ABIDE_fs-6.0.0/0050566/scripts/recon-all.log

Sun Oct  8 01:37:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050566 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050566/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050566
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-604 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   53756420   12237428    1741464          0   49932056
-/+ buffers/cache:    3824364   62169484
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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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: 2017/10/07-23:37:07-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-604  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-6.0.0/0050566

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050566/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050566/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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/Yale/0050566/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-6.0.0/0050566/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sun Oct  8 01:37:12 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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 float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sun Oct  8 01:37:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-604 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
Sun Oct  8 01:37:21 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.24582
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24582/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24582/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.24582/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:37:24 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.24582/nu0.mnc ./tmp.mri_nu_correct.mni.24582/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24582/0/ -iterations 1000 -distance 50
[ntraut@tars-604:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/] [2017-10-08 01:37:24] 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.24582/0/ ./tmp.mri_nu_correct.mni.24582/nu0.mnc ./tmp.mri_nu_correct.mni.24582/nu1.imp

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Number of iterations: 54 
CV of field change: 0.000992525
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.24582/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.24582/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.24582/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...
 
 
Sun Oct  8 01:38:38 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 Sun Oct 8 01:38:38 CEST 2017
Ended   at Sun Oct  8 01:39:09 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sun Oct  8 01:39:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6856, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach_avi.log 

TalAviQA: 0.97932
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sun Oct  8 01:39:11 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-6.0.0/0050566/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-604 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
Sun Oct  8 01:39:12 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.25515
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25515/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25515/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.25515/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:39:14 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.25515/nu0.mnc ./tmp.mri_nu_correct.mni.25515/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25515/0/
[ntraut@tars-604:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/] [2017-10-08 01:39:14] 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.25515/0/ ./tmp.mri_nu_correct.mni.25515/nu0.mnc ./tmp.mri_nu_correct.mni.25515/nu1.imp

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Number of iterations: 39 
CV of field change: 0.000961806
 
 
--------------------------------------------------------
Iteration 2 Sun Oct  8 01:40:02 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.25515/nu1.mnc ./tmp.mri_nu_correct.mni.25515/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25515/1/
[ntraut@tars-604:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/] [2017-10-08 01:40:02] 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.25515/1/ ./tmp.mri_nu_correct.mni.25515/nu1.mnc ./tmp.mri_nu_correct.mni.25515/nu2.imp

Processing:.................................................................Done
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Number of iterations: 22 
CV of field change: 0.000970114
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25515/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-6.0.0/0050566/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25515/ones.mgz 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.25515/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.25515/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.25515/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/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.25515/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/input.mean.dat 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.25515/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.25515/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25515/ones.mgz --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/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.25515/ones.mgz --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/output.mean.dat 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.25515/ones.mgz
Loading ./tmp.mri_nu_correct.mni.25515/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.25515/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.25515/nu2.mnc ./tmp.mri_nu_correct.mni.25515/nu2.mnc mul 1.01812367956321046405
Saving result to './tmp.mri_nu_correct.mni.25515/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.25515/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.25515/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.25515/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 ( 5, 116) to ( 3, 110)
 
 
Sun Oct  8 01:41:14 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sun Oct  8 01:41:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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
 1.12323   0.05093  -0.02905  -43.66782;
-0.02742   1.01447   0.40186   50.74092;
-0.01426  -0.33404   1.08284  -13.44376;
 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 = 14
Starting OpenSpline(): npoints = 14
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 55 (55), valley at 19 (19)
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 58 (58), valley at 18 (18)
csf peak at 30, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 57 seconds.
#--------------------------------------------
#@# Skull Stripping Sun Oct  8 01:43:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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=11.0
skull bounding box = (51, 76, 23) --> (200, 226, 209)
using (101, 126, 116) as brain centroid...
mean wm in atlas = 108, using box (83,108,93) --> (119, 144,138) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.9
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.698
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.364028 @ (9.091, -27.273, -9.091)
max log p =    -4.318834 @ (-4.545, -4.545, -4.545)
max log p =    -4.265907 @ (-6.818, 2.273, 2.273)
max log p =    -4.261907 @ (1.136, 1.136, 1.136)
max log p =    -4.246409 @ (0.568, -0.568, 0.568)
max log p =    -4.235481 @ (0.284, -0.284, -0.284)
Found translation: (-0.3, -29.3, -9.9): log p = -4.235
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.842, old_max_log_p =-4.235 (thresh=-4.2)
 1.15000   0.00000   0.00000  -19.05799;
 0.00000   1.11081   0.29764  -76.73383;
 0.00000  -0.27532   1.02750   33.93199;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.842, old_max_log_p =-3.842 (thresh=-3.8)
 1.15000   0.00000   0.00000  -19.05799;
 0.00000   1.11081   0.29764  -76.73383;
 0.00000  -0.27532   1.02750   33.93199;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.776, old_max_log_p =-3.842 (thresh=-3.8)
 1.12783   0.01157  -0.03350  -14.20147;
 0.00000   1.09043   0.36421  -81.30061;
 0.03692  -0.35346   1.02344   44.57402;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.775, old_max_log_p =-3.776 (thresh=-3.8)
 1.14898   0.01179  -0.03413  -16.80915;
-0.00121   1.10141   0.33053  -79.01006;
 0.03759  -0.32355   1.05421   35.91718;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.747, old_max_log_p =-3.775 (thresh=-3.8)
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.747, old_max_log_p =-3.747 (thresh=-3.7)
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3243 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.747 (old=-4.698)
transform before final EM align:
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 364799 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.2  tol 0.000000
final transform:
 1.15029   0.00281  -0.03710  -15.13517;
 0.00843   1.09493   0.33766  -79.51074;
 0.03762  -0.33138   1.04777   38.43645;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1244.197853
mri_em_register stimesec    1.343795
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   157061
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    336
mri_em_register ru_nivcsw   17717
registration took 10 minutes and 51 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=127 y=143 z=111 r=65
      first estimation of the main basin volume: 1151627 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        15 found in the rest of the brain 
      global maximum in x=146, y=135, z=80, Imax=255
      CSF=18, 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=8110681402 voxels, voxel volume =1.000 
                     = 8110681402 mmm3 = 8110681.600 cm3
done.
PostAnalyze...Basin Prior
 13 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=125,y=148, z=106, r=9451 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=23, CSF_MAX=58 , nb = 44074
  RIGHT_CER    CSF_MIN=0, CSF_intensity=23, CSF_MAX=56 , nb = -1029927675
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=86 , nb = -1031222087
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=23, CSF_MAX=52 , nb = 1110004096
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=23, CSF_MAX=66 , nb = 1061772250
    OTHER      CSF_MIN=11, CSF_intensity=25, CSF_MAX=55 , nb = 1082347322
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    58,      43,        36,   55
  after  analyzing :    37,      43,        43,   46
   RIGHT_CER   
  before analyzing :    56,      48,        43,   67
  after  analyzing :    41,      48,        48,   52
   LEFT_CER    
  before analyzing :    86,      50,        42,   61
  after  analyzing :    38,      50,        50,   52
  RIGHT_BRAIN  
  before analyzing :    52,      41,        34,   55
  after  analyzing :    36,      41,        41,   44
  LEFT_BRAIN   
  before analyzing :    66,      45,        37,   56
  after  analyzing :    39,      45,        45,   47
     OTHER     
  before analyzing :    55,      58,        62,   94
  after  analyzing :    55,      60,        62,   68
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...68 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 68.119, std = 7.127

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.57, sigma = 5.56
      after  rotation: sse = 3.57, sigma = 5.56
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.02, its var is  6.23   
      before Erosion-Dilatation  1.18% 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...36 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1528172 voxels, voxel volume = 1.000 mm3
           = 1528172 mmm3 = 1528.172 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    26.829921
mri_watershed stimesec    0.531919
mri_watershed ru_maxrss   818064
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   211644
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  4456
mri_watershed ru_oublock  2424
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    2012
mri_watershed ru_nivcsw   174
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct  8 01:54:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

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

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (60, 85, 32) --> (187, 226, 193)
using (102, 132, 113) as brain centroid...
mean wm in atlas = 107, using box (86,115,93) --> (117, 149,132) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.8
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.386
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.023443 @ (9.091, -27.273, -9.091)
max log p =    -3.926755 @ (-4.545, -4.545, 4.545)
max log p =    -3.823371 @ (-2.273, 2.273, -6.818)
max log p =    -3.811545 @ (-1.136, 1.136, 3.409)
max log p =    -3.787865 @ (0.568, -0.568, -0.568)
max log p =    -3.787865 @ (0.000, 0.000, 0.000)
Found translation: (1.7, -29.0, -8.5): log p = -3.788
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.510, old_max_log_p =-3.788 (thresh=-3.8)
 1.06375   0.00000   0.00000  -6.26628;
 0.00000   1.06753   0.42117  -79.48959;
 0.00000  -0.43171   0.98772   64.38564;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.510, old_max_log_p =-3.510 (thresh=-3.5)
 1.06375   0.00000   0.00000  -6.26628;
 0.00000   1.06753   0.42117  -79.48959;
 0.00000  -0.43171   0.98772   64.38564;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.315, old_max_log_p =-3.510 (thresh=-3.5)
 1.08085  -0.05724  -0.05528   4.05277;
 0.06734   1.06185   0.30742  -78.89843;
 0.03276  -0.31854   1.00387   40.20407;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.315, old_max_log_p =-3.315 (thresh=-3.3)
 1.08085  -0.05724  -0.05528   4.05277;
 0.06734   1.06185   0.30742  -78.89843;
 0.03276  -0.31854   1.00387   40.20407;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.280, old_max_log_p =-3.315 (thresh=-3.3)
 1.07959  -0.05717  -0.05522   4.66420;
 0.06763   1.05279   0.32267  -78.30307;
 0.03170  -0.33626   0.99987   44.31944;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.275, old_max_log_p =-3.280 (thresh=-3.3)
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.275, old_max_log_p =-3.275 (thresh=-3.3)
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.275 (old=-4.386)
transform before final EM align:
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 315557 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 010: -log(p) = 3.8
after pass:transform: ( 1.08, -0.06, -0.06, 4.52)
                      ( 0.07, 1.05, 0.32, -78.07)
                      ( 0.03, -0.34, 1.00, 44.39)
pass 2 through quasi-newton minimization...
outof QuasiNewtonEMA: 012: -log(p) =    3.8  tol 0.000000
final transform:
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1291.609645
mri_em_register stimesec    1.575760
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   158956
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    376
mri_em_register ru_nivcsw   18249
registration took 11 minutes and 14 seconds.
#--------------------------------------
#@# CA Normalize Sun Oct  8 02:05:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

