 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  30 found -  30 modified     |    TOTAL:  30
pass   2 (xy+):   0 found -  30 modified     |    TOTAL:  30
pass   1 (xy-):  22 found -  22 modified     |    TOTAL:  52
pass   2 (xy-):   0 found -  22 modified     |    TOTAL:  52
pass   1 (yz+):  38 found -  38 modified     |    TOTAL:  90
pass   2 (yz+):   0 found -  38 modified     |    TOTAL:  90
pass   1 (yz-):  28 found -  28 modified     |    TOTAL: 118
pass   2 (yz-):   0 found -  28 modified     |    TOTAL: 118
pass   1 (xz+):  29 found -  29 modified     |    TOTAL: 147
pass   2 (xz+):   0 found -  29 modified     |    TOTAL: 147
pass   1 (xz-):  21 found -  21 modified     |    TOTAL: 168
pass   2 (xz-):   0 found -  21 modified     |    TOTAL: 168
Iteration Number : 1
pass   1 (+++):  37 found -  37 modified     |    TOTAL:  37
pass   2 (+++):   0 found -  37 modified     |    TOTAL:  37
pass   1 (+++):  34 found -  34 modified     |    TOTAL:  71
pass   2 (+++):   0 found -  34 modified     |    TOTAL:  71
pass   1 (+++):  42 found -  42 modified     |    TOTAL: 113
pass   2 (+++):   0 found -  42 modified     |    TOTAL: 113
pass   1 (+++):  59 found -  59 modified     |    TOTAL: 172
pass   2 (+++):   0 found -  59 modified     |    TOTAL: 172
Iteration Number : 1
pass   1 (++): 155 found - 155 modified     |    TOTAL: 155
pass   2 (++):   0 found - 155 modified     |    TOTAL: 155
pass   1 (+-): 164 found - 164 modified     |    TOTAL: 319
pass   2 (+-):   0 found - 164 modified     |    TOTAL: 319
pass   1 (--): 154 found - 154 modified     |    TOTAL: 473
pass   2 (--):   1 found - 155 modified     |    TOTAL: 474
pass   3 (--):   0 found - 155 modified     |    TOTAL: 474
pass   1 (-+): 140 found - 140 modified     |    TOTAL: 614
pass   2 (-+):   0 found - 140 modified     |    TOTAL: 614
Iteration Number : 2
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):   8 found -   8 modified     |    TOTAL:  15
pass   2 (xy-):   0 found -   8 modified     |    TOTAL:  15
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:  18
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:  18
pass   1 (yz-):   7 found -   7 modified     |    TOTAL:  25
pass   2 (yz-):   0 found -   7 modified     |    TOTAL:  25
pass   1 (xz+):   8 found -   8 modified     |    TOTAL:  33
pass   2 (xz+):   0 found -   8 modified     |    TOTAL:  33
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  40
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  40
Iteration Number : 2
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 (+++):   4 found -   4 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   6
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   8
Iteration Number : 2
pass   1 (++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   5
pass   1 (--):   2 found -   2 modified     |    TOTAL:   7
pass   2 (--):   0 found -   2 modified     |    TOTAL:   7
pass   1 (-+):   5 found -   5 modified     |    TOTAL:  12
pass   2 (-+):   0 found -   5 modified     |    TOTAL:  12
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   6
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   2 found -   2 modified     |    TOTAL:   2
pass   2 (--):   0 found -   2 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1024 (out of 572602: 0.178833)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 21:19:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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
 0.97292  -0.09981  -0.07396   20.27187;
 0.16912   1.09963   0.26263  -52.41856;
 0.05747  -0.23025   0.99142   18.55815;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 0.97292  -0.09981  -0.07396   20.27187;
 0.16912   1.09963   0.26263  -52.41856;
 0.05747  -0.23025   0.99142   18.55815;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1807 (min = 350, max = 1400), aspect = 1.39 (min = 0.10, max = 0.75)
need search nearby
using seed (125, 110, 94), TAL = (3.0, -34.0, 18.0)
talairach voxel to voxel transform
 1.00734   0.10154   0.04825  -15.99355;
-0.13357   0.84814  -0.23464   51.52049;
-0.08942   0.19109   0.95137  -5.82654;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (125,  110,  94) --> (3.0, -34.0, 18.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (3.00, -34.00, 18.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, -34.00, 18.00) SRC: (107.50, 108.47, 95.05)
search lh wm seed point around talairach space (-15.00, -34.00, 18.00), SRC: (143.76, 103.66, 91.83)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 21:20:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   6
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   8
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   9
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
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 276587: 0.004339)
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: 4730 vertices, 5035 faces
slice 50: 16226 vertices, 16693 faces
slice 60: 29595 vertices, 30090 faces
slice 70: 42209 vertices, 42700 faces
slice 80: 54049 vertices, 54491 faces
slice 90: 66512 vertices, 67031 faces
slice 100: 79304 vertices, 79754 faces
slice 110: 91452 vertices, 91936 faces
slice 120: 102796 vertices, 103226 faces
slice 130: 114526 vertices, 114977 faces
slice 140: 124323 vertices, 124740 faces
slice 150: 134026 vertices, 134477 faces
slice 160: 142479 vertices, 142836 faces
slice 170: 149479 vertices, 149834 faces
slice 180: 154867 vertices, 155129 faces
slice 190: 158399 vertices, 158582 faces
slice 200: 158692 vertices, 158810 faces
slice 210: 158692 vertices, 158810 faces
slice 220: 158692 vertices, 158810 faces
slice 230: 158692 vertices, 158810 faces
slice 240: 158692 vertices, 158810 faces
slice 250: 158692 vertices, 158810 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...
   158692 voxel in cpt #1: X=-118 [v=158692,e=476430,f=317620] located at (-27.401867, -26.316563, 25.212992)
For the whole surface: X=-118 [v=158692,e=476430,f=317620]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 21:20:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   6
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 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
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 = 7 (out of 273560: 0.002559)
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: 1795 vertices, 1961 faces
slice 50: 9592 vertices, 9912 faces
slice 60: 20579 vertices, 21020 faces
slice 70: 33381 vertices, 33781 faces
slice 80: 45108 vertices, 45500 faces
slice 90: 57970 vertices, 58412 faces
slice 100: 70561 vertices, 71019 faces
slice 110: 82540 vertices, 82990 faces
slice 120: 94400 vertices, 94850 faces
slice 130: 106019 vertices, 106530 faces
slice 140: 117696 vertices, 118125 faces
slice 150: 128144 vertices, 128538 faces
slice 160: 137806 vertices, 138218 faces
slice 170: 145517 vertices, 145844 faces
slice 180: 152209 vertices, 152511 faces
slice 190: 156684 vertices, 156881 faces
slice 200: 157376 vertices, 157472 faces
slice 210: 157376 vertices, 157472 faces
slice 220: 157376 vertices, 157472 faces
slice 230: 157376 vertices, 157472 faces
slice 240: 157376 vertices, 157472 faces
slice 250: 157376 vertices, 157472 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...
   157376 voxel in cpt #1: X=-96 [v=157376,e=472416,f=314944] located at (30.532539, -20.421862, 19.279942)
For the whole surface: X=-96 [v=157376,e=472416,f=314944]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 21:20:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 21:20:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

Waiting for PID 5116 of (5116 5119) to complete...
Waiting for PID 5119 of (5116 5119) 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 (5116 5119) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 21:20:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 21:20:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

Waiting for PID 5164 of (5164 5167) to complete...
Waiting for PID 5167 of (5164 5167) 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 = 48.9 mm, total surface area = 82955 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.161 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.095 (target=0.015)   
step 015: RMS=0.082 (target=0.015)   
step 020: RMS=0.074 (target=0.015)   
step 025: RMS=0.065 (target=0.015)   
step 030: RMS=0.058 (target=0.015)   
step 035: RMS=0.055 (target=0.015)   
step 040: RMS=0.052 (target=0.015)   
step 045: RMS=0.050 (target=0.015)   
step 050: RMS=0.049 (target=0.015)   
step 055: RMS=0.050 (target=0.015)   
step 060: RMS=0.050 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.757435
mris_inflate stimesec    0.111982
mris_inflate ru_maxrss   231840
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33369
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11168
mris_inflate ru_oublock  11184
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2236
mris_inflate ru_nivcsw   3568

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 47.8 mm, total surface area = 82705 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.158 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.062 (target=0.015)   
step 030: RMS=0.056 (target=0.015)   
step 035: RMS=0.052 (target=0.015)   
step 040: RMS=0.049 (target=0.015)   
step 045: RMS=0.048 (target=0.015)   
step 050: RMS=0.046 (target=0.015)   
step 055: RMS=0.045 (target=0.015)   
step 060: RMS=0.045 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.341498
mris_inflate stimesec    0.113982
mris_inflate ru_maxrss   229732
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33352
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11096
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2044
mris_inflate ru_nivcsw   3555
PIDs (5164 5167) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 21:21:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 21:21:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

Waiting for PID 5242 of (5242 5246) to complete...
Waiting for PID 5246 of (5242 5246) 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 0.91 +- 0.57 (0.00-->6.68) (max @ vno 115211 --> 115212)
face area 0.02 +- 0.03 (-0.30-->0.71)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.302...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.858, avgs=0
005/300: dt: 0.9000, rms radial error=175.601, avgs=0
010/300: dt: 0.9000, rms radial error=175.050, avgs=0
015/300: dt: 0.9000, rms radial error=174.326, avgs=0
020/300: dt: 0.9000, rms radial error=173.500, avgs=0
025/300: dt: 0.9000, rms radial error=172.615, avgs=0
030/300: dt: 0.9000, rms radial error=171.697, avgs=0
035/300: dt: 0.9000, rms radial error=170.762, avgs=0
040/300: dt: 0.9000, rms radial error=169.820, avgs=0
045/300: dt: 0.9000, rms radial error=168.875, avgs=0
050/300: dt: 0.9000, rms radial error=167.931, avgs=0
055/300: dt: 0.9000, rms radial error=166.989, avgs=0
060/300: dt: 0.9000, rms radial error=166.050, avgs=0
065/300: dt: 0.9000, rms radial error=165.115, avgs=0
070/300: dt: 0.9000, rms radial error=164.184, avgs=0
075/300: dt: 0.9000, rms radial error=163.258, avgs=0
080/300: dt: 0.9000, rms radial error=162.337, avgs=0
085/300: dt: 0.9000, rms radial error=161.421, avgs=0
090/300: dt: 0.9000, rms radial error=160.508, avgs=0
095/300: dt: 0.9000, rms radial error=159.601, avgs=0
100/300: dt: 0.9000, rms radial error=158.698, avgs=0
105/300: dt: 0.9000, rms radial error=157.800, avgs=0
110/300: dt: 0.9000, rms radial error=156.907, avgs=0
115/300: dt: 0.9000, rms radial error=156.019, avgs=0
120/300: dt: 0.9000, rms radial error=155.135, avgs=0
125/300: dt: 0.9000, rms radial error=154.256, avgs=0
130/300: dt: 0.9000, rms radial error=153.382, avgs=0
135/300: dt: 0.9000, rms radial error=152.512, avgs=0
140/300: dt: 0.9000, rms radial error=151.648, avgs=0
145/300: dt: 0.9000, rms radial error=150.788, avgs=0
150/300: dt: 0.9000, rms radial error=149.933, avgs=0
155/300: dt: 0.9000, rms radial error=149.083, avgs=0
160/300: dt: 0.9000, rms radial error=148.237, avgs=0
165/300: dt: 0.9000, rms radial error=147.397, avgs=0
170/300: dt: 0.9000, rms radial error=146.560, avgs=0
175/300: dt: 0.9000, rms radial error=145.729, avgs=0
180/300: dt: 0.9000, rms radial error=144.901, avgs=0
185/300: dt: 0.9000, rms radial error=144.079, avgs=0
190/300: dt: 0.9000, rms radial error=143.261, avgs=0
195/300: dt: 0.9000, rms radial error=142.447, avgs=0
200/300: dt: 0.9000, rms radial error=141.638, avgs=0
205/300: dt: 0.9000, rms radial error=140.834, avgs=0
210/300: dt: 0.9000, rms radial error=140.034, avgs=0
215/300: dt: 0.9000, rms radial error=139.238, avgs=0
220/300: dt: 0.9000, rms radial error=138.446, avgs=0
225/300: dt: 0.9000, rms radial error=137.659, avgs=0
230/300: dt: 0.9000, rms radial error=136.877, avgs=0
235/300: dt: 0.9000, rms radial error=136.099, avgs=0
240/300: dt: 0.9000, rms radial error=135.328, avgs=0
245/300: dt: 0.9000, rms radial error=134.562, avgs=0
250/300: dt: 0.9000, rms radial error=133.801, avgs=0
255/300: dt: 0.9000, rms radial error=133.044, avgs=0
260/300: dt: 0.9000, rms radial error=132.291, avgs=0
265/300: dt: 0.9000, rms radial error=131.543, avgs=0
270/300: dt: 0.9000, rms radial error=130.798, avgs=0
275/300: dt: 0.9000, rms radial error=130.058, avgs=0
280/300: dt: 0.9000, rms radial error=129.322, avgs=0
285/300: dt: 0.9000, rms radial error=128.590, avgs=0
290/300: dt: 0.9000, rms radial error=127.863, avgs=0
295/300: dt: 0.9000, rms radial error=127.139, avgs=0
300/300: dt: 0.9000, rms radial error=126.420, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18828.41
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
epoch 2 (K=40.0), pass 1, starting sse = 3282.23
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00022
epoch 3 (K=160.0), pass 1, starting sse = 370.76
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00455
epoch 4 (K=640.0), pass 1, starting sse = 33.24
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.13/13 = 0.01023
final distance error %28.10
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    292.424544
mris_sphere stimesec    0.164974
mris_sphere ru_maxrss   232024
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33412
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11168
mris_sphere ru_oublock  11208
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    9488
mris_sphere ru_nivcsw   19588
FSRUNTIME@ mris_sphere  0.0803 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 0.93 +- 0.56 (0.00-->8.60) (max @ vno 105725 --> 105745)
face area 0.02 +- 0.03 (-0.22-->0.55)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.305...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.871, avgs=0
005/300: dt: 0.9000, rms radial error=175.617, avgs=0
010/300: dt: 0.9000, rms radial error=175.074, avgs=0
015/300: dt: 0.9000, rms radial error=174.359, avgs=0
020/300: dt: 0.9000, rms radial error=173.545, avgs=0
025/300: dt: 0.9000, rms radial error=172.667, avgs=0
030/300: dt: 0.9000, rms radial error=171.752, avgs=0
035/300: dt: 0.9000, rms radial error=170.816, avgs=0
040/300: dt: 0.9000, rms radial error=169.873, avgs=0
045/300: dt: 0.9000, rms radial error=168.928, avgs=0
050/300: dt: 0.9000, rms radial error=167.983, avgs=0
055/300: dt: 0.9000, rms radial error=167.041, avgs=0
060/300: dt: 0.9000, rms radial error=166.103, avgs=0
065/300: dt: 0.9000, rms radial error=165.173, avgs=0
070/300: dt: 0.9000, rms radial error=164.248, avgs=0
075/300: dt: 0.9000, rms radial error=163.327, avgs=0
080/300: dt: 0.9000, rms radial error=162.412, avgs=0
085/300: dt: 0.9000, rms radial error=161.502, avgs=0
090/300: dt: 0.9000, rms radial error=160.597, avgs=0
095/300: dt: 0.9000, rms radial error=159.696, avgs=0
100/300: dt: 0.9000, rms radial error=158.801, avgs=0
105/300: dt: 0.9000, rms radial error=157.910, avgs=0
110/300: dt: 0.9000, rms radial error=157.025, avgs=0
115/300: dt: 0.9000, rms radial error=156.144, avgs=0
120/300: dt: 0.9000, rms radial error=155.268, avgs=0
125/300: dt: 0.9000, rms radial error=154.397, avgs=0
130/300: dt: 0.9000, rms radial error=153.530, avgs=0
135/300: dt: 0.9000, rms radial error=152.668, avgs=0
140/300: dt: 0.9000, rms radial error=151.811, avgs=0
145/300: dt: 0.9000, rms radial error=150.959, avgs=0
150/300: dt: 0.9000, rms radial error=150.111, avgs=0
155/300: dt: 0.9000, rms radial error=149.267, avgs=0
160/300: dt: 0.9000, rms radial error=148.428, avgs=0
165/300: dt: 0.9000, rms radial error=147.594, avgs=0
170/300: dt: 0.9000, rms radial error=146.764, avgs=0
175/300: dt: 0.9000, rms radial error=145.939, avgs=0
180/300: dt: 0.9000, rms radial error=145.118, avgs=0
185/300: dt: 0.9000, rms radial error=144.302, avgs=0
190/300: dt: 0.9000, rms radial error=143.490, avgs=0
195/300: dt: 0.9000, rms radial error=142.683, avgs=0
200/300: dt: 0.9000, rms radial error=141.880, avgs=0
205/300: dt: 0.9000, rms radial error=141.082, avgs=0
210/300: dt: 0.9000, rms radial error=140.288, avgs=0
215/300: dt: 0.9000, rms radial error=139.498, avgs=0
220/300: dt: 0.9000, rms radial error=138.713, avgs=0
225/300: dt: 0.9000, rms radial error=137.932, avgs=0
230/300: dt: 0.9000, rms radial error=137.155, avgs=0
235/300: dt: 0.9000, rms radial error=136.383, avgs=0
240/300: dt: 0.9000, rms radial error=135.615, avgs=0
245/300: dt: 0.9000, rms radial error=134.851, avgs=0
250/300: dt: 0.9000, rms radial error=134.092, avgs=0
255/300: dt: 0.9000, rms radial error=133.336, avgs=0
260/300: dt: 0.9000, rms radial error=132.585, avgs=0
265/300: dt: 0.9000, rms radial error=131.838, avgs=0
270/300: dt: 0.9000, rms radial error=131.096, avgs=0
275/300: dt: 0.9000, rms radial error=130.357, avgs=0
280/300: dt: 0.9000, rms radial error=129.622, avgs=0
285/300: dt: 0.9000, rms radial error=128.892, avgs=0
290/300: dt: 0.9000, rms radial error=128.166, avgs=0
295/300: dt: 0.9000, rms radial error=127.443, avgs=0
300/300: dt: 0.9000, rms radial error=126.725, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18558.60
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 3169.29
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 339.98
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00419
epoch 4 (K=640.0), pass 1, starting sse = 25.37
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/11 = 0.00347
final distance error %28.02
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    282.954984
mris_sphere stimesec    0.168974
mris_sphere ru_maxrss   229920
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   32888
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11120
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8457
mris_sphere ru_nivcsw   20319
FSRUNTIME@ mris_sphere  0.0786 hours 1 threads
PIDs (5242 5246) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 21:26:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 21:26:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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


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

#@# Fix Topology lh Sat Oct  7 21:26:07 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051009 lh 

#@# Fix Topology rh Sat Oct  7 21:26:07 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051009 rh 

Waiting for PID 5765 of (5765 5768) to complete...
Waiting for PID 5768 of (5765 5768) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051009 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=-118 (nv=158692, nf=317620, ne=476430, g=60)
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...
10467 ambiguous faces found in tessellation
segmenting defects...
81 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
81 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8295  (-4.9148)
      -vertex     loglikelihood: -6.6312  (-3.3156)
      -normal dot loglikelihood: -3.6105  (-3.6105)
      -quad curv  loglikelihood: -6.3384  (-3.1692)
      Total Loglikelihood : -26.4097

CORRECTING DEFECT 0 (vertices=23, convex hull=25, v0=164)
After retessellation of defect 0 (v0=164), euler #=-75 (152382,454815,302358) : difference with theory (-78) = -3 

CORRECTING DEFECT 1 (vertices=77, convex hull=102, v0=415)
After retessellation of defect 1 (v0=415), euler #=-74 (152393,454891,302424) : difference with theory (-77) = -3 

CORRECTING DEFECT 2 (vertices=103, convex hull=124, v0=3714)
After retessellation of defect 2 (v0=3714), euler #=-73 (152431,455059,302555) : difference with theory (-76) = -3 

CORRECTING DEFECT 3 (vertices=147, convex hull=48, v0=3796)
After retessellation of defect 3 (v0=3796), euler #=-72 (152440,455106,302594) : difference with theory (-75) = -3 

CORRECTING DEFECT 4 (vertices=104, convex hull=54, v0=6434)
After retessellation of defect 4 (v0=6434), euler #=-71 (152449,455154,302634) : difference with theory (-74) = -3 

CORRECTING DEFECT 5 (vertices=438, convex hull=212, v0=6627)
After retessellation of defect 5 (v0=6627), euler #=-70 (152547,455548,302931) : difference with theory (-73) = -3 

CORRECTING DEFECT 6 (vertices=40, convex hull=59, v0=9176)
After retessellation of defect 6 (v0=9176), euler #=-69 (152555,455595,302971) : difference with theory (-72) = -3 

CORRECTING DEFECT 7 (vertices=819, convex hull=281, v0=11825)
After retessellation of defect 7 (v0=11825), euler #=-68 (152657,456038,303313) : difference with theory (-71) = -3 

