ABIDE_fs-6.0.0/0050233/scripts/recon-all.log

Sat Oct  7 19:27:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050233 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050233/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050233
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-112 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    10485760 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked 64 kbytes
maxproc      1024 

             total       used       free     shared    buffers     cached
Mem:     264574092  263364924    1209168    1740164          0  257214292
-/+ buffers/cache:    6150632  258423460
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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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: 2017/10/07-17:27:16-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-112  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-6.0.0/0050233

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050233/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050233/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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/Trinity/0050233/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-6.0.0/0050233/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 19:27:19 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 1, 0)
k_ras = (-0, -0, 1)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 19:27:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/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-112 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 19:27:26 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.14236
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14236/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.14236/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.14236/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 19:27:28 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.14236/nu0.mnc ./tmp.mri_nu_correct.mni.14236/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14236/0/ -iterations 1000 -distance 50
[ntraut@tars-112:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/] [2017-10-07 19:27:28] 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.14236/0/ ./tmp.mri_nu_correct.mni.14236/nu0.mnc ./tmp.mri_nu_correct.mni.14236/nu1.imp

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Number of iterations: 55 
CV of field change: 0.000955685
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.14236/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.14236/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.14236/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 19:28:48 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 19:28:48 CEST 2017
Ended   at Sat Oct  7 19:29:25 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 19:29:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6962, 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-6.0.0/0050233/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/transforms/talairach_avi.log 

TalAviQA: 0.97263
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 19:29:27 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-6.0.0/0050233/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-112 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 19:29:27 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.15192
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15192/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.15192/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.15192/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 19:29:29 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.15192/nu0.mnc ./tmp.mri_nu_correct.mni.15192/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15192/0/
[ntraut@tars-112:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/] [2017-10-07 19:29:29] 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.15192/0/ ./tmp.mri_nu_correct.mni.15192/nu0.mnc ./tmp.mri_nu_correct.mni.15192/nu1.imp

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Number of iterations: 45 
CV of field change: 0.000992707
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 19:30:20 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.15192/nu1.mnc ./tmp.mri_nu_correct.mni.15192/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.15192/1/
[ntraut@tars-112:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/] [2017-10-07 19:30:20] 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.15192/1/ ./tmp.mri_nu_correct.mni.15192/nu1.mnc ./tmp.mri_nu_correct.mni.15192/nu2.imp

Processing:.................................................................Done
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Number of iterations: 14 
CV of field change: 0.000982856
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.15192/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15192/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-6.0.0/0050233/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.15192/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15192/ones.mgz 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.15192/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.15192/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.15192/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15192/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15192/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.15192/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15192/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15192/input.mean.dat 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.15192/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.15192/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15192/ones.mgz --i ./tmp.mri_nu_correct.mni.15192/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15192/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15192/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.15192/ones.mgz --i ./tmp.mri_nu_correct.mni.15192/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15192/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15192/output.mean.dat 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.15192/ones.mgz
Loading ./tmp.mri_nu_correct.mni.15192/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.15192/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.15192/nu2.mnc ./tmp.mri_nu_correct.mni.15192/nu2.mnc mul .89879707061013723070
Saving result to './tmp.mri_nu_correct.mni.15192/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.15192/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.15192/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.15192/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 7 seconds.
mapping ( 5, 146) to ( 3, 110)
 