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

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (60, 85, 32) --> (187, 226, 193)
using (102, 132, 113) as brain centroid...
mean wm in atlas = 107, using box (86,115,93) --> (117, 149,132) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.8
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
 1.08085  -0.05724  -0.05528   4.52115;
 0.06755   1.05155   0.32229  -78.07096;
 0.03166  -0.33587   0.99870   44.39106;
 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 (123, 86, 35) --> (188, 195, 191)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 4977 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (65, 87, 35) --> (128, 189, 192)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 4956 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 172, 65) --> (174, 209, 117)
Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 194 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 172, 64) --> (127, 210, 118)
Right_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0
0 of 36 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 157, 98) --> (145, 221, 127)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 142 (0.0%) samples deleted
using 10305 total control points for intensity normalization...
bias field = 0.963 +- 0.048
102 of 10305 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 86, 35) --> (188, 195, 191)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
0 of 5291 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (65, 87, 35) --> (128, 189, 192)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 5483 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 172, 65) --> (174, 209, 117)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
25 of 307 (8.1%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 172, 64) --> (127, 210, 118)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 76 (1.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 157, 98) --> (145, 221, 127)
Brain_Stem: limiting intensities to 88.0 --> 132.0
84 of 265 (31.7%) samples deleted
using 11422 total control points for intensity normalization...
bias field = 1.029 +- 0.044
34 of 11239 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 86, 35) --> (188, 195, 191)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
1 of 5330 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (65, 87, 35) --> (128, 189, 192)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 5436 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 172, 65) --> (174, 209, 117)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
80 of 317 (25.2%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 172, 64) --> (127, 210, 118)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
24 of 96 (25.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 157, 98) --> (145, 221, 127)
Brain_Stem: limiting intensities to 88.0 --> 132.0
153 of 270 (56.7%) samples deleted
using 11449 total control points for intensity normalization...
bias field = 1.028 +- 0.038
14 of 10994 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 41 seconds.
#--------------------------------------
#@# CA Reg Sun Oct  8 02:07:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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) = 1.26 (predicted orig area = 6.4)
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=0.801, neg=0, invalid=762
0001: dt=231.608392, rms=0.720 (10.159%), neg=0, invalid=762
0002: dt=144.972376, rms=0.698 (2.959%), neg=0, invalid=762
0003: dt=254.645503, rms=0.687 (1.598%), neg=0, invalid=762
0004: dt=131.742690, rms=0.681 (0.874%), neg=0, invalid=762
0005: dt=369.920000, rms=0.676 (0.775%), neg=0, invalid=762
0006: dt=110.976000, rms=0.672 (0.586%), neg=0, invalid=762
0007: dt=517.888000, rms=0.668 (0.636%), neg=0, invalid=762
0008: dt=129.472000, rms=0.666 (0.303%), neg=0, invalid=762
0009: dt=295.936000, rms=0.664 (0.220%), neg=0, invalid=762
0010: dt=295.936000, rms=0.664 (-0.025%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.665, neg=0, invalid=762
0011: dt=129.472000, rms=0.662 (0.371%), neg=0, invalid=762
0012: dt=517.888000, rms=0.660 (0.299%), neg=0, invalid=762
0013: dt=129.472000, rms=0.659 (0.170%), neg=0, invalid=762
0014: dt=129.472000, rms=0.659 (0.073%), neg=0, invalid=762
0015: dt=129.472000, rms=0.658 (0.134%), neg=0, invalid=762
0016: dt=129.472000, rms=0.657 (0.190%), neg=0, invalid=762
0017: dt=129.472000, rms=0.655 (0.212%), neg=0, invalid=762
0018: dt=129.472000, rms=0.654 (0.222%), neg=0, invalid=762
0019: dt=129.472000, rms=0.652 (0.229%), neg=0, invalid=762
0020: dt=129.472000, rms=0.651 (0.232%), neg=0, invalid=762
0021: dt=129.472000, rms=0.649 (0.233%), neg=0, invalid=762
0022: dt=129.472000, rms=0.648 (0.219%), neg=0, invalid=762
0023: dt=129.472000, rms=0.647 (0.196%), neg=0, invalid=762
0024: dt=129.472000, rms=0.645 (0.182%), neg=0, invalid=762
0025: dt=129.472000, rms=0.644 (0.171%), neg=0, invalid=762
0026: dt=129.472000, rms=0.643 (0.156%), neg=0, invalid=762
0027: dt=129.472000, rms=0.642 (0.139%), neg=0, invalid=762
0028: dt=129.472000, rms=0.642 (0.123%), neg=0, invalid=762
0029: dt=129.472000, rms=0.641 (0.105%), neg=0, invalid=762
0030: dt=517.888000, rms=0.641 (0.052%), neg=0, invalid=762
0031: dt=517.888000, rms=0.641 (-0.219%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.645, neg=0, invalid=762
0032: dt=117.870504, rms=0.638 (0.998%), neg=0, invalid=762
0033: dt=110.625430, rms=0.631 (1.093%), neg=0, invalid=762
0034: dt=77.217391, rms=0.628 (0.508%), neg=0, invalid=762
0035: dt=108.178478, rms=0.624 (0.700%), neg=0, invalid=762
0036: dt=80.516129, rms=0.622 (0.338%), neg=0, invalid=762
0037: dt=95.255814, rms=0.618 (0.569%), neg=0, invalid=762
0038: dt=36.288000, rms=0.617 (0.224%), neg=0, invalid=762
0039: dt=36.288000, rms=0.616 (0.119%), neg=0, invalid=762
0040: dt=36.288000, rms=0.615 (0.221%), neg=0, invalid=762
0041: dt=36.288000, rms=0.613 (0.325%), neg=0, invalid=762
0042: dt=36.288000, rms=0.610 (0.404%), neg=0, invalid=762
0043: dt=36.288000, rms=0.608 (0.435%), neg=0, invalid=762
0044: dt=36.288000, rms=0.605 (0.434%), neg=0, invalid=762
0045: dt=36.288000, rms=0.602 (0.417%), neg=0, invalid=762
0046: dt=36.288000, rms=0.600 (0.378%), neg=0, invalid=762
0047: dt=36.288000, rms=0.598 (0.353%), neg=0, invalid=762
0048: dt=36.288000, rms=0.596 (0.326%), neg=0, invalid=762
0049: dt=36.288000, rms=0.594 (0.285%), neg=0, invalid=762
0050: dt=36.288000, rms=0.593 (0.255%), neg=0, invalid=762
0051: dt=36.288000, rms=0.591 (0.236%), neg=0, invalid=762
0052: dt=36.288000, rms=0.590 (0.223%), neg=0, invalid=762
0053: dt=36.288000, rms=0.589 (0.196%), neg=0, invalid=762
0054: dt=36.288000, rms=0.588 (0.177%), neg=0, invalid=762
0055: dt=36.288000, rms=0.587 (0.160%), neg=0, invalid=762
0056: dt=36.288000, rms=0.586 (0.128%), neg=0, invalid=762
0057: dt=36.288000, rms=0.586 (0.123%), neg=0, invalid=762
0058: dt=36.288000, rms=0.585 (0.115%), neg=0, invalid=762
0059: dt=414.720000, rms=0.584 (0.132%), neg=0, invalid=762
0060: dt=36.288000, rms=0.584 (0.046%), neg=0, invalid=762
0061: dt=36.288000, rms=0.584 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.585, neg=0, invalid=762
0062: dt=36.288000, rms=0.583 (0.212%), neg=0, invalid=762
0063: dt=36.288000, rms=0.583 (0.031%), neg=0, invalid=762
0064: dt=36.288000, rms=0.583 (0.021%), neg=0, invalid=762
0065: dt=36.288000, rms=0.583 (0.026%), neg=0, invalid=762
0066: dt=36.288000, rms=0.583 (-0.009%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.605, neg=0, invalid=762
0067: dt=8.000000, rms=0.604 (0.193%), neg=0, invalid=762
0068: dt=2.800000, rms=0.603 (0.012%), neg=0, invalid=762
0069: dt=2.800000, rms=0.603 (0.002%), neg=0, invalid=762
0070: dt=2.800000, rms=0.603 (-0.025%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.604, neg=0, invalid=762
0071: dt=0.000000, rms=0.603 (0.116%), neg=0, invalid=762
0072: dt=0.000000, rms=0.603 (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=0.659, neg=0, invalid=762
0073: dt=5.510730, rms=0.645 (2.152%), neg=0, invalid=762
0074: dt=2.561798, rms=0.644 (0.076%), neg=0, invalid=762
0075: dt=2.561798, rms=0.644 (-0.027%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.645, neg=0, invalid=762
0076: dt=0.000000, rms=0.644 (0.093%), neg=0, invalid=762
0077: dt=0.000000, rms=0.644 (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=0.702, neg=0, invalid=762
0078: dt=0.804124, rms=0.700 (0.333%), neg=0, invalid=762
0079: dt=1.792000, rms=0.697 (0.401%), neg=0, invalid=762
0080: dt=1.792000, rms=0.695 (0.323%), neg=0, invalid=762
0081: dt=1.280000, rms=0.694 (0.063%), neg=0, invalid=762
0082: dt=1.280000, rms=0.694 (0.019%), neg=0, invalid=762
0083: dt=1.280000, rms=0.694 (-0.023%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.695, neg=0, invalid=762
0084: dt=1.536000, rms=0.693 (0.251%), neg=0, invalid=762
0085: dt=0.000000, rms=0.693 (0.001%), neg=0, invalid=762
0086: dt=0.100000, rms=0.693 (-0.005%), 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=0.651, neg=0, invalid=762
0087: dt=0.836683, rms=0.633 (2.678%), neg=0, invalid=762
0088: dt=0.080000, rms=0.632 (0.152%), neg=0, invalid=762
0089: dt=0.080000, rms=0.632 (-0.081%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.633, neg=0, invalid=762
0090: dt=0.028000, rms=0.632 (0.113%), neg=0, invalid=762
0091: dt=0.000063, rms=0.632 (0.001%), neg=0, invalid=762
0092: dt=0.000063, rms=0.632 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.09608 (12)
Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (779 voxels, overlap=0.359)
Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (779 voxels, peak = 11), gca=10.9
gca peak = 0.15565 (16)
mri peak = 0.04813 (12)
Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (771 voxels, overlap=0.610)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (771 voxels, peak = 29), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.06036 (88)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (815 voxels, overlap=0.995)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (815 voxels, peak = 88), gca=87.8
gca peak = 0.20183 (93)
mri peak = 0.07597 (94)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (763 voxels, overlap=0.926)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (763 voxels, peak = 90), gca=89.7
gca peak = 0.21683 (55)
mri peak = 0.09189 (60)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (607 voxels, overlap=0.992)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (607 voxels, peak = 57), gca=57.5
gca peak = 0.30730 (58)
mri peak = 0.08633 (58)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (866 voxels, overlap=0.998)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (866 voxels, peak = 58), gca=58.0
gca peak = 0.11430 (101)
mri peak = 0.08703 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57357 voxels, overlap=0.748)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57357 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.09979 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (58063 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (58063 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.03769 (55)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (29446 voxels, overlap=0.970)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (29446 voxels, peak = 56), gca=55.8
gca peak = 0.15082 (58)
mri peak = 0.04026 (53)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (29163 voxels, overlap=0.950)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (29163 voxels, peak = 53), gca=53.1
gca peak = 0.14161 (67)
mri peak = 0.08816 (67)
Right_Caudate (50): linear fit = 0.98 x + 0.0 (861 voxels, overlap=0.900)
Right_Caudate (50): linear fit = 0.98 x + 0.0 (861 voxels, peak = 65), gca=65.3
gca peak = 0.15243 (71)
mri peak = 0.12715 (68)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (951 voxels, overlap=0.539)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (951 voxels, peak = 66), gca=65.7
gca peak = 0.13336 (57)
mri peak = 0.04892 (56)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (33034 voxels, overlap=0.990)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (33034 voxels, peak = 56), gca=56.1
gca peak = 0.13252 (56)
mri peak = 0.05006 (55)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (32983 voxels, overlap=0.964)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (32983 voxels, peak = 56), gca=55.7
gca peak = 0.18181 (84)
mri peak = 0.07121 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8874 voxels, overlap=0.633)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8874 voxels, peak = 90), gca=90.3
gca peak = 0.20573 (83)
mri peak = 0.05254 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7463 voxels, overlap=0.457)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7463 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.10245 (58)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, overlap=0.998)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, peak = 58), gca=58.4
gca peak = 0.39313 (56)
mri peak = 0.14683 (59)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (505 voxels, overlap=0.984)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (505 voxels, peak = 59), gca=58.5
gca peak = 0.14181 (85)
mri peak = 0.05595 (82)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5177 voxels, overlap=0.985)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5177 voxels, peak = 83), gca=82.9
gca peak = 0.11978 (83)
mri peak = 0.06415 (83)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4175 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4175 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.06234 (75)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2325 voxels, overlap=1.000)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2325 voxels, peak = 78), gca=77.8
gca peak = 0.14159 (79)
mri peak = 0.06107 (72)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (2196 voxels, overlap=0.923)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (2196 voxels, peak = 74), gca=73.9
gca peak = 0.10025 (80)
mri peak = 0.08218 (85)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (12046 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (12046 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.06335 (92)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1003 voxels, overlap=0.728)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1003 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.06764 (97)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1354 voxels, overlap=0.626)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1354 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
mri peak = 1.00000 (50)
gca peak = 0.15061 (21)
mri peak = 0.07757 (12)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (337 voxels, overlap=0.602)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (337 voxels, peak = 15), gca=14.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.92 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=0.655, neg=0, invalid=762
0093: dt=170.007722, rms=0.646 (1.288%), neg=0, invalid=762
0094: dt=129.472000, rms=0.644 (0.335%), neg=0, invalid=762
0095: dt=295.936000, rms=0.641 (0.463%), neg=0, invalid=762
0096: dt=92.480000, rms=0.640 (0.199%), neg=0, invalid=762
0097: dt=517.888000, rms=0.637 (0.447%), neg=0, invalid=762
0098: dt=73.984000, rms=0.636 (0.075%), neg=0, invalid=762
0099: dt=517.888000, rms=0.635 (0.187%), neg=0, invalid=762
0100: dt=129.472000, rms=0.634 (0.135%), neg=0, invalid=762
0101: dt=110.976000, rms=0.634 (0.020%), neg=0, invalid=762
0102: dt=110.976000, rms=0.634 (0.058%), neg=0, invalid=762
0103: dt=110.976000, rms=0.633 (0.079%), neg=0, invalid=762
0104: dt=110.976000, rms=0.633 (0.091%), neg=0, invalid=762
0105: dt=110.976000, rms=0.632 (0.112%), neg=0, invalid=762
0106: dt=110.976000, rms=0.631 (0.120%), neg=0, invalid=762
0107: dt=110.976000, rms=0.631 (0.123%), neg=0, invalid=762
0108: dt=110.976000, rms=0.630 (0.108%), neg=0, invalid=762
0109: dt=110.976000, rms=0.629 (0.091%), neg=0, invalid=762
0110: dt=110.976000, rms=0.629 (0.083%), neg=0, invalid=762
0111: dt=110.976000, rms=0.628 (0.076%), neg=0, invalid=762
0112: dt=110.976000, rms=0.628 (0.074%), neg=0, invalid=762
0113: dt=110.976000, rms=0.627 (0.065%), neg=0, invalid=762
0114: dt=110.976000, rms=0.627 (0.061%), neg=0, invalid=762
0115: dt=110.976000, rms=0.627 (0.061%), neg=0, invalid=762
0116: dt=110.976000, rms=0.626 (0.057%), neg=0, invalid=762
0117: dt=110.976000, rms=0.626 (0.051%), neg=0, invalid=762
0118: dt=110.976000, rms=0.626 (0.048%), neg=0, invalid=762
0119: dt=110.976000, rms=0.625 (0.047%), neg=0, invalid=762
0120: dt=110.976000, rms=0.625 (0.045%), neg=0, invalid=762
0121: dt=110.976000, rms=0.625 (0.046%), neg=0, invalid=762
0122: dt=110.976000, rms=0.625 (0.043%), neg=0, invalid=762
0123: dt=110.976000, rms=0.624 (0.051%), neg=0, invalid=762
0124: dt=110.976000, rms=0.624 (0.054%), neg=0, invalid=762
0125: dt=110.976000, rms=0.624 (0.050%), neg=0, invalid=762
0126: dt=110.976000, rms=0.623 (0.046%), neg=0, invalid=762
0127: dt=110.976000, rms=0.623 (0.044%), neg=0, invalid=762
0128: dt=110.976000, rms=0.623 (0.042%), neg=0, invalid=762
0129: dt=110.976000, rms=0.623 (0.040%), neg=0, invalid=762
0130: dt=110.976000, rms=0.622 (0.039%), neg=0, invalid=762
0131: dt=110.976000, rms=0.622 (0.039%), neg=0, invalid=762
0132: dt=110.976000, rms=0.622 (0.036%), neg=0, invalid=762
0133: dt=110.976000, rms=0.622 (0.035%), neg=0, invalid=762
0134: dt=110.976000, rms=0.621 (0.039%), neg=0, invalid=762
0135: dt=110.976000, rms=0.621 (0.032%), neg=0, invalid=762
0136: dt=110.976000, rms=0.621 (0.027%), neg=0, invalid=762
0137: dt=110.976000, rms=0.621 (0.030%), neg=0, invalid=762
0138: dt=110.976000, rms=0.621 (0.027%), neg=0, invalid=762
0139: dt=110.976000, rms=0.620 (0.032%), neg=0, invalid=762
0140: dt=110.976000, rms=0.620 (0.026%), neg=0, invalid=762
0141: dt=110.976000, rms=0.620 (0.026%), neg=0, invalid=762
0142: dt=110.976000, rms=0.620 (0.020%), neg=0, invalid=762
0143: dt=110.976000, rms=0.620 (0.022%), neg=0, invalid=762
0144: dt=110.976000, rms=0.620 (0.018%), neg=0, invalid=762
0145: dt=517.888000, rms=0.620 (0.008%), neg=0, invalid=762
0146: dt=517.888000, rms=0.620 (-0.091%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.620, neg=0, invalid=762
0147: dt=129.472000, rms=0.619 (0.220%), neg=0, invalid=762
0148: dt=369.920000, rms=0.619 (0.070%), neg=0, invalid=762
0149: dt=129.472000, rms=0.618 (0.025%), neg=0, invalid=762
0150: dt=129.472000, rms=0.618 (0.017%), neg=0, invalid=762
0151: dt=129.472000, rms=0.618 (0.025%), neg=0, invalid=762
0152: dt=129.472000, rms=0.618 (0.030%), neg=0, invalid=762
0153: dt=129.472000, rms=0.618 (0.027%), neg=0, invalid=762
0154: dt=129.472000, rms=0.618 (0.027%), neg=0, invalid=762
0155: dt=129.472000, rms=0.618 (0.028%), neg=0, invalid=762
0156: dt=129.472000, rms=0.617 (0.028%), neg=0, invalid=762
0157: dt=129.472000, rms=0.617 (0.031%), neg=0, invalid=762
0158: dt=129.472000, rms=0.617 (0.027%), neg=0, invalid=762
0159: dt=129.472000, rms=0.617 (0.023%), neg=0, invalid=762
0160: dt=129.472000, rms=0.617 (0.024%), neg=0, invalid=762
0161: dt=129.472000, rms=0.617 (0.020%), neg=0, invalid=762
0162: dt=295.936000, rms=0.617 (0.004%), neg=0, invalid=762
0163: dt=295.936000, rms=0.616 (0.016%), neg=0, invalid=762
0164: dt=295.936000, rms=0.616 (-0.010%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.618, neg=0, invalid=762
0165: dt=103.680000, rms=0.614 (0.645%), neg=0, invalid=762
0166: dt=132.266667, rms=0.609 (0.789%), neg=0, invalid=762
0167: dt=52.413793, rms=0.607 (0.376%), neg=0, invalid=762
0168: dt=145.152000, rms=0.603 (0.617%), neg=0, invalid=762
0169: dt=36.288000, rms=0.602 (0.187%), neg=0, invalid=762
0170: dt=580.608000, rms=0.594 (1.362%), neg=0, invalid=762
0171: dt=36.288000, rms=0.592 (0.344%), neg=0, invalid=762
0172: dt=145.152000, rms=0.590 (0.248%), neg=0, invalid=762
0173: dt=62.208000, rms=0.589 (0.117%), neg=0, invalid=762
0174: dt=145.152000, rms=0.588 (0.230%), neg=0, invalid=762
0175: dt=36.288000, rms=0.587 (0.098%), neg=0, invalid=762
0176: dt=580.608000, rms=0.584 (0.574%), neg=0, invalid=762
0177: dt=36.288000, rms=0.583 (0.263%), neg=0, invalid=762
0178: dt=331.776000, rms=0.581 (0.255%), neg=0, invalid=762
0179: dt=36.288000, rms=0.580 (0.176%), neg=0, invalid=762
0180: dt=145.152000, rms=0.579 (0.110%), neg=0, invalid=762
0181: dt=82.944000, rms=0.579 (0.126%), neg=0, invalid=762
0182: dt=62.208000, rms=0.578 (0.048%), neg=0, invalid=762
0183: dt=62.208000, rms=0.578 (0.080%), neg=0, invalid=762
0184: dt=62.208000, rms=0.577 (0.109%), neg=0, invalid=762
0185: dt=62.208000, rms=0.576 (0.144%), neg=0, invalid=762
0186: dt=62.208000, rms=0.576 (0.157%), neg=0, invalid=762
0187: dt=62.208000, rms=0.574 (0.212%), neg=0, invalid=762
0188: dt=62.208000, rms=0.573 (0.225%), neg=0, invalid=762
0189: dt=62.208000, rms=0.572 (0.214%), neg=0, invalid=762
0190: dt=62.208000, rms=0.571 (0.210%), neg=0, invalid=762
0191: dt=62.208000, rms=0.569 (0.225%), neg=0, invalid=762
0192: dt=62.208000, rms=0.568 (0.243%), neg=0, invalid=762
0193: dt=62.208000, rms=0.567 (0.230%), neg=0, invalid=762
0194: dt=62.208000, rms=0.565 (0.202%), neg=0, invalid=762
0195: dt=62.208000, rms=0.564 (0.185%), neg=0, invalid=762
0196: dt=62.208000, rms=0.563 (0.209%), neg=0, invalid=762
0197: dt=62.208000, rms=0.562 (0.193%), neg=0, invalid=762
0198: dt=62.208000, rms=0.561 (0.161%), neg=0, invalid=762
0199: dt=62.208000, rms=0.561 (0.019%), neg=0, invalid=762
0200: dt=62.208000, rms=0.561 (0.022%), neg=0, invalid=762
0201: dt=62.208000, rms=0.561 (0.052%), neg=0, invalid=762
0202: dt=62.208000, rms=0.560 (0.078%), neg=0, invalid=762
0203: dt=62.208000, rms=0.560 (0.069%), neg=0, invalid=762
0204: dt=62.208000, rms=0.560 (0.059%), neg=0, invalid=762
0205: dt=62.208000, rms=0.559 (0.075%), neg=0, invalid=762
0206: dt=62.208000, rms=0.559 (0.094%), neg=0, invalid=762
0207: dt=62.208000, rms=0.558 (0.097%), neg=0, invalid=762
0208: dt=15.552000, rms=0.558 (0.002%), neg=0, invalid=762
0209: dt=1.944000, rms=0.558 (0.002%), neg=0, invalid=762
0210: dt=0.972000, rms=0.558 (-0.000%), neg=0, invalid=762
0211: dt=1.620000, rms=0.558 (0.000%), neg=0, invalid=762
0212: dt=0.141750, rms=0.558 (0.001%), neg=0, invalid=762
0213: dt=0.035437, rms=0.558 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.559, neg=0, invalid=762
0214: dt=73.580838, rms=0.557 (0.322%), neg=0, invalid=762
0215: dt=124.416000, rms=0.556 (0.182%), neg=0, invalid=762
0216: dt=36.288000, rms=0.556 (0.074%), neg=0, invalid=762
0217: dt=414.720000, rms=0.555 (0.187%), neg=0, invalid=762
0218: dt=36.288000, rms=0.554 (0.111%), neg=0, invalid=762
0219: dt=145.152000, rms=0.554 (0.079%), neg=0, invalid=762
0220: dt=62.208000, rms=0.553 (0.039%), neg=0, invalid=762
0221: dt=62.208000, rms=0.553 (0.024%), neg=0, invalid=762
0222: dt=62.208000, rms=0.553 (0.047%), neg=0, invalid=762
0223: dt=62.208000, rms=0.553 (0.081%), neg=0, invalid=762
0224: dt=62.208000, rms=0.552 (0.074%), neg=0, invalid=762
0225: dt=62.208000, rms=0.552 (0.080%), neg=0, invalid=762
0226: dt=62.208000, rms=0.551 (0.093%), neg=0, invalid=762
0227: dt=62.208000, rms=0.551 (0.108%), neg=0, invalid=762
0228: dt=62.208000, rms=0.550 (0.098%), neg=0, invalid=762
0229: dt=62.208000, rms=0.550 (0.094%), neg=0, invalid=762
0230: dt=62.208000, rms=0.549 (0.085%), neg=0, invalid=762
0231: dt=62.208000, rms=0.548 (0.112%), neg=0, invalid=762
0232: dt=62.208000, rms=0.548 (0.100%), neg=0, invalid=762
0233: dt=62.208000, rms=0.547 (0.095%), neg=0, invalid=762
0234: dt=62.208000, rms=0.547 (0.069%), neg=0, invalid=762
0235: dt=62.208000, rms=0.546 (0.108%), neg=0, invalid=762
0236: dt=62.208000, rms=0.546 (0.087%), neg=0, invalid=762
0237: dt=62.208000, rms=0.545 (0.093%), neg=0, invalid=762
0238: dt=62.208000, rms=0.545 (0.065%), neg=0, invalid=762
0239: dt=62.208000, rms=0.545 (0.088%), neg=0, invalid=762
0240: dt=62.208000, rms=0.544 (0.073%), neg=0, invalid=762
0241: dt=62.208000, rms=0.544 (0.078%), neg=0, invalid=762
0242: dt=62.208000, rms=0.543 (0.066%), neg=0, invalid=762
0243: dt=62.208000, rms=0.543 (0.076%), neg=0, invalid=762
0244: dt=62.208000, rms=0.543 (0.070%), neg=0, invalid=762
0245: dt=62.208000, rms=0.542 (0.066%), neg=0, invalid=762
0246: dt=62.208000, rms=0.542 (0.061%), neg=0, invalid=762
0247: dt=62.208000, rms=0.542 (0.072%), neg=0, invalid=762
0248: dt=62.208000, rms=0.541 (0.058%), neg=0, invalid=762
0249: dt=62.208000, rms=0.541 (-0.006%), neg=0, invalid=762
0250: dt=25.920000, rms=0.541 (0.002%), neg=0, invalid=762
0251: dt=124.416000, rms=0.541 (0.010%), neg=0, invalid=762
0252: dt=9.072000, rms=0.541 (0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.549, neg=0, invalid=762
0253: dt=44.800000, rms=0.545 (0.819%), neg=0, invalid=762
0254: dt=11.200000, rms=0.543 (0.338%), neg=0, invalid=762
0255: dt=0.600000, rms=0.543 (0.011%), neg=0, invalid=762
0256: dt=0.009375, rms=0.543 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.544, neg=0, invalid=762
0257: dt=38.041298, rms=0.539 (0.757%), neg=0, invalid=762
0258: dt=29.310145, rms=0.537 (0.466%), neg=0, invalid=762
0259: dt=25.600000, rms=0.535 (0.368%), neg=0, invalid=762
0260: dt=32.000000, rms=0.533 (0.325%), neg=0, invalid=762
0261: dt=25.542169, rms=0.532 (0.302%), neg=0, invalid=762
0262: dt=25.600000, rms=0.530 (0.275%), neg=0, invalid=762
0263: dt=32.000000, rms=0.529 (0.236%), neg=0, invalid=762
0264: dt=24.671756, rms=0.527 (0.261%), neg=0, invalid=762
0265: dt=25.600000, rms=0.526 (0.204%), neg=0, invalid=762
0266: dt=32.000000, rms=0.525 (0.216%), neg=0, invalid=762
0267: dt=23.389558, rms=0.524 (0.179%), neg=0, invalid=762
0268: dt=32.000000, rms=0.523 (0.204%), neg=0, invalid=762
0269: dt=24.640000, rms=0.522 (0.158%), neg=0, invalid=762
0270: dt=25.600000, rms=0.522 (0.170%), neg=0, invalid=762
0271: dt=25.600000, rms=0.521 (0.121%), neg=0, invalid=762
0272: dt=25.600000, rms=0.520 (0.160%), neg=0, invalid=762
0273: dt=25.600000, rms=0.520 (0.105%), neg=0, invalid=762
0274: dt=32.000000, rms=0.519 (0.161%), neg=0, invalid=762
0275: dt=9.600000, rms=0.518 (0.073%), neg=0, invalid=762
0276: dt=0.175000, rms=0.518 (0.012%), neg=0, invalid=762
0277: dt=0.175000, rms=0.518 (0.001%), neg=0, invalid=762
0278: dt=0.087500, rms=0.518 (0.001%), neg=0, invalid=762
0279: dt=0.010937, rms=0.518 (-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=0.535, neg=0, invalid=762
0280: dt=2.880000, rms=0.534 (0.165%), neg=0, invalid=762
0281: dt=1.008000, rms=0.534 (0.006%), neg=0, invalid=762
0282: dt=1.008000, rms=0.534 (0.007%), neg=0, invalid=762
0283: dt=1.008000, rms=0.534 (0.001%), neg=0, invalid=762
0284: dt=1.008000, rms=0.534 (-0.034%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.534, neg=0, invalid=762
0285: dt=0.000000, rms=0.534 (0.127%), neg=0, invalid=762
0286: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762
0287: dt=0.150000, rms=0.534 (-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=0.563, neg=0, invalid=762
0288: dt=1.024000, rms=0.562 (0.217%), neg=0, invalid=762
0289: dt=0.096000, rms=0.562 (-0.002%), neg=0, invalid=762
0290: dt=0.096000, rms=0.562 (0.001%), neg=0, invalid=762
0291: dt=0.096000, rms=0.562 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.562, neg=0, invalid=762
0292: dt=1.280000, rms=0.561 (0.213%), neg=0, invalid=762
0293: dt=0.112000, rms=0.561 (-0.001%), neg=0, invalid=762
0294: dt=0.112000, rms=0.561 (0.001%), neg=0, invalid=762
0295: dt=0.112000, rms=0.561 (-0.001%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.525, neg=0, invalid=762
0296: dt=0.448000, rms=0.511 (2.674%), neg=0, invalid=762
0297: dt=0.448000, rms=0.507 (0.704%), neg=0, invalid=762
0298: dt=0.448000, rms=0.505 (0.407%), neg=0, invalid=762
0299: dt=0.448000, rms=0.504 (0.261%), neg=0, invalid=762
0300: dt=0.448000, rms=0.503 (0.193%), neg=0, invalid=762
0301: dt=0.448000, rms=0.502 (0.148%), neg=0, invalid=762
0302: dt=0.448000, rms=0.501 (0.115%), neg=0, invalid=762
0303: dt=0.448000, rms=0.501 (0.095%), neg=0, invalid=762
0304: dt=0.448000, rms=0.500 (0.078%), neg=0, invalid=762
0305: dt=0.448000, rms=0.500 (0.059%), neg=0, invalid=762
0306: dt=0.448000, rms=0.500 (0.059%), neg=0, invalid=762
0307: dt=0.448000, rms=0.500 (0.040%), neg=0, invalid=762
0308: dt=0.448000, rms=0.499 (0.046%), neg=0, invalid=762
0309: dt=0.448000, rms=0.499 (0.069%), neg=0, invalid=762
0310: dt=0.448000, rms=0.499 (0.082%), neg=0, invalid=762
0311: dt=0.448000, rms=0.498 (0.091%), neg=0, invalid=762
0312: dt=0.448000, rms=0.498 (0.008%), neg=0, invalid=762
0313: dt=0.448000, rms=0.498 (0.009%), neg=0, invalid=762
0314: dt=0.448000, rms=0.498 (0.000%), neg=0, invalid=762
0315: dt=0.320000, rms=0.498 (0.009%), neg=0, invalid=762
0316: dt=0.384000, rms=0.498 (0.011%), neg=0, invalid=762
0317: dt=0.192000, rms=0.498 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.499, neg=0, invalid=762
0318: dt=0.448000, rms=0.495 (0.812%), neg=0, invalid=762
0319: dt=0.448000, rms=0.494 (0.086%), neg=0, invalid=762
0320: dt=0.448000, rms=0.494 (0.026%), neg=0, invalid=762
0321: dt=0.448000, rms=0.494 (0.007%), neg=0, invalid=762
0322: dt=0.448000, rms=0.494 (0.001%), neg=0, invalid=762
0323: dt=0.224000, rms=0.494 (-0.005%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0324: dt=55.488000, rms=0.492 (0.170%), neg=0, invalid=762
0325: dt=0.000000, rms=0.492 (0.002%), neg=0, invalid=762
0326: dt=0.850000, rms=0.492 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0327: dt=23.120000, rms=0.492 (0.146%), neg=0, invalid=762
0328: dt=18.496000, rms=0.492 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0329: dt=36.288000, rms=0.491 (0.260%), neg=0, invalid=762
0330: dt=103.680000, rms=0.490 (0.137%), neg=0, invalid=762
0331: dt=103.680000, rms=0.490 (0.111%), neg=0, invalid=762
0332: dt=103.680000, rms=0.489 (0.109%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
0333: dt=103.680000, rms=0.489 (-0.042%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.490, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0334: dt=36.288000, rms=0.488 (0.333%), neg=0, invalid=762
0335: dt=145.152000, rms=0.487 (0.284%), neg=0, invalid=762
0336: dt=36.288000, rms=0.486 (0.110%), neg=0, invalid=762
0337: dt=36.288000, rms=0.486 (0.059%), neg=0, invalid=762
0338: dt=36.288000, rms=0.486 (0.064%), neg=0, invalid=762
0339: dt=36.288000, rms=0.486 (0.069%), neg=0, invalid=762
0340: dt=36.288000, rms=0.485 (0.066%), neg=0, invalid=762
0341: dt=36.288000, rms=0.485 (0.095%), neg=0, invalid=762
0342: dt=36.288000, rms=0.484 (0.096%), neg=0, invalid=762
0343: dt=36.288000, rms=0.484 (0.096%), neg=0, invalid=762
0344: dt=25.920000, rms=0.484 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.485, neg=0, invalid=762
iter 0, gcam->neg = 9
after 0 iterations, nbhd size=0, neg = 0
0345: dt=32.000000, rms=0.481 (0.764%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 12 iterations, nbhd size=1, neg = 0
0346: dt=44.800000, rms=0.478 (0.572%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0347: dt=11.200000, rms=0.477 (0.212%), neg=0, invalid=762
0348: dt=11.200000, rms=0.477 (0.133%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 9 iterations, nbhd size=1, neg = 0
0349: dt=11.200000, rms=0.476 (0.134%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 8 iterations, nbhd size=1, neg = 0
0350: dt=11.200000, rms=0.475 (0.212%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 8 iterations, nbhd size=1, neg = 0
0351: dt=11.200000, rms=0.474 (0.273%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 6 iterations, nbhd size=0, neg = 0
0352: dt=11.200000, rms=0.473 (0.257%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 5 iterations, nbhd size=0, neg = 0
0353: dt=11.200000, rms=0.472 (0.232%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 9 iterations, nbhd size=1, neg = 0
0354: dt=11.200000, rms=0.471 (0.184%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 10 iterations, nbhd size=0, neg = 0
0355: dt=11.200000, rms=0.470 (0.158%), neg=0, invalid=762
iter 0, gcam->neg = 16
after 12 iterations, nbhd size=1, neg = 0
0356: dt=11.200000, rms=0.469 (0.143%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 4 iterations, nbhd size=0, neg = 0
0357: dt=11.200000, rms=0.469 (0.152%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 8 iterations, nbhd size=1, neg = 0
0358: dt=11.200000, rms=0.468 (0.139%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 9 iterations, nbhd size=0, neg = 0
0359: dt=11.200000, rms=0.467 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 5 iterations, nbhd size=0, neg = 0
0360: dt=11.200000, rms=0.467 (0.136%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 11 iterations, nbhd size=1, neg = 0
0361: dt=11.200000, rms=0.466 (0.128%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 7 iterations, nbhd size=0, neg = 0
0362: dt=11.200000, rms=0.466 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 11 iterations, nbhd size=1, neg = 0
0363: dt=11.200000, rms=0.465 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 6 iterations, nbhd size=0, neg = 0
0364: dt=44.800000, rms=0.465 (0.095%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 16 iterations, nbhd size=1, neg = 0
0365: dt=44.800000, rms=0.465 (-0.090%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.465, neg=0, invalid=762
0366: dt=32.000000, rms=0.462 (0.633%), neg=0, invalid=762
0367: dt=32.000000, rms=0.461 (0.300%), neg=0, invalid=762
0368: dt=21.389474, rms=0.460 (0.150%), neg=0, invalid=762
0369: dt=21.389474, rms=0.460 (0.136%), neg=0, invalid=762
0370: dt=21.389474, rms=0.459 (0.148%), neg=0, invalid=762
0371: dt=21.389474, rms=0.458 (0.160%), neg=0, invalid=762
0372: dt=21.389474, rms=0.458 (0.102%), neg=0, invalid=762
0373: dt=21.389474, rms=0.457 (0.095%), neg=0, invalid=762
0374: dt=44.800000, rms=0.457 (0.086%), neg=0, invalid=762
0375: dt=44.800000, rms=0.457 (-0.081%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
0376: dt=2.814815, rms=0.463 (0.172%), neg=0, invalid=762
0377: dt=1.008000, rms=0.463 (0.008%), neg=0, invalid=762
0378: dt=1.008000, rms=0.463 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0379: dt=4.032000, rms=0.463 (0.202%), neg=0, invalid=762
0380: dt=3.456000, rms=0.463 (0.016%), neg=0, invalid=762
0381: dt=3.456000, rms=0.463 (0.015%), neg=0, invalid=762
0382: dt=3.456000, rms=0.463 (-0.023%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
0383: dt=0.000000, rms=0.472 (0.159%), neg=0, invalid=762
0384: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
0385: dt=0.448000, rms=0.472 (0.188%), neg=0, invalid=762
0386: dt=0.384000, rms=0.472 (0.010%), neg=0, invalid=762
0387: dt=0.384000, rms=0.472 (0.000%), neg=0, invalid=762
0388: dt=0.384000, rms=0.472 (-0.045%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
iter 0, gcam->neg = 796
after 13 iterations, nbhd size=1, neg = 0
0389: dt=2.112594, rms=0.432 (6.237%), neg=0, invalid=762
0390: dt=0.028000, rms=0.432 (0.023%), neg=0, invalid=762
0391: dt=0.028000, rms=0.432 (0.001%), neg=0, invalid=762
0392: dt=0.028000, rms=0.432 (-0.031%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0393: dt=0.048000, rms=0.432 (0.233%), neg=0, invalid=762
0394: dt=0.006000, rms=0.432 (-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=0.418, neg=0, invalid=762
0395: dt=1.734000, rms=0.418 (0.000%), neg=0, invalid=762
0396: dt=0.003613, rms=0.418 (0.000%), neg=0, invalid=762
0397: dt=0.003613, rms=0.418 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0398: dt=32.368000, rms=0.418 (0.004%), neg=0, invalid=762
0399: dt=32.368000, rms=0.418 (0.002%), neg=0, invalid=762
0400: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=762
0401: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=762
0402: dt=32.368000, rms=0.418 (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=0.418, neg=0, invalid=762
0403: dt=7.776000, rms=0.418 (0.008%), neg=0, invalid=762
0404: dt=0.324000, rms=0.418 (0.000%), neg=0, invalid=762
0405: dt=0.324000, rms=0.418 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0406: dt=103.680000, rms=0.418 (0.066%), neg=0, invalid=762
0407: dt=36.288000, rms=0.417 (0.047%), neg=0, invalid=762
0408: dt=36.288000, rms=0.417 (0.014%), neg=0, invalid=762
0409: dt=36.288000, rms=0.417 (0.024%), neg=0, invalid=762
0410: dt=36.288000, rms=0.417 (0.030%), neg=0, invalid=762
0411: dt=36.288000, rms=0.417 (0.032%), neg=0, invalid=762
0412: dt=36.288000, rms=0.417 (0.028%), neg=0, invalid=762
0413: dt=36.288000, rms=0.417 (0.022%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.417, neg=0, invalid=762
0414: dt=11.200000, rms=0.417 (0.096%), neg=0, invalid=762
0415: dt=9.600000, rms=0.417 (0.023%), neg=0, invalid=762
0416: dt=9.600000, rms=0.417 (0.013%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0417: dt=9.600000, rms=0.417 (-0.015%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.417, neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0418: dt=32.000000, rms=0.415 (0.398%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0419: dt=32.000000, rms=0.414 (0.268%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 9 iterations, nbhd size=1, neg = 0
0420: dt=25.600000, rms=0.414 (0.098%), neg=0, invalid=762
0421: dt=25.600000, rms=0.413 (0.140%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 2 iterations, nbhd size=0, neg = 0
0422: dt=25.600000, rms=0.412 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 2 iterations, nbhd size=0, neg = 0
0423: dt=25.600000, rms=0.412 (0.210%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 14 iterations, nbhd size=1, neg = 0
0424: dt=25.600000, rms=0.411 (0.157%), neg=0, invalid=762
iter 0, gcam->neg = 13
after 11 iterations, nbhd size=1, neg = 0
0425: dt=25.600000, rms=0.410 (0.194%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 12 iterations, nbhd size=1, neg = 0
0426: dt=25.600000, rms=0.410 (0.129%), neg=0, invalid=762
iter 0, gcam->neg = 20
after 4 iterations, nbhd size=0, neg = 0
0427: dt=25.600000, rms=0.409 (0.134%), neg=0, invalid=762
iter 0, gcam->neg = 24
after 19 iterations, nbhd size=1, neg = 0
0428: dt=25.600000, rms=0.409 (0.057%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 9 iterations, nbhd size=0, neg = 0
0429: dt=25.600000, rms=0.408 (0.101%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 11 iterations, nbhd size=1, neg = 0
0430: dt=25.600000, rms=0.408 (0.041%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0431: dt=25.600000, rms=0.408 (0.024%), neg=0, invalid=762
0432: dt=25.600000, rms=0.408 (0.031%), neg=0, invalid=762
0433: dt=25.600000, rms=0.408 (0.035%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0434: dt=25.600000, rms=0.408 (0.034%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 4 iterations, nbhd size=0, neg = 0
0435: dt=25.600000, rms=0.408 (0.019%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.412, neg=0, invalid=762
0436: dt=2.304000, rms=0.412 (0.020%), neg=0, invalid=762
0437: dt=0.576000, rms=0.412 (0.001%), neg=0, invalid=762
0438: dt=0.576000, rms=0.412 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.412, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0439: dt=4.750000, rms=0.412 (0.038%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0440: dt=4.032000, rms=0.412 (0.024%), neg=0, invalid=762
0441: dt=4.032000, rms=0.412 (0.020%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0442: dt=4.032000, rms=0.412 (0.013%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0443: dt=4.032000, rms=0.412 (-0.010%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0444: dt=0.000050, rms=0.419 (0.000%), neg=0, invalid=762
0445: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0446: dt=0.000000, rms=0.419 (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=0.407, neg=0, invalid=762
iter 0, gcam->neg = 685
after 18 iterations, nbhd size=1, neg = 0
0447: dt=1.168436, rms=0.397 (2.317%), neg=0, invalid=762
0448: dt=0.000023, rms=0.397 (0.000%), neg=0, invalid=762
0449: dt=0.000023, rms=0.397 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.397, neg=0, invalid=762
0450: dt=0.064000, rms=0.397 (0.018%), neg=0, invalid=762
0451: dt=0.028000, rms=0.397 (0.003%), neg=0, invalid=762
0452: dt=0.028000, rms=0.397 (0.001%), neg=0, invalid=762
0453: dt=0.028000, rms=0.397 (-0.008%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 24 minutes and 25 seconds.
mri_ca_register utimesec    9565.657798
mri_ca_register stimesec    9.174605
mri_ca_register ru_maxrss   1341756
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4156821
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  62952
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    4206
mri_ca_register ru_nivcsw   34739
FSRUNTIME@ mri_ca_register  2.4070 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 04:31:49 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-604
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-6.0.0/0050566/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.36
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 = 0.09388 (12)
Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (730 voxels, overlap=0.233)
Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (730 voxels, peak = 13), gca=13.3
gca peak = 0.17677 (13)
mri peak = 0.08343 (12)
Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (868 voxels, overlap=0.842)
Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (868 voxels, peak = 10), gca=10.1
gca peak = 0.28129 (95)
mri peak = 0.09037 (90)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (751 voxels, overlap=1.018)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (751 voxels, peak = 89), gca=88.8
gca peak = 0.16930 (96)
mri peak = 0.10694 (94)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (692 voxels, overlap=1.013)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (692 voxels, peak = 94), gca=93.6
gca peak = 0.24553 (55)
mri peak = 0.08758 (60)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1056 voxels, overlap=1.007)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1056 voxels, peak = 57), gca=57.5
gca peak = 0.30264 (59)
mri peak = 0.09937 (58)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (860 voxels, overlap=1.013)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (860 voxels, peak = 60), gca=60.5
gca peak = 0.07580 (103)
mri peak = 0.09470 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32978 voxels, overlap=0.643)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32978 voxels, peak = 106), gca=105.6
gca peak = 0.07714 (104)
mri peak = 0.10508 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (33541 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (33541 voxels, peak = 106), gca=105.6
gca peak = 0.09712 (58)
mri peak = 0.04317 (55)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (39158 voxels, overlap=0.911)
Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (39158 voxels, peak = 55), gca=54.8
gca peak = 0.11620 (58)
mri peak = 0.04299 (52)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (39473 voxels, overlap=0.918)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (39473 voxels, peak = 53), gca=53.1
gca peak = 0.30970 (66)
mri peak = 0.12730 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, peak = 66), gca=66.0
gca peak = 0.15280 (69)
mri peak = 0.15306 (67)
Left_Caudate (11): linear fit = 0.89 x + 0.0 (1078 voxels, overlap=0.415)
Left_Caudate (11): linear fit = 0.89 x + 0.0 (1078 voxels, peak = 62), gca=61.8
gca peak = 0.13902 (56)
mri peak = 0.05693 (56)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (37288 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (37288 voxels, peak = 55), gca=55.2
gca peak = 0.14777 (55)
mri peak = 0.05897 (56)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (37289 voxels, overlap=0.993)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (37289 voxels, peak = 57), gca=57.5
gca peak = 0.16765 (84)
mri peak = 0.10502 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5911 voxels, overlap=0.729)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5911 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.08673 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7171 voxels, overlap=0.557)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7171 voxels, peak = 91), gca=91.1
gca peak = 0.29869 (57)
mri peak = 0.09770 (58)
Left_Amygdala (18): linear fit = 0.96 x + 0.0 (530 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 0.96 x + 0.0 (530 voxels, peak = 55), gca=55.0
gca peak = 0.33601 (57)
mri peak = 0.13066 (59)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (575 voxels, overlap=0.983)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (575 voxels, peak = 60), gca=59.6
gca peak = 0.11131 (90)
mri peak = 0.09167 (82)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3720 voxels, overlap=0.915)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3720 voxels, peak = 86), gca=85.9
gca peak = 0.11793 (83)
mri peak = 0.07687 (82)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, overlap=0.974)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, peak = 83), gca=83.0
gca peak = 0.08324 (81)
mri peak = 0.08470 (75)
Left_Putamen (12): linear fit = 0.94 x + 0.0 (1889 voxels, overlap=0.795)
Left_Putamen (12): linear fit = 0.94 x + 0.0 (1889 voxels, peak = 77), gca=76.5
gca peak = 0.10360 (77)
mri peak = 0.07397 (72)
Right_Putamen (51): linear fit = 0.95 x + 0.0 (1778 voxels, overlap=0.750)
Right_Putamen (51): linear fit = 0.95 x + 0.0 (1778 voxels, peak = 74), gca=73.5
gca peak = 0.08424 (78)
mri peak = 0.07501 (85)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (12972 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (12972 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.07138 (97)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1668 voxels, overlap=0.756)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1668 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.06720 (97)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1757 voxels, overlap=0.725)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1757 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.07823 (33)
gca peak = 0.19357 (14)
mri peak = 0.10541 (12)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (349 voxels, overlap=0.713)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (349 voxels, peak = 10), gca=9.9
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.71 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.19552 (12)
mri peak = 0.09388 (12)
Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (730 voxels, overlap=0.922)
Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (730 voxels, peak = 12), gca=12.4
gca peak = 0.23646 (10)
mri peak = 0.08343 (12)
Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (868 voxels, overlap=0.967)
Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (868 voxels, peak = 10), gca=10.4
gca peak = 0.27117 (88)
mri peak = 0.09037 (90)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (751 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (751 voxels, peak = 87), gca=86.7
gca peak = 0.20112 (94)
mri peak = 0.10694 (94)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (692 voxels, overlap=1.009)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (692 voxels, peak = 95), gca=95.4
gca peak = 0.28858 (58)
mri peak = 0.08758 (60)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1056 voxels, overlap=1.005)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1056 voxels, peak = 59), gca=59.4
gca peak = 0.26523 (61)
mri peak = 0.09937 (58)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (860 voxels, overlap=1.012)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (860 voxels, peak = 60), gca=60.1
gca peak = 0.07610 (105)
mri peak = 0.09470 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32978 voxels, overlap=0.749)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32978 voxels, peak = 104), gca=104.5
gca peak = 0.07820 (106)
mri peak = 0.10508 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33541 voxels, overlap=0.679)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33541 voxels, peak = 106), gca=106.0
gca peak = 0.10323 (55)
mri peak = 0.04317 (55)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (39158 voxels, overlap=0.998)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (39158 voxels, peak = 54), gca=54.2
gca peak = 0.12626 (53)
mri peak = 0.04299 (52)
Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (39473 voxels, overlap=0.986)
Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (39473 voxels, peak = 55), gca=55.4
gca peak = 0.30217 (66)
mri peak = 0.12730 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, peak = 66), gca=66.0
gca peak = 0.13943 (68)
mri peak = 0.15306 (67)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1078 voxels, overlap=0.864)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1078 voxels, peak = 69), gca=69.0
gca peak = 0.14510 (55)
mri peak = 0.05693 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (37288 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (37288 voxels, peak = 55), gca=55.0
gca peak = 0.14202 (57)
mri peak = 0.05897 (56)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (37289 voxels, overlap=0.996)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (37289 voxels, peak = 55), gca=55.0
gca peak = 0.15888 (90)
mri peak = 0.10502 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5911 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5911 voxels, peak = 90), gca=89.6
gca peak = 0.14988 (91)
mri peak = 0.08673 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7171 voxels, overlap=0.956)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7171 voxels, peak = 91), gca=90.5
gca peak = 0.27905 (56)
mri peak = 0.09770 (58)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (530 voxels, overlap=1.015)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (530 voxels, peak = 59), gca=58.5
gca peak = 0.29016 (60)
mri peak = 0.13066 (59)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (575 voxels, overlap=1.006)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (575 voxels, peak = 62), gca=61.5
gca peak = 0.11376 (86)
mri peak = 0.09167 (82)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3720 voxels, overlap=0.954)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3720 voxels, peak = 85), gca=84.7
gca peak = 0.12266 (83)
mri peak = 0.07687 (82)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, overlap=0.971)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, peak = 83), gca=83.0
gca peak = 0.09390 (78)
mri peak = 0.08470 (75)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1889 voxels, overlap=0.918)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1889 voxels, peak = 78), gca=78.0
gca peak = 0.11277 (72)
mri peak = 0.07397 (72)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1778 voxels, overlap=0.940)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1778 voxels, peak = 71), gca=70.9
gca peak = 0.07149 (90)
mri peak = 0.07501 (85)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12972 voxels, overlap=0.847)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12972 voxels, peak = 90), gca=90.0
gca peak = 0.11321 (96)
mri peak = 0.07138 (97)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1668 voxels, overlap=0.910)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1668 voxels, peak = 95), gca=94.6
gca peak = 0.14451 (91)
mri peak = 0.06720 (97)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1757 voxels, overlap=0.931)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1757 voxels, peak = 93), gca=93.3
gca peak = 0.20920 (18)
mri peak = 0.07823 (33)
gca peak = 0.26059 (10)
mri peak = 0.10541 (12)
Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (349 voxels, overlap=0.887)
Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (349 voxels, peak = 10), gca=10.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15047 (33)
gca peak Left_Thalamus = 1.00000 (93)
gca peak Third_Ventricle = 0.20920 (18)
gca peak CSF = 0.29800 (26)
gca peak Left_Accumbens_area = 0.60061 (56)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.22003 (24)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82280 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65783 (23)
gca peak WM_hypointensities = 0.07165 (78)
gca peak non_WM_hypointensities = 0.08683 (44)
gca peak Optic_Chiasm = 0.70887 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.02 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
49824 voxels changed in iteration 0 of unlikely voxel relabeling
64 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
27992 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
339 hippocampal voxels changed.
1 amygdala voxels changed.
pass 1: 63868 changed. image ll: -2.099, PF=0.500
pass 2: 17777 changed. image ll: -2.099, PF=0.500
pass 3: 6160 changed.
pass 4: 2435 changed.
30391 voxels changed in iteration 0 of unlikely voxel relabeling
162 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5290 voxels changed in iteration 0 of unlikely voxel relabeling
20 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5254 voxels changed in iteration 0 of unlikely voxel relabeling
91 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5004 voxels changed in iteration 0 of unlikely voxel relabeling
39 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3110.188179
mri_ca_label stimesec    1.727737
mri_ca_label ru_maxrss   2108668
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   760315
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  62944
mri_ca_label ru_oublock  456
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    289
mri_ca_label ru_nivcsw   4617
auto-labeling took 51 minutes and 6 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/cc_up.lta 0050566 