CORRECTING DEFECT 8 (vertices=78, convex hull=102, v0=12189)
After retessellation of defect 8 (v0=12189), euler #=-67 (152692,456191,303432) : difference with theory (-70) = -3 

CORRECTING DEFECT 9 (vertices=140, convex hull=62, v0=13209)
After retessellation of defect 9 (v0=13209), euler #=-66 (152707,456264,303491) : difference with theory (-69) = -3 

CORRECTING DEFECT 10 (vertices=58, convex hull=98, v0=18877)
After retessellation of defect 10 (v0=18877), euler #=-65 (152718,456336,303553) : difference with theory (-68) = -3 

CORRECTING DEFECT 11 (vertices=22, convex hull=73, v0=20086)
After retessellation of defect 11 (v0=20086), euler #=-64 (152728,456393,303601) : difference with theory (-67) = -3 

CORRECTING DEFECT 12 (vertices=25, convex hull=67, v0=20587)
After retessellation of defect 12 (v0=20587), euler #=-63 (152738,456448,303647) : difference with theory (-66) = -3 

CORRECTING DEFECT 13 (vertices=15, convex hull=23, v0=22505)
After retessellation of defect 13 (v0=22505), euler #=-62 (152742,456470,303666) : difference with theory (-65) = -3 

CORRECTING DEFECT 14 (vertices=116, convex hull=133, v0=22582)
After retessellation of defect 14 (v0=22582), euler #=-61 (152765,456600,303774) : difference with theory (-64) = -3 

CORRECTING DEFECT 15 (vertices=83, convex hull=105, v0=23542)
After retessellation of defect 15 (v0=23542), euler #=-60 (152792,456726,303874) : difference with theory (-63) = -3 

CORRECTING DEFECT 16 (vertices=5, convex hull=27, v0=25003)
After retessellation of defect 16 (v0=25003), euler #=-59 (152793,456736,303884) : difference with theory (-62) = -3 

CORRECTING DEFECT 17 (vertices=203, convex hull=89, v0=26222)
After retessellation of defect 17 (v0=26222), euler #=-58 (152842,456922,304022) : difference with theory (-61) = -3 

CORRECTING DEFECT 18 (vertices=26, convex hull=32, v0=26726)
After retessellation of defect 18 (v0=26726), euler #=-57 (152844,456942,304041) : difference with theory (-60) = -3 

CORRECTING DEFECT 19 (vertices=10, convex hull=25, v0=29355)
After retessellation of defect 19 (v0=29355), euler #=-56 (152845,456952,304051) : difference with theory (-59) = -3 

CORRECTING DEFECT 20 (vertices=14, convex hull=26, v0=35711)
After retessellation of defect 20 (v0=35711), euler #=-55 (152849,456976,304072) : difference with theory (-58) = -3 

CORRECTING DEFECT 21 (vertices=52, convex hull=77, v0=37034)
After retessellation of defect 21 (v0=37034), euler #=-54 (152883,457114,304177) : difference with theory (-57) = -3 

CORRECTING DEFECT 22 (vertices=7, convex hull=21, v0=38130)
After retessellation of defect 22 (v0=38130), euler #=-53 (152884,457120,304183) : difference with theory (-56) = -3 

CORRECTING DEFECT 23 (vertices=67, convex hull=92, v0=38668)
After retessellation of defect 23 (v0=38668), euler #=-52 (152923,457277,304302) : difference with theory (-55) = -3 

CORRECTING DEFECT 24 (vertices=28, convex hull=63, v0=39752)
After retessellation of defect 24 (v0=39752), euler #=-51 (152942,457361,304368) : difference with theory (-54) = -3 

CORRECTING DEFECT 25 (vertices=10, convex hull=18, v0=52503)
After retessellation of defect 25 (v0=52503), euler #=-50 (152946,457380,304384) : difference with theory (-53) = -3 

CORRECTING DEFECT 26 (vertices=43, convex hull=70, v0=53620)
After retessellation of defect 26 (v0=53620), euler #=-49 (152955,457439,304435) : difference with theory (-52) = -3 

CORRECTING DEFECT 27 (vertices=94, convex hull=114, v0=55010)
After retessellation of defect 27 (v0=55010), euler #=-48 (152997,457612,304567) : difference with theory (-51) = -3 

CORRECTING DEFECT 28 (vertices=43, convex hull=32, v0=63524)
After retessellation of defect 28 (v0=63524), euler #=-47 (153005,457646,304594) : difference with theory (-50) = -3 

CORRECTING DEFECT 29 (vertices=121, convex hull=49, v0=66967)
After retessellation of defect 29 (v0=66967), euler #=-46 (153016,457697,304635) : difference with theory (-49) = -3 

CORRECTING DEFECT 30 (vertices=304, convex hull=297, v0=72950)
After retessellation of defect 30 (v0=72950), euler #=-45 (153148,458231,305038) : difference with theory (-48) = -3 

CORRECTING DEFECT 31 (vertices=15, convex hull=27, v0=73205)
After retessellation of defect 31 (v0=73205), euler #=-44 (153152,458253,305057) : difference with theory (-47) = -3 

CORRECTING DEFECT 32 (vertices=10, convex hull=24, v0=74066)
After retessellation of defect 32 (v0=74066), euler #=-43 (153154,458266,305069) : difference with theory (-46) = -3 

CORRECTING DEFECT 33 (vertices=22, convex hull=20, v0=75703)
After retessellation of defect 33 (v0=75703), euler #=-42 (153156,458280,305082) : difference with theory (-45) = -3 

CORRECTING DEFECT 34 (vertices=246, convex hull=49, v0=75981)
After retessellation of defect 34 (v0=75981), euler #=-41 (153173,458350,305136) : difference with theory (-44) = -3 

CORRECTING DEFECT 35 (vertices=79, convex hull=141, v0=78344)
After retessellation of defect 35 (v0=78344), euler #=-40 (153221,458555,305294) : difference with theory (-43) = -3 

CORRECTING DEFECT 36 (vertices=106, convex hull=48, v0=78539)
After retessellation of defect 36 (v0=78539), euler #=-39 (153231,458599,305329) : difference with theory (-42) = -3 

CORRECTING DEFECT 37 (vertices=8, convex hull=33, v0=81734)
After retessellation of defect 37 (v0=81734), euler #=-38 (153232,458612,305342) : difference with theory (-41) = -3 

CORRECTING DEFECT 38 (vertices=41, convex hull=40, v0=84230)
After retessellation of defect 38 (v0=84230), euler #=-37 (153239,458650,305374) : difference with theory (-40) = -3 

CORRECTING DEFECT 39 (vertices=39, convex hull=58, v0=85326)
After retessellation of defect 39 (v0=85326), euler #=-36 (153260,458738,305442) : difference with theory (-39) = -3 

CORRECTING DEFECT 40 (vertices=53, convex hull=73, v0=85403)
After retessellation of defect 40 (v0=85403), euler #=-35 (153281,458829,305513) : difference with theory (-38) = -3 

CORRECTING DEFECT 41 (vertices=31, convex hull=62, v0=87681)
After retessellation of defect 41 (v0=87681), euler #=-34 (153293,458892,305565) : difference with theory (-37) = -3 

CORRECTING DEFECT 42 (vertices=42, convex hull=29, v0=88847)
After retessellation of defect 42 (v0=88847), euler #=-33 (153304,458934,305597) : difference with theory (-36) = -3 

CORRECTING DEFECT 43 (vertices=13, convex hull=26, v0=89962)
After retessellation of defect 43 (v0=89962), euler #=-32 (153310,458959,305617) : difference with theory (-35) = -3 

CORRECTING DEFECT 44 (vertices=27, convex hull=62, v0=90958)
After retessellation of defect 44 (v0=90958), euler #=-31 (153324,459030,305675) : difference with theory (-34) = -3 

CORRECTING DEFECT 45 (vertices=16, convex hull=14, v0=93436)
After retessellation of defect 45 (v0=93436), euler #=-30 (153326,459040,305684) : difference with theory (-33) = -3 

CORRECTING DEFECT 46 (vertices=43, convex hull=80, v0=98112)
After retessellation of defect 46 (v0=98112), euler #=-29 (153351,459148,305768) : difference with theory (-32) = -3 

CORRECTING DEFECT 47 (vertices=37, convex hull=49, v0=98192)
After retessellation of defect 47 (v0=98192), euler #=-28 (153364,459203,305811) : difference with theory (-31) = -3 

CORRECTING DEFECT 48 (vertices=68, convex hull=30, v0=100589)
After retessellation of defect 48 (v0=100589), euler #=-27 (153370,459235,305838) : difference with theory (-30) = -3 

CORRECTING DEFECT 49 (vertices=14, convex hull=31, v0=102243)
After retessellation of defect 49 (v0=102243), euler #=-26 (153373,459256,305857) : difference with theory (-29) = -3 

CORRECTING DEFECT 50 (vertices=36, convex hull=61, v0=102344)
After retessellation of defect 50 (v0=102344), euler #=-25 (153395,459346,305926) : difference with theory (-28) = -3 

CORRECTING DEFECT 51 (vertices=39, convex hull=63, v0=104543)
After retessellation of defect 51 (v0=104543), euler #=-24 (153407,459407,305976) : difference with theory (-27) = -3 

CORRECTING DEFECT 52 (vertices=11, convex hull=30, v0=106100)
After retessellation of defect 52 (v0=106100), euler #=-23 (153408,459418,305987) : difference with theory (-26) = -3 

CORRECTING DEFECT 53 (vertices=62, convex hull=96, v0=107163)
After retessellation of defect 53 (v0=107163), euler #=-22 (153442,459563,306099) : difference with theory (-25) = -3 

CORRECTING DEFECT 54 (vertices=75, convex hull=83, v0=107504)
After retessellation of defect 54 (v0=107504), euler #=-21 (153467,459669,306181) : difference with theory (-24) = -3 

CORRECTING DEFECT 55 (vertices=51, convex hull=67, v0=108525)
After retessellation of defect 55 (v0=108525), euler #=-20 (153484,459743,306239) : difference with theory (-23) = -3 

CORRECTING DEFECT 56 (vertices=71, convex hull=99, v0=110026)
After retessellation of defect 56 (v0=110026), euler #=-19 (153493,459818,306306) : difference with theory (-22) = -3 

CORRECTING DEFECT 57 (vertices=66, convex hull=98, v0=110862)
After retessellation of defect 57 (v0=110862), euler #=-18 (153515,459928,306395) : difference with theory (-21) = -3 

CORRECTING DEFECT 58 (vertices=8, convex hull=21, v0=110987)
After retessellation of defect 58 (v0=110987), euler #=-17 (153520,459948,306411) : difference with theory (-20) = -3 

CORRECTING DEFECT 59 (vertices=22, convex hull=28, v0=113155)
After retessellation of defect 59 (v0=113155), euler #=-16 (153522,459964,306426) : difference with theory (-19) = -3 

CORRECTING DEFECT 60 (vertices=247, convex hull=46, v0=115313)
After retessellation of defect 60 (v0=115313), euler #=-17 (153532,460027,306478) : difference with theory (-18) = -1 

CORRECTING DEFECT 61 (vertices=35, convex hull=30, v0=116168)
After retessellation of defect 61 (v0=116168), euler #=-16 (153537,460052,306499) : difference with theory (-17) = -1 

CORRECTING DEFECT 62 (vertices=6, convex hull=22, v0=118213)
After retessellation of defect 62 (v0=118213), euler #=-15 (153539,460065,306511) : difference with theory (-16) = -1 

CORRECTING DEFECT 63 (vertices=47, convex hull=68, v0=119148)
After retessellation of defect 63 (v0=119148), euler #=-14 (153558,460151,306579) : difference with theory (-15) = -1 

CORRECTING DEFECT 64 (vertices=124, convex hull=127, v0=120193)
After retessellation of defect 64 (v0=120193), euler #=-13 (153600,460336,306723) : difference with theory (-14) = -1 

CORRECTING DEFECT 65 (vertices=42, convex hull=37, v0=122765)
After retessellation of defect 65 (v0=122765), euler #=-13 (153608,460378,306757) : difference with theory (-13) = 0 

CORRECTING DEFECT 66 (vertices=26, convex hull=70, v0=123206)
After retessellation of defect 66 (v0=123206), euler #=-12 (153619,460437,306806) : difference with theory (-12) = 0 

CORRECTING DEFECT 67 (vertices=38, convex hull=39, v0=124138)
After retessellation of defect 67 (v0=124138), euler #=-11 (153630,460485,306844) : difference with theory (-11) = 0 

CORRECTING DEFECT 68 (vertices=264, convex hull=60, v0=125091)
After retessellation of defect 68 (v0=125091), euler #=-10 (153654,460581,306917) : difference with theory (-10) = 0 

CORRECTING DEFECT 69 (vertices=48, convex hull=54, v0=125236)
After retessellation of defect 69 (v0=125236), euler #=-9 (153663,460633,306961) : difference with theory (-9) = 0 

CORRECTING DEFECT 70 (vertices=34, convex hull=36, v0=125895)
After retessellation of defect 70 (v0=125895), euler #=-8 (153672,460673,306993) : difference with theory (-8) = 0 

CORRECTING DEFECT 71 (vertices=41, convex hull=74, v0=127207)
After retessellation of defect 71 (v0=127207), euler #=-7 (153686,460746,307053) : difference with theory (-7) = 0 

CORRECTING DEFECT 72 (vertices=266, convex hull=90, v0=130735)
After retessellation of defect 72 (v0=130735), euler #=-6 (153722,460891,307163) : difference with theory (-6) = 0 

CORRECTING DEFECT 73 (vertices=44, convex hull=96, v0=134877)
After retessellation of defect 73 (v0=134877), euler #=-5 (153742,460989,307242) : difference with theory (-5) = 0 

CORRECTING DEFECT 74 (vertices=16, convex hull=24, v0=137822)
After retessellation of defect 74 (v0=137822), euler #=-4 (153745,461004,307255) : difference with theory (-4) = 0 

CORRECTING DEFECT 75 (vertices=92, convex hull=135, v0=142963)
After retessellation of defect 75 (v0=142963), euler #=-3 (153793,461208,307412) : difference with theory (-3) = 0 

CORRECTING DEFECT 76 (vertices=41, convex hull=83, v0=144044)
After retessellation of defect 76 (v0=144044), euler #=-2 (153812,461298,307484) : difference with theory (-2) = 0 

CORRECTING DEFECT 77 (vertices=57, convex hull=92, v0=145342)
After retessellation of defect 77 (v0=145342), euler #=-1 (153850,461453,307602) : difference with theory (-1) = 0 

CORRECTING DEFECT 78 (vertices=34, convex hull=25, v0=150120)
After retessellation of defect 78 (v0=150120), euler #=0 (153852,461466,307614) : difference with theory (0) = 0 

CORRECTING DEFECT 79 (vertices=25, convex hull=60, v0=150788)
After retessellation of defect 79 (v0=150788), euler #=1 (153861,461514,307654) : difference with theory (1) = 0 

CORRECTING DEFECT 80 (vertices=113, convex hull=122, v0=157306)
After retessellation of defect 80 (v0=157306), euler #=2 (153897,461685,307790) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.25 (0.04-->11.76) (max @ vno 109712 --> 119058)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.25 (0.04-->11.76) (max @ vno 109712 --> 119058)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
275 mutations (33.8%), 538 crossovers (66.2%), 271 vertices were eliminated
building final representation...
4795 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=153897, nf=307790, ne=461685, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 48.9 minutes
0 defective edges
removing intersecting faces
000: 532 intersecting
001: 25 intersecting
002: 6 intersecting
mris_fix_topology utimesec    2938.598265
mris_fix_topology stimesec    0.212967
mris_fix_topology ru_maxrss   502348
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56677
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  33504
mris_fix_topology ru_oublock  15008
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    678
mris_fix_topology ru_nivcsw   4192
FSRUNTIME@ mris_fix_topology lh  0.8156 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051009 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=-96 (nv=157376, nf=314944, ne=472416, g=49)
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...
7523 ambiguous faces found in tessellation
segmenting defects...
55 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 9 into 6
      -merging segment 24 into 21
      -merging segment 23 into 22
52 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7480  (-4.8740)
      -vertex     loglikelihood: -6.6098  (-3.3049)
      -normal dot loglikelihood: -3.5985  (-3.5985)
      -quad curv  loglikelihood: -6.3309  (-3.1654)
      Total Loglikelihood : -26.2872

CORRECTING DEFECT 0 (vertices=79, convex hull=70, v0=1687)
After retessellation of defect 0 (v0=1687), euler #=-52 (152865,456895,303978) : difference with theory (-49) = 3 

CORRECTING DEFECT 1 (vertices=74, convex hull=132, v0=6457)
After retessellation of defect 1 (v0=6457), euler #=-51 (152890,457026,304085) : difference with theory (-48) = 3 

CORRECTING DEFECT 2 (vertices=23, convex hull=73, v0=9752)
After retessellation of defect 2 (v0=9752), euler #=-50 (152901,457084,304133) : difference with theory (-47) = 3 

CORRECTING DEFECT 3 (vertices=27, convex hull=51, v0=9899)
After retessellation of defect 3 (v0=9899), euler #=-49 (152919,457160,304192) : difference with theory (-46) = 3 

CORRECTING DEFECT 4 (vertices=24, convex hull=57, v0=17219)
After retessellation of defect 4 (v0=17219), euler #=-48 (152928,457210,304234) : difference with theory (-45) = 3 

CORRECTING DEFECT 5 (vertices=152, convex hull=156, v0=28176)
After retessellation of defect 5 (v0=28176), euler #=-47 (152994,457486,304445) : difference with theory (-44) = 3 

CORRECTING DEFECT 6 (vertices=362, convex hull=266, v0=28339)
After retessellation of defect 6 (v0=28339), euler #=-45 (153060,457822,304717) : difference with theory (-43) = 2 

CORRECTING DEFECT 7 (vertices=24, convex hull=19, v0=34255)
After retessellation of defect 7 (v0=34255), euler #=-44 (153062,457835,304729) : difference with theory (-42) = 2 

CORRECTING DEFECT 8 (vertices=28, convex hull=66, v0=39430)
After retessellation of defect 8 (v0=39430), euler #=-43 (153076,457906,304787) : difference with theory (-41) = 2 

CORRECTING DEFECT 9 (vertices=46, convex hull=20, v0=47010)
After retessellation of defect 9 (v0=47010), euler #=-42 (153078,457922,304802) : difference with theory (-40) = 2 

CORRECTING DEFECT 10 (vertices=145, convex hull=61, v0=52394)
After retessellation of defect 10 (v0=52394), euler #=-41 (153095,457998,304862) : difference with theory (-39) = 2 

CORRECTING DEFECT 11 (vertices=403, convex hull=239, v0=56251)
After retessellation of defect 11 (v0=56251), euler #=-40 (153236,458544,305268) : difference with theory (-38) = 2 

CORRECTING DEFECT 12 (vertices=51, convex hull=84, v0=58531)
After retessellation of defect 12 (v0=58531), euler #=-39 (153265,458668,305364) : difference with theory (-37) = 2 

CORRECTING DEFECT 13 (vertices=43, convex hull=82, v0=60347)
After retessellation of defect 13 (v0=60347), euler #=-38 (153274,458726,305414) : difference with theory (-36) = 2 

CORRECTING DEFECT 14 (vertices=30, convex hull=54, v0=60388)
After retessellation of defect 14 (v0=60388), euler #=-37 (153289,458789,305463) : difference with theory (-35) = 2 

CORRECTING DEFECT 15 (vertices=59, convex hull=33, v0=64924)
After retessellation of defect 15 (v0=64924), euler #=-36 (153295,458816,305485) : difference with theory (-34) = 2 

CORRECTING DEFECT 16 (vertices=66, convex hull=95, v0=66003)
After retessellation of defect 16 (v0=66003), euler #=-35 (153309,458898,305554) : difference with theory (-33) = 2 

CORRECTING DEFECT 17 (vertices=63, convex hull=80, v0=70254)
After retessellation of defect 17 (v0=70254), euler #=-34 (153345,459040,305661) : difference with theory (-32) = 2 

CORRECTING DEFECT 18 (vertices=162, convex hull=104, v0=72953)
After retessellation of defect 18 (v0=72953), euler #=-33 (153388,459222,305801) : difference with theory (-31) = 2 

CORRECTING DEFECT 19 (vertices=28, convex hull=81, v0=79163)
After retessellation of defect 19 (v0=79163), euler #=-32 (153404,459301,305865) : difference with theory (-30) = 2 

CORRECTING DEFECT 20 (vertices=261, convex hull=335, v0=80052)
After retessellation of defect 20 (v0=80052), euler #=-30 (153575,459974,306369) : difference with theory (-29) = 1 

CORRECTING DEFECT 21 (vertices=51, convex hull=65, v0=81610)
After retessellation of defect 21 (v0=81610), euler #=-28 (153593,460055,306434) : difference with theory (-28) = 0 

CORRECTING DEFECT 22 (vertices=15, convex hull=25, v0=89692)
After retessellation of defect 22 (v0=89692), euler #=-27 (153594,460063,306442) : difference with theory (-27) = 0 