 
Sat Oct  7 19:31:44 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 19:31:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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
 1.07967  -0.00020  -0.02398   14.98109;
-0.02347   0.98524   0.32354   6.70668;
 0.01201  -0.30387   1.04002  -6.07681;
 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 = 21
Starting OpenSpline(): npoints = 21
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 73 (73), valley at 44 (44)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 73 (73), valley at 36 (36)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 9 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 19:33:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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=10.0
skull bounding box = (46, 18, 0) --> (209, 183, 225)
using (100, 73, 113) as brain centroid...
mean wm in atlas = 108, using box (80,53,85) --> (120, 93,140) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.7
after smoothing, mri peak at 108, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.378
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.296780 @ (-9.091, 9.091, -9.091)
max log p =    -4.096887 @ (4.545, 4.545, 4.545)
max log p =    -4.096887 @ (0.000, 0.000, 0.000)
max log p =    -4.064870 @ (1.136, 3.409, 3.409)
max log p =    -4.054307 @ (0.568, 0.568, 1.705)
max log p =    -4.052600 @ (-0.284, 0.284, -0.852)
Found translation: (-3.1, 17.9, -0.3): log p = -4.053
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.942, old_max_log_p =-4.053 (thresh=-4.0)
 1.00000   0.00000   0.00000  -3.12500;
 0.00000   1.03837   0.27823  -17.81205;
 0.00000  -0.23941   0.89348   33.81429;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.942, old_max_log_p =-3.942 (thresh=-3.9)
 1.00000   0.00000   0.00000  -3.12500;
 0.00000   1.03837   0.27823  -17.81205;
 0.00000  -0.23941   0.89348   33.81429;
 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=-3.891, old_max_log_p =-3.942 (thresh=-3.9)
 1.01820  -0.00339   0.03074  -8.57450;
 0.00000   1.06074   0.15923  -6.37862;
-0.03211  -0.09986   0.90438   23.25492;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.891, old_max_log_p =-3.891 (thresh=-3.9)
 1.01820  -0.00339   0.03074  -8.57450;
 0.00000   1.06074   0.15923  -6.37862;
-0.03211  -0.09986   0.90438   23.25492;
 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=-3.877, old_max_log_p =-3.891 (thresh=-3.9)
 1.01940  -0.00340   0.03077  -8.73088;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.875, old_max_log_p =-3.877 (thresh=-3.9)
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 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
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.875 (old=-4.378)
transform before final EM align:
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 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
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.3  tol 0.000000
final transform:
 1.02298  -0.00341   0.03088  -9.20095;
 0.00000   1.06447   0.15979  -7.37003;
-0.03203  -0.09963   0.90226   24.39789;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1035.681552
mri_em_register stimesec    3.544461
mri_em_register ru_maxrss   609828
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   162174
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    61
mri_em_register ru_nivcsw   1817
registration took 9 minutes and 7 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=129 y=97 z=113 r=75
      first estimation of the main basin volume: 1778692 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=109, y=79, z=77, Imax=255
      CSF=13, 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=9635132013 voxels, voxel volume =1.000 
                     = 9635132013 mmm3 = 9635132.416 cm3
done.
PostAnalyze...Basin Prior
 142 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=128,y=102, z=104, r=11062 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=3, CSF_MAX=22 , nb = 44705
  RIGHT_CER    CSF_MIN=0, CSF_intensity=3, CSF_MAX=20 , nb = -1030966806
  LEFT_CER     CSF_MIN=0, CSF_intensity=4, CSF_MAX=18 , nb = -1041450604
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=3, CSF_MAX=22 , nb = -1050553777
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 1081561702
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=72 , nb = 1074559016
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    22,      39,        53,   68
  after  analyzing :    22,      48,        53,   53
   RIGHT_CER   
  before analyzing :    20,      32,        51,   76
  after  analyzing :    20,      44,        51,   52
   LEFT_CER    
  before analyzing :    18,      27,        50,   84
  after  analyzing :    18,      42,        50,   52
  RIGHT_BRAIN  
  before analyzing :    22,      39,        53,   68
  after  analyzing :    22,      48,        53,   53
  LEFT_BRAIN   
  before analyzing :    19,      37,        53,   68
  after  analyzing :    19,      47,        53,   52
     OTHER     
  before analyzing :    72,      66,        65,   92
  after  analyzing :    36,      66,        66,   72
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...67 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.010
curvature mean = 74.474, std = 8.887