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-6.0.0/0050566/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/norm.mgz
30853 voxels in left wm, 62494 in right wm, xrange [119, 129]
searching rotation angles z=[-8  6], y=[-9  5]

searching scale 1 Z rot -8.2  
searching scale 1 Z rot -7.9  
searching scale 1 Z rot -7.7  
searching scale 1 Z rot -7.4  
searching scale 1 Z rot -7.2  
searching scale 1 Z rot -6.9  
searching scale 1 Z rot -6.7  
searching scale 1 Z rot -6.4  
searching scale 1 Z rot -6.2  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  global minimum found at slice 125.0, rotations (-1.94, -1.17)
final transformation (x=125.0, yr=-1.943, zr=-1.166):
 0.99922   0.02036  -0.03390   3.90892;
-0.02035   0.99979   0.00069   0.49977;
 0.03391   0.00000   0.99943   21.82046;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 130 102
eigenvectors:
-0.00055  -0.00577   0.99998;
-0.14033  -0.99009  -0.00579;
 0.99011  -0.14033  -0.00026;
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.9 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 05:23:48 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 05:23:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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...
1718 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 110
gm peak at 61 (61), valley at  0 (-1)
csf peak at 30, setting threshold to 50
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 60 (60), valley at  0 (-1)
csf peak at 30, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 57 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 05:26:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1516277 voxels in mask (pct=  9.04)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 05:26:47 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 104.4 +- 5.4 [79.0 --> 125.0]
GM (71.0) : 69.4 +- 9.5 [30.0 --> 95.0]
setting bottom of white matter range to 79.0
setting top of gray matter range to 88.5
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...
3572 sparsely connected voxels removed...
thickening thin strands....
20 segments, 6263 filled
2005 bright non-wm voxels segmented.
1648 diagonally connected voxels added...
white matter segmentation took 1.5 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.44 minutes
reading wm segmentation from wm.seg.mgz...
61 voxels added to wm to prevent paths from MTL structures to cortex
3322 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 41562 voxels turned on, 42119 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 107   new 107
115,126,128 old 107   new 107
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  22 found -  22 modified     |    TOTAL:  22
pass   2 (xy+):   0 found -  22 modified     |    TOTAL:  22
pass   1 (xy-):  17 found -  17 modified     |    TOTAL:  39
pass   2 (xy-):   0 found -  17 modified     |    TOTAL:  39
pass   1 (yz+):  24 found -  24 modified     |    TOTAL:  63
pass   2 (yz+):   0 found -  24 modified     |    TOTAL:  63
pass   1 (yz-):  28 found -  28 modified     |    TOTAL:  91
pass   2 (yz-):   0 found -  28 modified     |    TOTAL:  91
pass   1 (xz+):  20 found -  20 modified     |    TOTAL: 111
pass   2 (xz+):   0 found -  20 modified     |    TOTAL: 111
pass   1 (xz-):  19 found -  19 modified     |    TOTAL: 130
pass   2 (xz-):   0 found -  19 modified     |    TOTAL: 130
Iteration Number : 1
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  12
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  12
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  22
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  22
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  32
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  32
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  44
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  44
Iteration Number : 1
pass   1 (++):  40 found -  40 modified     |    TOTAL:  40
pass   2 (++):   0 found -  40 modified     |    TOTAL:  40
pass   1 (+-):  47 found -  47 modified     |    TOTAL:  87
pass   2 (+-):   0 found -  47 modified     |    TOTAL:  87
pass   1 (--): 119 found - 119 modified     |    TOTAL: 206
pass   2 (--):   1 found - 120 modified     |    TOTAL: 207
pass   3 (--):   0 found - 120 modified     |    TOTAL: 207
pass   1 (-+):  35 found -  35 modified     |    TOTAL: 242
pass   2 (-+):   0 found -  35 modified     |    TOTAL: 242
Iteration Number : 2
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:   8
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:  12
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:  12
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  15
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  15
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  17
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  17
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  20
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  20
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 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   6
pass   1 (--):   1 found -   1 modified     |    TOTAL:   7
pass   2 (--):   0 found -   1 modified     |    TOTAL:   7
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   9
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   9
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 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 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 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+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 6
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 : 6
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 : 6
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 = 455 (out of 497909: 0.091382)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 05:28:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.08085  -0.05724  -0.05528   4.52116;
 0.06755   1.05155   0.32229  -78.07095;
 0.03166  -0.33587   0.99870   44.39107;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.08085  -0.05724  -0.05528   4.52116;
 0.06755   1.05155   0.32229  -78.07095;
 0.03166  -0.33587   0.99870   44.39107;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1050 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75)
no need to search
using seed (125, 119, 150), TAL = (3.0, 22.0, 9.0)
talairach voxel to voxel transform
 0.92051   0.06018   0.03153  -0.86359;
-0.04550   0.85914  -0.27977   79.69904;
-0.04448   0.28702   0.90621  -17.61836;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (125,  119,  150) --> (3.0, 22.0, 9.0)
done.
writing output to filled.mgz...
filling took 0.6 minutes
talairach cc position changed to (3.00, 22.00, 9.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, 22.00, 9.00) SRC: (109.52, 135.10, 147.71)
search lh wm seed point around talairach space (-15.00, 22.00, 9.00), SRC: (142.66, 133.46, 146.11)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 05:29:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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


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

Total Number of Modified Voxels = 11 (out of 239637: 0.004590)
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: 1220 vertices, 1353 faces
slice 50: 8286 vertices, 8599 faces
slice 60: 18647 vertices, 19038 faces
slice 70: 29951 vertices, 30363 faces
slice 80: 40657 vertices, 41106 faces
slice 90: 51941 vertices, 52388 faces
slice 100: 62768 vertices, 63222 faces
slice 110: 73733 vertices, 74203 faces
slice 120: 84508 vertices, 85000 faces
slice 130: 94892 vertices, 95374 faces
slice 140: 105348 vertices, 105790 faces
slice 150: 114063 vertices, 114500 faces
slice 160: 122418 vertices, 122772 faces
slice 170: 128274 vertices, 128570 faces
slice 180: 132559 vertices, 132819 faces
slice 190: 134822 vertices, 134980 faces
slice 200: 134906 vertices, 135040 faces
slice 210: 134906 vertices, 135040 faces
slice 220: 134906 vertices, 135040 faces
slice 230: 134906 vertices, 135040 faces
slice 240: 134906 vertices, 135040 faces
slice 250: 134906 vertices, 135040 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...
   134906 voxel in cpt #1: X=-134 [v=134906,e=405120,f=270080] located at (-23.177553, -23.320089, -9.925511)
For the whole surface: X=-134 [v=134906,e=405120,f=270080]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 05:29:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
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 = 4 (out of 235310: 0.001700)
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: 937 vertices, 1014 faces
slice 50: 6953 vertices, 7209 faces
slice 60: 16590 vertices, 16985 faces
slice 70: 27248 vertices, 27605 faces
slice 80: 38276 vertices, 38665 faces
slice 90: 48896 vertices, 49256 faces
slice 100: 59629 vertices, 60033 faces
slice 110: 69679 vertices, 70079 faces
slice 120: 79888 vertices, 80273 faces
slice 130: 90128 vertices, 90514 faces
slice 140: 99718 vertices, 100102 faces
slice 150: 108656 vertices, 109010 faces
slice 160: 116359 vertices, 116663 faces
slice 170: 121863 vertices, 122104 faces
slice 180: 126187 vertices, 126394 faces
slice 190: 128431 vertices, 128542 faces
slice 200: 128566 vertices, 128644 faces
slice 210: 128566 vertices, 128644 faces
slice 220: 128566 vertices, 128644 faces
slice 230: 128566 vertices, 128644 faces
slice 240: 128566 vertices, 128644 faces
slice 250: 128566 vertices, 128644 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...
   128566 voxel in cpt #1: X=-78 [v=128566,e=385932,f=257288] located at (28.957212, -22.628572, -10.298430)
For the whole surface: X=-78 [v=128566,e=385932,f=257288]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 05:29:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 05:29:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

Waiting for PID 8532 of (8532 8535) to complete...
Waiting for PID 8535 of (8532 8535) 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 (8532 8535) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 05:29:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 05:29:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

Waiting for PID 8580 of (8580 8583) to complete...
Waiting for PID 8583 of (8580 8583) 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 = 46.8 mm, total surface area = 73098 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.7 minutes

step 000: RMS=0.158 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.087 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.073 (target=0.015)   
step 030: RMS=0.068 (target=0.015)   
step 035: RMS=0.064 (target=0.015)   
step 040: RMS=0.062 (target=0.015)   
step 045: RMS=0.059 (target=0.015)   
step 050: RMS=0.057 (target=0.015)   
step 055: RMS=0.056 (target=0.015)   
step 060: RMS=0.055 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    42.536533
mris_inflate stimesec    0.106983
mris_inflate ru_maxrss   196900
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   28721
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  9496
mris_inflate ru_oublock  9512
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2120
mris_inflate ru_nivcsw   3586

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 45.9 mm, total surface area = 69349 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.7 minutes

step 000: RMS=0.154 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.080 (target=0.015)   
step 020: RMS=0.073 (target=0.015)   
step 025: RMS=0.067 (target=0.015)   
step 030: RMS=0.061 (target=0.015)   
step 035: RMS=0.057 (target=0.015)   
step 040: RMS=0.054 (target=0.015)   
step 045: RMS=0.052 (target=0.015)   
step 050: RMS=0.050 (target=0.015)   
step 055: RMS=0.049 (target=0.015)   
step 060: RMS=0.049 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    40.779800
mris_inflate stimesec    0.098984
mris_inflate ru_maxrss   187956
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   26995
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  9048
mris_inflate ru_oublock  9064
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2018
mris_inflate ru_nivcsw   3325
PIDs (8580 8583) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 05:30:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 05:30:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

Waiting for PID 8668 of (8668 8672) to complete...
Waiting for PID 8672 of (8668 8672) 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 0.99 +- 0.62 (0.00-->6.31) (max @ vno 68929 --> 69966)
face area 0.03 +- 0.04 (-0.25-->0.63)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.322...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.513, avgs=0
005/300: dt: 0.9000, rms radial error=175.255, avgs=0
010/300: dt: 0.9000, rms radial error=174.700, avgs=0
015/300: dt: 0.9000, rms radial error=173.970, avgs=0
020/300: dt: 0.9000, rms radial error=173.138, avgs=0
025/300: dt: 0.9000, rms radial error=172.249, avgs=0
030/300: dt: 0.9000, rms radial error=171.335, avgs=0
035/300: dt: 0.9000, rms radial error=170.405, avgs=0
040/300: dt: 0.9000, rms radial error=169.467, avgs=0
045/300: dt: 0.9000, rms radial error=168.527, avgs=0
050/300: dt: 0.9000, rms radial error=167.588, avgs=0
055/300: dt: 0.9000, rms radial error=166.653, avgs=0
060/300: dt: 0.9000, rms radial error=165.721, avgs=0
065/300: dt: 0.9000, rms radial error=164.793, avgs=0
070/300: dt: 0.9000, rms radial error=163.869, avgs=0
075/300: dt: 0.9000, rms radial error=162.950, avgs=0
080/300: dt: 0.9000, rms radial error=162.036, avgs=0
085/300: dt: 0.9000, rms radial error=161.127, avgs=0
090/300: dt: 0.9000, rms radial error=160.223, avgs=0
095/300: dt: 0.9000, rms radial error=159.324, avgs=0
100/300: dt: 0.9000, rms radial error=158.429, avgs=0
105/300: dt: 0.9000, rms radial error=157.541, avgs=0
110/300: dt: 0.9000, rms radial error=156.657, avgs=0
115/300: dt: 0.9000, rms radial error=155.777, avgs=0
120/300: dt: 0.9000, rms radial error=154.903, avgs=0
125/300: dt: 0.9000, rms radial error=154.033, avgs=0
130/300: dt: 0.9000, rms radial error=153.167, avgs=0
135/300: dt: 0.9000, rms radial error=152.306, avgs=0
140/300: dt: 0.9000, rms radial error=151.450, avgs=0
145/300: dt: 0.9000, rms radial error=150.598, avgs=0
150/300: dt: 0.9000, rms radial error=149.751, avgs=0
155/300: dt: 0.9000, rms radial error=148.909, avgs=0
160/300: dt: 0.9000, rms radial error=148.070, avgs=0
165/300: dt: 0.9000, rms radial error=147.237, avgs=0
170/300: dt: 0.9000, rms radial error=146.408, avgs=0
175/300: dt: 0.9000, rms radial error=145.583, avgs=0
180/300: dt: 0.9000, rms radial error=144.763, avgs=0
185/300: dt: 0.9000, rms radial error=143.948, avgs=0
190/300: dt: 0.9000, rms radial error=143.137, avgs=0
195/300: dt: 0.9000, rms radial error=142.331, avgs=0
200/300: dt: 0.9000, rms radial error=141.530, avgs=0
205/300: dt: 0.9000, rms radial error=140.732, avgs=0
210/300: dt: 0.9000, rms radial error=139.939, avgs=0
215/300: dt: 0.9000, rms radial error=139.151, avgs=0
220/300: dt: 0.9000, rms radial error=138.367, avgs=0
225/300: dt: 0.9000, rms radial error=137.587, avgs=0
230/300: dt: 0.9000, rms radial error=136.811, avgs=0
235/300: dt: 0.9000, rms radial error=136.040, avgs=0
240/300: dt: 0.9000, rms radial error=135.273, avgs=0
245/300: dt: 0.9000, rms radial error=134.511, avgs=0
250/300: dt: 0.9000, rms radial error=133.752, avgs=0
255/300: dt: 0.9000, rms radial error=132.999, avgs=0
260/300: dt: 0.9000, rms radial error=132.249, avgs=0
265/300: dt: 0.9000, rms radial error=131.503, avgs=0
270/300: dt: 0.9000, rms radial error=130.762, avgs=0
275/300: dt: 0.9000, rms radial error=130.025, avgs=0
280/300: dt: 0.9000, rms radial error=129.292, avgs=0
285/300: dt: 0.9000, rms radial error=128.562, avgs=0
290/300: dt: 0.9000, rms radial error=127.837, avgs=0
295/300: dt: 0.9000, rms radial error=127.116, avgs=0
300/300: dt: 0.9000, rms radial error=126.400, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15616.91
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 2 (K=40.0), pass 1, starting sse = 2671.42
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 3 (K=160.0), pass 1, starting sse = 340.05
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00197
epoch 4 (K=640.0), pass 1, starting sse = 52.44
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/12 = 0.00749
final distance error %29.00
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    246.873469
mris_sphere stimesec    0.156976
mris_sphere ru_maxrss   197100
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   28770
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9536
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8376
mris_sphere ru_nivcsw   20486
FSRUNTIME@ mris_sphere  0.0682 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 1.01 +- 0.61 (0.00-->6.12) (max @ vno 59460 --> 60595)
face area 0.03 +- 0.04 (-0.05-->0.63)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.323...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.046, avgs=0
005/300: dt: 0.9000, rms radial error=175.789, avgs=0
010/300: dt: 0.9000, rms radial error=175.237, avgs=0
015/300: dt: 0.9000, rms radial error=174.513, avgs=0
020/300: dt: 0.9000, rms radial error=173.689, avgs=0
025/300: dt: 0.9000, rms radial error=172.808, avgs=0
030/300: dt: 0.9000, rms radial error=171.895, avgs=0
035/300: dt: 0.9000, rms radial error=170.965, avgs=0
040/300: dt: 0.9000, rms radial error=170.028, avgs=0
045/300: dt: 0.9000, rms radial error=169.087, avgs=0
050/300: dt: 0.9000, rms radial error=168.148, avgs=0
055/300: dt: 0.9000, rms radial error=167.210, avgs=0
060/300: dt: 0.9000, rms radial error=166.276, avgs=0
065/300: dt: 0.9000, rms radial error=165.346, avgs=0
070/300: dt: 0.9000, rms radial error=164.422, avgs=0
075/300: dt: 0.9000, rms radial error=163.503, avgs=0
080/300: dt: 0.9000, rms radial error=162.588, avgs=0
085/300: dt: 0.9000, rms radial error=161.679, avgs=0
090/300: dt: 0.9000, rms radial error=160.774, avgs=0
095/300: dt: 0.9000, rms radial error=159.873, avgs=0
100/300: dt: 0.9000, rms radial error=158.978, avgs=0
105/300: dt: 0.9000, rms radial error=158.087, avgs=0
110/300: dt: 0.9000, rms radial error=157.200, avgs=0
115/300: dt: 0.9000, rms radial error=156.319, avgs=0
120/300: dt: 0.9000, rms radial error=155.442, avgs=0
125/300: dt: 0.9000, rms radial error=154.569, avgs=0
130/300: dt: 0.9000, rms radial error=153.701, avgs=0
135/300: dt: 0.9000, rms radial error=152.837, avgs=0
140/300: dt: 0.9000, rms radial error=151.979, avgs=0
145/300: dt: 0.9000, rms radial error=151.124, avgs=0
150/300: dt: 0.9000, rms radial error=150.275, avgs=0
155/300: dt: 0.9000, rms radial error=149.430, avgs=0
160/300: dt: 0.9000, rms radial error=148.590, avgs=0
165/300: dt: 0.9000, rms radial error=147.754, avgs=0
170/300: dt: 0.9000, rms radial error=146.923, avgs=0
175/300: dt: 0.9000, rms radial error=146.097, avgs=0
180/300: dt: 0.9000, rms radial error=145.275, avgs=0
185/300: dt: 0.9000, rms radial error=144.457, avgs=0
190/300: dt: 0.9000, rms radial error=143.644, avgs=0
195/300: dt: 0.9000, rms radial error=142.835, avgs=0
200/300: dt: 0.9000, rms radial error=142.031, avgs=0
205/300: dt: 0.9000, rms radial error=141.231, avgs=0
210/300: dt: 0.9000, rms radial error=140.436, avgs=0
215/300: dt: 0.9000, rms radial error=139.646, avgs=0
220/300: dt: 0.9000, rms radial error=138.859, avgs=0
225/300: dt: 0.9000, rms radial error=138.077, avgs=0
230/300: dt: 0.9000, rms radial error=137.300, avgs=0
235/300: dt: 0.9000, rms radial error=136.526, avgs=0
240/300: dt: 0.9000, rms radial error=135.757, avgs=0
245/300: dt: 0.9000, rms radial error=134.992, avgs=0
250/300: dt: 0.9000, rms radial error=134.231, avgs=0
255/300: dt: 0.9000, rms radial error=133.475, avgs=0
260/300: dt: 0.9000, rms radial error=132.723, avgs=0
265/300: dt: 0.9000, rms radial error=131.975, avgs=0
270/300: dt: 0.9000, rms radial error=131.231, avgs=0
275/300: dt: 0.9000, rms radial error=130.491, avgs=0
280/300: dt: 0.9000, rms radial error=129.755, avgs=0
285/300: dt: 0.9000, rms radial error=129.024, avgs=0
290/300: dt: 0.9000, rms radial error=128.296, avgs=0
295/300: dt: 0.9000, rms radial error=127.573, avgs=0
300/300: dt: 0.9000, rms radial error=126.854, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 14809.65
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 2 (K=40.0), pass 1, starting sse = 2431.54
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 3 (K=160.0), pass 1, starting sse = 255.76
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/11 = 0.00890
epoch 4 (K=640.0), pass 1, starting sse = 19.78
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/13 = 0.00831
final distance error %26.45
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    242.156186
mris_sphere stimesec    0.176973
mris_sphere ru_maxrss   188160
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   27556
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9088
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8208
mris_sphere ru_nivcsw   18103
FSRUNTIME@ mris_sphere  0.0673 hours 1 threads
PIDs (8668 8672) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 05:34:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 05:34:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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