CORRECTING DEFECT 23 (vertices=60, convex hull=104, v0=90993)
After retessellation of defect 23 (v0=90993), euler #=-26 (153635,460228,306567) : difference with theory (-26) = 0 

CORRECTING DEFECT 24 (vertices=40, convex hull=66, v0=94076)
After retessellation of defect 24 (v0=94076), euler #=-25 (153662,460331,306644) : difference with theory (-25) = 0 

CORRECTING DEFECT 25 (vertices=11, convex hull=20, v0=95555)
After retessellation of defect 25 (v0=95555), euler #=-24 (153663,460340,306653) : difference with theory (-24) = 0 

CORRECTING DEFECT 26 (vertices=92, convex hull=68, v0=96136)
After retessellation of defect 26 (v0=96136), euler #=-23 (153686,460434,306725) : difference with theory (-23) = 0 

CORRECTING DEFECT 27 (vertices=18, convex hull=23, v0=99688)
After retessellation of defect 27 (v0=99688), euler #=-22 (153688,460446,306736) : difference with theory (-22) = 0 

CORRECTING DEFECT 28 (vertices=58, convex hull=79, v0=103130)
After retessellation of defect 28 (v0=103130), euler #=-21 (153704,460523,306798) : difference with theory (-21) = 0 

CORRECTING DEFECT 29 (vertices=248, convex hull=182, v0=103211)
After retessellation of defect 29 (v0=103211), euler #=-20 (153819,460956,307117) : difference with theory (-20) = 0 

CORRECTING DEFECT 30 (vertices=375, convex hull=57, v0=106838)
After retessellation of defect 30 (v0=106838), euler #=-19 (153836,461028,307173) : difference with theory (-19) = 0 

CORRECTING DEFECT 31 (vertices=52, convex hull=30, v0=110673)
After retessellation of defect 31 (v0=110673), euler #=-18 (153842,461056,307196) : difference with theory (-18) = 0 

CORRECTING DEFECT 32 (vertices=25, convex hull=34, v0=115157)
After retessellation of defect 32 (v0=115157), euler #=-17 (153848,461086,307221) : difference with theory (-17) = 0 

CORRECTING DEFECT 33 (vertices=28, convex hull=41, v0=115196)
After retessellation of defect 33 (v0=115196), euler #=-16 (153859,461133,307258) : difference with theory (-16) = 0 

CORRECTING DEFECT 34 (vertices=33, convex hull=68, v0=116151)
After retessellation of defect 34 (v0=116151), euler #=-15 (153879,461219,307325) : difference with theory (-15) = 0 

CORRECTING DEFECT 35 (vertices=220, convex hull=127, v0=117361)
After retessellation of defect 35 (v0=117361), euler #=-14 (153920,461399,307465) : difference with theory (-14) = 0 

CORRECTING DEFECT 36 (vertices=5, convex hull=16, v0=126247)
After retessellation of defect 36 (v0=126247), euler #=-13 (153920,461403,307470) : difference with theory (-13) = 0 

CORRECTING DEFECT 37 (vertices=97, convex hull=52, v0=126987)
After retessellation of defect 37 (v0=126987), euler #=-12 (153932,461458,307514) : difference with theory (-12) = 0 

CORRECTING DEFECT 38 (vertices=34, convex hull=63, v0=129243)
After retessellation of defect 38 (v0=129243), euler #=-11 (153952,461542,307579) : difference with theory (-11) = 0 

CORRECTING DEFECT 39 (vertices=15, convex hull=27, v0=132746)
After retessellation of defect 39 (v0=132746), euler #=-10 (153953,461552,307589) : difference with theory (-10) = 0 

CORRECTING DEFECT 40 (vertices=47, convex hull=26, v0=132770)
After retessellation of defect 40 (v0=132770), euler #=-9 (153957,461573,307607) : difference with theory (-9) = 0 

CORRECTING DEFECT 41 (vertices=50, convex hull=65, v0=132931)
After retessellation of defect 41 (v0=132931), euler #=-8 (153980,461672,307684) : difference with theory (-8) = 0 

CORRECTING DEFECT 42 (vertices=6, convex hull=21, v0=134271)
After retessellation of defect 42 (v0=134271), euler #=-7 (153982,461685,307696) : difference with theory (-7) = 0 

CORRECTING DEFECT 43 (vertices=15, convex hull=22, v0=134683)
After retessellation of defect 43 (v0=134683), euler #=-6 (153983,461697,307708) : difference with theory (-6) = 0 

CORRECTING DEFECT 44 (vertices=466, convex hull=112, v0=134784)
After retessellation of defect 44 (v0=134784), euler #=-5 (154036,461910,307869) : difference with theory (-5) = 0 

CORRECTING DEFECT 45 (vertices=33, convex hull=50, v0=137400)
After retessellation of defect 45 (v0=137400), euler #=-4 (154046,461964,307914) : difference with theory (-4) = 0 

CORRECTING DEFECT 46 (vertices=38, convex hull=80, v0=140309)
After retessellation of defect 46 (v0=140309), euler #=-3 (154073,462077,308001) : difference with theory (-3) = 0 

CORRECTING DEFECT 47 (vertices=48, convex hull=61, v0=146226)
After retessellation of defect 47 (v0=146226), euler #=-2 (154099,462182,308081) : difference with theory (-2) = 0 

CORRECTING DEFECT 48 (vertices=66, convex hull=48, v0=147630)
After retessellation of defect 48 (v0=147630), euler #=-1 (154103,462216,308112) : difference with theory (-1) = 0 

CORRECTING DEFECT 49 (vertices=13, convex hull=35, v0=152752)
After retessellation of defect 49 (v0=152752), euler #=0 (154104,462232,308128) : difference with theory (0) = 0 

CORRECTING DEFECT 50 (vertices=37, convex hull=80, v0=153298)
After retessellation of defect 50 (v0=153298), euler #=1 (154128,462338,308211) : difference with theory (1) = 0 

CORRECTING DEFECT 51 (vertices=77, convex hull=90, v0=153827)
After retessellation of defect 51 (v0=153827), euler #=2 (154166,462492,308328) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.08-->7.11) (max @ vno 93816 --> 96194)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.08-->7.11) (max @ vno 93816 --> 96194)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
158 mutations (36.7%), 272 crossovers (63.3%), 232 vertices were eliminated
building final representation...
3210 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=154166, nf=308328, ne=462492, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 34.9 minutes
0 defective edges
removing intersecting faces
000: 243 intersecting
001: 12 intersecting
mris_fix_topology utimesec    2093.407753
mris_fix_topology stimesec    0.208968
mris_fix_topology ru_maxrss   499304
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56108
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  11080
mris_fix_topology ru_oublock  14840
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    712
mris_fix_topology ru_nivcsw   6456
FSRUNTIME@ mris_fix_topology rh  0.5813 hours 1 threads
PIDs (5765 5768) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 153897 - 461685 + 307790 = 2 --> 0 holes
      F =2V-4:          307790 = 307794-4 (0)
      2E=3F:            923370 = 923370 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 154166 - 462492 + 308328 = 2 --> 0 holes
      F =2V-4:          308328 = 308332-4 (0)
      2E=3F:            924984 = 924984 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 76 intersecting
001: 14 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 39 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 22:15:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051009 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 22:15:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051009 rh 

Waiting for PID 7547 of (7547 7550) to complete...
Waiting for PID 7550 of (7547 7550) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051009 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-6.0.0/0051009/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
27343 bright wm thresholded.
7958 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.orig...
computing class statistics...
border white:    287611 voxels (1.71%)
border gray      356118 voxels (2.12%)
WM (96.0): 96.3 +- 9.9 [70.0 --> 110.0]
GM (63.0) : 63.4 +- 10.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 48.1 (was 70)
setting MAX_BORDER_WHITE to 111.9 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 37.2 (was 40)
setting MAX_GRAY to 92.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 48.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 26.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.03-->6.17) (max @ vno 28414 --> 152602)
face area 0.28 +- 0.13 (0.00-->5.67)
mean absolute distance = 0.58 +- 0.67
4377 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-7.8,    GM=59+-7.0
mean inside = 91.1, mean outside = 67.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=73.8, 93 (93) missing vertices, mean dist 0.3 [0.4 (%36.4)->0.7 (%63.6))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.06-->6.43) (max @ vno 28414 --> 152602)
face area 0.28 +- 0.13 (0.00-->5.69)
mean absolute distance = 0.26 +- 0.42
2647 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4908055.5, rms=12.034
001: dt: 0.5000, sse=2694228.8, rms=8.383 (30.338%)
002: dt: 0.5000, sse=1853432.9, rms=6.516 (22.280%)
003: dt: 0.5000, sse=1465221.8, rms=5.416 (16.869%)
004: dt: 0.5000, sse=1307999.1, rms=4.900 (9.529%)
005: dt: 0.5000, sse=1230328.1, rms=4.608 (5.965%)
006: dt: 0.5000, sse=1206914.0, rms=4.525 (1.798%)
007: dt: 0.5000, sse=1181951.9, rms=4.426 (2.196%)
rms = 4.42, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=1181086.5, rms=4.419 (0.143%)
009: dt: 0.2500, sse=867829.6, rms=2.896 (34.460%)
010: dt: 0.2500, sse=796657.2, rms=2.449 (15.447%)
011: dt: 0.2500, sse=783295.4, rms=2.344 (4.305%)
012: dt: 0.2500, sse=771889.9, rms=2.260 (3.549%)
rms = 2.23, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=767840.7, rms=2.232 (1.264%)
014: dt: 0.1250, sse=735098.2, rms=1.954 (12.467%)
rms = 1.92, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=733244.4, rms=1.917 (1.860%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 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 4 vertex label from ripped group
mean border=77.4, 91 (18) missing vertices, mean dist -0.2 [0.3 (%74.7)->0.2 (%25.3))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.10-->6.35) (max @ vno 28414 --> 152602)
face area 0.35 +- 0.16 (0.00-->6.99)
mean absolute distance = 0.20 +- 0.32
2880 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1509822.5, rms=4.981
016: dt: 0.5000, sse=1183352.1, rms=3.706 (25.600%)
rms = 4.22, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=961688.6, rms=2.505 (32.415%)
018: dt: 0.2500, sse=900601.3, rms=2.023 (19.238%)
019: dt: 0.2500, sse=871229.2, rms=1.794 (11.304%)
rms = 1.77, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=868049.4, rms=1.769 (1.412%)
021: dt: 0.1250, sse=847984.2, rms=1.553 (12.190%)
rms = 1.53, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=846118.8, rms=1.531 (1.431%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.0, 103 (13) missing vertices, mean dist -0.1 [0.2 (%62.6)->0.2 (%37.4))]
%89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.08-->6.31) (max @ vno 28414 --> 152602)
face area 0.34 +- 0.16 (0.00-->6.90)
mean absolute distance = 0.20 +- 0.29
2680 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=968306.6, rms=2.645
rms = 3.49, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=857920.6, rms=1.796 (32.090%)
024: dt: 0.2500, sse=845124.8, rms=1.500 (16.515%)
rms = 1.50, time step reduction 2 of 3 to 0.125...
025: dt: 0.1250, sse=827350.6, rms=1.448 (3.431%)
026: dt: 0.1250, sse=823898.8, rms=1.380 (4.735%)
rms = 1.38, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=820284.8, rms=1.375 (0.315%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=79.6, 122 (7) missing vertices, mean dist -0.0 [0.2 (%52.9)->0.2 (%47.1))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=837993.1, rms=1.635
rms = 2.32, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=797915.8, rms=1.155 (29.379%)
029: dt: 0.2500, sse=789781.9, rms=1.031 (10.750%)
rms = 1.03, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=786758.4, rms=1.029 (0.178%)
rms = 1.01, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=783675.1, rms=1.009 (1.964%)
positioning took 0.6 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7862 vertices
erasing segment 1 (vno[0] = 59573)
erasing segment 2 (vno[0] = 67419)
erasing segment 3 (vno[0] = 76981)
erasing segment 4 (vno[0] = 85108)
erasing segment 5 (vno[0] = 96988)
erasing segment 6 (vno[0] = 101689)
erasing segment 7 (vno[0] = 107502)
erasing segment 8 (vno[0] = 110758)
erasing segment 9 (vno[0] = 111520)
erasing segment 10 (vno[0] = 117306)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.area
vertex spacing 0.90 +- 0.25 (0.04-->6.27) (max @ vno 28414 --> 152602)
face area 0.34 +- 0.16 (0.00-->6.46)
refinement took 6.1 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051009 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-6.0.0/0051009/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
27343 bright wm thresholded.
7958 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.orig...
computing class statistics...
border white:    287611 voxels (1.71%)
border gray      356118 voxels (2.12%)
WM (96.0): 96.3 +- 9.9 [70.0 --> 110.0]
GM (63.0) : 63.4 +- 10.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 48.1 (was 70)
setting MAX_BORDER_WHITE to 112.9 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 37.2 (was 40)
setting MAX_GRAY to 93.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 48.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 26.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->4.01) (max @ vno 67338 --> 153106)
face area 0.28 +- 0.13 (0.00-->6.15)
mean absolute distance = 0.58 +- 0.66
4632 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=103+-7.8,    GM=59+-7.0
mean inside = 91.2, mean outside = 68.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=74.0, 80 (80) missing vertices, mean dist 0.3 [0.4 (%36.9)->0.7 (%63.1))]
%82 local maxima, %14 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 0.91 +- 0.25 (0.07-->3.99) (max @ vno 69907 --> 153135)
face area 0.28 +- 0.13 (0.00-->4.92)
mean absolute distance = 0.26 +- 0.41
2822 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4907192.5, rms=11.982
001: dt: 0.5000, sse=2664258.2, rms=8.331 (30.470%)
002: dt: 0.5000, sse=1840355.9, rms=6.468 (22.369%)
003: dt: 0.5000, sse=1461556.5, rms=5.392 (16.639%)
004: dt: 0.5000, sse=1291900.1, rms=4.833 (10.352%)
005: dt: 0.5000, sse=1234130.0, rms=4.565 (5.562%)
006: dt: 0.5000, sse=1190735.8, rms=4.454 (2.416%)
007: dt: 0.5000, sse=1177790.5, rms=4.389 (1.463%)
rms = 4.36, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=1166848.1, rms=4.359 (0.685%)
009: dt: 0.2500, sse=855403.8, rms=2.825 (35.197%)
010: dt: 0.2500, sse=785322.3, rms=2.369 (16.136%)
011: dt: 0.2500, sse=772207.9, rms=2.256 (4.774%)
012: dt: 0.2500, sse=767691.2, rms=2.172 (3.708%)
rms = 2.14, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=762261.6, rms=2.141 (1.458%)
014: dt: 0.1250, sse=723144.5, rms=1.845 (13.800%)
rms = 1.81, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=720645.8, rms=1.811 (1.848%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=77.6, 97 (23) missing vertices, mean dist -0.2 [0.3 (%75.1)->0.2 (%24.9))]
%88 local maxima, % 8 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 0.90 +- 0.24 (0.07-->4.11) (max @ vno 69907 --> 71088)
face area 0.35 +- 0.16 (0.00-->6.29)
mean absolute distance = 0.19 +- 0.31
2974 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1554554.5, rms=5.126
016: dt: 0.5000, sse=1179316.1, rms=3.684 (28.129%)
rms = 4.21, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=962919.8, rms=2.489 (32.435%)
018: dt: 0.2500, sse=897496.4, rms=1.986 (20.197%)
019: dt: 0.2500, sse=867455.8, rms=1.756 (11.571%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=864628.6, rms=1.726 (1.746%)
021: dt: 0.1250, sse=854734.5, rms=1.497 (13.284%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=852159.8, rms=1.470 (1.771%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=79.3, 93 (10) missing vertices, mean dist -0.1 [0.2 (%63.2)->0.2 (%36.8))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.24 (0.12-->4.21) (max @ vno 69907 --> 71088)
face area 0.34 +- 0.16 (0.00-->6.20)
mean absolute distance = 0.19 +- 0.28
2510 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=984691.8, rms=2.687
rms = 3.52, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=858101.6, rms=1.814 (32.509%)
024: dt: 0.2500, sse=824405.0, rms=1.465 (19.234%)
rms = 1.45, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=825591.1, rms=1.454 (0.752%)
026: dt: 0.1250, sse=811873.3, rms=1.320 (9.197%)
rms = 1.32, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=811404.5, rms=1.317 (0.235%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=79.9, 127 (5) missing vertices, mean dist -0.0 [0.2 (%53.4)->0.2 (%46.6))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=827157.9, rms=1.572
rms = 2.30, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=788620.1, rms=1.091 (30.615%)
029: dt: 0.2500, sse=783005.5, rms=0.978 (10.366%)
rms = 0.98, time step reduction 2 of 3 to 0.125...
rms = 0.97, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=780957.6, rms=0.971 (0.638%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 7394 vertices
erasing segment 1 (vno[0] = 62651)
erasing segment 2 (vno[0] = 67013)
erasing segment 3 (vno[0] = 104268)
erasing segment 4 (vno[0] = 105375)
erasing segment 5 (vno[0] = 105447)
erasing segment 6 (vno[0] = 105635)
erasing segment 7 (vno[0] = 113280)
erasing segment 8 (vno[0] = 114247)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.area
vertex spacing 0.90 +- 0.25 (0.04-->4.25) (max @ vno 69907 --> 71088)
face area 0.34 +- 0.16 (0.00-->6.17)
refinement took 6.0 minutes
PIDs (7547 7550) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 22:21:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 22:21:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

Waiting for PID 8017 of (8017 8020) to complete...
Waiting for PID 8020 of (8017 8020) 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 (8017 8020) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 22:21:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 22:21:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 8108 of (8108 8111) to complete...
Waiting for PID 8111 of (8108 8111) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 48.8 mm, total surface area = 94500 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.180 (target=0.015)   
step 005: RMS=0.127 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.053 (target=0.015)   
step 030: RMS=0.045 (target=0.015)   
step 035: RMS=0.038 (target=0.015)   
step 040: RMS=0.032 (target=0.015)   
step 045: RMS=0.028 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    49.899414
mris_inflate stimesec    0.113982
mris_inflate ru_maxrss   225056
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32823
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10832
mris_inflate ru_oublock  12056
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2339
mris_inflate ru_nivcsw   3530

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 47.8 mm, total surface area = 94580 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.179 (target=0.015)   
step 005: RMS=0.126 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.054 (target=0.015)   
step 030: RMS=0.045 (target=0.015)   
step 035: RMS=0.039 (target=0.015)   
step 040: RMS=0.034 (target=0.015)   
step 045: RMS=0.031 (target=0.015)   
step 050: RMS=0.028 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    49.826425
mris_inflate stimesec    0.135979
mris_inflate ru_maxrss   225212
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32350
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10848
mris_inflate ru_oublock  12072
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2350
mris_inflate ru_nivcsw   3682
PIDs (8108 8111) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 22:22:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 22:22:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 8208 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8211 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8214 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8217 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8220 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8223 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8226 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8229 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8232 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8235 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8238 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...
Waiting for PID 8241 of (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 3.634*4pi (45.670) --> -3 handles
ICI = 206.8, FI = 2028.8, variation=32437.584
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
203 vertices thresholded to be in k1 ~ [-0.27 0.23], k2 ~ [-0.10 0.05]
total integrated curvature = 0.470*4pi (5.906) --> 1 handles
ICI = 1.6, FI = 10.3, variation=177.182
138 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
171 vertices thresholded to be in [-0.15 0.11]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = -5.082*4pi (-63.866) --> 6 handles
ICI = 198.1, FI = 1937.1, variation=31135.605
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
175 vertices thresholded to be in k1 ~ [-0.24 0.37], k2 ~ [-0.09 0.08]
total integrated curvature = 0.427*4pi (5.365) --> 1 handles
ICI = 1.6, FI = 10.6, variation=182.994
149 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
148 vertices thresholded to be in [-0.14 0.15]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023
done.
PIDs (8208 8211 8214 8217 8220 8223 8226 8229 8232 8235 8238 8241) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 22:23:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051009 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      [ 0051009/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                      [ 312 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.487852
WARN:    S explicit min:                          0.000000	vertex = 245