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.32, sigma = 2.36
      after  rotation: sse = 1.32, sigma = 2.36
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  1.32, its var is  1.81   
      before Erosion-Dilatation  0.00% 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...49 iterations

      mri_strip_skull: done peeling brain

Brain Size = 2058167 voxels, voxel volume = 1.000 mm3
           = 2058167 mmm3 = 2058.167 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    24.757236
mri_watershed stimesec    0.410937
mri_watershed ru_maxrss   825916
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213817
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  3240
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1025
mri_watershed ru_nivcsw   43
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 19:43:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = (61, 35, 21) --> (196, 182, 201)
using (106, 84, 111) as brain centroid...
mean wm in atlas = 107, using box (89,66,89) --> (122, 102,133) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.5
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
initial log_p = -4.445
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.139557 @ (-9.091, 9.091, 9.091)
max log p =    -3.872151 @ (4.545, 13.636, -13.636)
max log p =    -3.780452 @ (2.273, -6.818, 2.273)
max log p =    -3.726594 @ (-1.136, 3.409, -1.136)
max log p =    -3.726594 @ (0.000, 0.000, 0.000)
max log p =    -3.726594 @ (0.000, 0.000, 0.000)
Found translation: (-3.4, 19.3, -3.4): log p = -3.727
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.616, old_max_log_p =-3.727 (thresh=-3.7)
 1.00000   0.00000   0.00000  -3.40909;
 0.00000   1.02750   0.27532  -13.40080;
 0.00000  -0.23650   0.88261   40.51162;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.584, old_max_log_p =-3.616 (thresh=-3.6)
 1.00000   0.00000   0.00000  -3.40909;
 0.00000   1.04958   0.15776  -3.79020;
 0.00000  -0.10036   0.91100   16.24751;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.584, old_max_log_p =-3.584 (thresh=-3.6)
 1.00000   0.00000   0.00000  -3.40909;
 0.00000   1.04958   0.15776  -3.79020;
 0.00000  -0.10036   0.91100   16.24751;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.443, old_max_log_p =-3.584 (thresh=-3.6)
 0.99893  -0.04038   0.02127  -1.27020;
 0.03331   1.00671   0.27082  -18.06612;
-0.03211  -0.24064   0.89806   39.66534;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.439, old_max_log_p =-3.443 (thresh=-3.4)
 0.98078  -0.00705   0.02861  -3.14125;
 0.00168   1.03385   0.24497  -14.03351;
-0.03158  -0.21146   0.92344   33.88944;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.439, old_max_log_p =-3.439 (thresh=-3.4)
 0.98078  -0.00705   0.02861  -3.14125;
 0.00168   1.03385   0.24497  -14.03351;
-0.03158  -0.21146   0.92344   33.88944;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.415, old_max_log_p =-3.439 (thresh=-3.4)
 0.98162  -0.00877   0.03643  -3.43053;
 0.00211   1.03477   0.22916  -12.04643;
-0.03978  -0.19385   0.92490   33.44336;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.407, old_max_log_p =-3.415 (thresh=-3.4)
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.407, old_max_log_p =-3.407 (thresh=-3.4)
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.407 (old=-4.445)
transform before final EM align:
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 315557 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 013: -log(p) =    3.9  tol 0.000000
final transform:
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1297.557741
mri_em_register stimesec    2.457626
mri_em_register ru_maxrss   599056
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   163562
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    120
mri_em_register ru_nivcsw   2430
registration took 11 minutes and 6 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 19:54:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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=26.0
skull bounding box = (61, 35, 21) --> (196, 182, 201)
using (106, 84, 111) as brain centroid...
mean wm in atlas = 107, using box (89,66,89) --> (122, 102,133) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.5
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
using 246344 sample points...
INFO: compute sample coordinates transform
 0.98047  -0.00876   0.03639  -3.27763;
 0.00146   1.02783   0.24341  -12.74146;
-0.03990  -0.21125   0.92319   35.43819;
 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 (129, 40, 25) --> (197, 152, 199)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0