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

#@# Fix Topology lh Sun Oct  8 05:34:31 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 lh 

#@# Fix Topology rh Sun Oct  8 05:34:31 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 rh 

Waiting for PID 8933 of (8933 8936) to complete...
Waiting for PID 8936 of (8933 8936) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 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=-134 (nv=134906, nf=270080, ne=405120, g=68)
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 9 iterations
marking ambiguous vertices...
28813 ambiguous faces found in tessellation
segmenting defects...
50 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 15 into 12
      -merging segment 43 into 37
48 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2964  (-4.6482)
      -vertex     loglikelihood: -6.2890  (-3.1445)
      -normal dot loglikelihood: -3.6136  (-3.6136)
      -quad curv  loglikelihood: -5.7849  (-2.8924)
      Total Loglikelihood : -24.9838

CORRECTING DEFECT 0 (vertices=94, convex hull=140, v0=67)
After retessellation of defect 0 (v0=67), euler #=-40 (119149,354567,235378) : difference with theory (-45) = -5 

CORRECTING DEFECT 1 (vertices=74, convex hull=122, v0=866)
After retessellation of defect 1 (v0=866), euler #=-39 (119183,354720,235498) : difference with theory (-44) = -5 

CORRECTING DEFECT 2 (vertices=306, convex hull=232, v0=2209)
After retessellation of defect 2 (v0=2209), euler #=-38 (119300,355178,235840) : difference with theory (-43) = -5 

CORRECTING DEFECT 3 (vertices=30, convex hull=72, v0=6846)
After retessellation of defect 3 (v0=6846), euler #=-37 (119319,355264,235908) : difference with theory (-42) = -5 

CORRECTING DEFECT 4 (vertices=88, convex hull=132, v0=7068)
After retessellation of defect 4 (v0=7068), euler #=-36 (119338,355387,236013) : difference with theory (-41) = -5 

CORRECTING DEFECT 5 (vertices=109, convex hull=109, v0=9079)
After retessellation of defect 5 (v0=9079), euler #=-35 (119397,355614,236182) : difference with theory (-40) = -5 

CORRECTING DEFECT 6 (vertices=311, convex hull=188, v0=9184)
After retessellation of defect 6 (v0=9184), euler #=-34 (119448,355856,236374) : difference with theory (-39) = -5 

CORRECTING DEFECT 7 (vertices=20, convex hull=28, v0=11170)
After retessellation of defect 7 (v0=11170), euler #=-33 (119449,355867,236385) : difference with theory (-38) = -5 

CORRECTING DEFECT 8 (vertices=417, convex hull=178, v0=11623)
After retessellation of defect 8 (v0=11623), euler #=-32 (119640,356529,236857) : difference with theory (-37) = -5 

CORRECTING DEFECT 9 (vertices=21, convex hull=67, v0=12130)
After retessellation of defect 9 (v0=12130), euler #=-31 (119653,356589,236905) : difference with theory (-36) = -5 

CORRECTING DEFECT 10 (vertices=8955, convex hull=1082, v0=13015)
XL defect detected...
After retessellation of defect 10 (v0=13015), euler #=-34 (119817,357670,237819) : difference with theory (-35) = -1 

CORRECTING DEFECT 11 (vertices=148, convex hull=137, v0=16381)
After retessellation of defect 11 (v0=16381), euler #=-33 (119877,357914,238004) : difference with theory (-34) = -1 

CORRECTING DEFECT 12 (vertices=648, convex hull=277, v0=18307)
After retessellation of defect 12 (v0=18307), euler #=-33 (120036,358547,238478) : difference with theory (-33) = 0 

CORRECTING DEFECT 13 (vertices=98, convex hull=83, v0=27097)
After retessellation of defect 13 (v0=27097), euler #=-32 (120080,358716,238604) : difference with theory (-32) = 0 

CORRECTING DEFECT 14 (vertices=132, convex hull=125, v0=27604)
normal vector of length zero at vertex 130549 with 3 faces
normal vector of length zero at vertex 130549 with 3 faces
After retessellation of defect 14 (v0=27604), euler #=-31 (120128,358916,238757) : difference with theory (-31) = 0 

CORRECTING DEFECT 15 (vertices=249, convex hull=169, v0=35914)
After retessellation of defect 15 (v0=35914), euler #=-30 (120230,359308,239048) : difference with theory (-30) = 0 

CORRECTING DEFECT 16 (vertices=281, convex hull=229, v0=38363)
After retessellation of defect 16 (v0=38363), euler #=-29 (120347,359777,239401) : difference with theory (-29) = 0 

CORRECTING DEFECT 17 (vertices=94, convex hull=90, v0=45202)
After retessellation of defect 17 (v0=45202), euler #=-28 (120380,359920,239512) : difference with theory (-28) = 0 

CORRECTING DEFECT 18 (vertices=61, convex hull=73, v0=51598)
After retessellation of defect 18 (v0=51598), euler #=-27 (120414,360053,239612) : difference with theory (-27) = 0 

CORRECTING DEFECT 19 (vertices=28, convex hull=62, v0=51913)
After retessellation of defect 19 (v0=51913), euler #=-26 (120423,360104,239655) : difference with theory (-26) = 0 

CORRECTING DEFECT 20 (vertices=51, convex hull=97, v0=52373)
After retessellation of defect 20 (v0=52373), euler #=-25 (120458,360250,239767) : difference with theory (-25) = 0 

CORRECTING DEFECT 21 (vertices=47, convex hull=83, v0=53985)
After retessellation of defect 21 (v0=53985), euler #=-24 (120490,360380,239866) : difference with theory (-24) = 0 

CORRECTING DEFECT 22 (vertices=141, convex hull=168, v0=54971)
normal vector of length zero at vertex 131494 with 4 faces
normal vector of length zero at vertex 131496 with 4 faces
normal vector of length zero at vertex 131496 with 4 faces
normal vector of length zero at vertex 131496 with 4 faces
normal vector of length zero at vertex 131508 with 4 faces
normal vector of length zero at vertex 131508 with 4 faces
normal vector of length zero at vertex 131508 with 4 faces
After retessellation of defect 22 (v0=54971), euler #=-23 (120532,360582,240027) : difference with theory (-23) = 0 

CORRECTING DEFECT 23 (vertices=37, convex hull=66, v0=56223)
After retessellation of defect 23 (v0=56223), euler #=-22 (120550,360664,240092) : difference with theory (-22) = 0 

CORRECTING DEFECT 24 (vertices=5, convex hull=26, v0=57303)
After retessellation of defect 24 (v0=57303), euler #=-21 (120551,360675,240103) : difference with theory (-21) = 0 

CORRECTING DEFECT 25 (vertices=25, convex hull=22, v0=59406)
After retessellation of defect 25 (v0=59406), euler #=-20 (120555,360692,240117) : difference with theory (-20) = 0 

CORRECTING DEFECT 26 (vertices=16, convex hull=46, v0=69489)
After retessellation of defect 26 (v0=69489), euler #=-19 (120562,360731,240150) : difference with theory (-19) = 0 

CORRECTING DEFECT 27 (vertices=8, convex hull=32, v0=69601)
After retessellation of defect 27 (v0=69601), euler #=-18 (120563,360743,240162) : difference with theory (-18) = 0 

CORRECTING DEFECT 28 (vertices=56, convex hull=112, v0=71664)
After retessellation of defect 28 (v0=71664), euler #=-17 (120599,360894,240278) : difference with theory (-17) = 0 

CORRECTING DEFECT 29 (vertices=9, convex hull=13, v0=76603)
After retessellation of defect 29 (v0=76603), euler #=-16 (120600,360899,240283) : difference with theory (-16) = 0 

CORRECTING DEFECT 30 (vertices=96, convex hull=101, v0=79241)
After retessellation of defect 30 (v0=79241), euler #=-15 (120639,361062,240408) : difference with theory (-15) = 0 

CORRECTING DEFECT 31 (vertices=125, convex hull=94, v0=82520)
After retessellation of defect 31 (v0=82520), euler #=-14 (120690,361255,240551) : difference with theory (-14) = 0 

CORRECTING DEFECT 32 (vertices=132, convex hull=100, v0=91064)
After retessellation of defect 32 (v0=91064), euler #=-13 (120736,361437,240688) : difference with theory (-13) = 0 

CORRECTING DEFECT 33 (vertices=185, convex hull=173, v0=91704)
After retessellation of defect 33 (v0=91704), euler #=-12 (120819,361766,240935) : difference with theory (-12) = 0 

CORRECTING DEFECT 34 (vertices=44, convex hull=77, v0=92508)
After retessellation of defect 34 (v0=92508), euler #=-11 (120846,361879,241022) : difference with theory (-11) = 0 

CORRECTING DEFECT 35 (vertices=9, convex hull=15, v0=96794)
After retessellation of defect 35 (v0=96794), euler #=-10 (120848,361890,241032) : difference with theory (-10) = 0 

CORRECTING DEFECT 36 (vertices=1537, convex hull=472, v0=100004)
XL defect detected...
After retessellation of defect 36 (v0=100004), euler #=-9 (121000,362606,241597) : difference with theory (-9) = 0 

CORRECTING DEFECT 37 (vertices=26, convex hull=30, v0=100182)
After retessellation of defect 37 (v0=100182), euler #=-8 (121009,362643,241626) : difference with theory (-8) = 0 

CORRECTING DEFECT 38 (vertices=67, convex hull=53, v0=102087)
After retessellation of defect 38 (v0=102087), euler #=-7 (121024,362710,241679) : difference with theory (-7) = 0 

CORRECTING DEFECT 39 (vertices=242, convex hull=93, v0=106163)
After retessellation of defect 39 (v0=106163), euler #=-6 (121037,362796,241753) : difference with theory (-6) = 0 

CORRECTING DEFECT 40 (vertices=154, convex hull=116, v0=107841)
After retessellation of defect 40 (v0=107841), euler #=-5 (121068,362939,241866) : difference with theory (-5) = 0 

CORRECTING DEFECT 41 (vertices=221, convex hull=86, v0=110725)
After retessellation of defect 41 (v0=110725), euler #=-4 (121118,363132,242010) : difference with theory (-4) = 0 

CORRECTING DEFECT 42 (vertices=108, convex hull=113, v0=123801)
After retessellation of defect 42 (v0=123801), euler #=-3 (121169,363341,242169) : difference with theory (-3) = 0 

CORRECTING DEFECT 43 (vertices=89, convex hull=91, v0=124505)
After retessellation of defect 43 (v0=124505), euler #=-2 (121206,363492,242284) : difference with theory (-2) = 0 

CORRECTING DEFECT 44 (vertices=10, convex hull=29, v0=126929)
After retessellation of defect 44 (v0=126929), euler #=-1 (121207,363505,242297) : difference with theory (-1) = 0 

CORRECTING DEFECT 45 (vertices=48, convex hull=72, v0=127314)
After retessellation of defect 45 (v0=127314), euler #=0 (121224,363587,242363) : difference with theory (0) = 0 

CORRECTING DEFECT 46 (vertices=76, convex hull=97, v0=127734)
After retessellation of defect 46 (v0=127734), euler #=1 (121272,363772,242501) : difference with theory (1) = 0 

CORRECTING DEFECT 47 (vertices=57, convex hull=75, v0=128038)
After retessellation of defect 47 (v0=128038), euler #=2 (121292,363870,242580) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.90 +- 0.30 (0.03-->20.04) (max @ vno 82463 --> 87703)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.90 +- 0.30 (0.03-->20.04) (max @ vno 82463 --> 87703)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
115 mutations (30.2%), 266 crossovers (69.8%), 2536 vertices were eliminated
building final representation...
13614 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=121292, nf=242580, ne=363870, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 216.7 minutes
0 defective edges
removing intersecting faces
000: 854 intersecting
001: 21 intersecting
002: 4 intersecting
mris_fix_topology utimesec    13008.547400
mris_fix_topology stimesec    2.420632
mris_fix_topology ru_maxrss   676892
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   116465
mris_fix_topology ru_majflt   1
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  2528
mris_fix_topology ru_oublock  11992
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    327
mris_fix_topology ru_nivcsw   24162
FSRUNTIME@ mris_fix_topology lh  3.6122 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 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=-78 (nv=128566, nf=257288, ne=385932, g=40)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
6950 ambiguous faces found in tessellation
segmenting defects...
48 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
48 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4102  (-4.7051)
      -vertex     loglikelihood: -6.2925  (-3.1462)
      -normal dot loglikelihood: -3.5568  (-3.5568)
      -quad curv  loglikelihood: -6.1537  (-3.0769)
      Total Loglikelihood : -25.4131

CORRECTING DEFECT 0 (vertices=37, convex hull=47, v0=211)
After retessellation of defect 0 (v0=211), euler #=-45 (124381,371574,247148) : difference with theory (-45) = 0 

CORRECTING DEFECT 1 (vertices=6, convex hull=25, v0=3233)
After retessellation of defect 1 (v0=3233), euler #=-44 (124382,371583,247157) : difference with theory (-44) = 0 

CORRECTING DEFECT 2 (vertices=87, convex hull=111, v0=3442)
After retessellation of defect 2 (v0=3442), euler #=-43 (124432,371779,247304) : difference with theory (-43) = 0 

CORRECTING DEFECT 3 (vertices=42, convex hull=40, v0=4047)
After retessellation of defect 3 (v0=4047), euler #=-42 (124439,371819,247338) : difference with theory (-42) = 0 

CORRECTING DEFECT 4 (vertices=25, convex hull=71, v0=4547)
After retessellation of defect 4 (v0=4547), euler #=-41 (124452,371887,247394) : difference with theory (-41) = 0 

CORRECTING DEFECT 5 (vertices=76, convex hull=130, v0=7313)
After retessellation of defect 5 (v0=7313), euler #=-40 (124494,372072,247538) : difference with theory (-40) = 0 

CORRECTING DEFECT 6 (vertices=63, convex hull=128, v0=9734)
After retessellation of defect 6 (v0=9734), euler #=-39 (124532,372240,247669) : difference with theory (-39) = 0 

CORRECTING DEFECT 7 (vertices=229, convex hull=95, v0=10203)
After retessellation of defect 7 (v0=10203), euler #=-38 (124576,372418,247804) : difference with theory (-38) = 0 

CORRECTING DEFECT 8 (vertices=74, convex hull=84, v0=12513)
After retessellation of defect 8 (v0=12513), euler #=-37 (124600,372526,247889) : difference with theory (-37) = 0 

CORRECTING DEFECT 9 (vertices=19, convex hull=45, v0=13344)
After retessellation of defect 9 (v0=13344), euler #=-36 (124611,372574,247927) : difference with theory (-36) = 0 

CORRECTING DEFECT 10 (vertices=90, convex hull=100, v0=18771)
After retessellation of defect 10 (v0=18771), euler #=-35 (124653,372742,248054) : difference with theory (-35) = 0 

CORRECTING DEFECT 11 (vertices=86, convex hull=101, v0=18798)
After retessellation of defect 11 (v0=18798), euler #=-34 (124690,372891,248167) : difference with theory (-34) = 0 

CORRECTING DEFECT 12 (vertices=35, convex hull=75, v0=23275)
After retessellation of defect 12 (v0=23275), euler #=-33 (124715,372997,248249) : difference with theory (-33) = 0 

CORRECTING DEFECT 13 (vertices=88, convex hull=110, v0=25872)
After retessellation of defect 13 (v0=25872), euler #=-32 (124757,373174,248385) : difference with theory (-32) = 0 

CORRECTING DEFECT 14 (vertices=67, convex hull=43, v0=26213)
After retessellation of defect 14 (v0=26213), euler #=-31 (124764,373212,248417) : difference with theory (-31) = 0 

CORRECTING DEFECT 15 (vertices=86, convex hull=86, v0=35165)
After retessellation of defect 15 (v0=35165), euler #=-30 (124802,373365,248533) : difference with theory (-30) = 0 

CORRECTING DEFECT 16 (vertices=14, convex hull=31, v0=36941)
After retessellation of defect 16 (v0=36941), euler #=-29 (124806,373388,248553) : difference with theory (-29) = 0 

CORRECTING DEFECT 17 (vertices=99, convex hull=110, v0=46867)
After retessellation of defect 17 (v0=46867), euler #=-28 (124850,373573,248695) : difference with theory (-28) = 0 

CORRECTING DEFECT 18 (vertices=216, convex hull=97, v0=51128)
After retessellation of defect 18 (v0=51128), euler #=-27 (124887,373729,248815) : difference with theory (-27) = 0 

CORRECTING DEFECT 19 (vertices=40, convex hull=73, v0=55511)
After retessellation of defect 19 (v0=55511), euler #=-26 (124914,373839,248899) : difference with theory (-26) = 0 

CORRECTING DEFECT 20 (vertices=20, convex hull=21, v0=57050)
After retessellation of defect 20 (v0=57050), euler #=-25 (124917,373856,248914) : difference with theory (-25) = 0 

CORRECTING DEFECT 21 (vertices=85, convex hull=89, v0=59884)
After retessellation of defect 21 (v0=59884), euler #=-24 (124944,373979,249011) : difference with theory (-24) = 0 

CORRECTING DEFECT 22 (vertices=226, convex hull=168, v0=60691)
After retessellation of defect 22 (v0=60691), euler #=-23 (125004,374237,249210) : difference with theory (-23) = 0 

CORRECTING DEFECT 23 (vertices=20, convex hull=25, v0=68057)
After retessellation of defect 23 (v0=68057), euler #=-22 (125009,374259,249228) : difference with theory (-22) = 0 

CORRECTING DEFECT 24 (vertices=123, convex hull=46, v0=73747)
After retessellation of defect 24 (v0=73747), euler #=-21 (125023,374317,249273) : difference with theory (-21) = 0 

CORRECTING DEFECT 25 (vertices=37, convex hull=45, v0=83856)
After retessellation of defect 25 (v0=83856), euler #=-20 (125027,374345,249298) : difference with theory (-20) = 0 

CORRECTING DEFECT 26 (vertices=47, convex hull=79, v0=89152)
After retessellation of defect 26 (v0=89152), euler #=-19 (125036,374404,249349) : difference with theory (-19) = 0 

CORRECTING DEFECT 27 (vertices=31, convex hull=46, v0=92707)
After retessellation of defect 27 (v0=92707), euler #=-18 (125055,374472,249399) : difference with theory (-18) = 0 

CORRECTING DEFECT 28 (vertices=33, convex hull=68, v0=92994)
After retessellation of defect 28 (v0=92994), euler #=-17 (125073,374556,249466) : difference with theory (-17) = 0 

CORRECTING DEFECT 29 (vertices=331, convex hull=73, v0=96584)
After retessellation of defect 29 (v0=96584), euler #=-16 (125093,374648,249539) : difference with theory (-16) = 0 

CORRECTING DEFECT 30 (vertices=506, convex hull=207, v0=96669)
After retessellation of defect 30 (v0=96669), euler #=-15 (125169,374986,249802) : difference with theory (-15) = 0 

CORRECTING DEFECT 31 (vertices=116, convex hull=70, v0=97612)
After retessellation of defect 31 (v0=97612), euler #=-14 (125178,375040,249848) : difference with theory (-14) = 0 

CORRECTING DEFECT 32 (vertices=12, convex hull=27, v0=99413)
After retessellation of defect 32 (v0=99413), euler #=-13 (125180,375055,249862) : difference with theory (-13) = 0 

CORRECTING DEFECT 33 (vertices=63, convex hull=72, v0=100203)
After retessellation of defect 33 (v0=100203), euler #=-12 (125209,375173,249952) : difference with theory (-12) = 0 

CORRECTING DEFECT 34 (vertices=82, convex hull=122, v0=104288)
After retessellation of defect 34 (v0=104288), euler #=-11 (125253,375354,250090) : difference with theory (-11) = 0 

CORRECTING DEFECT 35 (vertices=188, convex hull=90, v0=104948)
After retessellation of defect 35 (v0=104948), euler #=-10 (125278,375470,250182) : difference with theory (-10) = 0 

CORRECTING DEFECT 36 (vertices=191, convex hull=79, v0=105190)
After retessellation of defect 36 (v0=105190), euler #=-9 (125308,375595,250278) : difference with theory (-9) = 0 

CORRECTING DEFECT 37 (vertices=41, convex hull=62, v0=106093)
After retessellation of defect 37 (v0=106093), euler #=-8 (125327,375679,250344) : difference with theory (-8) = 0 

CORRECTING DEFECT 38 (vertices=107, convex hull=111, v0=108443)
After retessellation of defect 38 (v0=108443), euler #=-7 (125347,375792,250438) : difference with theory (-7) = 0 

CORRECTING DEFECT 39 (vertices=92, convex hull=33, v0=110799)
After retessellation of defect 39 (v0=110799), euler #=-6 (125350,375817,250461) : difference with theory (-6) = 0 

CORRECTING DEFECT 40 (vertices=47, convex hull=83, v0=111705)
After retessellation of defect 40 (v0=111705), euler #=-5 (125368,375909,250536) : difference with theory (-5) = 0 

CORRECTING DEFECT 41 (vertices=22, convex hull=65, v0=114840)
After retessellation of defect 41 (v0=114840), euler #=-4 (125375,375955,250576) : difference with theory (-4) = 0 

CORRECTING DEFECT 42 (vertices=62, convex hull=36, v0=116278)
After retessellation of defect 42 (v0=116278), euler #=-3 (125383,375993,250607) : difference with theory (-3) = 0 

CORRECTING DEFECT 43 (vertices=32, convex hull=77, v0=122447)
After retessellation of defect 43 (v0=122447), euler #=-2 (125399,376070,250669) : difference with theory (-2) = 0 

CORRECTING DEFECT 44 (vertices=33, convex hull=27, v0=123772)
After retessellation of defect 44 (v0=123772), euler #=-1 (125401,376086,250684) : difference with theory (-1) = 0 

CORRECTING DEFECT 45 (vertices=95, convex hull=129, v0=125895)
After retessellation of defect 45 (v0=125895), euler #=0 (125432,376236,250804) : difference with theory (0) = 0 

CORRECTING DEFECT 46 (vertices=57, convex hull=103, v0=126630)
After retessellation of defect 46 (v0=126630), euler #=1 (125462,376369,250908) : difference with theory (1) = 0 

CORRECTING DEFECT 47 (vertices=14, convex hull=31, v0=128426)
After retessellation of defect 47 (v0=128426), euler #=2 (125464,376386,250924) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.03-->9.05) (max @ vno 59464 --> 63269)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.23 (0.03-->9.05) (max @ vno 59464 --> 63269)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
136 mutations (31.7%), 293 crossovers (68.3%), 146 vertices were eliminated
building final representation...
3102 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=125464, nf=250924, ne=376386, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 24.1 minutes
0 defective edges
removing intersecting faces
000: 273 intersecting
001: 21 intersecting
mris_fix_topology utimesec    1445.988176
mris_fix_topology stimesec    0.273958
mris_fix_topology ru_maxrss   410432
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   53990
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  7680
mris_fix_topology ru_oublock  12088
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    331
mris_fix_topology ru_nivcsw   9722
FSRUNTIME@ mris_fix_topology rh  0.4022 hours 1 threads
PIDs (8933 8936) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 121292 - 363870 + 242580 = 2 --> 0 holes
      F =2V-4:          242580 = 242584-4 (0)
      2E=3F:            727740 = 727740 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 125464 - 376386 + 250924 = 2 --> 0 holes
      F =2V-4:          250924 = 250928-4 (0)
      2E=3F:            752772 = 752772 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 244 intersecting
001: 8 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 13 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 09:11:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 09:11:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 rh 