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 22:23:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051009 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      [ 0051009/rh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 297 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.400579
WARN:    S explicit min:                          0.000000	vertex = 18
#--------------------------------------------
#@# Sphere lh Sat Oct  7 22:24:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 22:24:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 8379 of (8379 8382) to complete...
Waiting for PID 8382 of (8379 8382) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0.281...
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 %20.37
pass 1: epoch 2 of 3 starting distance error %20.40
unfolding complete - removing small folds...
starting distance error %20.32
removing remaining folds...
final distance error %20.34
MRISunfold() return, current seed 1234
-01: dt=0.0000, 159 negative triangles
203: dt=0.9900, 159 negative triangles
204: dt=0.9900, 51 negative triangles
205: dt=0.9900, 32 negative triangles
206: dt=0.9900, 30 negative triangles
207: dt=0.9900, 21 negative triangles
208: dt=0.9900, 18 negative triangles
209: dt=0.9900, 13 negative triangles
210: dt=0.9900, 12 negative triangles
211: dt=0.9900, 13 negative triangles
212: dt=0.9900, 5 negative triangles
213: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.04 hours
mris_sphere utimesec    3748.142195
mris_sphere stimesec    1.082835
mris_sphere ru_maxrss   316416
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55297
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10864
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    140209
mris_sphere ru_nivcsw   300281
FSRUNTIME@ mris_sphere  1.0413 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0.283...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.12
pass 1: epoch 2 of 3 starting distance error %21.08
unfolding complete - removing small folds...
starting distance error %20.96
removing remaining folds...
final distance error %20.99
MRISunfold() return, current seed 1234
-01: dt=0.0000, 170 negative triangles
201: dt=0.9900, 170 negative triangles
202: dt=0.9900, 97 negative triangles
203: dt=0.9900, 89 negative triangles
204: dt=0.9900, 72 negative triangles
205: dt=0.9900, 50 negative triangles
206: dt=0.9900, 37 negative triangles
207: dt=0.9900, 35 negative triangles
208: dt=0.9900, 40 negative triangles
209: dt=0.9900, 37 negative triangles
210: dt=0.9900, 43 negative triangles
211: dt=0.9900, 48 negative triangles
212: dt=0.9900, 40 negative triangles
213: dt=0.9900, 38 negative triangles
214: dt=0.9900, 41 negative triangles
215: dt=0.9900, 41 negative triangles
216: dt=0.9900, 38 negative triangles
217: dt=0.9405, 42 negative triangles
218: dt=0.9405, 36 negative triangles
219: dt=0.9405, 36 negative triangles
220: dt=0.9405, 40 negative triangles
221: dt=0.9405, 36 negative triangles
222: dt=0.9405, 36 negative triangles
223: dt=0.9405, 38 negative triangles
224: dt=0.9405, 32 negative triangles
225: dt=0.9405, 30 negative triangles
226: dt=0.9405, 30 negative triangles
227: dt=0.9405, 29 negative triangles
228: dt=0.9405, 30 negative triangles
229: dt=0.9405, 31 negative triangles
230: dt=0.9405, 24 negative triangles
231: dt=0.9405, 23 negative triangles
232: dt=0.9405, 22 negative triangles
233: dt=0.9405, 19 negative triangles
234: dt=0.9405, 26 negative triangles
235: dt=0.9405, 21 negative triangles
236: dt=0.9405, 20 negative triangles
237: dt=0.9405, 21 negative triangles
238: dt=0.9405, 21 negative triangles
239: dt=0.9405, 17 negative triangles
240: dt=0.9405, 24 negative triangles
241: dt=0.9405, 20 negative triangles
242: dt=0.9405, 19 negative triangles
243: dt=0.9405, 17 negative triangles
244: dt=0.9405, 20 negative triangles
245: dt=0.9405, 13 negative triangles
246: dt=0.9405, 16 negative triangles
247: dt=0.9405, 12 negative triangles
248: dt=0.9405, 14 negative triangles
249: dt=0.9405, 14 negative triangles
250: dt=0.9405, 14 negative triangles
251: dt=0.9405, 12 negative triangles
252: dt=0.9405, 14 negative triangles
253: dt=0.9405, 12 negative triangles
254: dt=0.9405, 19 negative triangles
255: dt=0.9405, 16 negative triangles
256: dt=0.9405, 12 negative triangles
257: dt=0.9405, 11 negative triangles
258: dt=0.9405, 11 negative triangles
259: dt=0.9405, 7 negative triangles
260: dt=0.9405, 13 negative triangles
261: dt=0.9405, 9 negative triangles
262: dt=0.9405, 13 negative triangles
263: dt=0.9405, 9 negative triangles
264: dt=0.9405, 11 negative triangles
265: dt=0.9405, 9 negative triangles
266: dt=0.9405, 11 negative triangles
267: dt=0.9405, 10 negative triangles
268: dt=0.9405, 11 negative triangles
269: dt=0.8935, 9 negative triangles
270: dt=0.8935, 9 negative triangles
271: dt=0.8935, 10 negative triangles
272: dt=0.8935, 6 negative triangles
273: dt=0.8935, 4 negative triangles
274: dt=0.8935, 8 negative triangles
275: dt=0.8935, 5 negative triangles
276: dt=0.8935, 4 negative triangles
277: dt=0.8935, 8 negative triangles
278: dt=0.8935, 5 negative triangles
279: dt=0.8935, 3 negative triangles
280: dt=0.8935, 6 negative triangles
281: dt=0.8935, 2 negative triangles
282: dt=0.8935, 4 negative triangles
283: dt=0.8935, 2 negative triangles
284: dt=0.8935, 4 negative triangles
285: dt=0.8935, 4 negative triangles
286: dt=0.8935, 5 negative triangles
287: dt=0.8935, 2 negative triangles
288: dt=0.8935, 3 negative triangles
289: dt=0.8935, 1 negative triangles
290: dt=0.8935, 3 negative triangles
291: dt=0.8935, 1 negative triangles
292: dt=0.8935, 1 negative triangles
293: dt=0.8935, 5 negative triangles
294: dt=0.8935, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.05 hours
mris_sphere utimesec    3841.572992
mris_sphere stimesec    1.138826
mris_sphere ru_maxrss   316840
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55907
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10936
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    141936
mris_sphere ru_nivcsw   296491
FSRUNTIME@ mris_sphere  1.0544 hours 1 threads
PIDs (8379 8382) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sat Oct  7 23:27:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 Sat Oct  7 23:27:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 11745 of (11745 11748) to complete...
Waiting for PID 11748 of (11745 11748) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 5.693
curvature mean = 0.030, std = 0.816
curvature mean = 0.015, std = 0.854
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 318633.8, tmin=1.1961
  d=32.00 min @ (-8.00, 0.00, 0.00) sse = 304495.0, tmin=2.4322
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 281684.5, tmin=3.6770
  d=8.00 min @ (-2.00, -2.00, 2.00) sse = 269001.2, tmin=4.9078
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 267743.3, tmin=6.1567
  d=1.00 min @ (-0.25, 0.25, -0.25) sse = 267554.9, tmin=8.6267
  d=0.50 min @ (0.00, -0.12, 0.12) sse = 267521.6, tmin=9.8608
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   9.86 min
curvature mean = 0.011, std = 0.823
curvature mean = 0.008, std = 0.942
curvature mean = 0.008, std = 0.832
curvature mean = 0.003, std = 0.976
curvature mean = 0.007, std = 0.834
curvature mean = 0.001, std = 0.990
2 Reading smoothwm
curvature mean = -0.028, std = 0.296
curvature mean = 0.042, std = 0.244
curvature mean = 0.071, std = 0.322
curvature mean = 0.037, std = 0.303
curvature mean = 0.044, std = 0.499
curvature mean = 0.036, std = 0.330
curvature mean = 0.026, std = 0.641
curvature mean = 0.035, std = 0.343
curvature mean = 0.009, std = 0.758
MRISregister() return, current seed 0
-01: dt=0.0000, 48 negative triangles
123: dt=0.9900, 48 negative triangles
expanding nbhd size to 1
124: dt=0.9900, 71 negative triangles
125: dt=0.9900, 45 negative triangles
126: dt=0.9900, 45 negative triangles
127: dt=0.9900, 40 negative triangles
128: dt=0.9900, 35 negative triangles
129: dt=0.9900, 35 negative triangles
130: dt=0.9900, 33 negative triangles
131: dt=0.9900, 28 negative triangles
132: dt=0.9900, 26 negative triangles
133: dt=0.9900, 20 negative triangles
134: dt=0.9900, 20 negative triangles
135: dt=0.9900, 19 negative triangles
136: dt=0.9900, 16 negative triangles
137: dt=0.9900, 15 negative triangles
138: dt=0.9900, 12 negative triangles
139: dt=0.9900, 10 negative triangles
140: dt=0.9900, 13 negative triangles
141: dt=0.9900, 7 negative triangles
142: dt=0.9900, 5 negative triangles
143: dt=0.9900, 5 negative triangles
144: dt=0.9900, 2 negative triangles
145: dt=0.9900, 3 negative triangles
146: dt=0.9900, 1 negative triangles
147: dt=0.9900, 1 negative triangles
148: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.55 hours
mris_register utimesec    5623.042167
mris_register stimesec    2.868563
mris_register ru_maxrss   278604
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38363
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10920
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    411703
mris_register ru_nivcsw   252998
FSRUNTIME@ mris_register  1.5468 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 5.766
curvature mean = 0.011, std = 0.802
curvature mean = 0.016, std = 0.854
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 323172.8, tmin=1.1963
  d=32.00 min @ (-8.00, 0.00, 0.00) sse = 301227.7, tmin=2.4324
  d=16.00 min @ (4.00, 0.00, 4.00) sse = 254428.2, tmin=3.6772
  d=8.00 min @ (0.00, 2.00, -2.00) sse = 239296.6, tmin=4.9362
  d=4.00 min @ (1.00, 0.00, 1.00) sse = 236091.7, tmin=6.2127
  d=2.00 min @ (-0.50, 0.00, 0.00) sse = 235968.5, tmin=7.4858
  d=1.00 min @ (0.25, 0.00, 0.00) sse = 235876.8, tmin=8.7390
  d=0.50 min @ (0.00, 0.12, -0.12) sse = 235781.9, tmin=9.9867
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   9.99 min
curvature mean = -0.004, std = 0.809
curvature mean = 0.007, std = 0.943
curvature mean = -0.007, std = 0.817
curvature mean = 0.002, std = 0.976
curvature mean = -0.007, std = 0.818
curvature mean = 0.001, std = 0.990
2 Reading smoothwm
curvature mean = -0.029, std = 0.320
curvature mean = 0.037, std = 0.237
curvature mean = 0.065, std = 0.304
curvature mean = 0.033, std = 0.296
curvature mean = 0.041, std = 0.473
curvature mean = 0.033, std = 0.322
curvature mean = 0.022, std = 0.617
curvature mean = 0.033, std = 0.333
curvature mean = 0.007, std = 0.738
MRISregister() return, current seed 0
-01: dt=0.0000, 103 negative triangles
118: dt=0.9900, 103 negative triangles
expanding nbhd size to 1
119: dt=0.9900, 125 negative triangles
120: dt=0.9405, 105 negative triangles
121: dt=0.9405, 104 negative triangles
122: dt=0.9405, 94 negative triangles
123: dt=0.9405, 99 negative triangles
124: dt=0.9405, 92 negative triangles
125: dt=0.9405, 90 negative triangles
126: dt=0.9405, 93 negative triangles
127: dt=0.9405, 92 negative triangles
128: dt=0.9405, 91 negative triangles
129: dt=0.9405, 88 negative triangles
130: dt=0.9405, 86 negative triangles
131: dt=0.9405, 82 negative triangles
132: dt=0.9405, 81 negative triangles
133: dt=0.9405, 81 negative triangles
134: dt=0.9405, 76 negative triangles
135: dt=0.9405, 75 negative triangles
136: dt=0.9405, 77 negative triangles
137: dt=0.9405, 74 negative triangles
138: dt=0.9405, 75 negative triangles
139: dt=0.9405, 72 negative triangles
140: dt=0.9405, 71 negative triangles
141: dt=0.9405, 69 negative triangles
142: dt=0.9405, 69 negative triangles
143: dt=0.9405, 69 negative triangles
144: dt=0.9405, 69 negative triangles
145: dt=0.9405, 66 negative triangles
146: dt=0.9405, 64 negative triangles
147: dt=0.9405, 61 negative triangles
148: dt=0.9405, 60 negative triangles
149: dt=0.9405, 59 negative triangles
150: dt=0.9405, 61 negative triangles
151: dt=0.9405, 58 negative triangles
152: dt=0.9405, 55 negative triangles
153: dt=0.9405, 53 negative triangles
154: dt=0.9405, 49 negative triangles
155: dt=0.9405, 48 negative triangles
156: dt=0.9405, 50 negative triangles
157: dt=0.9405, 48 negative triangles
158: dt=0.9405, 48 negative triangles
159: dt=0.9405, 48 negative triangles
160: dt=0.9405, 46 negative triangles
161: dt=0.9405, 41 negative triangles
162: dt=0.9405, 44 negative triangles
163: dt=0.9405, 43 negative triangles
164: dt=0.9405, 41 negative triangles
165: dt=0.9405, 38 negative triangles
166: dt=0.9405, 33 negative triangles
167: dt=0.9405, 32 negative triangles
168: dt=0.9405, 30 negative triangles
169: dt=0.9405, 28 negative triangles
170: dt=0.9405, 23 negative triangles
171: dt=0.9405, 19 negative triangles
172: dt=0.9405, 20 negative triangles
173: dt=0.9405, 18 negative triangles
174: dt=0.9405, 17 negative triangles
175: dt=0.9405, 14 negative triangles
176: dt=0.9405, 13 negative triangles
177: dt=0.9405, 10 negative triangles
178: dt=0.9405, 10 negative triangles
179: dt=0.9405, 10 negative triangles
180: dt=0.9405, 9 negative triangles
181: dt=0.9405, 6 negative triangles
182: dt=0.9405, 6 negative triangles
183: dt=0.9405, 4 negative triangles
184: dt=0.9405, 5 negative triangles
185: dt=0.9405, 3 negative triangles
186: dt=0.9405, 3 negative triangles
187: dt=0.9405, 2 negative triangles
188: dt=0.9405, 3 negative triangles
189: dt=0.9405, 3 negative triangles
190: dt=0.9405, 2 negative triangles
191: dt=0.9405, 3 negative triangles
192: dt=0.9405, 2 negative triangles
193: dt=0.9405, 2 negative triangles
194: dt=0.9405, 1 negative triangles
195: dt=0.9405, 2 negative triangles
196: dt=0.9405, 1 negative triangles
197: dt=0.9405, 1 negative triangles
198: dt=0.9405, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.52 hours
mris_register utimesec    5473.860846
mris_register stimesec    2.572608
mris_register ru_maxrss   280184
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39435
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10960
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    397801
mris_register ru_nivcsw   258377
FSRUNTIME@ mris_register  1.5208 hours 1 threads
PIDs (11745 11748) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 01:00:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 01:00:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

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

Waiting for PID 15982 of (15982 15985) to complete...
Waiting for PID 15985 of (15982 15985) 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 (15982 15985) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 01:00:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 01:00:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 16027 of (16027 16030) to complete...
Waiting for PID 16030 of (16027 16030) 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 (16027 16030) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 01:00:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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 01:00:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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 16074 of (16074 16077) to complete...
Waiting for PID 16077 of (16074 16077) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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...
1922 labels changed using aseg
relabeling using gibbs priors...
000:   3523 changed, 153897 examined...
001:    847 changed, 14836 examined...
002:    224 changed, 4667 examined...
003:     81 changed, 1316 examined...
004:     36 changed, 471 examined...
005:     16 changed, 223 examined...
006:     10 changed, 96 examined...
007:      3 changed, 56 examined...
008:      1 changed, 20 examined...
009:      1 changed, 7 examined...
010:      1 changed, 5 examined...
011:      0 changed, 7 examined...
250 labels changed using aseg
000: 148 total segments, 105 labels (651 vertices) changed
001: 45 total segments, 7 labels (13 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
9 filter iterations complete (10 requested, 0 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2057 vertices marked for relabeling...
2057 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 0051009 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...
1296 labels changed using aseg
relabeling using gibbs priors...
000:   2992 changed, 154166 examined...
001:    672 changed, 12954 examined...
002:    164 changed, 3778 examined...
003:     46 changed, 969 examined...
004:      9 changed, 282 examined...
005:      4 changed, 51 examined...
006:      1 changed, 19 examined...
007:      2 changed, 7 examined...
008:      0 changed, 17 examined...
114 labels changed using aseg
000: 104 total segments, 67 labels (348 vertices) changed
001: 39 total segments, 2 labels (5 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1817 vertices marked for relabeling...
1817 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 17 seconds.
PIDs (16074 16077) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 01:00:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051009 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 01:00:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051009 rh 