Waiting for PID 19846 of (19846 19849) to complete...
Waiting for PID 19849 of (19846 19849) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
12664 bright wm thresholded.
2174 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.orig...
computing class statistics...
border white:    240984 voxels (1.44%)
border gray      284361 voxels (1.69%)
WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0]
GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 54.4 (was 70)
setting MAX_BORDER_WHITE to 109.6 (was 105)
setting MIN_BORDER_WHITE to 65.0 (was 85)
setting MAX_CSF to 43.9 (was 40)
setting MAX_GRAY to 92.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.84 +- 0.24 (0.03-->4.97) (max @ vno 7895 --> 119426)
face area 0.29 +- 0.14 (0.00-->5.27)
mean absolute distance = 0.62 +- 0.73
3485 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.0,    GM=65+-7.0
mean inside = 91.4, mean outside = 73.7
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=77.7, 89 (89) missing vertices, mean dist 0.3 [0.4 (%33.6)->0.7 (%66.4))]
%75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.27 (0.13-->4.83) (max @ vno 120250 --> 120298)
face area 0.29 +- 0.15 (0.00-->4.35)
mean absolute distance = 0.29 +- 0.51
2361 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2784216.2, rms=9.905
001: dt: 0.5000, sse=1638215.8, rms=7.009 (29.231%)
002: dt: 0.5000, sse=1146538.2, rms=5.294 (24.473%)
003: dt: 0.5000, sse=918095.4, rms=4.261 (19.505%)
004: dt: 0.5000, sse=815291.6, rms=3.709 (12.973%)
005: dt: 0.5000, sse=782778.9, rms=3.439 (7.275%)
006: dt: 0.5000, sse=753442.6, rms=3.318 (3.502%)
007: dt: 0.5000, sse=743844.2, rms=3.256 (1.875%)
rms = 3.22, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=739923.2, rms=3.224 (1.000%)
009: dt: 0.2500, sse=596442.7, rms=1.929 (40.155%)
010: dt: 0.2500, sse=574940.8, rms=1.654 (14.259%)
011: dt: 0.2500, sse=570057.6, rms=1.584 (4.250%)
rms = 1.55, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=567648.5, rms=1.546 (2.398%)
rms = 1.50, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=564331.2, rms=1.500 (2.957%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=79.8, 117 (43) missing vertices, mean dist -0.1 [0.3 (%69.3)->0.3 (%30.7))]
%80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.93 +- 0.26 (0.10-->4.86) (max @ vno 14221 --> 119427)
face area 0.36 +- 0.18 (0.00-->5.58)
mean absolute distance = 0.25 +- 0.41
2591 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=954143.4, rms=3.712
014: dt: 0.5000, sse=774203.7, rms=2.447 (34.078%)
rms = 2.65, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=709294.1, rms=1.795 (26.654%)
016: dt: 0.2500, sse=683722.0, rms=1.446 (19.452%)
017: dt: 0.2500, sse=677159.2, rms=1.340 (7.320%)
rms = 1.31, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=674556.2, rms=1.308 (2.371%)
rms = 1.27, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=674501.4, rms=1.273 (2.666%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 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=81.4, 118 (39) missing vertices, mean dist -0.1 [0.3 (%63.8)->0.2 (%36.2))]
%84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.26 (0.05-->4.95) (max @ vno 120883 --> 91955)
face area 0.36 +- 0.18 (0.00-->5.71)
mean absolute distance = 0.24 +- 0.36
2509 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=772011.7, rms=2.477
020: dt: 0.5000, sse=753286.9, rms=2.252 (9.078%)
rms = 2.54, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=691038.1, rms=1.537 (31.774%)
022: dt: 0.2500, sse=677510.9, rms=1.242 (19.161%)
023: dt: 0.2500, sse=661213.2, rms=1.170 (5.834%)
rms = 1.16, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=660185.1, rms=1.163 (0.576%)
rms = 1.13, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=657667.4, rms=1.134 (2.512%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=82.1, 130 (38) missing vertices, mean dist -0.0 [0.3 (%54.4)->0.2 (%45.6))]
%86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=670070.2, rms=1.444
rms = 1.49, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=649025.1, rms=1.086 (24.823%)
027: dt: 0.2500, sse=645450.9, rms=0.894 (17.656%)
rms = 0.89, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=642983.0, rms=0.891 (0.395%)
rms = 0.89, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=642777.4, rms=0.886 (0.541%)
positioning took 0.4 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7382 vertices
erasing segment 0 (vno[0] = 32688)
erasing segment 1 (vno[0] = 32720)
erasing segment 2 (vno[0] = 33594)
erasing segment 3 (vno[0] = 37419)
erasing segment 4 (vno[0] = 38419)
erasing segment 6 (vno[0] = 88196)
erasing segment 7 (vno[0] = 88295)
erasing segment 8 (vno[0] = 90067)
erasing segment 9 (vno[0] = 120851)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.area
vertex spacing 0.92 +- 0.27 (0.03-->5.05) (max @ vno 91955 --> 120883)
face area 0.35 +- 0.18 (0.00-->5.79)
refinement took 4.3 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
12664 bright wm thresholded.
2174 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.orig...
computing class statistics...
border white:    240984 voxels (1.44%)
border gray      284361 voxels (1.69%)
WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0]
GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 53.4 (was 70)
setting MAX_BORDER_WHITE to 109.6 (was 105)
setting MIN_BORDER_WHITE to 64.0 (was 85)
setting MAX_CSF to 42.9 (was 40)
setting MAX_GRAY to 92.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.83 +- 0.22 (0.03-->3.43) (max @ vno 64931 --> 66846)
face area 0.29 +- 0.12 (0.00-->2.27)
mean absolute distance = 0.62 +- 0.72
4110 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.0,    GM=64+-8.7
mean inside = 91.7, mean outside = 73.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=77.5, 60 (60) missing vertices, mean dist 0.4 [0.4 (%31.4)->0.7 (%68.6))]
%76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.25 (0.08-->3.65) (max @ vno 124624 --> 124652)
face area 0.29 +- 0.13 (0.00-->2.44)
mean absolute distance = 0.28 +- 0.48
2851 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2996296.2, rms=10.166
001: dt: 0.5000, sse=1757392.4, rms=7.227 (28.911%)
002: dt: 0.5000, sse=1205797.8, rms=5.414 (25.089%)
003: dt: 0.5000, sse=949113.4, rms=4.320 (20.199%)
004: dt: 0.5000, sse=838049.2, rms=3.741 (13.416%)
005: dt: 0.5000, sse=791101.1, rms=3.464 (7.385%)
006: dt: 0.5000, sse=771127.3, rms=3.331 (3.852%)
007: dt: 0.5000, sse=760110.4, rms=3.263 (2.030%)
rms = 3.22, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=754191.6, rms=3.225 (1.183%)
009: dt: 0.2500, sse=602436.1, rms=1.886 (41.514%)
010: dt: 0.2500, sse=579271.2, rms=1.598 (15.264%)
011: dt: 0.2500, sse=573103.2, rms=1.517 (5.093%)
rms = 1.47, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=570230.2, rms=1.474 (2.847%)
013: dt: 0.1250, sse=566874.5, rms=1.420 (3.643%)
rms = 1.41, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=566209.9, rms=1.410 (0.696%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
mean border=79.7, 44 (4) missing vertices, mean dist -0.1 [0.3 (%69.0)->0.3 (%31.0))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.25 (0.10-->3.91) (max @ vno 124624 --> 124652)
face area 0.36 +- 0.16 (0.00-->2.83)
mean absolute distance = 0.25 +- 0.40
3382 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=982169.1, rms=3.747
015: dt: 0.5000, sse=788934.2, rms=2.456 (34.448%)
rms = 2.64, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=720692.5, rms=1.779 (27.578%)
017: dt: 0.2500, sse=693278.5, rms=1.386 (22.067%)
018: dt: 0.2500, sse=682687.3, rms=1.251 (9.761%)
rms = 1.21, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=680249.5, rms=1.210 (3.311%)
rms = 1.17, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=678136.2, rms=1.171 (3.189%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.3, 40 (2) missing vertices, mean dist -0.1 [0.3 (%64.1)->0.2 (%35.9))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.24 (0.09-->3.89) (max @ vno 124624 --> 124652)
face area 0.35 +- 0.16 (0.00-->2.75)
mean absolute distance = 0.25 +- 0.36
2729 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=793674.1, rms=2.547
021: dt: 0.5000, sse=759713.2, rms=2.258 (11.351%)
rms = 2.51, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=694395.1, rms=1.533 (32.101%)
023: dt: 0.2500, sse=672469.6, rms=1.199 (21.778%)
024: dt: 0.2500, sse=666716.6, rms=1.100 (8.285%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=665669.7, rms=1.085 (1.318%)
rms = 1.05, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=664011.6, rms=1.053 (3.019%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=82.0, 55 (1) missing vertices, mean dist -0.0 [0.3 (%55.0)->0.2 (%45.0))]
%86 local maxima, % 9 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-6.0.0/0050566/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=682505.8, rms=1.463
rms = 1.45, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=680687.2, rms=1.454 (0.618%)
028: dt: 0.2500, sse=655120.9, rms=1.024 (29.582%)
029: dt: 0.2500, sse=648259.6, rms=0.895 (12.595%)
rms = 0.94, time step reduction 2 of 3 to 0.125...
rms = 0.86, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=646584.3, rms=0.857 (4.162%)
positioning took 0.4 minutes
generating cortex label...
3 non-cortical segments detected
only using segment with 7628 vertices
erasing segment 0 (vno[0] = 37911)
erasing segment 2 (vno[0] = 91649)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.area
vertex spacing 0.91 +- 0.25 (0.03-->3.58) (max @ vno 124624 --> 124652)
face area 0.35 +- 0.16 (0.00-->2.61)
refinement took 4.6 minutes
PIDs (19846 19849) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 09:15:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 09:15:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

Waiting for PID 20022 of (20022 20025) to complete...
Waiting for PID 20025 of (20022 20025) 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 (20022 20025) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 09:16:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 09:16:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 20070 of (20070 20073) to complete...
Waiting for PID 20073 of (20070 20073) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 46.4 mm, total surface area = 77743 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.176 (target=0.015)   
step 005: RMS=0.126 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.079 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.056 (target=0.015)   
step 030: RMS=0.047 (target=0.015)   
step 035: RMS=0.039 (target=0.015)   
step 040: RMS=0.035 (target=0.015)   
step 045: RMS=0.031 (target=0.015)   
step 050: RMS=0.027 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.025 (target=0.015)   
inflation complete.
inflation took 0.6 minutes
mris_inflate utimesec    38.736111
mris_inflate stimesec    0.100984
mris_inflate ru_maxrss   178024
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   26182
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  9504
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5761
mris_inflate ru_nivcsw   4239

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 45.9 mm, total surface area = 79613 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.173 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.048 (target=0.015)   
step 035: RMS=0.041 (target=0.015)   
step 040: RMS=0.036 (target=0.015)   
step 045: RMS=0.032 (target=0.015)   
step 050: RMS=0.029 (target=0.015)   
step 055: RMS=0.028 (target=0.015)   
step 060: RMS=0.028 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    39.868939
mris_inflate stimesec    0.107983
mris_inflate ru_maxrss   183620
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   27070
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  9832
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    4565
mris_inflate ru_nivcsw   4844
PIDs (20070 20073) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 09:16:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 09:16:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 20177 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20180 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20183 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20186 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20189 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20192 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20195 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20198 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20201 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20204 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20207 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...
Waiting for PID 20211 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 13.746*4pi (172.736) --> -13 handles
ICI = 149.1, FI = 1418.6, variation=22634.810
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
138 vertices thresholded to be in k1 ~ [-0.28 0.39], k2 ~ [-0.13 0.07]
total integrated curvature = 0.365*4pi (4.581) --> 1 handles
ICI = 1.2, FI = 8.1, variation=139.504
100 vertices thresholded to be in [-0.02 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
124 vertices thresholded to be in [-0.16 0.18]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 20.324*4pi (255.397) --> -19 handles
ICI = 151.5, FI = 1462.2, variation=23131.480
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
162 vertices thresholded to be in k1 ~ [-0.30 0.79], k2 ~ [-0.24 0.16]
total integrated curvature = 0.419*4pi (5.261) --> 1 handles
ICI = 1.4, FI = 8.8, variation=151.127
119 vertices thresholded to be in [-0.07 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
106 vertices thresholded to be in [-0.16 0.22]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023
done.
PIDs (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 09:17:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050566 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      [ 0050566/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                      [ 230 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.358928
WARN:    S explicit min:                          0.000000	vertex = 2260

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 09:18:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050566 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      [ 0050566/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                      [ 254 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.267072
WARN:    S explicit min:                          0.000000	vertex = 1250
#--------------------------------------------
#@# Sphere lh Sun Oct  8 09:18:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 09:18:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 20350 of (20350 20353) to complete...
Waiting for PID 20353 of (20350 20353) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0.304...
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 %43.79
pass 1: epoch 2 of 3 starting distance error %21.42
unfolding complete - removing small folds...
starting distance error %21.13
removing remaining folds...
final distance error %21.16
MRISunfold() return, current seed 1234
-01: dt=0.0000, 30 negative triangles
186: dt=0.9900, 30 negative triangles
187: dt=0.9900, 10 negative triangles
188: dt=0.9900, 9 negative triangles
189: dt=0.9900, 8 negative triangles
190: dt=0.9900, 6 negative triangles
191: dt=0.9900, 6 negative triangles
192: dt=0.9900, 2 negative triangles
193: dt=0.9900, 3 negative triangles
194: dt=0.9900, 2 negative triangles
195: dt=0.9900, 4 negative triangles
196: dt=0.9900, 6 negative triangles
197: dt=0.9900, 4 negative triangles
198: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.55 hours
mris_sphere utimesec    1969.463596
mris_sphere stimesec    0.831873
mris_sphere ru_maxrss   250072
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   44834
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  8568
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    91506
mris_sphere ru_nivcsw   162004
FSRUNTIME@ mris_sphere  0.5476 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0.301...
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 %21.23
pass 1: epoch 2 of 3 starting distance error %21.16
unfolding complete - removing small folds...
starting distance error %21.03
removing remaining folds...
final distance error %21.07
MRISunfold() return, current seed 1234
-01: dt=0.0000, 52 negative triangles
235: dt=0.9900, 52 negative triangles
236: dt=0.9900, 26 negative triangles
237: dt=0.9900, 17 negative triangles
238: dt=0.9900, 20 negative triangles
239: dt=0.9900, 13 negative triangles
240: dt=0.9900, 12 negative triangles
241: dt=0.9900, 17 negative triangles
242: dt=0.9900, 13 negative triangles
243: dt=0.9900, 13 negative triangles
244: dt=0.9900, 12 negative triangles
245: dt=0.9900, 5 negative triangles
246: dt=0.9900, 10 negative triangles
247: dt=0.9900, 10 negative triangles
248: dt=0.9900, 8 negative triangles
249: dt=0.9900, 8 negative triangles
250: dt=0.9900, 8 negative triangles
251: dt=0.9900, 8 negative triangles
252: dt=0.9900, 3 negative triangles
253: dt=0.9900, 6 negative triangles
254: dt=0.9900, 4 negative triangles
255: dt=0.9900, 7 negative triangles
256: dt=0.9900, 2 negative triangles
257: dt=0.9900, 5 negative triangles
258: dt=0.9900, 5 negative triangles
259: dt=0.9900, 5 negative triangles
260: dt=0.9900, 3 negative triangles
261: dt=0.9900, 7 negative triangles
262: dt=0.9900, 5 negative triangles
263: dt=0.9900, 2 negative triangles
264: dt=0.9900, 2 negative triangles
265: dt=0.9900, 2 negative triangles
266: dt=0.9405, 5 negative triangles
267: dt=0.9405, 2 negative triangles
268: dt=0.9405, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.75 hours
mris_sphere utimesec    3319.245398
mris_sphere stimesec    1.165822
mris_sphere ru_maxrss   258568
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   45927
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  8864
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    109825
mris_sphere ru_nivcsw   165902
FSRUNTIME@ mris_sphere  0.7496 hours 1 threads
PIDs (20350 20353) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 10:03:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 10:03:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 22035 of (22035 22038) to complete...
Waiting for PID 22038 of (22035 22038) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 5.738
curvature mean = 0.040, std = 0.821
curvature mean = 0.008, std = 0.875
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 301173.9, tmin=0.9338
  d=32.00 min @ (-8.00, -8.00, 0.00) sse = 209498.0, tmin=1.8855
  d=16.00 min @ (-4.00, 0.00, 0.00) sse = 202056.6, tmin=2.8476
  d=8.00 min @ (2.00, 2.00, 0.00) sse = 193921.5, tmin=3.8146
  d=4.00 min @ (0.00, -1.00, -1.00) sse = 192118.0, tmin=4.7899
  d=2.00 min @ (0.00, 0.50, 0.00) sse = 192070.1, tmin=5.7718
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 192000.1, tmin=6.7522
  d=0.50 min @ (0.12, 0.00, -0.12) sse = 191972.3, tmin=7.7332
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   7.73 min
curvature mean = 0.009, std = 0.835
curvature mean = 0.003, std = 0.954
curvature mean = 0.007, std = 0.846
curvature mean = 0.002, std = 0.982
curvature mean = 0.006, std = 0.849
curvature mean = 0.000, std = 0.993
2 Reading smoothwm
curvature mean = -0.030, std = 0.265
curvature mean = 0.043, std = 0.246
curvature mean = 0.049, std = 0.406
curvature mean = 0.037, std = 0.305
curvature mean = 0.037, std = 0.583
curvature mean = 0.036, std = 0.332
curvature mean = 0.020, std = 0.722
curvature mean = 0.036, std = 0.343
curvature mean = 0.007, std = 0.825
MRISregister() return, current seed 0
-01: dt=0.0000, 42 negative triangles
111: dt=0.9900, 42 negative triangles
expanding nbhd size to 1
112: dt=0.9900, 55 negative triangles
113: dt=0.9900, 27 negative triangles
114: dt=0.9900, 27 negative triangles
115: dt=0.9900, 22 negative triangles
116: dt=0.9900, 24 negative triangles
117: dt=0.9900, 19 negative triangles
118: dt=0.9900, 15 negative triangles
119: dt=0.9900, 16 negative triangles
120: dt=0.9900, 15 negative triangles
121: dt=0.9900, 10 negative triangles
122: dt=0.9900, 11 negative triangles
123: dt=0.9900, 10 negative triangles
124: dt=0.9900, 8 negative triangles
125: dt=0.9900, 5 negative triangles
126: dt=0.9900, 4 negative triangles
127: dt=0.9900, 6 negative triangles
128: dt=0.9900, 3 negative triangles
129: dt=0.9900, 3 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.04 hours
mris_register utimesec    3757.921709
mris_register stimesec    2.764579
mris_register ru_maxrss   233232
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   33233
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  8632
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    329895
mris_register ru_nivcsw   201008
FSRUNTIME@ mris_register  1.0444 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 5.803
curvature mean = 0.035, std = 0.814
curvature mean = 0.007, std = 0.876
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 306683.7, tmin=0.9667
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 196065.8, tmin=1.9505
  d=8.00 min @ (0.00, 0.00, 2.00) sse = 191396.3, tmin=3.9429
  d=4.00 min @ (1.00, 0.00, -1.00) sse = 190387.2, tmin=4.9432
  d=2.00 min @ (-0.50, 0.00, 0.50) sse = 189694.4, tmin=5.9531
  d=1.00 min @ (0.00, -0.25, -0.25) sse = 189452.9, tmin=6.9660
  d=0.50 min @ (-0.12, 0.00, 0.00) sse = 189428.7, tmin=7.9993
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   8.00 min
curvature mean = 0.025, std = 0.833
curvature mean = 0.002, std = 0.955
curvature mean = 0.024, std = 0.845
curvature mean = 0.001, std = 0.982
curvature mean = 0.023, std = 0.848
curvature mean = 0.000, std = 0.993
2 Reading smoothwm
curvature mean = -0.030, std = 0.264
curvature mean = 0.041, std = 0.240
curvature mean = 0.049, std = 0.405
curvature mean = 0.034, std = 0.300
curvature mean = 0.037, std = 0.587
curvature mean = 0.033, std = 0.327
curvature mean = 0.019, std = 0.725
curvature mean = 0.032, std = 0.339
curvature mean = 0.006, std = 0.823
MRISregister() return, current seed 0
-01: dt=0.0000, 75 negative triangles
113: dt=0.9900, 75 negative triangles
expanding nbhd size to 1
114: dt=0.9900, 87 negative triangles
115: dt=0.9900, 73 negative triangles
116: dt=0.9900, 68 negative triangles
117: dt=0.9900, 72 negative triangles
118: dt=0.9900, 61 negative triangles
119: dt=0.9900, 56 negative triangles
120: dt=0.9900, 55 negative triangles
121: dt=0.9900, 54 negative triangles
122: dt=0.9900, 45 negative triangles
123: dt=0.9900, 43 negative triangles
124: dt=0.9900, 37 negative triangles
125: dt=0.9900, 35 negative triangles
126: dt=0.9900, 32 negative triangles
127: dt=0.9900, 35 negative triangles
128: dt=0.9900, 28 negative triangles
129: dt=0.9900, 28 negative triangles
130: dt=0.9900, 27 negative triangles
131: dt=0.9900, 22 negative triangles
132: dt=0.9900, 23 negative triangles
133: dt=0.9900, 22 negative triangles
134: dt=0.9900, 16 negative triangles
135: dt=0.9900, 14 negative triangles
136: dt=0.9900, 14 negative triangles
137: dt=0.9900, 12 negative triangles
138: dt=0.9900, 11 negative triangles
139: dt=0.9900, 13 negative triangles
140: dt=0.9900, 12 negative triangles
141: dt=0.9900, 10 negative triangles
142: dt=0.9900, 9 negative triangles
143: dt=0.9900, 8 negative triangles
144: dt=0.9900, 12 negative triangles
145: dt=0.9900, 7 negative triangles
146: dt=0.9900, 11 negative triangles
147: dt=0.9900, 8 negative triangles
148: dt=0.9900, 7 negative triangles
149: dt=0.9900, 7 negative triangles
150: dt=0.9900, 4 negative triangles
151: dt=0.9900, 5 negative triangles
152: dt=0.9900, 4 negative triangles
153: dt=0.9900, 5 negative triangles
154: dt=0.9900, 2 negative triangles
155: dt=0.9900, 1 negative triangles
156: dt=0.9900, 5 negative triangles
157: dt=0.9900, 3 negative triangles
158: dt=0.9900, 2 negative triangles
159: dt=0.9900, 1 negative triangles
160: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.15 hours
mris_register utimesec    4353.764127
mris_register stimesec    2.722586
mris_register ru_maxrss   238168
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   34759
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  8832
mris_register ru_oublock  8920
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    353905
mris_register ru_nivcsw   204788
FSRUNTIME@ mris_register  1.1528 hours 1 threads
PIDs (22035 22038) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 11:12:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 11:12:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

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

Waiting for PID 24617 of (24617 24620) to complete...
Waiting for PID 24620 of (24617 24620) 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 (24617 24620) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 11:12:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 11:12:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 24665 of (24665 24668) to complete...
Waiting for PID 24668 of (24665 24668) 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 (24665 24668) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 11:12:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 11:12:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 24710 of (24710 24713) to complete...
Waiting for PID 24713 of (24710 24713) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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...
954 labels changed using aseg
relabeling using gibbs priors...
000:   2741 changed, 121292 examined...
001:    629 changed, 11432 examined...
002:    125 changed, 3537 examined...
003:     42 changed, 778 examined...
004:     13 changed, 253 examined...
005:      7 changed, 81 examined...
006:      2 changed, 44 examined...
007:      2 changed, 14 examined...
008:      1 changed, 11 examined...
009:      0 changed, 5 examined...
191 labels changed using aseg
000: 105 total segments, 59 labels (215 vertices) changed
001: 43 total segments, 3 labels (6 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1230 vertices marked for relabeling...
1230 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 13 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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...
982 labels changed using aseg
relabeling using gibbs priors...
000:   2591 changed, 125464 examined...
001:    595 changed, 11415 examined...
002:    117 changed, 3319 examined...
003:     50 changed, 747 examined...
004:     18 changed, 306 examined...
005:      7 changed, 107 examined...
006:      7 changed, 51 examined...
007:      1 changed, 33 examined...
008:      0 changed, 7 examined...
163 labels changed using aseg
000: 95 total segments, 58 labels (202 vertices) changed
001: 39 total segments, 2 labels (2 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1066 vertices marked for relabeling...
1066 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 13 seconds.
PIDs (24710 24713) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 11:12:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 11:12:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 rh 

Waiting for PID 24766 of (24766 24769) to complete...
Waiting for PID 24769 of (24766 24769) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
12664 bright wm thresholded.
2174 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.orig...
computing class statistics...
border white:    240984 voxels (1.44%)
border gray      284361 voxels (1.69%)
WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0]
GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 54.4 (was 70)
setting MAX_BORDER_WHITE to 109.6 (was 105)
setting MIN_BORDER_WHITE to 65.0 (was 85)
setting MAX_CSF to 43.9 (was 40)
setting MAX_GRAY to 92.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.0,    GM=65+-7.0
mean inside = 91.4, mean outside = 73.7
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 0.92 +- 0.27 (0.03-->5.05) (max @ vno 91955 --> 120883)
face area 0.35 +- 0.18 (0.00-->5.75)
mean absolute distance = 0.44 +- 0.69
2261 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 15 points - only 0.00% unknown
deleting segment 1 with 90 points - only 0.00% unknown
deleting segment 2 with 20 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 6 with 14 points - only 0.00% unknown
deleting segment 7 with 160 points - only 0.00% unknown
deleting segment 8 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 35 points - only 0.00% unknown
deleting segment 11 with 15 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 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 19 points - only 0.00% unknown
deleting segment 15 with 6 points - only 0.00% unknown
mean border=77.2, 101 (100) missing vertices, mean dist 0.3 [0.5 (%17.5)->0.4 (%82.5))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.94 +- 0.28 (0.11-->5.51) (max @ vno 120883 --> 91955)
face area 0.35 +- 0.18 (0.00-->5.21)
mean absolute distance = 0.29 +- 0.54
2255 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1621828.2, rms=6.576
001: dt: 0.5000, sse=970163.8, rms=3.904 (40.632%)
002: dt: 0.5000, sse=833555.8, rms=3.082 (21.069%)
003: dt: 0.5000, sse=825576.4, rms=3.031 (1.630%)
004: dt: 0.5000, sse=807652.2, rms=2.910 (4.004%)
rms = 3.03, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=715992.2, rms=2.058 (29.265%)
006: dt: 0.2500, sse=686215.2, rms=1.676 (18.570%)
007: dt: 0.2500, sse=678197.9, rms=1.577 (5.893%)
rms = 1.56, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=677294.4, rms=1.556 (1.330%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=677685.2, rms=1.523 (2.112%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
deleting segment 1 with 99 points - only 0.00% unknown
deleting segment 2 with 18 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 4 with 108 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 53 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
mean border=79.6, 120 (64) missing vertices, mean dist -0.2 [0.3 (%70.5)->0.2 (%29.5))]
%80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.93 +- 0.27 (0.07-->5.62) (max @ vno 120883 --> 91955)
face area 0.37 +- 0.19 (0.00-->5.56)
mean absolute distance = 0.25 +- 0.43
2481 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=974661.2, rms=3.712
010: dt: 0.5000, sse=783132.2, rms=2.380 (35.879%)
rms = 2.57, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=725141.4, rms=1.747 (26.608%)
012: dt: 0.2500, sse=698320.5, rms=1.398 (19.951%)
013: dt: 0.2500, sse=691907.8, rms=1.296 (7.318%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=690368.8, rms=1.271 (1.949%)
rms = 1.24, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=688785.7, rms=1.242 (2.261%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
deleting segment 1 with 113 points - only 0.00% unknown
deleting segment 2 with 19 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 4 with 106 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 53 points - only 0.00% unknown
deleting segment 7 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
mean border=81.3, 127 (59) missing vertices, mean dist -0.1 [0.3 (%64.2)->0.2 (%35.8))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.27 (0.10-->5.78) (max @ vno 120883 --> 91955)
face area 0.36 +- 0.19 (0.00-->5.63)
mean absolute distance = 0.25 +- 0.37
2431 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=782290.3, rms=2.492
016: dt: 0.5000, sse=754797.3, rms=2.233 (10.391%)
rms = 2.50, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=692352.2, rms=1.519 (31.989%)
018: dt: 0.2500, sse=674258.9, rms=1.219 (19.746%)
019: dt: 0.2500, sse=668790.6, rms=1.152 (5.506%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=668469.5, rms=1.148 (0.301%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=666976.9, rms=1.123 (2.195%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
deleting segment 1 with 108 points - only 0.00% unknown
deleting segment 2 with 21 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 113 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
deleting segment 7 with 53 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
deleting segment 12 with 26 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 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 5 points - only 0.00% unknown
mean border=82.0, 146 (55) missing vertices, mean dist -0.0 [0.3 (%54.6)->0.2 (%45.4))]
%87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=677431.0, rms=1.432
rms = 1.49, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=656268.9, rms=1.063 (25.793%)
023: dt: 0.2500, sse=648780.9, rms=0.870 (18.177%)
rms = 0.87, time step reduction 2 of 3 to 0.125...
rms = 0.87, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=647529.4, rms=0.868 (0.226%)
positioning took 0.4 minutes
generating cortex label...
7 non-cortical segments detected
only using segment with 7396 vertices
erasing segment 0 (vno[0] = 33594)
erasing segment 1 (vno[0] = 34474)
erasing segment 3 (vno[0] = 88196)
erasing segment 4 (vno[0] = 88295)
erasing segment 5 (vno[0] = 90067)
erasing segment 6 (vno[0] = 120851)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.area
vertex spacing 0.92 +- 0.27 (0.03-->5.79) (max @ vno 91955 --> 120883)
face area 0.36 +- 0.19 (0.00-->5.71)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 29 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=53.0, 107 (107) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.7 (%100.0))]
% 9 local maxima, %48 large gradients and %38 min vals, 887 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=20769124.0, rms=29.574
001: dt: 0.0500, sse=18332574.0, rms=27.728 (6.241%)
002: dt: 0.0500, sse=16579036.0, rms=26.320 (5.079%)
003: dt: 0.0500, sse=15227909.0, rms=25.181 (4.327%)
004: dt: 0.0500, sse=14127705.0, rms=24.214 (3.841%)
005: dt: 0.0500, sse=13195252.0, rms=23.363 (3.515%)
006: dt: 0.0500, sse=12384146.0, rms=22.596 (3.281%)
007: dt: 0.0500, sse=11662920.0, rms=21.892 (3.116%)
008: dt: 0.0500, sse=11012877.0, rms=21.237 (2.991%)
009: dt: 0.0500, sse=10420728.0, rms=20.623 (2.894%)
010: dt: 0.0500, sse=9877192.0, rms=20.042 (2.816%)
positioning took 0.8 minutes
mean border=52.9, 110 (73) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.2 (%100.0))]
%10 local maxima, %47 large gradients and %38 min vals, 850 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=10474192.0, rms=20.678
011: dt: 0.0500, sse=9968826.0, rms=20.140 (2.601%)
012: dt: 0.0500, sse=9499765.0, rms=19.627 (2.545%)
013: dt: 0.0500, sse=9063099.0, rms=19.138 (2.494%)
014: dt: 0.0500, sse=8656216.0, rms=18.670 (2.444%)
015: dt: 0.0500, sse=8276600.0, rms=18.222 (2.396%)
016: dt: 0.0500, sse=7922216.5, rms=17.795 (2.348%)
017: dt: 0.0500, sse=7591744.0, rms=17.386 (2.296%)
018: dt: 0.0500, sse=7283855.5, rms=16.996 (2.241%)
019: dt: 0.0500, sse=6996662.0, rms=16.624 (2.188%)
020: dt: 0.0500, sse=6728686.0, rms=16.270 (2.134%)
positioning took 0.8 minutes
mean border=52.7, 101 (57) missing vertices, mean dist 1.2 [0.1 (%0.8)->1.9 (%99.2))]
%10 local maxima, %47 large gradients and %38 min vals, 852 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=6819666.0, rms=16.395
021: dt: 0.0500, sse=6564234.5, rms=16.052 (2.091%)
022: dt: 0.0500, sse=6326888.5, rms=15.727 (2.027%)
023: dt: 0.0500, sse=6105191.0, rms=15.416 (1.973%)
024: dt: 0.0500, sse=5899113.5, rms=15.122 (1.909%)
025: dt: 0.0500, sse=5707338.0, rms=14.843 (1.846%)
026: dt: 0.0500, sse=5528651.5, rms=14.578 (1.786%)
027: dt: 0.0500, sse=5361297.0, rms=14.325 (1.734%)
028: dt: 0.0500, sse=5203107.0, rms=14.082 (1.698%)
029: dt: 0.0500, sse=5053418.0, rms=13.847 (1.664%)
030: dt: 0.0500, sse=4911743.0, rms=13.622 (1.629%)
positioning took 0.8 minutes
mean border=52.7, 122 (50) missing vertices, mean dist 1.0 [0.1 (%12.1)->1.8 (%87.9))]
%10 local maxima, %48 large gradients and %37 min vals, 847 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=4969178.0, rms=13.712
031: dt: 0.5000, sse=3990408.2, rms=12.051 (12.109%)
032: dt: 0.5000, sse=3364963.5, rms=10.849 (9.975%)
033: dt: 0.5000, sse=2932365.0, rms=9.933 (8.445%)
034: dt: 0.5000, sse=2643731.5, rms=9.262 (6.752%)
035: dt: 0.5000, sse=2436878.2, rms=8.749 (5.537%)
036: dt: 0.5000, sse=2283431.8, rms=8.345 (4.624%)
037: dt: 0.5000, sse=2148397.8, rms=7.975 (4.434%)
038: dt: 0.5000, sse=2026504.0, rms=7.625 (4.387%)
039: dt: 0.5000, sse=1907428.2, rms=7.271 (4.640%)
040: dt: 0.5000, sse=1807158.8, rms=6.958 (4.301%)
041: dt: 0.5000, sse=1715035.4, rms=6.661 (4.269%)
042: dt: 0.5000, sse=1648534.1, rms=6.436 (3.377%)
043: dt: 0.5000, sse=1588641.5, rms=6.229 (3.218%)
044: dt: 0.5000, sse=1555030.2, rms=6.107 (1.959%)
045: dt: 0.5000, sse=1521268.1, rms=5.987 (1.972%)
046: dt: 0.5000, sse=1506267.5, rms=5.929 (0.972%)
047: dt: 0.5000, sse=1488130.4, rms=5.862 (1.127%)
rms = 5.84, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1482808.5, rms=5.840 (0.380%)
049: dt: 0.2500, sse=1443116.1, rms=5.662 (3.048%)
050: dt: 0.2500, sse=1428818.5, rms=5.605 (1.007%)
rms = 5.60, time step reduction 2 of 3 to 0.125...
051: dt: 0.2500, sse=1427664.9, rms=5.598 (0.108%)
rms = 5.56, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1418147.0, rms=5.558 (0.726%)
positioning took 2.4 minutes
mean border=52.1, 2070 (19) missing vertices, mean dist 0.2 [0.2 (%54.0)->1.0 (%46.0))]
%19 local maxima, %41 large gradients and %34 min vals, 460 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=1567036.8, rms=5.263
053: dt: 0.5000, sse=1506328.2, rms=5.012 (4.781%)
054: dt: 0.5000, sse=1477280.1, rms=4.905 (2.140%)
rms = 5.01, time step reduction 1 of 3 to 0.250...
055: dt: 0.2500, sse=1444698.2, rms=4.731 (3.535%)
rms = 4.75, time step reduction 2 of 3 to 0.125...
rms = 4.71, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1440784.9, rms=4.709 (0.474%)
positioning took 0.7 minutes
mean border=51.3, 2285 (10) missing vertices, mean dist 0.2 [0.2 (%49.1)->0.8 (%50.9))]
%30 local maxima, %30 large gradients and %33 min vals, 512 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=1521435.2, rms=5.013
rms = 5.09, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1491000.1, rms=4.869 (2.856%)
rms = 4.84, time step reduction 2 of 3 to 0.125...
058: dt: 0.2500, sse=1486173.2, rms=4.845 (0.504%)
rms = 4.82, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1482024.9, rms=4.822 (0.479%)
positioning took 0.5 minutes
mean border=50.7, 5179 (7) missing vertices, mean dist 0.2 [0.2 (%47.8)->0.6 (%52.2))]
%36 local maxima, %23 large gradients and %32 min vals, 546 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-6.0.0/0050566/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1510204.5, rms=4.929
060: dt: 0.5000, sse=1473245.1, rms=4.794 (2.728%)
061: dt: 0.5000, sse=1427920.9, rms=4.629 (3.438%)
062: dt: 0.5000, sse=1413049.4, rms=4.570 (1.285%)
063: dt: 0.5000, sse=1387293.4, rms=4.463 (2.347%)
rms = 4.43, time step reduction 1 of 3 to 0.250...
064: dt: 0.5000, sse=1378639.9, rms=4.427 (0.805%)
065: dt: 0.2500, sse=1327745.2, rms=4.121 (6.902%)
066: dt: 0.2500, sse=1307189.4, rms=4.016 (2.542%)
rms = 4.05, time step reduction 2 of 3 to 0.125...
rms = 3.97, time step reduction 3 of 3 to 0.062...
067: dt: 0.1250, sse=1299327.6, rms=3.970 (1.163%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.area.pial
vertex spacing 1.10 +- 0.50 (0.08-->8.24) (max @ vno 82855 --> 82845)
face area 0.47 +- 0.40 (0.00-->8.33)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 121292 vertices processed
25000 of 121292 vertices processed
50000 of 121292 vertices processed
75000 of 121292 vertices processed
100000 of 121292 vertices processed
0 of 121292 vertices processed
25000 of 121292 vertices processed
50000 of 121292 vertices processed
75000 of 121292 vertices processed
100000 of 121292 vertices processed
thickness calculation complete, 781:3388 truncations.
27634 vertices at 0 distance
80520 vertices at 1 distance
72282 vertices at 2 distance
33173 vertices at 3 distance
11185 vertices at 4 distance
3494 vertices at 5 distance
1187 vertices at 6 distance
458 vertices at 7 distance
204 vertices at 8 distance
137 vertices at 9 distance
78 vertices at 10 distance
54 vertices at 11 distance
48 vertices at 12 distance
42 vertices at 13 distance
28 vertices at 14 distance
26 vertices at 15 distance
24 vertices at 16 distance
11 vertices at 17 distance
13 vertices at 18 distance
8 vertices at 19 distance
10 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.thickness
positioning took 13.2 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
12664 bright wm thresholded.
2174 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.orig...
computing class statistics...
border white:    240984 voxels (1.44%)
border gray      284361 voxels (1.69%)
WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0]
GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 53.4 (was 70)
setting MAX_BORDER_WHITE to 109.6 (was 105)
setting MIN_BORDER_WHITE to 64.0 (was 85)
setting MAX_CSF to 42.9 (was 40)
setting MAX_GRAY to 92.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.0,    GM=64+-8.7
mean inside = 91.7, mean outside = 73.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.91 +- 0.25 (0.03-->3.58) (max @ vno 124624 --> 124652)
face area 0.35 +- 0.16 (0.00-->2.58)
mean absolute distance = 0.45 +- 0.70
3242 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 32 points - only 0.00% unknown
deleting segment 3 with 189 points - only 0.00% unknown
deleting segment 4 with 52 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
deleting segment 6 with 10 points - only 0.00% unknown
mean border=77.0, 110 (100) missing vertices, mean dist 0.3 [0.5 (%17.7)->0.5 (%82.3))]
%73 local maxima, %22 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 0.94 +- 0.26 (0.11-->4.03) (max @ vno 124624 --> 124652)
face area 0.35 +- 0.16 (0.00-->2.60)
mean absolute distance = 0.29 +- 0.51
2758 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1717081.2, rms=6.759
001: dt: 0.5000, sse=1013887.4, rms=4.038 (40.259%)
002: dt: 0.5000, sse=862353.4, rms=3.173 (21.424%)
003: dt: 0.5000, sse=848221.7, rms=3.087 (2.716%)
004: dt: 0.5000, sse=834038.0, rms=2.931 (5.045%)
rms = 3.04, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=726701.8, rms=2.039 (30.428%)
006: dt: 0.2500, sse=690992.4, rms=1.618 (20.631%)
007: dt: 0.2500, sse=682703.8, rms=1.496 (7.537%)
rms = 1.45, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=679845.2, rms=1.454 (2.872%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=677341.2, rms=1.405 (3.354%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 29 points - only 0.00% unknown
deleting segment 1 with 118 points - only 0.00% unknown
deleting segment 2 with 42 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
mean border=79.5, 46 (12) missing vertices, mean dist -0.2 [0.3 (%70.9)->0.2 (%29.1))]
%80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.93 +- 0.25 (0.11-->3.82) (max @ vno 124624 --> 124652)
face area 0.37 +- 0.17 (0.00-->2.95)
mean absolute distance = 0.26 +- 0.41
2973 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1008036.4, rms=3.784
010: dt: 0.5000, sse=806037.6, rms=2.418 (36.110%)
rms = 2.58, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=738050.2, rms=1.756 (27.362%)
012: dt: 0.2500, sse=708878.9, rms=1.356 (22.770%)
013: dt: 0.2500, sse=699353.2, rms=1.215 (10.395%)
rms = 1.17, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=698006.9, rms=1.174 (3.441%)
rms = 1.14, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=695374.9, rms=1.141 (2.757%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 30 points - only 0.00% unknown
deleting segment 1 with 120 points - only 0.00% unknown
deleting segment 2 with 43 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
mean border=81.2, 48 (8) missing vertices, mean dist -0.1 [0.3 (%64.6)->0.2 (%35.4))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.25 (0.06-->3.74) (max @ vno 124624 --> 124652)
face area 0.36 +- 0.17 (0.00-->2.91)
mean absolute distance = 0.25 +- 0.36
2733 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=807220.2, rms=2.581
016: dt: 0.5000, sse=770339.3, rms=2.263 (12.327%)
rms = 2.49, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=704492.2, rms=1.537 (32.096%)
018: dt: 0.2500, sse=681535.8, rms=1.189 (22.651%)
019: dt: 0.2500, sse=675996.5, rms=1.091 (8.202%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=683215.8, rms=1.075 (1.467%)
rms = 1.04, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=672889.8, rms=1.040 (3.274%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 27 points - only 0.00% unknown
deleting segment 1 with 121 points - only 0.00% unknown
deleting segment 2 with 47 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
mean border=81.9, 51 (4) missing vertices, mean dist -0.0 [0.3 (%55.1)->0.2 (%44.9))]
%86 local maxima, % 9 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-6.0.0/0050566/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=690469.6, rms=1.473
rms = 1.47, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=696567.0, rms=1.466 (0.464%)
023: dt: 0.2500, sse=663522.4, rms=1.024 (30.132%)
024: dt: 0.2500, sse=662714.9, rms=0.892 (12.870%)
rms = 0.93, time step reduction 2 of 3 to 0.125...
rms = 0.86, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=661098.9, rms=0.857 (4.005%)
positioning took 0.4 minutes
generating cortex label...
3 non-cortical segments detected
only using segment with 7637 vertices
erasing segment 0 (vno[0] = 39048)
erasing segment 2 (vno[0] = 91649)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.area
vertex spacing 0.91 +- 0.25 (0.03-->3.51) (max @ vno 49445 --> 49452)
face area 0.35 +- 0.16 (0.00-->2.89)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 30 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=52.4, 146 (146) missing vertices, mean dist 1.5 [3.8 (%0.0)->2.8 (%100.0))]
% 9 local maxima, %44 large gradients and %42 min vals, 761 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=22358734.0, rms=30.207
001: dt: 0.0500, sse=19784170.0, rms=28.361 (6.110%)
002: dt: 0.0500, sse=17935920.0, rms=26.958 (4.947%)
003: dt: 0.0500, sse=16508529.0, rms=25.822 (4.213%)
004: dt: 0.0500, sse=15344590.0, rms=24.858 (3.736%)
005: dt: 0.0500, sse=14357010.0, rms=24.009 (3.415%)
006: dt: 0.0500, sse=13494368.0, rms=23.242 (3.194%)
007: dt: 0.0500, sse=12726657.0, rms=22.537 (3.031%)
008: dt: 0.0500, sse=12032543.0, rms=21.881 (2.914%)
009: dt: 0.0500, sse=11398805.0, rms=21.263 (2.821%)
010: dt: 0.0500, sse=10815420.0, rms=20.679 (2.749%)
positioning took 0.9 minutes
mean border=52.2, 103 (76) missing vertices, mean dist 1.3 [3.1 (%0.0)->2.3 (%100.0))]
%10 local maxima, %44 large gradients and %41 min vals, 753 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=11538971.0, rms=21.397
011: dt: 0.0500, sse=10994248.0, rms=20.855 (2.531%)
012: dt: 0.0500, sse=10487013.0, rms=20.338 (2.481%)
013: dt: 0.0500, sse=10013911.0, rms=19.843 (2.433%)
014: dt: 0.0500, sse=9572053.0, rms=19.369 (2.387%)
015: dt: 0.0500, sse=9159382.0, rms=18.916 (2.340%)
016: dt: 0.0500, sse=8773994.0, rms=18.483 (2.291%)
017: dt: 0.0500, sse=8413631.0, rms=18.068 (2.244%)
018: dt: 0.0500, sse=8077839.0, rms=17.673 (2.188%)
019: dt: 0.0500, sse=7763779.0, rms=17.295 (2.139%)
020: dt: 0.0500, sse=7471131.0, rms=16.935 (2.081%)
positioning took 0.9 minutes
mean border=52.0, 146 (63) missing vertices, mean dist 1.1 [0.1 (%0.8)->2.0 (%99.2))]
%10 local maxima, %44 large gradients and %41 min vals, 747 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=7567063.0, rms=17.057
021: dt: 0.0500, sse=7286535.0, rms=16.707 (2.051%)
022: dt: 0.0500, sse=7025741.5, rms=16.375 (1.988%)
023: dt: 0.0500, sse=6781530.0, rms=16.057 (1.938%)
024: dt: 0.0500, sse=6554461.0, rms=15.757 (1.874%)
025: dt: 0.0500, sse=6342810.5, rms=15.471 (1.814%)
026: dt: 0.0500, sse=6145838.5, rms=15.200 (1.752%)
027: dt: 0.0500, sse=5961316.0, rms=14.941 (1.700%)
028: dt: 0.0500, sse=5787314.0, rms=14.693 (1.660%)
029: dt: 0.0500, sse=5622573.0, rms=14.455 (1.625%)
030: dt: 0.0500, sse=5466583.5, rms=14.225 (1.591%)
positioning took 0.9 minutes
mean border=51.9, 188 (54) missing vertices, mean dist 1.0 [0.1 (%12.6)->1.9 (%87.4))]
%10 local maxima, %44 large gradients and %41 min vals, 722 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=5549698.5, rms=14.345
031: dt: 0.5000, sse=4481932.5, rms=12.675 (11.639%)
032: dt: 0.5000, sse=3790270.2, rms=11.456 (9.620%)
033: dt: 0.5000, sse=3304117.8, rms=10.514 (8.220%)
034: dt: 0.5000, sse=2970424.8, rms=9.807 (6.724%)
035: dt: 0.5000, sse=2723287.2, rms=9.248 (5.701%)
036: dt: 0.5000, sse=2520815.5, rms=8.761 (5.269%)
037: dt: 0.5000, sse=2337009.0, rms=8.297 (5.290%)
038: dt: 0.5000, sse=2169452.8, rms=7.850 (5.387%)
039: dt: 0.5000, sse=2005191.5, rms=7.391 (5.853%)
040: dt: 0.5000, sse=1866066.4, rms=6.975 (5.622%)
041: dt: 0.5000, sse=1750328.5, rms=6.614 (5.174%)
042: dt: 0.5000, sse=1662337.9, rms=6.322 (4.423%)
043: dt: 0.5000, sse=1597132.6, rms=6.100 (3.504%)
044: dt: 0.5000, sse=1550144.6, rms=5.931 (2.775%)
045: dt: 0.5000, sse=1513595.1, rms=5.800 (2.209%)
046: dt: 0.5000, sse=1486593.9, rms=5.698 (1.758%)
047: dt: 0.5000, sse=1464102.8, rms=5.615 (1.457%)
048: dt: 0.5000, sse=1449521.5, rms=5.558 (1.018%)
049: dt: 0.5000, sse=1435256.4, rms=5.504 (0.961%)
rms = 5.47, time step reduction 1 of 3 to 0.250...
050: dt: 0.5000, sse=1427120.8, rms=5.471 (0.606%)
051: dt: 0.2500, sse=1386133.4, rms=5.281 (3.476%)
052: dt: 0.2500, sse=1371881.8, rms=5.223 (1.105%)
rms = 5.23, time step reduction 2 of 3 to 0.125...
rms = 5.20, time step reduction 3 of 3 to 0.062...
053: dt: 0.1250, sse=1367870.2, rms=5.205 (0.342%)
positioning took 2.7 minutes
mean border=51.4, 2541 (13) missing vertices, mean dist 0.2 [0.2 (%53.7)->0.9 (%46.3))]
%19 local maxima, %38 large gradients and %36 min vals, 332 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=1594510.6, rms=5.141
054: dt: 0.5000, sse=1529758.4, rms=4.874 (5.202%)
055: dt: 0.5000, sse=1482305.4, rms=4.686 (3.853%)
rms = 4.72, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1442797.2, rms=4.474 (4.516%)
rms = 4.43, time step reduction 2 of 3 to 0.125...
057: dt: 0.2500, sse=1436049.1, rms=4.429 (1.011%)
058: dt: 0.1250, sse=1424321.0, rms=4.366 (1.427%)
rms = 4.35, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1420498.5, rms=4.348 (0.414%)
positioning took 0.9 minutes
mean border=50.8, 3017 (13) missing vertices, mean dist 0.2 [0.2 (%51.0)->0.7 (%49.0))]
%28 local maxima, %29 large gradients and %36 min vals, 403 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=1485253.2, rms=4.608
rms = 4.60, time step reduction 1 of 3 to 0.250...
060: dt: 0.5000, sse=1480814.4, rms=4.602 (0.126%)
061: dt: 0.2500, sse=1440656.5, rms=4.411 (4.158%)
062: dt: 0.2500, sse=1425294.9, rms=4.340 (1.605%)
rms = 4.32, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1420042.0, rms=4.317 (0.516%)
064: dt: 0.1250, sse=1401261.9, rms=4.220 (2.261%)
rms = 4.19, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1394510.6, rms=4.188 (0.746%)
positioning took 0.9 minutes
mean border=50.2, 5869 (12) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.5 (%51.7))]
%34 local maxima, %22 large gradients and %34 min vals, 458 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-6.0.0/0050566/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1428204.1, rms=4.265
rms = 4.24, time step reduction 1 of 3 to 0.250...
066: dt: 0.5000, sse=1418002.8, rms=4.239 (0.616%)
067: dt: 0.2500, sse=1370524.6, rms=3.989 (5.885%)
068: dt: 0.2500, sse=1351386.1, rms=3.897 (2.327%)
rms = 3.87, time step reduction 2 of 3 to 0.125...
069: dt: 0.2500, sse=1345021.0, rms=3.866 (0.793%)
070: dt: 0.1250, sse=1323515.2, rms=3.740 (3.244%)
rms = 3.71, time step reduction 3 of 3 to 0.062...
071: dt: 0.1250, sse=1316838.8, rms=3.706 (0.910%)
positioning took 0.9 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.area.pial
vertex spacing 1.09 +- 0.51 (0.07-->9.38) (max @ vno 95512 --> 95531)
face area 0.47 +- 0.40 (0.00-->9.67)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 125464 vertices processed
25000 of 125464 vertices processed
50000 of 125464 vertices processed
75000 of 125464 vertices processed
100000 of 125464 vertices processed
125000 of 125464 vertices processed
0 of 125464 vertices processed
25000 of 125464 vertices processed
50000 of 125464 vertices processed
75000 of 125464 vertices processed
100000 of 125464 vertices processed
125000 of 125464 vertices processed
thickness calculation complete, 815:4164 truncations.
27925 vertices at 0 distance
82016 vertices at 1 distance
74735 vertices at 2 distance
34727 vertices at 3 distance
12421 vertices at 4 distance
3866 vertices at 5 distance
1324 vertices at 6 distance
504 vertices at 7 distance
228 vertices at 8 distance
197 vertices at 9 distance
136 vertices at 10 distance
82 vertices at 11 distance
72 vertices at 12 distance
54 vertices at 13 distance
46 vertices at 14 distance
41 vertices at 15 distance
48 vertices at 16 distance
20 vertices at 17 distance
16 vertices at 18 distance
18 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.thickness
positioning took 14.3 minutes
PIDs (24766 24769) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 11:26:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label
Total face volume 255377
Total vertex volume 251169 (mask=0)
#@# 0050566 lh 251169
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 11:26:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label
Total face volume 268912
Total vertex volume 264656 (mask=0)
#@# 0050566 rh 264656
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 11:26:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 

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 = 213
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/ribbon.mgz
mris_volmask took 10.87 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 11:37:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 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 0050566 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 11:37:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 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 0050566 rh pial 