Waiting for PID 16138 of (16138 16141) to complete...
Waiting for PID 16141 of (16138 16141) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051009 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-6.0.0/0051009/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
27343 bright wm thresholded.
7958 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.orig...
computing class statistics...
border white:    287611 voxels (1.71%)
border gray      356118 voxels (2.12%)
WM (96.0): 96.3 +- 9.9 [70.0 --> 110.0]
GM (63.0) : 63.4 +- 10.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 48.1 (was 70)
setting MAX_BORDER_WHITE to 111.9 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 37.2 (was 40)
setting MAX_GRAY to 92.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 48.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 26.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-7.8,    GM=59+-7.0
mean inside = 91.1, mean outside = 67.9
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.25 (0.04-->6.27) (max @ vno 28414 --> 152602)
face area 0.34 +- 0.16 (0.00-->6.43)
mean absolute distance = 0.44 +- 0.62
3145 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 88 points - only 0.00% unknown
deleting segment 1 with 9 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 347 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 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
deleting segment 12 with 15 points - only 0.00% unknown
deleting segment 13 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
deleting segment 15 with 9 points - only 0.00% unknown
deleting segment 16 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 17 with 4 points - only 0.00% unknown
deleting segment 18 with 7 points - only 0.00% unknown
mean border=73.2, 81 (81) missing vertices, mean dist 0.3 [0.4 (%16.6)->0.4 (%83.4))]
%79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.10-->6.22) (max @ vno 28414 --> 152602)
face area 0.34 +- 0.16 (0.00-->6.32)
mean absolute distance = 0.27 +- 0.42
2499 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2736780.2, rms=8.199
001: dt: 0.5000, sse=1478562.9, rms=4.960 (39.499%)
002: dt: 0.5000, sse=1301931.9, rms=4.333 (12.653%)
rms = 4.33, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=1038763.4, rms=3.124 (27.898%)
004: dt: 0.2500, sse=947027.6, rms=2.568 (17.810%)
005: dt: 0.2500, sse=908016.8, rms=2.287 (10.939%)
006: dt: 0.2500, sse=898211.6, rms=2.199 (3.841%)
007: dt: 0.2500, sse=888484.1, rms=2.120 (3.605%)
rms = 2.08, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=883681.9, rms=2.084 (1.671%)
009: dt: 0.1250, sse=866004.9, rms=1.927 (7.548%)
rms = 1.90, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=863137.2, rms=1.901 (1.329%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 83 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 166 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 7 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
deleting segment 16 with 7 points - only 0.00% unknown
mean border=77.2, 92 (27) missing vertices, mean dist -0.2 [0.3 (%77.6)->0.2 (%22.4))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.06-->6.15) (max @ vno 28414 --> 152602)
face area 0.36 +- 0.17 (0.00-->6.62)
mean absolute distance = 0.20 +- 0.32
2680 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1557561.9, rms=5.085
011: dt: 0.5000, sse=1182657.9, rms=3.614 (28.913%)
rms = 4.11, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=967984.9, rms=2.410 (33.320%)
013: dt: 0.2500, sse=905742.2, rms=1.914 (20.567%)
014: dt: 0.2500, sse=880098.2, rms=1.690 (11.709%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=879032.4, rms=1.678 (0.747%)
016: dt: 0.1250, sse=859738.9, rms=1.466 (12.612%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=858174.8, rms=1.447 (1.306%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 83 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 9 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 250 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 12 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
mean border=78.9, 106 (19) missing vertices, mean dist -0.1 [0.2 (%63.0)->0.2 (%37.0))]
%89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.91 +- 0.26 (0.08-->6.14) (max @ vno 28414 --> 152602)
face area 0.35 +- 0.17 (0.00-->6.56)
mean absolute distance = 0.20 +- 0.30
2636 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=975300.4, rms=2.619
rms = 3.48, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=863253.0, rms=1.744 (33.419%)
019: dt: 0.2500, sse=836633.9, rms=1.443 (17.233%)
rms = 1.44, time step reduction 2 of 3 to 0.125...
020: dt: 0.1250, sse=840065.6, rms=1.390 (3.713%)
021: dt: 0.1250, sse=825610.4, rms=1.319 (5.086%)
rms = 1.32, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=827659.4, rms=1.318 (0.069%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 82 points - only 0.00% unknown
deleting segment 1 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 11 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 263 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
deleting segment 9 with 16 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
deleting segment 14 with 7 points - only 0.00% unknown
mean border=79.5, 126 (17) missing vertices, mean dist -0.0 [0.2 (%53.2)->0.2 (%46.8))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=846066.0, rms=1.603
rms = 2.29, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=804315.8, rms=1.106 (31.012%)
024: dt: 0.2500, sse=795399.5, rms=0.981 (11.269%)
rms = 0.99, time step reduction 2 of 3 to 0.125...
rms = 0.97, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=793991.8, rms=0.973 (0.855%)
positioning took 0.5 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7835 vertices
erasing segment 1 (vno[0] = 67419)
erasing segment 2 (vno[0] = 76981)
erasing segment 3 (vno[0] = 85108)
erasing segment 4 (vno[0] = 101689)
erasing segment 5 (vno[0] = 106412)
erasing segment 6 (vno[0] = 107502)
erasing segment 7 (vno[0] = 111520)
erasing segment 8 (vno[0] = 117307)
erasing segment 9 (vno[0] = 153248)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.area
vertex spacing 0.90 +- 0.26 (0.04-->6.10) (max @ vno 28414 --> 152602)
face area 0.34 +- 0.17 (0.00-->6.29)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=47.3, 99 (99) missing vertices, mean dist 1.3 [2.9 (%0.0)->3.1 (%100.0))]
% 9 local maxima, %32 large gradients and %55 min vals, 590 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=32662826.0, rms=32.860
001: dt: 0.0500, sse=28064592.0, rms=30.400 (7.487%)
002: dt: 0.0500, sse=24802230.0, rms=28.526 (6.165%)
003: dt: 0.0500, sse=22336454.0, rms=27.023 (5.268%)
004: dt: 0.0500, sse=20372124.0, rms=25.764 (4.662%)
005: dt: 0.0500, sse=18746414.0, rms=24.672 (4.236%)
006: dt: 0.0500, sse=17363684.0, rms=23.704 (3.923%)
007: dt: 0.0500, sse=16164215.0, rms=22.831 (3.682%)
008: dt: 0.0500, sse=15108406.0, rms=22.034 (3.491%)
009: dt: 0.0500, sse=14168400.0, rms=21.300 (3.335%)
010: dt: 0.0500, sse=13324793.0, rms=20.618 (3.201%)
positioning took 1.1 minutes
mean border=46.8, 109 (54) missing vertices, mean dist 1.2 [0.1 (%0.0)->2.7 (%100.0))]
%11 local maxima, %33 large gradients and %52 min vals, 506 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=14517571.0, rms=21.580
011: dt: 0.0500, sse=13738330.0, rms=20.960 (2.875%)
012: dt: 0.0500, sse=13030939.0, rms=20.380 (2.765%)
013: dt: 0.0500, sse=12387148.0, rms=19.838 (2.661%)
014: dt: 0.0500, sse=11799892.0, rms=19.330 (2.561%)
015: dt: 0.0500, sse=11263957.0, rms=18.854 (2.461%)
016: dt: 0.0500, sse=10774131.0, rms=18.409 (2.363%)
017: dt: 0.0500, sse=10326319.0, rms=17.991 (2.266%)
018: dt: 0.0500, sse=9916784.0, rms=17.601 (2.169%)
019: dt: 0.0500, sse=9542086.0, rms=17.236 (2.073%)
020: dt: 0.0500, sse=9198905.0, rms=16.895 (1.979%)
positioning took 1.1 minutes
mean border=46.7, 144 (43) missing vertices, mean dist 1.1 [0.1 (%0.8)->2.4 (%99.2))]
%11 local maxima, %33 large gradients and %52 min vals, 508 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=9280998.0, rms=16.985
021: dt: 0.0500, sse=8961965.0, rms=16.664 (1.895%)
022: dt: 0.0500, sse=8669373.0, rms=16.363 (1.805%)
023: dt: 0.0500, sse=8399748.0, rms=16.081 (1.725%)
024: dt: 0.0500, sse=8152512.5, rms=15.817 (1.637%)
025: dt: 0.0500, sse=7925165.0, rms=15.571 (1.556%)
026: dt: 0.0500, sse=7715531.5, rms=15.341 (1.481%)
027: dt: 0.0500, sse=7520914.5, rms=15.123 (1.417%)
028: dt: 0.0500, sse=7339081.0, rms=14.917 (1.362%)
029: dt: 0.0500, sse=7168951.0, rms=14.722 (1.310%)
030: dt: 0.0500, sse=7009311.0, rms=14.536 (1.263%)
positioning took 1.1 minutes
mean border=46.7, 192 (34) missing vertices, mean dist 1.0 [0.1 (%6.0)->2.2 (%94.0))]
%11 local maxima, %33 large gradients and %51 min vals, 490 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=7057402.5, rms=14.592
031: dt: 0.5000, sse=5943149.5, rms=13.229 (9.343%)
032: dt: 0.5000, sse=5212775.0, rms=12.244 (7.444%)
033: dt: 0.5000, sse=4659353.0, rms=11.439 (6.575%)
034: dt: 0.5000, sse=4206941.0, rms=10.731 (6.191%)
035: dt: 0.5000, sse=3822028.0, rms=10.091 (5.962%)
036: dt: 0.5000, sse=3468145.5, rms=9.465 (6.207%)
037: dt: 0.5000, sse=3139600.0, rms=8.848 (6.516%)
038: dt: 0.5000, sse=2855222.5, rms=8.276 (6.463%)
039: dt: 0.5000, sse=2620444.0, rms=7.775 (6.058%)
040: dt: 0.5000, sse=2434612.5, rms=7.352 (5.439%)
041: dt: 0.5000, sse=2290014.5, rms=7.007 (4.690%)
042: dt: 0.5000, sse=2191936.5, rms=6.759 (3.536%)
043: dt: 0.5000, sse=2119929.5, rms=6.576 (2.718%)
044: dt: 0.5000, sse=2074137.0, rms=6.452 (1.874%)
045: dt: 0.5000, sse=2034671.5, rms=6.347 (1.640%)
046: dt: 0.5000, sse=2014340.1, rms=6.290 (0.894%)
047: dt: 0.5000, sse=1995277.8, rms=6.238 (0.824%)
rms = 6.21, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1985615.8, rms=6.209 (0.465%)
049: dt: 0.2500, sse=1916020.5, rms=5.980 (3.695%)
050: dt: 0.2500, sse=1889523.4, rms=5.904 (1.268%)
rms = 5.91, time step reduction 2 of 3 to 0.125...
rms = 5.88, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1881647.0, rms=5.878 (0.430%)
positioning took 3.4 minutes
mean border=46.5, 6511 (15) missing vertices, mean dist 0.1 [0.2 (%47.9)->0.7 (%52.1))]
%19 local maxima, %26 large gradients and %47 min vals, 262 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=2057342.4, rms=5.567
052: dt: 0.5000, sse=1970943.0, rms=5.301 (4.777%)
rms = 5.27, time step reduction 1 of 3 to 0.250...
053: dt: 0.5000, sse=1953502.4, rms=5.271 (0.573%)
054: dt: 0.2500, sse=1902185.4, rms=5.051 (4.177%)
rms = 5.00, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1888007.4, rms=5.003 (0.936%)
056: dt: 0.1250, sse=1871654.4, rms=4.938 (1.312%)
rms = 4.94, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1872241.8, rms=4.940 (-0.048%)
positioning took 1.2 minutes
mean border=46.1, 7216 (10) missing vertices, mean dist 0.1 [0.2 (%48.5)->0.5 (%51.5))]
%27 local maxima, %19 large gradients and %45 min vals, 342 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=1912910.2, rms=5.062
rms = 5.33, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1890326.6, rms=4.982 (1.588%)
rms = 5.03, time step reduction 2 of 3 to 0.125...
rms = 4.97, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1887835.4, rms=4.972 (0.203%)
positioning took 0.7 minutes
mean border=45.6, 12312 (9) missing vertices, mean dist 0.1 [0.2 (%45.9)->0.4 (%54.1))]
%29 local maxima, %16 large gradients and %43 min vals, 377 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-6.0.0/0051009/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1935130.2, rms=5.134
060: dt: 0.5000, sse=1880230.0, rms=5.004 (2.548%)
061: dt: 0.5000, sse=1846676.9, rms=4.948 (1.104%)
062: dt: 0.5000, sse=1823478.9, rms=4.874 (1.508%)
rms = 4.83, time step reduction 1 of 3 to 0.250...
063: dt: 0.5000, sse=1806293.5, rms=4.835 (0.803%)
064: dt: 0.2500, sse=1700101.9, rms=4.383 (9.342%)
065: dt: 0.2500, sse=1664823.2, rms=4.250 (3.030%)
rms = 4.24, time step reduction 2 of 3 to 0.125...
066: dt: 0.2500, sse=1663470.9, rms=4.245 (0.123%)
067: dt: 0.1250, sse=1632482.4, rms=4.109 (3.211%)
rms = 4.08, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1624027.6, rms=4.077 (0.773%)
positioning took 1.9 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.area.pial
vertex spacing 1.06 +- 0.49 (0.04-->7.10) (max @ vno 100487 --> 99383)
face area 0.44 +- 0.36 (0.00-->9.56)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 153897 vertices processed
25000 of 153897 vertices processed
50000 of 153897 vertices processed
75000 of 153897 vertices processed
100000 of 153897 vertices processed
125000 of 153897 vertices processed
150000 of 153897 vertices processed
0 of 153897 vertices processed
25000 of 153897 vertices processed
50000 of 153897 vertices processed
75000 of 153897 vertices processed
100000 of 153897 vertices processed
125000 of 153897 vertices processed
150000 of 153897 vertices processed
thickness calculation complete, 382:1879 truncations.
24009 vertices at 0 distance
89196 vertices at 1 distance
101217 vertices at 2 distance
52502 vertices at 3 distance
19092 vertices at 4 distance
5987 vertices at 5 distance
1929 vertices at 6 distance
714 vertices at 7 distance
301 vertices at 8 distance
196 vertices at 9 distance
106 vertices at 10 distance
86 vertices at 11 distance
70 vertices at 12 distance
61 vertices at 13 distance
50 vertices at 14 distance
29 vertices at 15 distance
40 vertices at 16 distance
38 vertices at 17 distance
26 vertices at 18 distance
14 vertices at 19 distance
19 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.thickness
positioning took 18.8 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051009 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-6.0.0/0051009/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
27343 bright wm thresholded.
7958 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.orig...
computing class statistics...
border white:    287611 voxels (1.71%)
border gray      356118 voxels (2.12%)
WM (96.0): 96.3 +- 9.9 [70.0 --> 110.0]
GM (63.0) : 63.4 +- 10.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 48.1 (was 70)
setting MAX_BORDER_WHITE to 112.9 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 37.2 (was 40)
setting MAX_GRAY to 93.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 48.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 26.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-7.8,    GM=59+-7.0
mean inside = 91.2, mean outside = 68.0
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.25 (0.04-->4.25) (max @ vno 69907 --> 71088)
face area 0.34 +- 0.16 (0.00-->6.15)
mean absolute distance = 0.44 +- 0.62
3354 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 80 points - only 0.00% unknown
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
deleting segment 5 with 214 points - only 0.00% unknown
deleting segment 6 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
deleting segment 10 with 45 points - only 0.00% unknown
deleting segment 11 with 29 points - only 0.00% unknown
deleting segment 12 with 30 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
deleting segment 14 with 17 points - only 0.00% unknown
deleting segment 15 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 16 with 2 points - only 0.00% unknown
deleting segment 17 with 6 points - only 0.00% unknown
mean border=73.4, 113 (113) missing vertices, mean dist 0.3 [0.4 (%17.3)->0.5 (%82.7))]
%79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.09-->4.42) (max @ vno 69907 --> 71088)
face area 0.34 +- 0.16 (0.00-->5.83)
mean absolute distance = 0.27 +- 0.42
2893 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2872696.5, rms=8.457
001: dt: 0.5000, sse=1503468.0, rms=5.040 (40.400%)
002: dt: 0.5000, sse=1307097.2, rms=4.362 (13.457%)
003: dt: 0.5000, sse=1285210.5, rms=4.281 (1.852%)
004: dt: 0.5000, sse=1256221.2, rms=4.168 (2.641%)
rms = 4.23, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=983903.6, rms=2.817 (32.413%)
006: dt: 0.2500, sse=901870.9, rms=2.251 (20.100%)
007: dt: 0.2500, sse=875863.7, rms=2.035 (9.611%)
rms = 1.99, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=870069.5, rms=1.989 (2.251%)
009: dt: 0.1250, sse=848803.8, rms=1.791 (9.957%)
rms = 1.76, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=845965.1, rms=1.761 (1.683%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 79 points - only 0.00% unknown
deleting segment 1 with 7 points - only 0.00% unknown
deleting segment 2 with 148 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
deleting segment 4 with 10 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 23 points - only 0.00% unknown
deleting segment 7 with 7 points - only 0.00% unknown
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
mean border=77.4, 99 (34) missing vertices, mean dist -0.2 [0.3 (%77.9)->0.2 (%22.1))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.10-->4.51) (max @ vno 69907 --> 71088)
face area 0.36 +- 0.17 (0.00-->6.36)
mean absolute distance = 0.20 +- 0.31
2907 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1603858.1, rms=5.221
011: dt: 0.5000, sse=1198417.5, rms=3.639 (30.307%)
rms = 4.12, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=976667.4, rms=2.438 (32.987%)
013: dt: 0.2500, sse=910565.8, rms=1.908 (21.744%)
014: dt: 0.2500, sse=880696.4, rms=1.673 (12.329%)
rms = 1.64, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=876633.5, rms=1.643 (1.821%)
016: dt: 0.1250, sse=858821.3, rms=1.413 (13.977%)
rms = 1.39, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=854649.4, rms=1.388 (1.733%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 73 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 75 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 23 points - only 0.00% unknown
deleting segment 8 with 15 points - only 0.00% unknown
deleting segment 9 with 11 points - only 0.00% unknown
deleting segment 10 with 25 points - only 0.00% unknown
deleting segment 11 with 8 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
deleting segment 13 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
deleting segment 15 with 7 points - only 0.00% unknown
mean border=79.2, 80 (21) missing vertices, mean dist -0.1 [0.2 (%63.8)->0.2 (%36.2))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.11-->4.56) (max @ vno 69907 --> 71088)
face area 0.34 +- 0.16 (0.00-->6.21)
mean absolute distance = 0.20 +- 0.29
2506 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=982461.9, rms=2.672
rms = 3.51, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=864233.4, rms=1.768 (33.833%)
019: dt: 0.2500, sse=843324.1, rms=1.401 (20.764%)
rms = 1.39, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=832302.8, rms=1.392 (0.650%)
021: dt: 0.1250, sse=818694.6, rms=1.255 (9.823%)
rms = 1.25, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=818077.2, rms=1.255 (0.031%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 70 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
deleting segment 3 with 46 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
deleting segment 8 with 35 points - only 0.00% unknown
deleting segment 9 with 23 points - only 0.00% unknown
deleting segment 10 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
deleting segment 13 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
deleting segment 15 with 6 points - only 0.00% unknown
mean border=79.8, 110 (17) missing vertices, mean dist -0.0 [0.2 (%53.5)->0.2 (%46.5))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=834694.7, rms=1.543
rms = 2.30, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=796107.7, rms=1.044 (32.386%)
024: dt: 0.2500, sse=793260.4, rms=0.933 (10.573%)
rms = 0.95, time step reduction 2 of 3 to 0.125...
rms = 0.93, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=792230.9, rms=0.928 (0.604%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7376 vertices
erasing segment 1 (vno[0] = 62651)
erasing segment 2 (vno[0] = 104268)
erasing segment 3 (vno[0] = 105375)
erasing segment 4 (vno[0] = 105447)
erasing segment 5 (vno[0] = 110073)
erasing segment 6 (vno[0] = 113280)
erasing segment 7 (vno[0] = 114247)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.area
vertex spacing 0.90 +- 0.26 (0.04-->4.58) (max @ vno 69907 --> 71088)
face area 0.34 +- 0.16 (0.00-->6.18)
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=47.5, 120 (120) missing vertices, mean dist 1.3 [0.2 (%0.0)->3.2 (%100.0))]
% 9 local maxima, %30 large gradients and %57 min vals, 550 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=32885772.0, rms=32.931
001: dt: 0.0500, sse=28229532.0, rms=30.452 (7.529%)
002: dt: 0.0500, sse=24927626.0, rms=28.563 (6.202%)
003: dt: 0.0500, sse=22438164.0, rms=27.052 (5.290%)
004: dt: 0.0500, sse=20460774.0, rms=25.789 (4.670%)
005: dt: 0.0500, sse=18827290.0, rms=24.696 (4.236%)
006: dt: 0.0500, sse=17441410.0, rms=23.730 (3.913%)
007: dt: 0.0500, sse=16239947.0, rms=22.859 (3.670%)
008: dt: 0.0500, sse=15182394.0, rms=22.064 (3.478%)
009: dt: 0.0500, sse=14241462.0, rms=21.332 (3.319%)
010: dt: 0.0500, sse=13396254.0, rms=20.652 (3.188%)
positioning took 1.1 minutes
mean border=47.1, 114 (67) missing vertices, mean dist 1.2 [0.1 (%0.0)->2.7 (%100.0))]
%10 local maxima, %31 large gradients and %54 min vals, 519 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=14508516.0, rms=21.546
011: dt: 0.0500, sse=13730157.0, rms=20.927 (2.872%)
012: dt: 0.0500, sse=13023880.0, rms=20.349 (2.762%)
013: dt: 0.0500, sse=12380421.0, rms=19.808 (2.660%)
014: dt: 0.0500, sse=11793595.0, rms=19.301 (2.559%)
015: dt: 0.0500, sse=11257884.0, rms=18.826 (2.460%)
016: dt: 0.0500, sse=10768318.0, rms=18.382 (2.362%)
017: dt: 0.0500, sse=10319988.0, rms=17.965 (2.269%)
018: dt: 0.0500, sse=9909944.0, rms=17.574 (2.172%)
019: dt: 0.0500, sse=9534148.0, rms=17.209 (2.079%)
020: dt: 0.0500, sse=9189167.0, rms=16.867 (1.990%)
positioning took 1.1 minutes
mean border=47.1, 139 (51) missing vertices, mean dist 1.0 [0.1 (%0.7)->2.4 (%99.3))]
%11 local maxima, %31 large gradients and %54 min vals, 498 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=9297233.0, rms=16.982
021: dt: 0.0500, sse=8976795.0, rms=16.660 (1.898%)
022: dt: 0.0500, sse=8682182.0, rms=16.358 (1.813%)
023: dt: 0.0500, sse=8410439.0, rms=16.074 (1.734%)
024: dt: 0.0500, sse=8160707.5, rms=15.809 (1.650%)
025: dt: 0.0500, sse=7930312.0, rms=15.560 (1.574%)
026: dt: 0.0500, sse=7717190.5, rms=15.326 (1.503%)
027: dt: 0.0500, sse=7519107.0, rms=15.105 (1.440%)
028: dt: 0.0500, sse=7333648.5, rms=14.895 (1.389%)
029: dt: 0.0500, sse=7159821.5, rms=14.696 (1.339%)
030: dt: 0.0500, sse=6996110.0, rms=14.506 (1.296%)
positioning took 1.1 minutes
mean border=47.1, 191 (40) missing vertices, mean dist 0.9 [0.1 (%5.2)->2.2 (%94.8))]
%11 local maxima, %31 large gradients and %53 min vals, 443 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=7022704.0, rms=14.537
031: dt: 0.5000, sse=5880509.5, rms=13.136 (9.638%)
032: dt: 0.5000, sse=5121685.5, rms=12.107 (7.835%)
033: dt: 0.5000, sse=4554151.0, rms=11.273 (6.888%)
034: dt: 0.5000, sse=4105127.2, rms=10.561 (6.310%)
035: dt: 0.5000, sse=3726377.0, rms=9.922 (6.054%)
036: dt: 0.5000, sse=3378295.5, rms=9.297 (6.299%)
037: dt: 0.5000, sse=3048977.0, rms=8.668 (6.764%)
038: dt: 0.5000, sse=2766051.5, rms=8.089 (6.681%)
039: dt: 0.5000, sse=2520591.8, rms=7.552 (6.633%)
040: dt: 0.5000, sse=2329096.0, rms=7.106 (5.909%)
041: dt: 0.5000, sse=2185270.0, rms=6.751 (4.996%)
042: dt: 0.5000, sse=2097803.8, rms=6.525 (3.346%)
043: dt: 0.5000, sse=2035525.5, rms=6.359 (2.551%)
044: dt: 0.5000, sse=2004711.2, rms=6.274 (1.327%)
045: dt: 0.5000, sse=1972874.9, rms=6.186 (1.410%)
046: dt: 0.5000, sse=1953435.2, rms=6.131 (0.888%)
rms = 6.08, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1936899.1, rms=6.083 (0.782%)
048: dt: 0.2500, sse=1865571.1, rms=5.843 (3.936%)
049: dt: 0.2500, sse=1839059.9, rms=5.766 (1.324%)
rms = 5.78, time step reduction 2 of 3 to 0.125...
rms = 5.74, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1831242.9, rms=5.740 (0.449%)
positioning took 3.3 minutes
mean border=46.9, 6361 (16) missing vertices, mean dist 0.1 [0.2 (%46.8)->0.7 (%53.2))]
%18 local maxima, %25 large gradients and %49 min vals, 220 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=2003321.0, rms=5.475
051: dt: 0.5000, sse=1935042.2, rms=5.262 (3.898%)
rms = 5.27, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1854366.2, rms=4.969 (5.559%)
rms = 4.96, time step reduction 2 of 3 to 0.125...
053: dt: 0.2500, sse=1852834.2, rms=4.956 (0.271%)
054: dt: 0.1250, sse=1836942.8, rms=4.890 (1.327%)
rms = 4.90, time step reduction 3 of 3 to 0.062...
055: dt: 0.1250, sse=1840152.1, rms=4.902 (-0.240%)
positioning took 1.1 minutes
mean border=46.5, 6709 (14) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))]
%25 local maxima, %18 large gradients and %48 min vals, 253 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=1866459.2, rms=5.013
rms = 5.32, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1844217.0, rms=4.934 (1.575%)
rms = 5.02, time step reduction 2 of 3 to 0.125...
rms = 4.93, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1842844.9, rms=4.928 (0.126%)
positioning took 0.7 minutes
mean border=45.9, 12575 (14) missing vertices, mean dist 0.1 [0.2 (%45.3)->0.4 (%54.7))]
%28 local maxima, %15 large gradients and %45 min vals, 273 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-6.0.0/0051009/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1883939.4, rms=5.067
058: dt: 0.5000, sse=1823862.8, rms=4.920 (2.902%)
rms = 4.88, time step reduction 1 of 3 to 0.250...
059: dt: 0.5000, sse=1795072.4, rms=4.879 (0.827%)
060: dt: 0.2500, sse=1688971.9, rms=4.443 (8.934%)
061: dt: 0.2500, sse=1652097.2, rms=4.306 (3.075%)
rms = 4.28, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1644070.4, rms=4.276 (0.711%)
063: dt: 0.1250, sse=1610903.5, rms=4.133 (3.334%)
rms = 4.10, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1601391.9, rms=4.098 (0.865%)
positioning took 1.5 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.area.pial
vertex spacing 1.05 +- 0.48 (0.05-->8.47) (max @ vno 71080 --> 71088)
face area 0.43 +- 0.35 (0.00-->8.73)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 154166 vertices processed
25000 of 154166 vertices processed
50000 of 154166 vertices processed
75000 of 154166 vertices processed
100000 of 154166 vertices processed
125000 of 154166 vertices processed
150000 of 154166 vertices processed
0 of 154166 vertices processed
25000 of 154166 vertices processed
50000 of 154166 vertices processed
75000 of 154166 vertices processed
100000 of 154166 vertices processed
125000 of 154166 vertices processed
150000 of 154166 vertices processed
thickness calculation complete, 496:1268 truncations.
26438 vertices at 0 distance
95364 vertices at 1 distance
100122 vertices at 2 distance
48683 vertices at 3 distance
16916 vertices at 4 distance
5409 vertices at 5 distance
1930 vertices at 6 distance
747 vertices at 7 distance
354 vertices at 8 distance
157 vertices at 9 distance
108 vertices at 10 distance
71 vertices at 11 distance
53 vertices at 12 distance
34 vertices at 13 distance
40 vertices at 14 distance
25 vertices at 15 distance
15 vertices at 16 distance
9 vertices at 17 distance
21 vertices at 18 distance
22 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.thickness
positioning took 18.1 minutes
PIDs (16138 16141) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 01:19:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label
Total face volume 332878
Total vertex volume 328569 (mask=0)
#@# 0051009 lh 328569
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 01:19:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label
Total face volume 323359
Total vertex volume 319050 (mask=0)
#@# 0051009 rh 319050
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 01:19:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 