Waiting for PID 25691 of (25691 25694 25697 25700) to complete...
Waiting for PID 25694 of (25691 25694 25697 25700) to complete...
Waiting for PID 25697 of (25691 25694 25697 25700) to complete...
Waiting for PID 25700 of (25691 25694 25697 25700) 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 0050566 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377
Total vertex volume 251169 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1093    787   1750  2.383 0.440     0.090     0.015        6     0.6  bankssts
  718    498   1763  2.936 0.677     0.123     0.016       10     0.4  caudalanteriorcingulate
 3552   2395   7403  2.640 0.708     0.106     0.017       28     2.4  caudalmiddlefrontal
 1786   1354   3073  2.152 0.600     0.156     0.037       24     3.0  cuneus
  545    384   2177  3.842 0.867     0.112     0.025        4     0.6  entorhinal
 3405   2556   9505  2.929 0.775     0.139     0.029       44     4.2  fusiform
 7136   5013  15225  2.511 0.683     0.126     0.028       95     8.5  inferiorparietal
 4288   3111  10408  2.584 0.774     0.141     0.041       73     7.9  inferiortemporal
 1465    972   3043  2.656 0.862     0.121     0.029       16     1.7  isthmuscingulate
 7428   5174  12923  2.195 0.649     0.138     0.032       93     9.6  lateraloccipital
 3413   2464   8884  2.940 0.864     0.129     0.028       37     4.0  lateralorbitofrontal
 4425   3258   8241  2.267 0.722     0.142     0.035       55     6.6  lingual
 2186   1567   5101  2.772 0.729     0.133     0.030       30     2.7  medialorbitofrontal
 3822   2785   9426  2.545 0.752     0.127     0.028       49     4.7  middletemporal
  839    583   2189  3.185 0.821     0.102     0.023        6     0.6  parahippocampal
 2005   1408   3796  2.495 0.657     0.121     0.023       18     1.8  paracentral
 2115   1512   4613  2.493 0.707     0.115     0.022       25     2.1  parsopercularis
  953    686   2960  3.081 0.861     0.129     0.026       12     1.0  parsorbitalis
 1681   1188   3849  2.601 0.672     0.131     0.032       20     2.1  parstriangularis
 1866   1457   2449  1.756 0.595     0.155     0.040       23     3.3  pericalcarine
 5372   3752  10486  2.221 0.788     0.110     0.021       45     4.7  postcentral
 1559   1100   3522  2.674 0.855     0.129     0.026       17     1.7  posteriorcingulate
 6316   4458  13317  2.544 0.643     0.116     0.021       57     5.4  precentral
 4962   3508  12135  2.794 0.762     0.130     0.031       57     6.4  precuneus
  925    590   2579  3.211 0.949     0.111     0.032       10     1.1  rostralanteriorcingulate
 8412   5951  17989  2.405 0.730     0.133     0.033      120    12.2  rostralmiddlefrontal
10419   7517  24866  2.824 0.741     0.125     0.027      107    11.7  superiorfrontal
 8117   5883  17585  2.464 0.748     0.130     0.026       89     8.9  superiorparietal
 4272   3017   9278  2.470 0.778     0.099     0.021       40     3.9  superiortemporal
 4115   2958   8445  2.367 0.678     0.141     0.033       55     5.9  supramarginal
  330    248   1404  3.050 0.875     0.144     0.049        7     0.6  frontalpole
  569    462   3590  4.501 0.550     0.160     0.049        7     1.2  temporalpole
  546    376    786  2.030 0.378     0.149     0.024        7     0.5  transversetemporal
 2831   1932   6401  3.143 0.847     0.120     0.032       25     3.6  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 0050566 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377
Total vertex volume 251169 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1093    697   1750  2.383 0.440     0.113     0.029       27     1.3  bankssts
  718    700   1763  2.936 0.677     0.166     0.035       12     1.2  caudalanteriorcingulate
 3552   3184   7403  2.640 0.708     0.152     0.034       39     5.9  caudalmiddlefrontal
 1786   1601   3073  2.152 0.600     0.155     0.038       22     3.2  cuneus
  545    766   2177  3.842 0.867     0.209     0.044        6     1.2  entorhinal
 3405   3685   9505  2.929 0.775     0.190     0.043       47     7.5  fusiform
 7136   6984  15225  2.511 0.683     0.173     0.038       96    13.2  inferiorparietal
 4288   4779  10408  2.584 0.774     0.208     0.050       77    10.5  inferiortemporal
 1465   1312   3043  2.656 0.862     0.175     0.046       29     2.9  isthmuscingulate
 7428   6526  12923  2.195 0.649     0.148     0.034       98    12.0  lateraloccipital
 3413   3461   8884  2.940 0.864     0.190     0.045       59     8.0  lateralorbitofrontal
 4425   4054   8241  2.267 0.722     0.172     0.043       73     9.2  lingual
 2186   2120   5101  2.772 0.729     0.186     0.049       36     5.1  medialorbitofrontal
 3822   4265   9426  2.545 0.752     0.202     0.043       51     8.4  middletemporal
  839    784   2189  3.185 0.821     0.173     0.048       11     1.9  parahippocampal
 2005   1649   3796  2.495 0.657     0.138     0.030       26     2.6  paracentral
 2115   2218   4613  2.493 0.707     0.177     0.040       26     4.2  parsopercularis
  953   1177   2960  3.081 0.861     0.197     0.038       11     1.7  parsorbitalis
 1681   1720   3849  2.601 0.672     0.203     0.044       28     3.2  parstriangularis
 1866   1361   2449  1.756 0.595     0.145     0.044       30     3.3  pericalcarine
 5372   5497  10486  2.221 0.788     0.169     0.036       57    10.2  postcentral
 1559   1388   3522  2.674 0.855     0.166     0.049       65     3.1  posteriorcingulate
 6316   5667  13317  2.544 0.643     0.144     0.030       83     9.0  precentral
 4962   4855  12135  2.794 0.762     0.187     0.048       93    11.1  precuneus
  925    907   2579  3.211 0.949     0.188     0.052       17     2.1  rostralanteriorcingulate
 8412   8588  17989  2.405 0.730     0.188     0.041      112    18.2  rostralmiddlefrontal
10419   9903  24866  2.824 0.741     0.166     0.039      153    19.1  superiorfrontal
 8117   7933  17585  2.464 0.748     0.167     0.038      103    15.1  superiorparietal
 4272   4220   9278  2.470 0.778     0.170     0.036       58     8.0  superiortemporal
 4115   4022   8445  2.367 0.678     0.181     0.039       53     7.9  supramarginal
  330    629   1404  3.050 0.875     0.306     0.051        5     1.0  frontalpole
  569   1042   3590  4.501 0.550     0.239     0.039        4     1.2  temporalpole
  546    420    786  2.030 0.378     0.147     0.037        6     0.9  transversetemporal
 2831   2091   6401  3.143 0.847     0.171     0.050       55     6.7  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 0050566 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912
Total vertex volume 264656 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1285    919   2410  2.583 0.587     0.101     0.014        8     0.8  bankssts
 1270    899   2612  2.711 0.707     0.138     0.016       20     0.9  caudalanteriorcingulate
 3152   2178   7387  2.831 0.732     0.109     0.019       24     2.5  caudalmiddlefrontal
 2321   1699   3830  2.063 0.575     0.149     0.034       30     3.3  cuneus
  583    407   2167  3.609 0.828     0.114     0.024        4     0.6  entorhinal
 3782   2688   9770  2.896 0.828     0.136     0.032       48     4.8  fusiform
 7491   5294  17345  2.639 0.709     0.128     0.030       93     9.4  inferiorparietal
 3424   2515   9444  2.760 0.829     0.140     0.034       53     5.2  inferiortemporal
 1144    771   2468  2.665 0.871     0.123     0.030       15     1.0  isthmuscingulate
 7558   5106  12776  2.212 0.716     0.135     0.032       98     9.7  lateraloccipital
 2866   2077   8866  3.250 0.926     0.136     0.038       38     4.4  lateralorbitofrontal
 4625   3426   8878  2.284 0.706     0.152     0.039       64     8.4  lingual
 2448   1774   6212  2.725 0.826     0.142     0.041       45     4.2  medialorbitofrontal
 4073   3014  11286  2.773 0.879     0.139     0.032       67     5.8  middletemporal
  911    610   2138  2.812 0.957     0.093     0.019        7     0.5  parahippocampal
 2271   1585   4517  2.574 0.582     0.129     0.029       22     2.8  paracentral
 2081   1494   5019  2.699 0.703     0.124     0.022       25     1.9  parsopercularis
 1032    754   3823  3.452 0.942     0.141     0.030       14     1.3  parsorbitalis
 2195   1542   5226  2.564 0.766     0.118     0.022       23     2.0  parstriangularis
 2413   1702   2442  1.658 0.394     0.137     0.033       27     3.4  pericalcarine
 5534   3653   9641  2.123 0.810     0.101     0.022       57     5.3  postcentral
 1715   1240   3759  2.692 0.813     0.144     0.030       24     2.2  posteriorcingulate
 6303   4251  12092  2.453 0.793     0.110     0.023       65     6.5  precentral
 5510   3844  12152  2.702 0.809     0.129     0.025       60     6.0  precuneus
  742    472   1768  3.014 0.892     0.142     0.036       11     1.2  rostralanteriorcingulate
 7581   5391  18158  2.635 0.765     0.136     0.033      102    10.7  rostralmiddlefrontal
10097   7057  25797  2.890 0.749     0.124     0.027      107    10.7  superiorfrontal
 8561   5895  17554  2.473 0.764     0.115     0.023       71     8.1  superiorparietal
 4835   3483  11835  2.612 0.938     0.098     0.017       40     3.8  superiortemporal
 4725   3285  11204  2.591 0.824     0.129     0.026       59     5.3  supramarginal
  473    348   1792  2.965 0.787     0.195     0.058       11     1.3  frontalpole
  641    517   2566  3.522 0.970     0.158     0.030       10     1.1  temporalpole
  573    390    848  1.939 0.428     0.145     0.026       10     0.6  transversetemporal
 3028   2068   6855  3.087 0.882     0.122     0.028       30     3.4  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 0050566 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912
Total vertex volume 264656 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1285    911   2410  2.583 0.587     0.141     0.030       16     1.8  bankssts
 1270   1002   2612  2.711 0.707     0.145     0.032       28     1.7  caudalanteriorcingulate
 3152   2906   7387  2.831 0.732     0.144     0.030       36     4.6  caudalmiddlefrontal
 2321   2165   3830  2.063 0.575     0.154     0.035       33     3.8  cuneus
  583    804   2167  3.609 0.828     0.206     0.044        8     1.3  entorhinal
 3782   3756   9770  2.896 0.828     0.162     0.037       60     6.3  fusiform
 7491   7489  17345  2.639 0.709     0.170     0.034       98    12.8  inferiorparietal
 3424   3947   9444  2.760 0.829     0.207     0.048       60     8.2  inferiortemporal
 1144   1047   2468  2.665 0.871     0.170     0.047       47     2.3  isthmuscingulate
 7558   6416  12776  2.212 0.716     0.136     0.033      115    11.2  lateraloccipital
 2866   3051   8866  3.250 0.926     0.205     0.052       64     7.2  lateralorbitofrontal
 4625   4422   8878  2.284 0.706     0.174     0.041       71     9.5  lingual
 2448   2740   6212  2.725 0.826     0.211     0.052       41     6.2  medialorbitofrontal
 4073   4839  11286  2.773 0.879     0.199     0.038      102     7.7  middletemporal
  911    845   2138  2.812 0.957     0.168     0.044       12     1.9  parahippocampal
 2271   1888   4517  2.574 0.582     0.143     0.035       27     3.6  paracentral
 2081   2099   5019  2.699 0.703     0.173     0.033       28     3.3  parsopercularis
 1032   1406   3823  3.452 0.942     0.211     0.043       17     2.1  parsorbitalis
 2195   2406   5226  2.564 0.766     0.191     0.037       29     4.0  parstriangularis
 2413   1437   2442  1.658 0.394     0.114     0.031       34     3.5  pericalcarine
 5534   5003   9641  2.123 0.810     0.138     0.029       56     8.0  postcentral
 1715   1531   3759  2.692 0.813     0.171     0.049       49     3.9  posteriorcingulate
 6303   5390  12092  2.453 0.793     0.133     0.026       75     8.0  precentral
 5510   4897  12152  2.702 0.809     0.165     0.042       85    10.5  precuneus
  742    681   1768  3.014 0.892     0.179     0.048       13     1.7  rostralanteriorcingulate
 7581   7830  18158  2.635 0.765     0.187     0.043      108    16.3  rostralmiddlefrontal
10097  10227  25797  2.890 0.749     0.174     0.040      133    19.4  superiorfrontal
 8561   7760  17554  2.473 0.764     0.145     0.030       97    12.6  superiorparietal
 4835   5063  11835  2.612 0.938     0.166     0.033       58     8.0  superiortemporal
 4725   4806  11204  2.591 0.824     0.175     0.039       60     9.1  supramarginal
  473    862   1792  2.965 0.787     0.313     0.066        9     1.7  frontalpole
  641    982   2566  3.522 0.970     0.229     0.047        7     1.5  temporalpole
  573    486    848  1.939 0.428     0.151     0.039        7     1.0  transversetemporal
 3028   2120   6855  3.087 0.882     0.161     0.053       60     7.8  insula
PIDs (25691 25694 25697 25700) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 11:38:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 11:38:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 25803 of (25803 25806) to complete...
Waiting for PID 25806 of (25803 25806) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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...
42 labels changed using aseg
relabeling using gibbs priors...
000:   7819 changed, 121292 examined...
001:   1734 changed, 30607 examined...
002:    494 changed, 9321 examined...
003:    210 changed, 2846 examined...
004:    104 changed, 1222 examined...
005:     58 changed, 625 examined...
006:     28 changed, 325 examined...
007:     12 changed, 163 examined...
008:      7 changed, 81 examined...
009:      2 changed, 38 examined...
010:      1 changed, 14 examined...
011:      0 changed, 7 examined...
18 labels changed using aseg
000: 233 total segments, 149 labels (1720 vertices) changed
001: 90 total segments, 7 labels (27 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 27 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
728 vertices marked for relabeling...
728 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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...
66 labels changed using aseg
relabeling using gibbs priors...
000:   7972 changed, 125464 examined...
001:   1746 changed, 31120 examined...
002:    503 changed, 9260 examined...
003:    203 changed, 2863 examined...
004:     95 changed, 1154 examined...
005:     43 changed, 541 examined...
006:     28 changed, 227 examined...
007:     14 changed, 159 examined...
008:      9 changed, 80 examined...
009:      5 changed, 45 examined...
010:      5 changed, 31 examined...
011:      2 changed, 24 examined...
012:      0 changed, 8 examined...
42 labels changed using aseg
000: 210 total segments, 126 labels (1848 vertices) changed
001: 92 total segments, 9 labels (67 vertices) changed
002: 84 total segments, 1 labels (1 vertices) changed
003: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 27 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
809 vertices marked for relabeling...
809 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 17 seconds.
PIDs (25803 25806) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 11:39:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 11:39:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh white 

Waiting for PID 25852 of (25852 25855) to complete...
Waiting for PID 25855 of (25852 25855) 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 0050566 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377
Total vertex volume 251169 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1118    801   2667  2.406 1.062     0.142     0.040       16     1.9  G&S_frontomargin
 1267    963   2822  2.392 0.710     0.147     0.031       17     1.6  G&S_occipital_inf
 1701   1183   3421  2.318 0.577     0.133     0.028       17     2.1  G&S_paracentral
 1183    866   3246  2.665 0.751     0.138     0.033       16     1.4  G&S_subcentral
  559    397   1802  2.805 0.780     0.137     0.049       13     1.0  G&S_transv_frontopol
 1934   1335   4554  2.968 0.795     0.107     0.022       13     1.6  G&S_cingul-Ant
 1028    722   2323  2.784 0.680     0.102     0.017        7     0.7  G&S_cingul-Mid-Ant
 1246    887   2694  2.822 0.730     0.118     0.025        9     1.3  G&S_cingul-Mid-Post
  464    334   1595  3.209 0.704     0.157     0.040        6     0.7  G_cingul-Post-dorsal
  271    184    754  2.983 0.890     0.144     0.044        4     0.4  G_cingul-Post-ventral
 1760   1371   3319  2.133 0.607     0.173     0.044       29     3.6  G_cuneus
 1204    843   3277  2.696 0.798     0.126     0.029       20     1.5  G_front_inf-Opercular
  340    234   1227  3.478 0.442     0.151     0.038        6     0.6  G_front_inf-Orbital
  904    642   2513  2.682 0.598     0.150     0.045       16     1.6  G_front_inf-Triangul
 4647   3265  12934  2.754 0.784     0.146     0.038       86     7.8  G_front_middle
 7202   5146  19785  3.019 0.722     0.139     0.033       94    10.0  G_front_sup
  569    376   1505  3.402 0.834     0.134     0.044        8     1.0  G_Ins_lg&S_cent_ins
  647    446   2290  3.536 0.813     0.129     0.040        7     1.0  G_insular_short
 2339   1564   5857  2.726 0.694     0.143     0.033       36     3.2  G_occipital_middle
 1548   1144   2815  2.062 0.500     0.140     0.024       20     1.5  G_occipital_sup
 1302    957   4467  3.246 0.657     0.146     0.029       22     1.5  G_oc-temp_lat-fusifor
 2936   2115   5731  2.266 0.726     0.154     0.041       43     5.3  G_oc-temp_med-Lingual
 1005    691   3383  3.546 0.795     0.104     0.024        6     0.8  G_oc-temp_med-Parahip
 2304   1699   7346  3.049 0.795     0.143     0.036       34     3.3  G_orbital
 2735   1942   7024  2.557 0.797     0.156     0.044       51     5.5  G_pariet_inf-Angular
 2075   1494   5244  2.548 0.719     0.159     0.039       39     3.7  G_pariet_inf-Supramar
 2908   2224   8692  2.790 0.810     0.153     0.035       44     4.4  G_parietal_sup
 2102   1473   4897  2.403 0.821     0.129     0.026       23     2.2  G_postcentral
 2121   1545   5777  2.765 0.661     0.134     0.028       26     2.4  G_precentral
 2425   1745   8681  3.207 0.746     0.155     0.042       40     4.3  G_precuneus
  767    610   2345  2.752 0.652     0.181     0.045       17     1.5  G_rectus
  402    239    728  2.748 0.778     0.077     0.028        3     0.3  G_subcallosal
  334    230    614  2.223 0.549     0.139     0.026        4     0.3  G_temp_sup-G_T_transv
 1526   1149   5166  2.787 0.898     0.155     0.038       30     2.9  G_temp_sup-Lateral
  667    454   1925  3.413 1.001     0.089     0.026        8     0.5  G_temp_sup-Plan_polar
  512    364    767  1.933 0.414     0.048     0.013        1     0.1  G_temp_sup-Plan_tempo
 2522   1875   6839  2.552 0.753     0.171     0.059       64     7.0  G_temporal_inf
 2023   1516   6193  2.683 0.733     0.155     0.041       43     3.7  G_temporal_middle
  263    187    530  2.646 0.835     0.107     0.016        2     0.1  Lat_Fis-ant-Horizont
  226    170    404  2.481 0.647     0.106     0.015        1     0.1  Lat_Fis-ant-Vertical
  819    555    997  2.095 0.511     0.108     0.017        5     0.6  Lat_Fis-post
 2099   1455   2968  1.856 0.509     0.151     0.040       33     3.4  Pole_occipital
 1426   1099   6939  3.756 0.945     0.157     0.045       22     2.6  Pole_temporal
 2428   1869   3187  1.930 0.761     0.139     0.036       26     3.7  S_calcarine
 2668   1869   3338  1.946 0.604     0.095     0.014       14     1.4  S_central
 1083    745   1638  2.254 0.576     0.089     0.011        5     0.5  S_cingul-Marginalis
  527    385   1026  3.048 0.694     0.089     0.015        2     0.3  S_circular_insula_ant
 1217    820   1916  2.635 0.770     0.091     0.012        5     0.6  S_circular_insula_inf
 1398    972   2262  2.709 0.559     0.101     0.017        6     1.0  S_circular_insula_sup
  829    627   1618  2.601 0.535     0.117     0.019        6     0.7  S_collat_transv_ant
  451    302    565  2.153 0.385     0.111     0.018        3     0.4  S_collat_transv_post
 2544   1748   3891  2.218 0.512     0.107     0.020       17     2.1  S_front_inf
 1545   1076   2100  2.173 0.491     0.101     0.019        8     1.1  S_front_middle
 2856   2146   5162  2.321 0.541     0.103     0.016       21     1.9  S_front_sup
  191    147    240  1.799 0.305     0.140     0.043        2     0.2  S_interm_prim-Jensen
 2509   1752   3706  2.234 0.559     0.109     0.017       19     1.8  S_intrapariet&P_trans
 1105    755   1314  2.024 0.415     0.123     0.027        8     1.1  S_oc_middle&Lunatus
 1594   1077   2109  2.170 0.626     0.112     0.021       12     1.3  S_oc_sup&transversal
  787    534   1127  2.235 0.563     0.083     0.012        3     0.4  S_occipital_ant
  692    497   1201  2.524 0.813     0.127     0.029        8     0.7  S_oc-temp_lat
 1906   1420   3669  2.634 0.633     0.122     0.024       14     1.9  S_oc-temp_med&Lingual
  337    235    461  1.997 0.424     0.096     0.012        1     0.2  S_orbital_lateral
  456    357   1028  3.072 0.975     0.118     0.024        4     0.4  S_orbital_med-olfact
 1304    880   2772  2.748 0.981     0.112     0.019       10     1.0  S_orbital-H_Shaped
 1738   1248   3080  2.529 0.676     0.101     0.016       11     1.0  S_parieto_occipital
 1121    694   1101  2.070 0.618     0.117     0.021       18     1.0  S_pericallosal
 2881   1962   4515  2.396 0.553     0.094     0.017       16     1.9  S_postcentral
 1682   1158   2806  2.383 0.615     0.101     0.014       11     1.0  S_precentral-inf-part
 1384    980   2169  2.415 0.529     0.091     0.011        6     0.6  S_precentral-sup-part
  617    406   1151  2.780 0.756     0.115     0.020        6     0.5  S_suborbital
 1100    727   1647  2.351 0.575     0.113     0.023        7     1.1  S_subparietal
 1449   1009   2031  2.135 0.644     0.106     0.016        8     1.0  S_temporal_inf
 5380   3815   8963  2.377 0.520     0.095     0.015       34     3.3  S_temporal_sup
  227    181    317  1.897 0.311     0.100     0.007        1     0.1  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 0050566 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912
Total vertex volume 264656 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
  808    600   1966  2.362 0.695     0.174     0.052       16     1.9  G&S_frontomargin
 1157    832   2597  2.707 0.674     0.133     0.027       14     1.3  G&S_occipital_inf
 1606   1047   2762  2.226 0.637     0.142     0.042       28     3.2  G&S_paracentral
  997    729   3073  2.837 0.941     0.129     0.028       11     1.0  G&S_subcentral
 1089    801   3378  2.833 0.821     0.159     0.032       18     1.5  G&S_transv_frontopol
 2921   2046   6635  2.759 0.770     0.131     0.030       40     3.4  G&S_cingul-Ant
 1731   1212   3766  2.826 0.629     0.128     0.022       19     1.5  G&S_cingul-Mid-Ant
 1648   1188   3597  2.728 0.756     0.133     0.028       18     2.1  G&S_cingul-Mid-Post
  399    313   1236  2.832 0.575     0.169     0.050        6     0.8  G_cingul-Post-dorsal
  300    190   1024  3.398 1.101     0.140     0.036        5     0.4  G_cingul-Post-ventral
 2299   1697   3852  1.954 0.580     0.151     0.034       31     3.2  G_cuneus
 1240    904   3878  2.957 0.826     0.155     0.038       24     2.1  G_front_inf-Opercular
  362    245   1172  3.045 0.700     0.125     0.023        4     0.4  G_front_inf-Orbital
 1001    720   3207  2.908 0.719     0.145     0.031       17     1.4  G_front_inf-Triangul
 3847   2689  12438  3.038 0.822     0.152     0.040       68     6.7  G_front_middle
 5864   4080  18161  3.146 0.693     0.135     0.031       77     7.2  G_front_sup
  507    357   1227  2.862 0.941     0.135     0.033        8     0.6  G_Ins_lg&S_cent_ins
  852    555   2453  3.291 1.073     0.123     0.044       11     1.4  G_insular_short
 2216   1551   6149  2.756 0.713     0.169     0.045       44     4.2  G_occipital_middle
 1530   1026   2965  2.335 0.627     0.129     0.033       18     2.1  G_occipital_sup
 1878   1382   5327  2.877 0.760     0.161     0.043       31     3.7  G_oc-temp_lat-fusifor
 3102   2322   6838  2.378 0.713     0.170     0.047       52     6.7  G_oc-temp_med-Lingual
  950    634   3094  3.400 0.886     0.108     0.024        8     0.7  G_oc-temp_med-Parahip
 2179   1625   8822  3.522 0.913     0.161     0.045       39     4.3  G_orbital
 2904   2147   9241  2.911 0.824     0.157     0.040       57     5.0  G_pariet_inf-Angular
 2287   1611   6995  2.829 0.942     0.148     0.036       38     3.7  G_pariet_inf-Supramar
 2881   2065   8133  2.729 0.881     0.136     0.033       32     3.9  G_parietal_sup
 2030   1320   4078  2.228 0.777     0.123     0.030       26     2.7  G_postcentral
 2521   1674   6098  2.684 0.847     0.123     0.029       40     3.3  G_precentral
 2255   1683   6833  2.999 0.836     0.147     0.032       32     3.3  G_precuneus
  796    626   2778  2.841 0.879     0.189     0.067       19     2.5  G_rectus
  149     85    342  2.901 1.206     0.123     0.088        4     0.5  G_subcallosal
  420    298    844  2.112 0.535     0.136     0.025        8     0.4  G_temp_sup-G_T_transv
 1524   1191   5707  3.040 0.863     0.154     0.030       28     2.3  G_temp_sup-Lateral
  775    560   2186  3.407 0.993     0.082     0.016        3     0.5  G_temp_sup-Plan_polar
  670    483   1377  2.456 0.573     0.057     0.006        1     0.2  G_temp_sup-Plan_tempo
 1745   1295   6203  2.953 0.834     0.152     0.042       34     3.5  G_temporal_inf
 2166   1655   7597  2.978 0.862     0.167     0.048       53     4.6  G_temporal_middle
  380    261    474  2.036 0.541     0.079     0.009        1     0.1  Lat_Fis-ant-Horizont
  309    222    482  2.228 0.566     0.082     0.011        1     0.1  Lat_Fis-ant-Vertical
 1156    793   1657  2.460 0.589     0.112     0.020        9     0.9  Lat_Fis-post
 3953   2641   5150  1.806 0.598     0.142     0.038       56     6.3  Pole_occipital
 1720   1313   6930  3.591 0.952     0.146     0.027       29     2.3  Pole_temporal
 2327   1621   2894  2.063 0.821     0.114     0.024       17     2.3  S_calcarine
 2510   1644   2502  1.720 0.520     0.076     0.010       10     1.0  S_central
 1358    943   2387  2.570 0.626     0.122     0.021       12     1.2  S_cingul-Marginalis
  464    320   1021  3.327 0.812     0.079     0.013        1     0.2  S_circular_insula_ant
 1079    731   1571  2.384 0.835     0.084     0.010        4     0.4  S_circular_insula_inf
 1361    934   2302  2.851 0.605     0.105     0.016        7     1.0  S_circular_insula_sup
  714    499   1242  2.392 0.609     0.099     0.015        4     0.3  S_collat_transv_ant
  384    268    405  1.930 0.381     0.124     0.027        3     0.4  S_collat_transv_post
 2035   1374   3263  2.471 0.578     0.097     0.015       12     1.3  S_front_inf
 2002   1437   3652  2.480 0.594     0.105     0.020       12     1.4  S_front_middle
 2664   1909   4726  2.537 0.537     0.097     0.017       15     1.8  S_front_sup
  241    161    276  1.792 0.478     0.108     0.014        2     0.2  S_interm_prim-Jensen
 3682   2467   5736  2.295 0.645     0.092     0.013       22     1.8  S_intrapariet&P_trans
  997    669   1200  1.954 0.418     0.113     0.020        7     0.9  S_oc_middle&Lunatus
 1428    962   2034  2.348 0.488     0.100     0.016        9     0.9  S_oc_sup&transversal
  624    458    876  2.361 0.572     0.128     0.026        5     0.7  S_occipital_ant
  737    530   1686  2.801 0.819     0.143     0.039        9     1.0  S_oc-temp_lat
 1997   1393   3303  2.516 0.595     0.104     0.015       13     1.2  S_oc-temp_med&Lingual
  358    245    460  2.067 0.413     0.114     0.021        2     0.3  S_orbital_lateral
  476    341   1441  3.595 0.961     0.103     0.032        5     0.5  S_orbital_med-olfact
 1023    739   2391  2.804 0.951     0.139     0.030       11     1.4  S_orbital-H_Shaped
 2096   1438   3144  2.378 0.626     0.117     0.019       16     1.6  S_parieto_occipital
 1300    822   1258  2.047 0.588     0.120     0.017       23     0.8  S_pericallosal
 2712   1781   3546  2.250 0.503     0.085     0.014       11     1.5  S_postcentral
 1584   1084   2353  2.189 0.616     0.093     0.012        9     0.8  S_precentral-inf-part
 1250    876   2298  2.734 0.564     0.098     0.014        7     0.7  S_precentral-sup-part
  362    247    481  2.254 0.597     0.080     0.009        2     0.1  S_suborbital
 1252    849   2069  2.378 0.545     0.116     0.022       12     1.1  S_subparietal
  953    701   1484  2.181 0.563     0.115     0.017        5     0.7  S_temporal_inf
 5864   4035   9631  2.436 0.638     0.094     0.015       36     3.5  S_temporal_sup
  288    198    301  1.896 0.374     0.142     0.014        4     0.2  S_temporal_transverse
PIDs (25852 25855) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 11:39:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 11:39:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 25919 of (25919 25922) to complete...
Waiting for PID 25922 of (25919 25922) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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...
1277 labels changed using aseg
relabeling using gibbs priors...
000:   1779 changed, 121292 examined...
001:    411 changed, 8322 examined...
002:    114 changed, 2369 examined...
003:     59 changed, 665 examined...
004:     28 changed, 311 examined...
005:     14 changed, 163 examined...
006:      7 changed, 90 examined...
007:      6 changed, 49 examined...
008:      4 changed, 37 examined...
009:      4 changed, 23 examined...
010:      1 changed, 23 examined...
011:      1 changed, 8 examined...
012:      2 changed, 6 examined...
013:      2 changed, 12 examined...
014:      1 changed, 13 examined...
015:      1 changed, 6 examined...
016:      1 changed, 7 examined...
017:      0 changed, 7 examined...
230 labels changed using aseg
000: 52 total segments, 19 labels (123 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 9 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
597 vertices marked for relabeling...
597 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 13 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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...
1150 labels changed using aseg
relabeling using gibbs priors...
000:   1925 changed, 125464 examined...
001:    427 changed, 8986 examined...
002:    121 changed, 2392 examined...
003:     49 changed, 684 examined...
004:     31 changed, 267 examined...
005:     21 changed, 154 examined...
006:     18 changed, 113 examined...
007:     17 changed, 91 examined...
008:      8 changed, 77 examined...
009:      7 changed, 40 examined...
010:      8 changed, 35 examined...
011:      6 changed, 39 examined...
012:      7 changed, 35 examined...
013:      6 changed, 35 examined...
014:      5 changed, 34 examined...
015:      3 changed, 23 examined...
016:      2 changed, 17 examined...
017:      4 changed, 16 examined...
018:      4 changed, 19 examined...
019:      3 changed, 22 examined...
020:      1 changed, 15 examined...
021:      0 changed, 5 examined...
256 labels changed using aseg
000: 51 total segments, 18 labels (150 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
614 vertices marked for relabeling...
614 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 14 seconds.
PIDs (25919 25922) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 11:40:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 11:40:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh white 

Waiting for PID 25986 of (25986 25989) to complete...
Waiting for PID 25989 of (25986 25989) 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 0050566 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377
Total vertex volume 251169 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1294    888   2836  2.817 0.664     0.110     0.018       13     0.8  caudalanteriorcingulate
 3813   2586   7826  2.609 0.706     0.106     0.017       30     2.6  caudalmiddlefrontal
 2500   1856   4388  2.186 0.558     0.146     0.032       31     3.6  cuneus
  470    330   1851  3.796 0.804     0.106     0.024        3     0.5  entorhinal
 3111   2323   7847  2.835 0.731     0.133     0.026       35     3.3  fusiform
 7138   4991  14871  2.481 0.691     0.127     0.029       91     8.7  inferiorparietal
 4266   3142  11863  2.713 0.849     0.150     0.045       81     8.6  inferiortemporal
 1451    962   3050  2.666 0.859     0.122     0.030       16     1.7  isthmuscingulate
 7406   5162  12993  2.203 0.650     0.139     0.032       95     9.6  lateraloccipital
 3593   2608  10473  3.069 0.937     0.135     0.035       46     5.2  lateralorbitofrontal
 4550   3323   8289  2.246 0.716     0.143     0.035       57     6.8  lingual
 1737   1274   4314  2.791 0.701     0.140     0.031       26     2.2  medialorbitofrontal
 5235   3797  11814  2.502 0.698     0.119     0.026       63     5.6  middletemporal
  878    609   2297  3.198 0.813     0.100     0.022        6     0.6  parahippocampal
 2334   1649   4714  2.560 0.650     0.123     0.024       22     2.3  paracentral
 1928   1379   4203  2.513 0.698     0.117     0.023       24     1.9  parsopercularis
  984    690   2520  2.931 0.787     0.115     0.024       10     1.0  parsorbitalis
 2109   1484   4315  2.416 0.636     0.122     0.028       22     2.3  parstriangularis
 1870   1458   2400  1.743 0.588     0.156     0.040       24     3.3  pericalcarine
 6243   4376  11993  2.218 0.762     0.112     0.021       52     5.4  postcentral
 1707   1207   3664  2.644 0.854     0.129     0.026       18     1.9  posteriorcingulate
 6222   4380  13136  2.551 0.647     0.115     0.022       55     5.3  precentral
 4885   3501  12566  2.832 0.766     0.136     0.033       61     6.8  precuneus
 1307    860   3394  3.173 0.894     0.115     0.030       15     1.5  rostralanteriorcingulate
 6185   4384  13272  2.398 0.690     0.135     0.033       90     9.0  rostralmiddlefrontal
11499   8271  27778  2.772 0.775     0.127     0.028      128    13.7  superiorfrontal
 6378   4613  14010  2.508 0.773     0.124     0.025       64     6.6  superiorparietal
 5570   3997  14083  2.689 0.975     0.107     0.025       54     5.9  superiortemporal
 3710   2685   7811  2.418 0.676     0.142     0.032       50     5.6  supramarginal
  547    378    786  2.017 0.391     0.147     0.023        7     0.5  transversetemporal
 2516   1722   5813  3.098 0.771     0.118     0.028       22     2.8  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050566 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912
Total vertex volume 264656 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1555   1072   3531  2.811 0.760     0.137     0.019       25     1.2  caudalanteriorcingulate
 3273   2263   7609  2.826 0.730     0.109     0.019       25     2.5  caudalmiddlefrontal
 2827   2033   4766  2.113 0.615     0.145     0.033       34     3.8  cuneus
  567    397   1969  3.603 0.827     0.111     0.023        4     0.5  entorhinal
 3412   2461   8455  2.785 0.731     0.137     0.033       44     4.5  fusiform
 7419   5241  17186  2.650 0.700     0.128     0.029       92     9.3  inferiorparietal
 3798   2754  10936  2.876 0.906     0.137     0.033       57     5.5  inferiortemporal
 1132    756   2416  2.666 0.861     0.122     0.030       15     0.9  isthmuscingulate
 7642   5168  12871  2.200 0.712     0.136     0.032      100     9.8  lateraloccipital
 3266   2376   9934  3.101 1.037     0.145     0.044       49     6.0  lateralorbitofrontal
 4541   3368   8724  2.284 0.704     0.153     0.040       63     8.3  lingual
 1732   1272   4878  2.850 0.877     0.144     0.047       31     3.4  medialorbitofrontal
 5077   3723  13091  2.726 0.842     0.132     0.029       74     6.5  middletemporal
  939    630   2202  2.804 0.950     0.092     0.019        7     0.6  parahippocampal
 2380   1656   4800  2.583 0.584     0.126     0.029       23     2.8  paracentral
 2319   1667   5473  2.688 0.697     0.125     0.022       27     2.2  parsopercularis
  972    666   3011  3.177 0.849     0.121     0.025        9     1.1  parsorbitalis
 2087   1472   4936  2.544 0.757     0.118     0.023       22     1.9  parstriangularis
 2387   1683   2440  1.665 0.398     0.135     0.032       26     3.3  pericalcarine
 6246   4147  10917  2.140 0.803     0.103     0.022       62     6.0  postcentral
 1860   1367   4240  2.689 0.796     0.151     0.034       28     2.9  posteriorcingulate
 6064   4040  11481  2.429 0.805     0.109     0.023       63     6.2  precentral
 5605   3923  12503  2.715 0.805     0.127     0.025       60     6.0  precuneus
  917    597   2178  3.000 0.852     0.138     0.033       12     1.2  rostralanteriorcingulate
 5423   3835  13576  2.721 0.791     0.139     0.035       77     8.2  rostralmiddlefrontal
12596   8900  31729  2.828 0.743     0.127     0.027      144    13.7  superiorfrontal
 7257   4977  14938  2.480 0.778     0.113     0.023       60     6.8  superiorparietal
 6300   4600  16124  2.722 0.953     0.107     0.019       57     5.6  superiortemporal
 4435   3095  10660  2.608 0.833     0.129     0.026       55     5.0  supramarginal
  562    382    846  1.939 0.436     0.139     0.026        9     0.6  transversetemporal
 2656   1823   6236  3.151 0.860     0.118     0.023       24     2.4  insula
PIDs (25986 25989) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 11:40:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 pctsurfcon --s 0050566 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 11:40:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts

 pctsurfcon --s 0050566 --rh-only 

Waiting for PID 26051 of (26051 26063) to complete...
Waiting for PID 26063 of (26051 26063) to complete...

 pctsurfcon --s 0050566 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts/pctsurfcon.log
Sun Oct  8 11:40:40 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-604 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-6.0.0/0050566/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.wm.mgh --regheader 0050566 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 70663
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.wm.mgh
Dim: 121292 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.gm.mgh --projfrac 0.3 --regheader 0050566 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 82900
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.gm.mgh
Dim: 121292 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.w-g.pct.mgh --annot 0050566 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/lh.w-g.pct.mgh --annot 0050566 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/lh.w-g.pct.mgh
Vertex Area is 0.709777 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 0050566 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts/pctsurfcon.log
Sun Oct  8 11:40:40 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-604 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-6.0.0/0050566/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.wm.mgh --regheader 0050566 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 72864
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.wm.mgh
Dim: 125464 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.gm.mgh --projfrac 0.3 --regheader 0050566 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 85791
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.gm.mgh
Dim: 125464 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.w-g.pct.mgh --annot 0050566 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.w-g.pct.mgh --annot 0050566 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.w-g.pct.mgh
Vertex Area is 0.699236 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 (26051 26063) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 11:40:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1954 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1631 voxels changed to hypointensity...
3698 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 11:41:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566

 mri_aparc2aseg --s 0050566 --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 11:41:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566

 mri_aparc2aseg --s 0050566 --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 11:41:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566

 mri_aparc2aseg --s 0050566 --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 26219 of (26219 26222 26225) to complete...
Waiting for PID 26222 of (26219 26222 26225) to complete...
Waiting for PID 26225 of (26219 26222 26225) to complete...

 mri_aparc2aseg --s 0050566 --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 0050566
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-6.0.0/0050566/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.36
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 --> 54
rescaling Left_Lateral_Ventricle from 13 --> 12
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 55
rescaling Left_Thalamus from 94 --> 95
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 19
rescaling Fourth_Ventricle from 22 --> 10
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 59
rescaling CSF from 32 --> 27
rescaling Left_Accumbens_area from 62 --> 57
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 55
rescaling Right_Lateral_Ventricle from 13 --> 10
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 55
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 71
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 59
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 24
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512199
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 127 changed.
pass 2: 8 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050566 --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 0050566
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-6.0.0/0050566/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.36
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 --> 54
rescaling Left_Lateral_Ventricle from 13 --> 12
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 55
rescaling Left_Thalamus from 94 --> 95
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 19
rescaling Fourth_Ventricle from 22 --> 10
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 59
rescaling CSF from 32 --> 27
rescaling Left_Accumbens_area from 62 --> 57
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 55
rescaling Right_Lateral_Ventricle from 13 --> 10
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 55
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 71
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 59
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 24
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512138
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 127 changed.
pass 2: 8 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050566 --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 0050566
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-6.0.0/0050566/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.36
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 --> 54
rescaling Left_Lateral_Ventricle from 13 --> 12
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 55
rescaling Left_Thalamus from 94 --> 95
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 19
rescaling Fourth_Ventricle from 22 --> 10
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 59
rescaling CSF from 32 --> 27
rescaling Left_Accumbens_area from 62 --> 57
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 55
rescaling Right_Lateral_Ventricle from 13 --> 10
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 55
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 66
rescaling Right_Putamen from 80 --> 71
rescaling Right_Pallidum from 97 --> 87
rescaling Right_Hippocampus from 53 --> 59
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 65
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 24
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512138
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 127 changed.
pass 2: 8 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (26219 26222 26225) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 11:47:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri

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

Sun Oct  8 11:47:56 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-6.0.0/0050566/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-604 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-6.0.0/0050566/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-604
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 11:47:56 CEST 2017 
Ended   at Sun Oct  8 11:48:02 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 11:48:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566

 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 0050566 


$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 0050566 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1406379 mm^3    (det: 1.385193 )
Computing euler number
orig.nofix lheno = -134, rheno = -78
orig.nofix lhholes =   68, rhholes = 40
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
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 11:49:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566

 mri_aparc2aseg --s 0050566 --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 0050566
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-6.0.0/0050566/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7826 vertices from left hemi
Ripped 8221 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-6.0.0/0050566/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 936872
Used brute-force search on 203 voxels
Fixing Parahip LH WM
  Found 5 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 1497.000000
     3 k 1.000000
     4 k 16.000000
Fixing Parahip RH WM
  Found 7 clusters
     0 k 1426.000000
     1 k 1.000000
     2 k 2.000000
     3 k 26.000000
     4 k 1.000000
     5 k 1.000000
     6 k 2.000000
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 0050566 --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 0050566 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-604
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1406379 mm^3    (det: 1.385193 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
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-6.0.0/0050566/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 11:58:21 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 26927 of (26927 26933 26939 26947 26954) to complete...
Waiting for PID 26933 of (26927 26933 26939 26947 26954) to complete...
Waiting for PID 26939 of (26927 26933 26939 26947 26954) to complete...
Waiting for PID 26947 of (26927 26933 26939 26947 26954) to complete...
Waiting for PID 26954 of (26927 26933 26939 26947 26954) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4129 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 203
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4332
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7909 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 373
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8282
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4077 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4162
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5983 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 141
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6124
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5784 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 220
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6004
mri_label2label: Done

PIDs (26927 26933 26939 26947 26954) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 27007 of (27007 27013 27019 27024) to complete...
Waiting for PID 27013 of (27007 27013 27019 27024) to complete...
Waiting for PID 27019 of (27007 27013 27019 27024) to complete...
Waiting for PID 27024 of (27007 27013 27019 27024) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4070 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 70
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4140
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  13589 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 1108
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14697
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4181 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 304
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4485
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3422 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 577
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 3999
mri_label2label: Done

PIDs (27007 27013 27019 27024) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 27073 of (27073 27079 27085 27091 27097) to complete...
Waiting for PID 27079 of (27073 27079 27085 27091 27097) to complete...
Waiting for PID 27085 of (27073 27079 27085 27091 27097) to complete...
Waiting for PID 27091 of (27073 27079 27085 27091 27097) to complete...
Waiting for PID 27097 of (27073 27079 27085 27091 27097) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4641 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 1155
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5796
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8114 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 2403
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10517
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2018 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 418
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2436
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1290 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 46
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1336
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1199 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1262
mri_label2label: Done

PIDs (27073 27079 27085 27091 27097) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 27150 of (27150 27156 27162 27168 27173) to complete...
Waiting for PID 27156 of (27150 27156 27162 27168 27173) to complete...
Waiting for PID 27162 of (27150 27156 27162 27168 27173) to complete...
Waiting for PID 27168 of (27150 27156 27162 27168 27173) to complete...
Waiting for PID 27173 of (27150 27156 27162 27168 27173) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1014 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 74
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1088
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2092 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 118
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2210
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1504 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 22
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1526
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1996 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 83
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2079
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2319 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 100
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2419
mri_label2label: Done

PIDs (27150 27156 27162 27168 27173) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 27223 of (27223 27229 27235 27240) to complete...
Waiting for PID 27229 of (27223 27229 27235 27240) to complete...
Waiting for PID 27235 of (27223 27229 27235 27240) to complete...
Waiting for PID 27240 of (27223 27229 27235 27240) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1549 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 31
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1580
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7035 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 467
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7502
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1912 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 158
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2070
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1151 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 167
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1318
mri_label2label: Done

PIDs (27223 27229 27235 27240) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 27310 of (27310 27316 27322 27328 27332) to complete...
Waiting for PID 27316 of (27310 27316 27322 27328 27332) to complete...
Waiting for PID 27322 of (27310 27316 27322 27328 27332) to complete...
Waiting for PID 27328 of (27310 27316 27322 27328 27332) to complete...
Waiting for PID 27332 of (27310 27316 27322 27328 27332) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3405 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 779
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4184
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3334 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 1125
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4459
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  513 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 120
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 633
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  470 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 22
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 492
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  450 nlabel points
Performing mapping from target back to the source label 121292
Number of reverse mapping hits = 7
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 457
mri_label2label: Done

PIDs (27310 27316 27322 27328 27332) completed and logs appended.

 mris_label2annot --s 0050566 --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-6.0.0/0050566/label
cmdline mris_label2annot --s 0050566 --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-604
machine  x86_64
user     ntraut

subject 0050566
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-6.0.0/0050566/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 82973 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050566 --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-6.0.0/0050566/label
cmdline mris_label2annot --s 0050566 --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-604
machine  x86_64
user     ntraut

subject 0050566
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-6.0.0/0050566/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 99059 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 255377
Total vertex volume 251169 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
 1003    710   2771  2.571 0.917     0.143     0.030       11     1.2  BA1_exvivo
 3721   2531   6306  2.380 0.555     0.098     0.017       22     2.7  BA2_exvivo
  889    624    885  1.836 0.428     0.140     0.025        9     0.7  BA3a_exvivo
 1869   1346   3601  1.979 0.833     0.112     0.021       18     1.6  BA3b_exvivo
 1511   1030   3337  2.627 0.653     0.120     0.026       14     1.8  BA4a_exvivo
 1023    722   1720  2.428 0.499     0.092     0.013        5     0.6  BA4p_exvivo
 8900   6391  21275  2.748 0.725     0.121     0.024       86     8.8  BA6_exvivo
 2217   1571   4959  2.462 0.726     0.124     0.027       30     2.5  BA44_exvivo
 2785   1970   5812  2.406 0.611     0.128     0.030       31     3.3  BA45_exvivo
 3273   2548   4507  1.718 0.596     0.158     0.042       45     6.3  V1_exvivo
 7925   5642  13508  2.190 0.605     0.151     0.037      110    12.3  V2_exvivo
 2081   1436   4258  2.503 0.700     0.112     0.023       19     1.8  MT_exvivo
  533    359   1960  3.639 0.803     0.110     0.022        4     0.5  perirhinal_exvivo
  589    476   2017  3.480 0.926     0.141     0.034        7     0.8  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 0050566 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 255377
Total vertex volume 251169 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
  641    432   1929  2.800 0.970     0.168     0.037       11     1.0  BA1_exvivo
 1517   1027   2757  2.422 0.503     0.089     0.014        9     0.8  BA2_exvivo
  734    517    715  1.881 0.420     0.147     0.027        8     0.6  BA3a_exvivo
 1229    914   1818  1.646 0.582     0.085     0.012        5     0.6  BA3b_exvivo
 1382    971   3020  2.623 0.649     0.108     0.022       10     1.3  BA4a_exvivo
  897    624   1445  2.387 0.489     0.097     0.015        5     0.6  BA4p_exvivo
 4853   3526  12040  2.805 0.694     0.128     0.026       51     5.2  BA6_exvivo
 1379    982   3181  2.441 0.736     0.136     0.029       24     1.8  BA44_exvivo
 1049    746   2664  2.579 0.577     0.142     0.040       16     1.6  BA45_exvivo
 3482   2701   4878  1.705 0.582     0.151     0.041       44     6.3  V1_exvivo
 3943   2882   6963  2.200 0.658     0.165     0.044       63     7.5  V2_exvivo
  558    388   1274  2.657 0.756     0.121     0.023        5     0.5  MT_exvivo
  275    192   1160  3.779 0.698     0.093     0.014        1     0.2  perirhinal_exvivo
  294    223    833  3.433 0.719     0.093     0.017        1     0.1  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 12:01:18 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 27461 of (27461 27467 27473 27478 27483) to complete...
Waiting for PID 27467 of (27461 27467 27473 27478 27483) to complete...
Waiting for PID 27473 of (27461 27467 27473 27478 27483) to complete...
Waiting for PID 27478 of (27461 27467 27473 27478 27483) to complete...
Waiting for PID 27483 of (27461 27467 27473 27478 27483) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 353
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4315
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 474
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7161
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 53
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4033
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 224
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4746
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 316
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6063
mri_label2label: Done

PIDs (27461 27467 27473 27478 27483) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 27677 of (27677 27683 27689 27694) to complete...
Waiting for PID 27683 of (27677 27683 27689 27694) to complete...
Waiting for PID 27689 of (27677 27683 27689 27694) to complete...
Waiting for PID 27694 of (27677 27683 27689 27694) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4613
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 663
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 12919
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 564
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7476
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 650
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6005
mri_label2label: Done

PIDs (27677 27683 27689 27694) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 27745 of (27745 27751 27757 27762 27767) to complete...
Waiting for PID 27751 of (27745 27751 27757 27762 27767) to complete...
Waiting for PID 27757 of (27745 27751 27757 27762 27767) to complete...
Waiting for PID 27762 of (27745 27751 27757 27762 27767) to complete...
Waiting for PID 27767 of (27745 27751 27757 27762 27767) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 1772
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6499
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 2802
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10818
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 292
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2224
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1125
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 75
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 827
mri_label2label: Done

PIDs (27745 27751 27757 27762 27767) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27823 of (27823 27829 27835 27840 27847) to complete...
Waiting for PID 27829 of (27823 27829 27835 27840 27847) to complete...
Waiting for PID 27835 of (27823 27829 27835 27840 27847) to complete...
Waiting for PID 27840 of (27823 27829 27835 27840 27847) to complete...
Waiting for PID 27847 of (27823 27829 27835 27840 27847) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 97
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 973
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 139
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2827
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1728
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 80
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2263
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 88
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1476
mri_label2label: Done

PIDs (27823 27829 27835 27840 27847) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27896 of (27896 27902 27908 27913) to complete...
Waiting for PID 27902 of (27896 27902 27908 27913) to complete...
Waiting for PID 27908 of (27896 27902 27908 27913) to complete...
Waiting for PID 27913 of (27896 27902 27908 27913) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 12
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1501
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 374
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7333
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 151
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1163
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 167
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1345
mri_label2label: Done

PIDs (27896 27902 27908 27913) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27959 of (27959 27965 27971 27975 27982) to complete...
Waiting for PID 27965 of (27959 27965 27971 27975 27982) to complete...
Waiting for PID 27971 of (27959 27965 27971 27975 27982) to complete...
Waiting for PID 27975 of (27959 27965 27971 27975 27982) to complete...
Waiting for PID 27982 of (27959 27965 27971 27975 27982) 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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 1231
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4463
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 1291
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4728
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 44
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 312
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 43
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 737
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 0050566 --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 = 0050566
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-6.0.0/0050566/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464
Number of reverse mapping hits = 15
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 306
mri_label2label: Done

PIDs (27959 27965 27971 27975 27982) completed and logs appended.

 mris_label2annot --s 0050566 --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-6.0.0/0050566/label
cmdline mris_label2annot --s 0050566 --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-604
machine  x86_64
user     ntraut

subject 0050566
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-6.0.0/0050566/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 86226 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050566 --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-6.0.0/0050566/label
cmdline mris_label2annot --s 0050566 --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-604
machine  x86_64
user     ntraut

subject 0050566
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-6.0.0/0050566/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 103091 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 268912
Total vertex volume 264656 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
  965    633   2047  2.262 0.867     0.175     0.050       30     2.5  BA1_exvivo
 3281   2146   4879  2.259 0.615     0.089     0.016       16     2.0  BA2_exvivo
  974    603    814  1.680 0.472     0.115     0.017        8     0.6  BA3a_exvivo
 1663   1113   2751  1.879 0.847     0.086     0.020       12     1.3  BA3b_exvivo
 1385    901   2787  2.588 0.597     0.108     0.027       10     1.7  BA4a_exvivo
  923    659   1386  2.189 0.604     0.080     0.014        3     0.6  BA4p_exvivo
 7441   5119  18165  2.833 0.772     0.118     0.026       84     8.0  BA6_exvivo
 3468   2440   7348  2.560 0.748     0.117     0.023       36     3.5  BA44_exvivo
 3839   2694   9273  2.613 0.787     0.118     0.022       39     3.5  BA45_exvivo
 4286   3003   5822  1.782 0.577     0.145     0.039       56     7.1  V1_exvivo
 8202   5799  13451  2.132 0.683     0.144     0.035      107    12.1  V2_exvivo
 1845   1288   3528  2.549 0.616     0.137     0.030       23     2.2  MT_exvivo
  583    385   2258  3.622 0.882     0.101     0.022        4     0.5  perirhinal_exvivo
  383    250   1064  3.316 0.845     0.110     0.023        3     0.4  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050566 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 268912
Total vertex volume 264656 (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) = 1406379 mm^3    (det: 1.385193 )
lhCtxGM: 250308.108 250379.000  diff=  -70.9  pctdiff=-0.028
rhCtxGM: 262877.757 263225.000  diff= -347.2  pctdiff=-0.132
lhCtxWM: 211302.320 211100.000  diff=  202.3  pctdiff= 0.096
rhCtxWM: 214124.692 214747.000  diff= -622.3  pctdiff=-0.291
SubCortGMVol  58322.000
SupraTentVol  1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179
SupraTentVolNotVent  999594.877 (997783.000) diff=1811.877 pctdiff=0.181
BrainSegVol  1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219
BrainSegVolNotVent  1156881.000 (1155925.877) diff=955.123 pctdiff=0.083
BrainSegVolNotVent  1156881.000
CerebellumVol 158981.000
VentChorVol   11760.000
3rd4th5thCSF   3469.000
CSFVol   898.000, OptChiasmVol   117.000
MaskVol 1524839.000
  629    433   1277  2.143 0.745     0.166     0.046       14     1.3  BA1_exvivo
 1860   1177   2891  2.210 0.604     0.073     0.012        7     1.0  BA2_exvivo
  873    538    626  1.605 0.349     0.115     0.016        7     0.5  BA3a_exvivo
 1314    883   1686  1.614 0.605     0.070     0.013        7     0.6  BA3b_exvivo
  937    595   1814  2.662 0.562     0.123     0.038        8     1.5  BA4a_exvivo
  779    549   1160  2.309 0.609     0.071     0.012        2     0.4  BA4p_exvivo
 4751   3258  11662  2.832 0.772     0.123     0.027       62     5.6  BA6_exvivo
  923    683   2716  2.826 0.776     0.163     0.034       18     1.4  BA44_exvivo
 1076    770   3412  2.857 0.840     0.139     0.030       17     1.4  BA45_exvivo
 4067   2848   5226  1.739 0.519     0.144     0.037       52     6.6  V1_exvivo
 4314   3142   7546  2.148 0.768     0.154     0.039       61     7.3  V2_exvivo
  264    183    729  2.845 0.623     0.152     0.028        5     0.3  MT_exvivo
  337    227   1261  3.581 0.860     0.076     0.016        1     0.2  perirhinal_exvivo
  249    170    715  3.320 0.783     0.110     0.020        1     0.2  entorhinal_exvivo

Started at Sun Oct 8 01:37:07 CEST 2017 
Ended   at Sun Oct 8 12:04:18 CEST 2017
#@#%# recon-all-run-time-hours 10.453
recon-all -s 0050566 finished without error at Sun Oct  8 12:04:18 CEST 2017