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 = 189
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/ribbon.mgz
mris_volmask took 20.88 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 01:40:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 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 0051009 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 01:40:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 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 0051009 rh pial 

Waiting for PID 17495 of (17495 17498 17501 17504) to complete...
Waiting for PID 17498 of (17495 17498 17501 17504) to complete...
Waiting for PID 17501 of (17495 17498 17501 17504) to complete...
Waiting for PID 17504 of (17495 17498 17501 17504) 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 0051009 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 332878
Total vertex volume 328569 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1668   1166   3097  2.719 0.554     0.095     0.016       10     1.0  bankssts
 1326    855   2840  3.151 0.542     0.124     0.026       18     1.3  caudalanteriorcingulate
 4040   2805   9816  2.912 0.687     0.125     0.028       41     4.5  caudalmiddlefrontal
 2568   1748   4171  2.224 0.582     0.152     0.040       44     4.0  cuneus
  791    565   2300  3.443 0.649     0.126     0.026        7     0.9  entorhinal
 4918   3441  12196  2.884 0.676     0.138     0.040       77     7.6  fusiform
 8163   5545  17945  2.820 0.561     0.118     0.026       90     8.0  inferiorparietal
 4895   3331  12377  3.030 0.701     0.120     0.030       59     6.0  inferiortemporal
 2028   1369   4069  2.509 0.944     0.126     0.038       30     2.7  isthmuscingulate
 7684   5322  14180  2.356 0.644     0.149     0.044      119    13.1  lateraloccipital
 5007   3427  11864  3.139 0.727     0.130     0.037       58     7.9  lateralorbitofrontal
 4480   3260   9030  2.401 0.635     0.150     0.042       79     7.6  lingual
 3181   2242   7656  2.957 0.692     0.140     0.037       69     4.7  medialorbitofrontal
 5070   3577  15349  3.204 0.705     0.135     0.037       76     7.4  middletemporal
 1224    813   2912  2.832 0.844     0.102     0.029       13     1.2  parahippocampal
 2221   1474   4821  2.853 0.608     0.112     0.027       21     2.2  paracentral
 2486   1781   5752  2.710 0.633     0.128     0.031       40     3.0  parsopercularis
 1334    964   3739  2.977 0.677     0.148     0.035       24     2.1  parsorbitalis
 2108   1469   5478  2.936 0.622     0.125     0.032       30     2.5  parstriangularis
 1688   1197   2244  2.074 0.606     0.137     0.042       18     2.9  pericalcarine
 7000   4704  13247  2.430 0.697     0.113     0.029       68     7.7  postcentral
 2109   1425   4217  2.622 0.698     0.109     0.019       24     1.5  posteriorcingulate
 6983   4653  15311  2.823 0.660     0.116     0.029       68     8.0  precentral
 7717   5276  16134  2.745 0.598     0.116     0.026       81     8.1  precuneus
 1782   1174   3610  2.814 0.708     0.118     0.029       24     2.3  rostralanteriorcingulate
 9782   6712  22821  2.810 0.624     0.129     0.034      150    13.9  rostralmiddlefrontal
11834   8109  29948  3.100 0.707     0.124     0.031      130    14.5  superiorfrontal
10573   7168  21976  2.604 0.601     0.123     0.030      121    12.4  superiorparietal
 6473   4308  14570  2.988 0.647     0.108     0.025       66     6.8  superiortemporal
 8021   5482  19680  2.995 0.640     0.122     0.031       94    10.2  supramarginal
  543    361   1638  3.076 0.532     0.160     0.044       15     1.0  frontalpole
  769    557   2883  3.549 0.806     0.129     0.031       10     1.0  temporalpole
  813    530   1759  2.784 0.485     0.100     0.023        9     0.7  transversetemporal
 4200   2863   8920  3.096 0.714     0.131     0.050       84     9.6  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 0051009 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 332878
Total vertex volume 328569 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1668   1169   3097  2.719 0.554     0.157     0.045       35     3.6  bankssts
 1326   1065   2840  3.151 0.542     0.187     0.060       38     3.7  caudalanteriorcingulate
 4040   3867   9816  2.912 0.687     0.178     0.047       91     9.0  caudalmiddlefrontal
 2568   2112   4171  2.224 0.582     0.163     0.044       41     5.1  cuneus
  791    811   2300  3.443 0.649     0.182     0.046       18     1.7  entorhinal
 4918   4788  12196  2.884 0.676     0.195     0.058      104    13.5  fusiform
 8163   6992  17945  2.820 0.561     0.152     0.038      125    14.3  inferiorparietal
 4895   4544  12377  3.030 0.701     0.182     0.052       96    12.2  inferiortemporal
 2028   1837   4069  2.509 0.944     0.176     0.048       36     4.4  isthmuscingulate
 7684   6583  14180  2.356 0.644     0.167     0.044      153    16.1  lateraloccipital
 5007   4234  11864  3.139 0.727     0.184     0.056      129    13.8  lateralorbitofrontal
 4480   4389   9030  2.401 0.635     0.197     0.056       83    12.2  lingual
 3181   3025   7656  2.957 0.692     0.203     0.059       78     9.1  medialorbitofrontal
 5070   5757  15349  3.204 0.705     0.191     0.045       83    11.1  middletemporal
 1224   1271   2912  2.832 0.844     0.195     0.057       18     3.7  parahippocampal
 2221   1855   4821  2.853 0.608     0.162     0.046       51     4.6  paracentral
 2486   2519   5752  2.710 0.633     0.211     0.060       92     8.0  parsopercularis
 1334   1466   3739  2.977 0.677     0.213     0.052       37     3.1  parsorbitalis
 2108   2216   5478  2.936 0.622     0.207     0.050       40     5.6  parstriangularis
 1688   1025   2244  2.074 0.606     0.137     0.044       28     3.4  pericalcarine
 7000   6225  13247  2.430 0.697     0.156     0.039       80    13.2  postcentral
 2109   1843   4217  2.622 0.698     0.198     0.056       58     5.9  posteriorcingulate
 6983   5903  15311  2.823 0.660     0.154     0.042      119    13.4  precentral
 7717   6252  16134  2.745 0.598     0.159     0.044      136    15.6  precuneus
 1782   1563   3610  2.814 0.708     0.214     0.068       42     6.0  rostralanteriorcingulate
 9782   9125  22821  2.810 0.624     0.183     0.047      181    22.1  rostralmiddlefrontal
11834  10990  29948  3.100 0.707     0.189     0.055      233    31.7  superiorfrontal
10573   9174  21976  2.604 0.601     0.154     0.037      141    17.4  superiorparietal
 6473   5631  14570  2.988 0.647     0.175     0.048      114    15.2  superiortemporal
 8021   7441  19680  2.995 0.640     0.182     0.049      154    19.1  supramarginal
  543    710   1638  3.076 0.532     0.225     0.045        7     1.3  frontalpole
  769   1067   2883  3.549 0.806     0.205     0.044        8     1.6  temporalpole
  813    800   1759  2.784 0.485     0.182     0.050       10     2.0  transversetemporal
 4200   2926   8920  3.096 0.714     0.181     0.067      122    12.7  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 0051009 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 323359
Total vertex volume 319050 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1111    786   1978  2.572 0.579     0.105     0.021        9     0.8  bankssts
  994    651   2174  2.675 1.033     0.114     0.019       12     0.8  caudalanteriorcingulate
 3409   2358   7988  2.893 0.603     0.119     0.029       39     3.9  caudalmiddlefrontal
 2910   1935   5131  2.205 0.573     0.146     0.042       47     4.6  cuneus
  740    525   2158  3.310 0.722     0.114     0.030        6     1.1  entorhinal
 4641   3180  10365  2.823 0.576     0.131     0.031       67     5.6  fusiform
 8084   5505  18009  2.799 0.572     0.119     0.027       91     8.5  inferiorparietal
 5511   3745  13417  2.963 0.710     0.128     0.036       84     7.8  inferiortemporal
 1822   1209   3364  2.298 0.962     0.113     0.024       25     1.7  isthmuscingulate
 8424   5698  16462  2.525 0.600     0.136     0.036      110    11.7  lateraloccipital
 4902   3318  10845  2.962 0.776     0.131     0.043       72     7.9  lateralorbitofrontal
 5455   3730  10102  2.446 0.674     0.147     0.043       87     9.4  lingual
 3398   2277   7088  2.833 0.683     0.122     0.033       51     4.1  medialorbitofrontal
 5734   4066  15137  2.997 0.696     0.128     0.031       83     7.5  middletemporal
 1052    749   2410  2.976 0.571     0.119     0.029       14     1.1  parahippocampal
 2141   1413   4816  2.982 0.597     0.113     0.032       17     2.3  paracentral
 2179   1465   4777  2.792 0.644     0.116     0.025       24     2.0  parsopercularis
 1677   1087   4200  3.171 0.724     0.118     0.032       24     2.1  parsorbitalis
 2737   1872   6575  2.950 0.618     0.131     0.033       39     3.5  parstriangularis
 2516   1726   2868  1.863 0.472     0.126     0.035       26     3.3  pericalcarine
 7758   5173  14307  2.382 0.712     0.112     0.031       83     9.7  postcentral
 1882   1284   3412  2.509 0.768     0.122     0.026       28     1.8  posteriorcingulate
 8120   5406  16816  2.709 0.642     0.118     0.032       91    10.7  precentral
 8520   5828  17554  2.707 0.585     0.123     0.030       94    10.0  precuneus
  937    676   2057  2.685 0.673     0.147     0.048       19     1.7  rostralanteriorcingulate
10054   6935  23022  2.803 0.633     0.128     0.032      143    13.0  rostralmiddlefrontal
13240   9098  32478  3.035 0.641     0.124     0.032      154    16.2  superiorfrontal
 8921   5899  18109  2.603 0.613     0.120     0.029       97    10.2  superiorparietal
 5675   3779  14352  3.272 0.658     0.102     0.022       49     5.0  superiortemporal
 6166   4274  14205  2.935 0.541     0.130     0.031       81     7.4  supramarginal
  528    329   1461  3.094 0.788     0.160     0.055       12     1.1  frontalpole
  688    492   2683  3.547 0.759     0.119     0.035       10     0.9  temporalpole
  578    364   1161  2.780 0.622     0.127     0.034        8     0.7  transversetemporal
 3797   2567   7503  3.059 0.742     0.130     0.043       47     7.0  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 0051009 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 323359
Total vertex volume 319050 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1111    768   1978  2.572 0.579     0.156     0.051       20     2.7  bankssts
  994    897   2174  2.675 1.033     0.173     0.048       29     2.2  caudalanteriorcingulate
 3409   3086   7988  2.893 0.603     0.157     0.041       48     6.3  caudalmiddlefrontal
 2910   2673   5131  2.205 0.573     0.170     0.043       41     6.1  cuneus
  740    750   2158  3.310 0.722     0.166     0.041       15     1.5  entorhinal
 4641   4204  10365  2.823 0.576     0.183     0.049       99    11.1  fusiform
 8084   7126  18009  2.799 0.572     0.158     0.037      102    13.6  inferiorparietal
 5511   5189  13417  2.963 0.710     0.179     0.048      101    12.6  inferiortemporal
 1822   1611   3364  2.298 0.962     0.160     0.041       27     3.2  isthmuscingulate
 8424   7251  16462  2.525 0.600     0.161     0.041      141    16.3  lateraloccipital
 4902   4030  10845  2.962 0.776     0.183     0.058      121    13.2  lateralorbitofrontal
 5455   4817  10102  2.446 0.674     0.182     0.053      142    13.8  lingual
 3398   2934   7088  2.833 0.683     0.186     0.056       85     8.8  medialorbitofrontal
 5734   6044  15137  2.997 0.696     0.195     0.050      102    14.7  middletemporal
 1052    933   2410  2.976 0.571     0.185     0.056       21     2.6  parahippocampal
 2141   1761   4816  2.982 0.597     0.157     0.043       33     4.2  paracentral
 2179   1999   4777  2.792 0.644     0.197     0.061       39     6.6  parsopercularis
 1677   1551   4200  3.171 0.724     0.164     0.047       26     4.0  parsorbitalis
 2737   2677   6575  2.950 0.618     0.205     0.054       49     7.8  parstriangularis
 2516   1490   2868  1.863 0.472     0.117     0.032       55     3.4  pericalcarine
 7758   6669  14307  2.382 0.712     0.154     0.039       95    14.5  postcentral
 1882   1467   3412  2.509 0.768     0.166     0.045       46     4.0  posteriorcingulate
 8120   6632  16816  2.709 0.642     0.152     0.047      140    18.2  precentral
 8520   6938  17554  2.707 0.585     0.164     0.046      154    18.9  precuneus
  937    896   2057  2.685 0.673     0.219     0.067      100     2.9  rostralanteriorcingulate
10054   9202  23022  2.803 0.633     0.178     0.048      197    22.1  rostralmiddlefrontal
13240  12053  32478  3.035 0.641     0.179     0.049      260    31.1  superiorfrontal
 8921   7554  18109  2.603 0.613     0.150     0.036      114    14.4  superiorparietal
 5675   5148  14352  3.272 0.658     0.179     0.050       97    13.3  superiortemporal
 6166   5467  14205  2.935 0.541     0.179     0.048      119    14.1  supramarginal
  528    597   1461  3.094 0.788     0.211     0.048        7     1.2  frontalpole
  688    980   2683  3.547 0.759     0.220     0.052        7     1.8  temporalpole
  578    484   1161  2.780 0.622     0.182     0.059        8     1.7  transversetemporal
 3797   2434   7503  3.059 0.742     0.188     0.216      441    56.6  insula
PIDs (17495 17498 17501 17504) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 01:41:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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 01:41:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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 17587 of (17587 17590) to complete...
Waiting for PID 17590 of (17587 17590) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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...
3 labels changed using aseg
relabeling using gibbs priors...
000:  10173 changed, 153897 examined...
001:   2334 changed, 39471 examined...
002:    706 changed, 12265 examined...
003:    290 changed, 3937 examined...
004:    145 changed, 1699 examined...
005:     75 changed, 828 examined...
006:     29 changed, 421 examined...
007:     17 changed, 176 examined...
008:      6 changed, 89 examined...
009:      1 changed, 21 examined...
010:      0 changed, 7 examined...
0 labels changed using aseg
000: 305 total segments, 218 labels (2651 vertices) changed
001: 99 total segments, 11 labels (34 vertices) changed
002: 88 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 31 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1324 vertices marked for relabeling...
1324 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 22 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 719 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1 labels changed using aseg
relabeling using gibbs priors...
000:  10027 changed, 154166 examined...
001:   2303 changed, 39477 examined...
002:    728 changed, 12357 examined...
003:    323 changed, 4190 examined...
004:    133 changed, 1835 examined...
005:     68 changed, 775 examined...
006:     36 changed, 398 examined...
007:     15 changed, 203 examined...
008:      3 changed, 81 examined...
009:      1 changed, 22 examined...
010:      0 changed, 7 examined...
1 labels changed using aseg
000: 289 total segments, 199 labels (3528 vertices) changed
001: 99 total segments, 10 labels (29 vertices) changed
002: 89 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 32 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1296 vertices marked for relabeling...
1296 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 22 seconds.
PIDs (17587 17590) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 01:42:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 01:42:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 rh white 

Waiting for PID 17669 of (17669 17672) to complete...
Waiting for PID 17672 of (17669 17672) 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 0051009 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 332878
Total vertex volume 328569 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1700   1192   4109  2.934 0.650     0.143     0.037       27     3.0  G&S_frontomargin
 1909   1365   4282  2.611 0.691     0.161     0.043       30     3.4  G&S_occipital_inf
 1774   1118   3662  2.635 0.604     0.109     0.029       16     1.8  G&S_paracentral
 1738   1207   4151  2.818 0.619     0.132     0.032       24     2.0  G&S_subcentral
  860    604   2304  2.785 0.625     0.156     0.039       28     1.4  G&S_transv_frontopol
 2773   1883   5646  2.959 0.634     0.115     0.025       29     3.0  G&S_cingul-Ant
 1583   1054   3201  2.995 0.533     0.102     0.022       14     1.2  G&S_cingul-Mid-Ant
 1580   1077   3281  2.855 0.631     0.105     0.020       13     1.1  G&S_cingul-Mid-Post
  721    521   2369  3.207 0.565     0.151     0.046       13     1.3  G_cingul-Post-dorsal
  443    275   1091  3.007 0.751     0.133     0.044        7     0.7  G_cingul-Post-ventral
 2148   1478   3646  2.123 0.559     0.159     0.046       41     3.8  G_cuneus
 1496   1065   4155  2.783 0.698     0.153     0.044       37     2.7  G_front_inf-Opercular
  677    474   1953  2.872 0.597     0.152     0.034       15     1.0  G_front_inf-Orbital
 1079    753   3350  3.096 0.613     0.133     0.040       19     1.5  G_front_inf-Triangul
 5772   3931  17154  3.047 0.697     0.145     0.041      111     9.7  G_front_middle
 7641   5208  22368  3.265 0.694     0.135     0.038      110    11.3  G_front_sup
  895    639   2128  3.117 0.741     0.148     0.050       16     1.6  G_Ins_lg&S_cent_ins
  919    617   2582  3.144 1.010     0.163     0.073       25     3.3  G_insular_short
 2580   1695   6642  2.834 0.545     0.153     0.050       52     4.5  G_occipital_middle
 1715   1153   3174  2.239 0.593     0.132     0.038       24     2.6  G_occipital_sup
 1936   1348   5362  3.042 0.620     0.152     0.049       37     3.9  G_oc-temp_lat-fusifor
 2888   2111   6497  2.417 0.659     0.168     0.053       66     6.1  G_oc-temp_med-Lingual
 1664   1147   4913  3.256 0.794     0.125     0.037       25     2.3  G_oc-temp_med-Parahip
 2964   2047   9111  3.161 0.772     0.146     0.047       53     5.8  G_orbital
 3227   2146   9293  3.052 0.630     0.130     0.033       51     4.0  G_pariet_inf-Angular
 3773   2558  11058  3.179 0.665     0.134     0.039       58     5.8  G_pariet_inf-Supramar
 4136   2847  10758  2.832 0.647     0.133     0.035       55     5.4  G_parietal_sup
 2606   1710   5791  2.536 0.685     0.124     0.038       33     3.7  G_postcentral
 2375   1586   7219  3.192 0.701     0.128     0.039       33     3.4  G_precentral
 3488   2489  10045  2.963 0.627     0.139     0.037       58     5.0  G_precuneus
 1159    831   3447  3.003 0.795     0.166     0.056       41     2.6  G_rectus
  308    195    702  3.218 0.725     0.099     0.030        4     0.3  G_subcallosal
  552    368   1430  2.787 0.501     0.115     0.029        8     0.7  G_temp_sup-G_T_transv
 2178   1461   6199  2.955 0.762     0.127     0.033       38     3.2  G_temp_sup-Lateral
  918    626   2230  3.045 0.707     0.079     0.015        3     0.6  G_temp_sup-Plan_polar
 1569   1072   3427  2.998 0.512     0.110     0.024       14     1.5  G_temp_sup-Plan_tempo
 2138   1459   6956  3.228 0.700     0.134     0.039       39     3.1  G_temporal_inf
 2930   2094  11031  3.496 0.607     0.151     0.046       58     5.4  G_temporal_middle
  329    237    590  2.615 0.581     0.108     0.019        2     0.3  Lat_Fis-ant-Horizont
  333    234    541  2.460 0.547     0.111     0.018        2     0.3  Lat_Fis-ant-Vertical
 1489    995   2295  2.765 0.459     0.109     0.021       11     1.2  Lat_Fis-post
 1797   1300   3089  2.074 0.690     0.168     0.060       35     4.2  Pole_occipital
 1648   1204   6414  3.538 0.721     0.148     0.039       29     2.6  Pole_temporal
 2196   1554   3054  2.206 0.650     0.135     0.037       25     3.3  S_calcarine
 2894   1970   3896  2.185 0.593     0.099     0.022       15     2.7  S_central
 1288    855   2107  2.561 0.654     0.087     0.014        6     0.8  S_cingul-Marginalis
  862    584   1561  3.231 0.550     0.095     0.019        4     0.7  S_circular_insula_ant
 1529   1043   2854  3.218 0.522     0.092     0.016        6     1.1  S_circular_insula_inf
 2183   1493   3721  2.932 0.545     0.106     0.037       38     4.0  S_circular_insula_sup
  841    604   1924  2.986 0.666     0.114     0.024        8     0.7  S_collat_transv_ant
  585    396    923  2.509 0.550     0.117     0.027        4     0.7  S_collat_transv_post
 2527   1734   4626  2.698 0.486     0.103     0.020       17     1.9  S_front_inf
 1364    980   2524  2.585 0.478     0.104     0.022       10     1.1  S_front_middle
 3806   2664   7209  2.664 0.547     0.109     0.022       25     3.5  S_front_sup
  420    307    867  2.770 0.688     0.112     0.020        3     0.3  S_interm_prim-Jensen
 3439   2344   5493  2.498 0.417     0.103     0.020       24     2.8  S_intrapariet&P_trans
 1080    721   1298  1.969 0.442     0.095     0.020        5     0.9  S_oc_middle&Lunatus
 1734   1179   2540  2.347 0.384     0.116     0.025       16     1.8  S_oc_sup&transversal
 1034    703   1431  2.399 0.438     0.116     0.022        9     1.0  S_occipital_ant
  968    657   1821  2.760 0.487     0.119     0.032       10     1.2  S_oc-temp_lat
 2534   1766   4208  2.482 0.650     0.111     0.024       21     2.5  S_oc-temp_med&Lingual
  489    347    855  2.411 0.521     0.129     0.032        5     0.6  S_orbital_lateral
  691    486   1281  2.797 0.732     0.133     0.034        7     1.1  S_orbital_med-olfact
 2013   1376   4385  3.206 0.648     0.130     0.032       20     2.8  S_orbital-H_Shaped
 3408   2269   5648  2.692 0.496     0.111     0.023       28     3.1  S_parieto_occipital
 1900   1194   2243  2.219 0.927     0.107     0.022       26     1.2  S_pericallosal
 4093   2734   6729  2.588 0.523     0.101     0.021       27     3.4  S_postcentral
 1818   1229   2871  2.576 0.538     0.108     0.022       13     1.6  S_precentral-inf-part
 1221    809   1943  2.698 0.544     0.109     0.021        8     1.1  S_precentral-sup-part
 1145    813   2268  2.869 0.560     0.126     0.019       13     1.0  S_suborbital
 1581   1069   2480  2.559 0.482     0.107     0.020        8     1.4  S_subparietal
 2184   1454   3395  2.651 0.547     0.103     0.019       11     1.9  S_temporal_inf
 6726   4632  11990  2.760 0.565     0.108     0.022       53     5.8  S_temporal_sup
  519    338    775  2.729 0.403     0.082     0.014        2     0.3  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051009 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 323359
Total vertex volume 319050 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1132    753   2419  2.818 0.758     0.146     0.040       19     2.0  G&S_frontomargin
 1346    922   3192  2.993 0.656     0.160     0.044       24     2.5  G&S_occipital_inf
 1497    915   3068  2.603 0.729     0.143     0.071       29     4.5  G&S_paracentral
 1513   1005   3511  2.859 0.599     0.126     0.037       21     2.1  G&S_subcentral
 1352    941   3949  3.131 0.557     0.150     0.048       27     2.4  G&S_transv_frontopol
 3437   2404   7405  2.924 0.637     0.119     0.029       40     4.2  G&S_cingul-Ant
 1659   1115   3674  3.112 0.570     0.112     0.023       13     1.6  G&S_cingul-Mid-Ant
 1652   1131   3381  2.918 0.554     0.115     0.027       15     1.8  G&S_cingul-Mid-Post
  793    517   2153  2.959 0.654     0.149     0.036       19     1.1  G_cingul-Post-dorsal
  317    216    860  2.854 0.777     0.145     0.036        6     0.4  G_cingul-Post-ventral
 2592   1765   4501  2.085 0.580     0.147     0.044       43     4.1  G_cuneus
 1351    902   3642  2.907 0.599     0.134     0.032       22     1.5  G_front_inf-Opercular
  531    379   1543  2.757 0.586     0.160     0.049       12     1.1  G_front_inf-Orbital
 1342    899   3794  3.131 0.583     0.148     0.042       25     2.0  G_front_inf-Triangul
 4423   3103  13768  3.094 0.617     0.147     0.041       90     7.1  G_front_middle
 8567   5903  24257  3.144 0.646     0.132     0.037      122    11.4  G_front_sup
  674    461   1632  3.304 0.839     0.135     0.048       11     1.3  G_Ins_lg&S_cent_ins
 1110    726   2211  2.761 0.823     0.170     0.076       25     3.5  G_insular_short
 2376   1580   6353  2.851 0.548     0.147     0.040       46     3.6  G_occipital_middle
 1850   1160   3387  2.441 0.486     0.130     0.033       24     2.2  G_occipital_sup
 1772   1185   4502  2.857 0.588     0.141     0.037       36     2.1  G_oc-temp_lat-fusifor
 3613   2461   7403  2.478 0.702     0.156     0.046       59     6.5  G_oc-temp_med-Lingual
 1441   1018   4193  3.259 0.680     0.127     0.034       20     2.0  G_oc-temp_med-Parahip
 3256   2173   9279  3.107 0.870     0.142     0.052       68     6.7  G_orbital
 2859   1973   8698  3.121 0.589     0.138     0.034       49     3.6  G_pariet_inf-Angular
 3266   2274   8716  2.926 0.530     0.139     0.035       56     4.6  G_pariet_inf-Supramar
 2838   1899   7615  2.898 0.684     0.135     0.035       43     4.1  G_parietal_sup
 2774   1826   6162  2.507 0.725     0.127     0.038       37     3.7  G_postcentral
 3144   2082   8449  2.890 0.685     0.131     0.042       50     5.4  G_precentral
 3560   2441   9243  2.893 0.557     0.137     0.038       55     5.3  G_precuneus
  733    506   1778  2.568 0.647     0.152     0.047       18     1.3  G_rectus
  713    446   1452  3.056 1.054     0.121     0.064       14     1.2  G_subcallosal
  399    250    905  2.735 0.716     0.149     0.043        8     0.6  G_temp_sup-G_T_transv
 1913   1259   6539  3.612 0.672     0.124     0.033       26     2.3  G_temp_sup-Lateral
  991    653   2297  3.093 0.575     0.073     0.016        4     0.8  G_temp_sup-Plan_polar
  818    557   1697  2.957 0.436     0.097     0.023        5     0.7  G_temp_sup-Plan_tempo
 2924   1989   8698  3.082 0.798     0.144     0.046       64     5.5  G_temporal_inf
 3172   2280   9892  3.083 0.720     0.143     0.041       63     5.4  G_temporal_middle
  416    291    590  2.387 0.507     0.093     0.016        2     0.3  Lat_Fis-ant-Horizont
  236    165    386  2.651 0.537     0.114     0.017        1     0.2  Lat_Fis-ant-Vertical
 1414    949   2325  3.050 0.490     0.102     0.018        8     1.0  Lat_Fis-post
 3690   2464   6356  2.226 0.588     0.142     0.047       62     6.6  Pole_occipital
 1919   1305   6632  3.420 0.768     0.142     0.039       36     3.1  Pole_temporal
 2805   1912   3753  2.217 0.643     0.122     0.029       28     3.2  S_calcarine
 3191   2152   4034  2.173 0.633     0.088     0.015       13     2.0  S_central
 1554   1103   2913  2.636 0.518     0.108     0.022       12     1.3  S_cingul-Marginalis
  804    552   1428  3.147 0.633     0.100     0.020        3     0.7  S_circular_insula_ant
 1266    858   2040  2.963 0.604     0.094     0.016        7     0.9  S_circular_insula_inf
 1573   1070   2749  3.081 0.664     0.108     0.023        8     1.6  S_circular_insula_sup
 1271    871   2320  2.742 0.498     0.105     0.019       10     0.9  S_collat_transv_ant
  493    332    630  2.434 0.444     0.118     0.020        3     0.5  S_collat_transv_post
 2094   1425   3478  2.661 0.573     0.105     0.021       16     1.6  S_front_inf
 2771   1873   5108  2.593 0.522     0.117     0.026       30     2.9  S_front_middle
 3139   2152   5213  2.593 0.499     0.098     0.019       16     2.6  S_front_sup
  176    128    428  3.048 0.408     0.102     0.017        1     0.1  S_interm_prim-Jensen
 3337   2263   5773  2.520 0.536     0.111     0.023       27     3.0  S_intrapariet&P_trans
 1453   1004   2153  2.234 0.517     0.116     0.024       11     1.4  S_oc_middle&Lunatus
 1451    984   2306  2.387 0.438     0.108     0.026       10     1.4  S_oc_sup&transversal
  924    649   1844  2.782 0.501     0.110     0.021        6     0.8  S_occipital_ant
 1402    953   2672  2.857 0.481     0.132     0.031       14     1.9  S_oc-temp_lat
 2063   1477   3461  2.728 0.574     0.107     0.021       12     1.7  S_oc-temp_med&Lingual
  755    507   1192  2.718 0.489     0.097     0.018        3     0.7  S_orbital_lateral
  630    444   1017  2.536 0.552     0.120     0.022        6     0.5  S_orbital_med-olfact
 1901   1294   3913  3.118 0.614     0.118     0.026       15     2.0  S_orbital-H_Shaped
 3542   2319   5578  2.516 0.531     0.108     0.023       27     3.2  S_parieto_occipital
 1725   1084   1354  1.518 0.549     0.105     0.018       23     1.0  S_pericallosal
 4134   2802   6623  2.521 0.582     0.104     0.021       28     3.7  S_postcentral
 2034   1368   3220  2.559 0.556     0.105     0.020       14     1.7  S_precentral-inf-part
 1555   1060   2688  2.684 0.511     0.105     0.022       11     1.4  S_precentral-sup-part
  619    425   1020  2.766 0.509     0.126     0.025        8     0.6  S_suborbital
 1829   1278   3430  2.708 0.495     0.115     0.024       16     1.7  S_subparietal
 1539   1072   2350  2.564 0.489     0.110     0.019        8     1.4  S_temporal_inf
 6626   4533  11231  2.744 0.560     0.101     0.019       42     5.1  S_temporal_sup
  301    215    625  3.073 0.614     0.083     0.016        1     0.2  S_temporal_transverse
PIDs (17669 17672) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 01:43:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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 01:43:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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 17765 of (17765 17768) to complete...
Waiting for PID 17768 of (17765 17768) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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...
1491 labels changed using aseg
relabeling using gibbs priors...
000:   2091 changed, 153897 examined...
001:    455 changed, 9845 examined...
002:    119 changed, 2584 examined...
003:     44 changed, 694 examined...
004:     19 changed, 264 examined...
005:      9 changed, 106 examined...
006:      6 changed, 57 examined...
007:      1 changed, 29 examined...
008:      1 changed, 7 examined...
009:      1 changed, 8 examined...
010:      2 changed, 7 examined...
011:      2 changed, 11 examined...
012:      0 changed, 10 examined...
115 labels changed using aseg
000: 51 total segments, 18 labels (177 vertices) changed
001: 34 total segments, 1 labels (2 vertices) changed
002: 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...
1017 vertices marked for relabeling...
1017 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051009 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...
1352 labels changed using aseg
relabeling using gibbs priors...
000:   2278 changed, 154166 examined...
001:    534 changed, 10351 examined...
002:    138 changed, 3049 examined...
003:     53 changed, 825 examined...
004:     26 changed, 333 examined...
005:     17 changed, 160 examined...
006:      8 changed, 94 examined...
007:      5 changed, 43 examined...
008:      4 changed, 30 examined...
009:      2 changed, 18 examined...
010:      0 changed, 12 examined...
117 labels changed using aseg
000: 63 total segments, 30 labels (198 vertices) changed
001: 34 total segments, 1 labels (2 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 10 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1000 vertices marked for relabeling...
1000 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 18 seconds.
PIDs (17765 17768) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 01:43:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 01:43:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 rh white 

Waiting for PID 17830 of (17830 17833) to complete...
Waiting for PID 17833 of (17830 17833) 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 0051009 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 332878
Total vertex volume 328569 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1994   1305   3882  3.085 0.545     0.112     0.023       22     1.6  caudalanteriorcingulate
 4347   2999  10443  2.900 0.680     0.126     0.029       45     4.9  caudalmiddlefrontal
 3792   2566   6326  2.341 0.601     0.139     0.037       56     5.4  cuneus
  672    480   1976  3.420 0.620     0.118     0.024        5     0.7  entorhinal
 4620   3197  11027  2.885 0.657     0.135     0.040       69     7.1  fusiform
 8044   5458  17752  2.821 0.581     0.119     0.027       90     8.1  inferiorparietal
 4734   3282  12631  3.040 0.712     0.125     0.031       61     5.9  inferiortemporal
 2003   1354   4042  2.523 0.937     0.128     0.038       30     2.7  isthmuscingulate
 7657   5290  13944  2.331 0.630     0.149     0.044      119    13.1  lateraloccipital
 5304   3645  13551  3.179 0.727     0.138     0.042       74     9.3  lateralorbitofrontal
 4600   3351   9280  2.392 0.641     0.151     0.042       80     7.9  lingual
 2631   1862   6695  2.942 0.711     0.143     0.041       61     4.4  medialorbitofrontal
 6837   4775  18811  3.103 0.705     0.129     0.033       92     9.1  middletemporal
 1304    873   3117  2.873 0.866     0.104     0.030       14     1.2  parahippocampal
 2541   1700   5506  2.847 0.588     0.112     0.027       23     2.5  paracentral
 2356   1669   5296  2.684 0.637     0.132     0.032       41     3.0  parsopercularis
 1387    965   3387  2.974 0.689     0.132     0.028       21     1.6  parsorbitalis
 2424   1703   5873  2.905 0.606     0.115     0.029       27     2.5  parstriangularis
 1698   1193   2226  2.072 0.602     0.135     0.041       18     2.9  pericalcarine
 8024   5380  15023  2.454 0.690     0.113     0.029       75     8.7  postcentral
 2191   1490   4415  2.607 0.714     0.111     0.020       25     1.6  posteriorcingulate
 6882   4603  15144  2.827 0.656     0.117     0.029       69     7.9  precentral
 7497   5137  16134  2.753 0.603     0.119     0.027       83     8.0  precuneus
 2419   1615   4729  2.832 0.668     0.121     0.028       31     2.9  rostralanteriorcingulate
 7229   4938  17222  2.810 0.627     0.132     0.035      116    10.7  rostralmiddlefrontal
13350   9183  34097  3.061 0.706     0.126     0.032      168    16.9  superiorfrontal
 8452   5753  18014  2.626 0.589     0.122     0.030       97    10.0  superiorparietal
 8733   5876  20404  3.017 0.674     0.109     0.026       91     9.5  superiortemporal
 7468   5109  18297  3.001 0.634     0.121     0.030       85     9.1  supramarginal
  789    512   1711  2.776 0.493     0.099     0.024        9     0.7  transversetemporal
 3501   2409   7614  3.124 0.719     0.129     0.048       73     8.1  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0051009 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 323359
Total vertex volume 319050 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1145    748   2493  2.709 1.010     0.119     0.022       15     1.0  caudalanteriorcingulate
 3534   2447   8170  2.868 0.621     0.118     0.028       39     4.1  caudalmiddlefrontal
 3624   2415   6260  2.269 0.574     0.140     0.039       53     5.3  cuneus
  636    457   1875  3.275 0.719     0.112     0.027        5     0.9  entorhinal
 4133   2841   9033  2.816 0.574     0.127     0.029       56     4.3  fusiform
 7894   5393  17737  2.804 0.572     0.120     0.027       91     8.4  inferiorparietal
 6047   4106  14739  2.945 0.699     0.131     0.037       95     9.1  inferiortemporal
 1858   1236   3453  2.314 0.950     0.113     0.022       25     1.6  isthmuscingulate
 8455   5726  16504  2.511 0.600     0.136     0.037      111    11.8  lateraloccipital
 5212   3533  11955  2.929 0.826     0.138     0.046       84     9.6  lateralorbitofrontal
 5343   3649   9897  2.446 0.666     0.147     0.042       87     9.3  lingual
 2453   1654   5141  2.776 0.726     0.130     0.039       43     3.3  medialorbitofrontal
 6713   4721  16630  2.926 0.704     0.125     0.030       92     8.4  middletemporal
 1157    822   2676  3.041 0.603     0.122     0.032       16     1.4  parahippocampal
 2265   1493   5104  2.987 0.598     0.112     0.032       18     2.4  paracentral
 2587   1725   5601  2.804 0.645     0.117     0.026       29     2.5  parsopercularis
 1538   1017   3603  2.999 0.676     0.131     0.037       26     2.4  parsorbitalis
 2526   1727   5876  2.940 0.598     0.128     0.030       33     3.0  parstriangularis
 2479   1704   2808  1.848 0.469     0.126     0.034       25     3.1  pericalcarine
 8608   5751  15960  2.406 0.701     0.113     0.031       92    10.9  postcentral
 2058   1399   3819  2.568 0.763     0.125     0.028       30     2.3  posteriorcingulate
 7795   5193  16196  2.711 0.634     0.119     0.032       90    10.3  precentral
 8558   5847  17724  2.696 0.586     0.123     0.030       95    10.0  precuneus
 1277    900   2567  2.728 0.668     0.138     0.044       22     2.0  rostralanteriorcingulate
 6938   4742  16077  2.841 0.652     0.125     0.031       94     8.2  rostralmiddlefrontal
16955  11643  41275  3.003 0.631     0.123     0.031      204    20.5  superiorfrontal
 7187   4738  15006  2.632 0.634     0.119     0.028       78     8.2  superiorparietal
 7251   4885  18888  3.259 0.679     0.103     0.024       64     6.6  superiortemporal
 5992   4150  13825  2.936 0.545     0.130     0.031       79     7.3  supramarginal
  576    361   1164  2.792 0.632     0.128     0.034        8     0.7  transversetemporal
 3538   2383   6991  3.068 0.746     0.132     0.043       45     6.4  insula
PIDs (17830 17833) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 01:44:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 pctsurfcon --s 0051009 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 01:44:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts

 pctsurfcon --s 0051009 --rh-only 

Waiting for PID 17886 of (17886 17898) to complete...
Waiting for PID 17898 of (17886 17898) to complete...

 pctsurfcon --s 0051009 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts/pctsurfcon.log
Sun Oct  8 01:44:04 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-6.0.0/0051009/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-576 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-6.0.0/0051009/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17886/lh.wm.mgh --regheader 0051009 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 75036
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17886/lh.wm.mgh
Dim: 153897 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17886/lh.gm.mgh --projfrac 0.3 --regheader 0051009 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 90890
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17886/lh.gm.mgh
Dim: 153897 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17886/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17886/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.w-g.pct.mgh --annot 0051009 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/lh.w-g.pct.mgh --annot 0051009 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/lh.w-g.pct.mgh
Vertex Area is 0.681989 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 0051009 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/scripts/pctsurfcon.log
Sun Oct  8 01:44:04 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-6.0.0/0051009/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-576 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-6.0.0/0051009/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17898/rh.wm.mgh --regheader 0051009 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 74506
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17898/rh.wm.mgh
Dim: 154166 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17898/rh.gm.mgh --projfrac 0.3 --regheader 0051009 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 90734
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17898/rh.gm.mgh
Dim: 154166 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17898/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/tmp.pctsurfcon.17898/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.w-g.pct.mgh --annot 0051009 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.w-g.pct.mgh --annot 0051009 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.w-g.pct.mgh
Vertex Area is 0.678837 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 (17886 17898) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 01:44:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1260 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
922 voxels changed to hypointensity...
2349 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 01:44:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009

 mri_aparc2aseg --s 0051009 --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 01:44:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009

 mri_aparc2aseg --s 0051009 --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 01:44:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009

 mri_aparc2aseg --s 0051009 --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 18063 of (18063 18066 18069) to complete...
Waiting for PID 18066 of (18063 18066 18069) to complete...
Waiting for PID 18069 of (18063 18066 18069) to complete...

 mri_aparc2aseg --s 0051009 --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 0051009
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/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-6.0.0/0051009/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.00
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 52
rescaling Left_Lateral_Ventricle from 13 -->  5
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 85
rescaling Left_Cerebellum_Cortex from 60 --> 51
rescaling Left_Thalamus from 94 --> 85
rescaling Left_Thalamus_Proper from 84 --> 82
rescaling Left_Caudate from 75 --> 68
rescaling Left_Putamen from 80 --> 74
rescaling Left_Pallidum from 98 --> 87
rescaling Third_Ventricle from 25 --> 10
rescaling Fourth_Ventricle from 22 -->  8
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 52
rescaling Left_Amygdala from 56 --> 54
rescaling CSF from 32 --> 14
rescaling Left_Accumbens_area from 62 --> 54
rescaling Left_VentralDC from 87 --> 86
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 52
rescaling Right_Lateral_Ventricle from 13 -->  5
rescaling Right_Inf_Lat_Vent from 25 --> 21
rescaling Right_Cerebellum_White_Matter from 87 --> 84
rescaling Right_Cerebellum_Cortex from 59 --> 50
rescaling Right_Thalamus_Proper from 85 --> 79
rescaling Right_Caudate from 62 --> 65
rescaling Right_Putamen from 80 --> 69
rescaling Right_Pallidum from 97 --> 85
rescaling Right_Hippocampus from 53 --> 50
rescaling Right_Amygdala from 55 --> 54
rescaling Right_Accumbens_area from 65 --> 64
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 14
rescaling WM_hypointensities from 78 --> 80
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 642359
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 5 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051009 --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 0051009
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/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-6.0.0/0051009/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.00
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 52
rescaling Left_Lateral_Ventricle from 13 -->  5
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 85
rescaling Left_Cerebellum_Cortex from 60 --> 51
rescaling Left_Thalamus from 94 --> 85
rescaling Left_Thalamus_Proper from 84 --> 82
rescaling Left_Caudate from 75 --> 68
rescaling Left_Putamen from 80 --> 74
rescaling Left_Pallidum from 98 --> 87
rescaling Third_Ventricle from 25 --> 10
rescaling Fourth_Ventricle from 22 -->  8
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 52
rescaling Left_Amygdala from 56 --> 54
rescaling CSF from 32 --> 14
rescaling Left_Accumbens_area from 62 --> 54
rescaling Left_VentralDC from 87 --> 86
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 52
rescaling Right_Lateral_Ventricle from 13 -->  5
rescaling Right_Inf_Lat_Vent from 25 --> 21
rescaling Right_Cerebellum_White_Matter from 87 --> 84
rescaling Right_Cerebellum_Cortex from 59 --> 50
rescaling Right_Thalamus_Proper from 85 --> 79
rescaling Right_Caudate from 62 --> 65
rescaling Right_Putamen from 80 --> 69
rescaling Right_Pallidum from 97 --> 85
rescaling Right_Hippocampus from 53 --> 50
rescaling Right_Amygdala from 55 --> 54
rescaling Right_Accumbens_area from 65 --> 64
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 14
rescaling WM_hypointensities from 78 --> 80
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 642414
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 5 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051009 --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 0051009
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/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-6.0.0/0051009/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.00
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 52
rescaling Left_Lateral_Ventricle from 13 -->  5
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 85
rescaling Left_Cerebellum_Cortex from 60 --> 51
rescaling Left_Thalamus from 94 --> 85
rescaling Left_Thalamus_Proper from 84 --> 82
rescaling Left_Caudate from 75 --> 68
rescaling Left_Putamen from 80 --> 74
rescaling Left_Pallidum from 98 --> 87
rescaling Third_Ventricle from 25 --> 10
rescaling Fourth_Ventricle from 22 -->  8
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 52
rescaling Left_Amygdala from 56 --> 54
rescaling CSF from 32 --> 14
rescaling Left_Accumbens_area from 62 --> 54
rescaling Left_VentralDC from 87 --> 86
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 52
rescaling Right_Lateral_Ventricle from 13 -->  5
rescaling Right_Inf_Lat_Vent from 25 --> 21
rescaling Right_Cerebellum_White_Matter from 87 --> 84
rescaling Right_Cerebellum_Cortex from 59 --> 50
rescaling Right_Thalamus_Proper from 85 --> 79
rescaling Right_Caudate from 62 --> 65
rescaling Right_Putamen from 80 --> 69
rescaling Right_Pallidum from 97 --> 85
rescaling Right_Hippocampus from 53 --> 50
rescaling Right_Amygdala from 55 --> 54
rescaling Right_Accumbens_area from 65 --> 64
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 14
rescaling WM_hypointensities from 78 --> 80
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 642414
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 5 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (18063 18066 18069) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 01:52:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri

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

Sun Oct  8 01:52:30 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-6.0.0/0051009/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-576 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-6.0.0/0051009/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-576
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 01:52:30 CEST 2017 
Ended   at Sun Oct  8 01:52:36 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 01:52:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009

 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 0051009 


$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 0051009 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1647491 mm^3    (det: 1.182468 )
Computing euler number
orig.nofix lheno = -118, rheno = -96
orig.nofix lhholes =   60, rhholes = 49
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
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 01:54:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009

 mri_aparc2aseg --s 0051009 --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 0051009
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-6.0.0/0051009/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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-6.0.0/0051009/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8418 vertices from left hemi
Ripped 7865 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-6.0.0/0051009/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 = 1132860
Used brute-force search on 196 voxels
Fixing Parahip LH WM
  Found 15 clusters
     0 k 3.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 2.000000
     5 k 1.000000
     6 k 7.000000
     7 k 1.000000
     8 k 7.000000
     9 k 1.000000
     10 k 4.000000
     11 k 8.000000
     12 k 1548.000000
     13 k 3.000000
     14 k 3.000000
Fixing Parahip RH WM
  Found 14 clusters
     0 k 2.000000
     1 k 2.000000
     2 k 1.000000
     3 k 1755.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 3.000000
     8 k 11.000000
     9 k 2.000000
     10 k 1.000000
     11 k 1.000000
     12 k 2.000000
     13 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0051009 --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 0051009 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-576
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1647491 mm^3    (det: 1.182468 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
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-6.0.0/0051009/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 02:04:33 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 19365 of (19365 19371 19377 19382 19389) to complete...
Waiting for PID 19371 of (19365 19371 19377 19382 19389) to complete...
Waiting for PID 19377 of (19365 19371 19377 19382 19389) to complete...
Waiting for PID 19382 of (19365 19371 19377 19382 19389) to complete...
Waiting for PID 19389 of (19365 19371 19377 19382 19389) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 411
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4540
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 1134
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9043
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 143
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4220
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 523
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6506
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 256
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6040
mri_label2label: Done

PIDs (19365 19371 19377 19382 19389) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 19432 of (19432 19438 19444 19450) to complete...
Waiting for PID 19438 of (19432 19438 19444 19450) to complete...
Waiting for PID 19444 of (19432 19438 19444 19450) to complete...
Waiting for PID 19450 of (19432 19438 19444 19450) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 165
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4235
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 1376
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14965
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 428
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4609
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 792
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4214
mri_label2label: Done

PIDs (19432 19438 19444 19450) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 19510 of (19510 19516 19522 19528 19533) to complete...
Waiting for PID 19516 of (19510 19516 19522 19528 19533) to complete...
Waiting for PID 19522 of (19510 19516 19522 19528 19533) to complete...
Waiting for PID 19528 of (19510 19516 19522 19528 19533) to complete...
Waiting for PID 19533 of (19510 19516 19522 19528 19533) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 1016
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5657
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 2764
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10878
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 541
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2559
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 183
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1473
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 180
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1379
mri_label2label: Done

PIDs (19510 19516 19522 19528 19533) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 19582 of (19582 19588 19594 19598 19605) to complete...
Waiting for PID 19588 of (19582 19588 19594 19598 19605) to complete...
Waiting for PID 19594 of (19582 19588 19594 19598 19605) to complete...
Waiting for PID 19598 of (19582 19588 19594 19598 19605) to complete...
Waiting for PID 19605 of (19582 19588 19594 19598 19605) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 169
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1183
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 212
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2304
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 32
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1536
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 109
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2105
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 89
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2408
mri_label2label: Done

PIDs (19582 19588 19594 19598 19605) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 19649 of (19649 19655 19661 19667) to complete...
Waiting for PID 19655 of (19649 19655 19661 19667) to complete...
Waiting for PID 19661 of (19649 19655 19661 19667) to complete...
Waiting for PID 19667 of (19649 19655 19661 19667) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 46
Checking for and removing duplicates
Writing label file ./lh.BA4p_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.BA6_exvivo.thresh.label --trgsubject 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 466
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7501
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2086
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 306
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1457
mri_label2label: Done

PIDs (19649 19655 19661 19667) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 19726 of (19726 19732 19738 19744 19749) to complete...
Waiting for PID 19732 of (19726 19732 19738 19744 19749) to complete...
Waiting for PID 19738 of (19726 19732 19738 19744 19749) to complete...
Waiting for PID 19744 of (19726 19732 19738 19744 19749) to complete...
Waiting for PID 19749 of (19726 19732 19738 19744 19749) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 710
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4115
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 1145
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4479
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 146
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 659
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 44
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 514
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.sphere.reg
Rescaling ...  original radius = 99.9999
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 153897
Number of reverse mapping hits = 62
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 512
mri_label2label: Done

PIDs (19726 19732 19738 19744 19749) completed and logs appended.

 mris_label2annot --s 0051009 --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-6.0.0/0051009/label
cmdline mris_label2annot --s 0051009 --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-576
machine  x86_64
user     ntraut

subject 0051009
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-6.0.0/0051009/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 110928 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051009 --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-6.0.0/0051009/label
cmdline mris_label2annot --s 0051009 --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-576
machine  x86_64
user     ntraut

subject 0051009
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-6.0.0/0051009/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 130551 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 332878
Total vertex volume 328569 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1331    832   3101  2.623 0.723     0.135     0.044       19     2.2  BA1_exvivo
 5176   3487   9881  2.634 0.575     0.108     0.026       44     5.4  BA2_exvivo
 1004    681   1142  2.082 0.498     0.125     0.028        7     1.1  BA3a_exvivo
 2521   1733   4228  2.199 0.694     0.107     0.028       25     2.8  BA3b_exvivo
 1608   1020   3746  2.950 0.559     0.113     0.031       15     2.0  BA4a_exvivo
 1107    733   1844  2.601 0.534     0.101     0.029        7     1.2  BA4p_exvivo
 9698   6617  25612  3.109 0.720     0.125     0.032      105    12.1  BA6_exvivo
 2365   1665   5542  2.739 0.635     0.127     0.029       35     2.8  BA44_exvivo
 3190   2212   7729  2.812 0.649     0.122     0.034       43     3.9  BA45_exvivo
 3047   2195   4676  1.993 0.581     0.151     0.049       49     6.0  V1_exvivo
 8173   5769  15028  2.340 0.654     0.156     0.046      141    14.9  V2_exvivo
 2265   1550   4493  2.514 0.576     0.135     0.033       28     2.9  MT_exvivo
  676    446   2123  3.392 0.778     0.099     0.024        5     0.6  perirhinal_exvivo
  808    591   2019  3.166 0.755     0.137     0.037       11     1.2  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 0051009 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 332878
Total vertex volume 328569 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
  908    541   2159  2.631 0.774     0.151     0.053       17     1.8  BA1_exvivo
 1759   1213   3467  2.538 0.532     0.098     0.023       11     1.5  BA2_exvivo
  797    537    848  2.054 0.464     0.130     0.030        6     0.9  BA3a_exvivo
 1387    984   1820  1.806 0.454     0.093     0.021        8     1.2  BA3b_exvivo
 1408    942   3234  2.884 0.574     0.108     0.030       11     1.7  BA4a_exvivo
  905    610   1524  2.604 0.532     0.098     0.027        5     0.9  BA4p_exvivo
 4983   3365  13597  3.157 0.732     0.128     0.034       58     6.4  BA6_exvivo
 1465   1050   3633  2.714 0.677     0.137     0.033       27     2.0  BA44_exvivo
 1262    876   3495  2.967 0.634     0.130     0.036       20     1.7  BA45_exvivo
 3220   2319   5060  2.012 0.588     0.152     0.050       55     6.4  V1_exvivo
 3899   2809   6992  2.234 0.661     0.165     0.049       73     7.6  V2_exvivo
  604    414   1125  2.467 0.532     0.150     0.037        8     1.0  MT_exvivo
  321    221   1186  3.723 0.606     0.081     0.019        1     0.2  perirhinal_exvivo
  428    320   1097  3.448 0.788     0.137     0.029        5     0.6  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 02:07:45 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 19862 of (19862 19868 19874 19879 19884) to complete...
Waiting for PID 19868 of (19862 19868 19874 19879 19884) to complete...
Waiting for PID 19874 of (19862 19868 19874 19879 19884) to complete...
Waiting for PID 19879 of (19862 19868 19874 19879 19884) to complete...
Waiting for PID 19884 of (19862 19868 19874 19879 19884) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 631
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4593
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 1164
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7851
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 138
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4118
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 381
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4903
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 513
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6260
mri_label2label: Done

PIDs (19862 19868 19874 19879 19884) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 19936 of (19936 19942 19948 19953) to complete...
Waiting for PID 19942 of (19936 19942 19948 19953) to complete...
Waiting for PID 19948 of (19936 19942 19948 19953) to complete...
Waiting for PID 19953 of (19936 19942 19948 19953) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 294
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4767
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 1777
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14033
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 975
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7887
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 1432
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6787
mri_label2label: Done

PIDs (19936 19942 19948 19953) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 20013 of (20013 20019 20025 20030 20037) to complete...
Waiting for PID 20019 of (20013 20019 20025 20030 20037) to complete...
Waiting for PID 20025 of (20013 20019 20025 20030 20037) to complete...
Waiting for PID 20030 of (20013 20019 20025 20030 20037) to complete...
Waiting for PID 20037 of (20013 20019 20025 20030 20037) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 1863
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6590
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 3516
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11532
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 840
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2772
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 170
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1208
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 169
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 921
mri_label2label: Done

PIDs (20013 20019 20025 20030 20037) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 20088 of (20088 20094 20100 20106 20112) to complete...
Waiting for PID 20094 of (20088 20094 20100 20106 20112) to complete...
Waiting for PID 20100 of (20088 20094 20100 20106 20112) to complete...
Waiting for PID 20106 of (20088 20094 20100 20106 20112) to complete...
Waiting for PID 20112 of (20088 20094 20100 20106 20112) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 136
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1012
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 552
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3240
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 39
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1737
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2357
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 136
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1524
mri_label2label: Done

PIDs (20088 20094 20100 20106 20112) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 20167 of (20167 20173 20179 20184) to complete...
Waiting for PID 20173 of (20167 20173 20179 20184) to complete...
Waiting for PID 20179 of (20167 20173 20179 20184) to complete...
Waiting for PID 20184 of (20167 20173 20179 20184) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 100
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1589
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 926
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7885
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 211
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1223
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 287
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1465
mri_label2label: Done

PIDs (20167 20173 20179 20184) 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 0051009 --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 0051009 --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 0051009 --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 0051009 --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 0051009 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 20227 of (20227 20233 20239 20244 20250) to complete...
Waiting for PID 20233 of (20227 20233 20239 20244 20250) to complete...
Waiting for PID 20239 of (20227 20233 20239 20244 20250) to complete...
Waiting for PID 20244 of (20227 20233 20239 20244 20250) to complete...
Waiting for PID 20250 of (20227 20233 20239 20244 20250) 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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 1264
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4496
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 1696
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5133
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 164
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 432
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 88
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 782
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 0051009 --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 = 0051009
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-6.0.0/0051009/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 154166
Number of reverse mapping hits = 57
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 348
mri_label2label: Done

PIDs (20227 20233 20239 20244 20250) completed and logs appended.

 mris_label2annot --s 0051009 --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-6.0.0/0051009/label
cmdline mris_label2annot --s 0051009 --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-576
machine  x86_64
user     ntraut

subject 0051009
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-6.0.0/0051009/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 106011 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051009 --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-6.0.0/0051009/label
cmdline mris_label2annot --s 0051009 --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-576
machine  x86_64
user     ntraut

subject 0051009
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-6.0.0/0051009/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 127370 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/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 0051009 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 323359
Total vertex volume 319050 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
 1191    732   2797  2.639 0.701     0.140     0.059       22     2.8  BA1_exvivo
 4854   3260   9041  2.515 0.619     0.112     0.026       48     5.0  BA2_exvivo
 1100    739   1176  2.099 0.459     0.111     0.021        6     1.0  BA3a_exvivo
 2109   1395   3162  1.922 0.662     0.099     0.030       18     2.4  BA3b_exvivo
 1549    967   3651  2.983 0.646     0.113     0.051       21     3.3  BA4a_exvivo
 1293    846   2169  2.629 0.558     0.105     0.033       13     1.8  BA4p_exvivo
 9833   6680  24417  2.989 0.674     0.121     0.030      105    11.5  BA6_exvivo
 3959   2661   8448  2.758 0.590     0.120     0.027       47     3.9  BA44_exvivo
 4992   3366  11298  2.879 0.635     0.130     0.033       73     6.6  BA45_exvivo
 4277   2935   6021  1.934 0.548     0.142     0.046       69     7.5  V1_exvivo
 9168   6156  16493  2.378 0.590     0.141     0.039      124    13.5  V2_exvivo
 2653   1798   5378  2.691 0.574     0.117     0.026       28     2.8  MT_exvivo
  660    492   2102  3.411 0.702     0.105     0.028        4     0.9  perirhinal_exvivo
  517    347   1114  2.983 0.656     0.135     0.035        9     0.9  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051009 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051009/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 323359
Total vertex volume 319050 (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) = 1647491 mm^3    (det: 1.182468 )
lhCtxGM: 326923.472 326404.000  diff=  519.5  pctdiff= 0.159
rhCtxGM: 317632.306 317446.000  diff=  186.3  pctdiff= 0.059
lhCtxWM: 247314.583 247586.000  diff= -271.4  pctdiff=-0.110
rhCtxWM: 244124.021 244513.000  diff= -389.0  pctdiff=-0.159
SubCortGMVol  66702.000
SupraTentVol  1212204.382 (1209486.000) diff=2718.382 pctdiff=0.224
SupraTentVolNotVent  1205402.382 (1202684.000) diff=2718.382 pctdiff=0.226
BrainSegVol  1368252.000 (1365892.000) diff=2360.000 pctdiff=0.172
BrainSegVolNotVent  1358456.000 (1358325.382) diff=130.618 pctdiff=0.010
BrainSegVolNotVent  1358456.000
CerebellumVol 155596.000
VentChorVol    6802.000
3rd4th5thCSF   2994.000
CSFVol   634.000, OptChiasmVol   176.000
MaskVol 1779299.000
  785    502   1911  2.548 0.704     0.142     0.048       13     1.3  BA1_exvivo
 2827   1912   5538  2.561 0.631     0.107     0.023       26     2.6  BA2_exvivo
  984    653    954  2.088 0.443     0.111     0.021        6     0.8  BA3a_exvivo
 1665   1144   2089  1.739 0.480     0.084     0.016        7     1.1  BA3b_exvivo
  948    574   2297  2.946 0.794     0.144     0.073       21     3.1  BA4a_exvivo
 1050    702   1753  2.628 0.503     0.098     0.031        8     1.2  BA4p_exvivo
 6152   4208  15183  2.950 0.674     0.120     0.030       65     7.2  BA6_exvivo
 1082    720   2578  2.784 0.626     0.127     0.027       14     1.2  BA44_exvivo
 1281    867   3463  3.102 0.575     0.149     0.040       24     1.8  BA45_exvivo
 4084   2792   5599  1.919 0.549     0.140     0.045       65     7.2  V1_exvivo
 4803   3256   8829  2.349 0.606     0.148     0.043       73     7.8  V2_exvivo
  423    276   1066  2.797 0.448     0.134     0.031        7     0.6  MT_exvivo
  398    288   1389  3.574 0.644     0.088     0.018        2     0.3  perirhinal_exvivo
  314    230    712  3.075 0.724     0.103     0.017        2     0.2  entorhinal_exvivo

Started at Sat Oct 7 17:18:08 CEST 2017 
Ended   at Sun Oct 8 02:11:05 CEST 2017
#@#%# recon-all-run-time-hours 8.882
recon-all -s 0051009 finished without error at Sun Oct  8 02:11:05 CEST 2017