4 of 4154 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 40, 23) --> (130, 148, 198)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
1 of 4743 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 128, 56) --> (181, 169, 112)
Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 121 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 128, 51) --> (131, 168, 112)
Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0
1 of 41 (2.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 114, 92) --> (147, 182, 124)
Brain_Stem: limiting intensities to 90.0 --> 132.0
0 of 49 (0.0%) samples deleted
using 9108 total control points for intensity normalization...
bias field = 0.975 +- 0.040
130 of 9102 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 40, 25) --> (197, 152, 199)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 4861 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 40, 23) --> (130, 148, 198)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
4 of 5319 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 128, 56) --> (181, 169, 112)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 216 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 128, 51) --> (131, 168, 112)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 75 (1.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 114, 92) --> (147, 182, 124)
Brain_Stem: limiting intensities to 88.0 --> 110.0
11 of 118 (9.3%) samples deleted
using 10589 total control points for intensity normalization...
bias field = 1.031 +- 0.042
52 of 10488 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 40, 25) --> (197, 152, 199)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
5 of 4849 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 40, 23) --> (130, 148, 198)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
6 of 5180 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 128, 56) --> (181, 169, 112)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
14 of 253 (5.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 128, 51) --> (131, 168, 112)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
20 of 107 (18.7%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 114, 92) --> (147, 182, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
60 of 207 (29.0%) samples deleted
using 10596 total control points for intensity normalization...
bias field = 1.028 +- 0.040
56 of 10348 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 42 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 19:56:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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) = 0.98 (predicted orig area = 8.1)
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=0.804, neg=0, invalid=762
0001: dt=246.671587, rms=0.747 (7.093%), neg=0, invalid=762
0002: dt=155.175385, rms=0.732 (1.994%), neg=0, invalid=762
0003: dt=369.920000, rms=0.721 (1.525%), neg=0, invalid=762
0004: dt=129.472000, rms=0.717 (0.551%), neg=0, invalid=762
0005: dt=517.888000, rms=0.712 (0.785%), neg=0, invalid=762
0006: dt=110.976000, rms=0.710 (0.202%), neg=0, invalid=762
0007: dt=110.976000, rms=0.709 (0.101%), neg=0, invalid=762
0008: dt=110.976000, rms=0.708 (0.185%), neg=0, invalid=762
0009: dt=110.976000, rms=0.706 (0.246%), neg=0, invalid=762
0010: dt=110.976000, rms=0.705 (0.257%), neg=0, invalid=762
0011: dt=110.976000, rms=0.703 (0.242%), neg=0, invalid=762
0012: dt=110.976000, rms=0.702 (0.197%), neg=0, invalid=762
0013: dt=110.976000, rms=0.700 (0.178%), neg=0, invalid=762
0014: dt=110.976000, rms=0.699 (0.149%), neg=0, invalid=762
0015: dt=110.976000, rms=0.698 (0.127%), neg=0, invalid=762
0016: dt=110.976000, rms=0.698 (0.091%), neg=0, invalid=762
0017: dt=110.976000, rms=0.697 (0.090%), neg=0, invalid=762
0018: dt=2071.552000, rms=0.695 (0.356%), neg=0, invalid=762
0019: dt=129.472000, rms=0.694 (0.071%), neg=0, invalid=762
0020: dt=129.472000, rms=0.694 (0.027%), neg=0, invalid=762
0021: dt=129.472000, rms=0.694 (0.032%), neg=0, invalid=762
0022: dt=129.472000, rms=0.693 (0.041%), neg=0, invalid=762
0023: dt=129.472000, rms=0.693 (0.056%), neg=0, invalid=762
0024: dt=129.472000, rms=0.693 (0.069%), neg=0, invalid=762
0025: dt=129.472000, rms=0.692 (0.083%), neg=0, invalid=762
0026: dt=129.472000, rms=0.691 (0.080%), neg=0, invalid=762
0027: dt=129.472000, rms=0.691 (0.074%), neg=0, invalid=762
0028: dt=443.904000, rms=0.691 (0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.691, neg=0, invalid=762
0029: dt=295.936000, rms=0.689 (0.390%), neg=0, invalid=762
0030: dt=129.472000, rms=0.688 (0.062%), neg=0, invalid=762
0031: dt=129.472000, rms=0.688 (0.040%), neg=0, invalid=762
0032: dt=129.472000, rms=0.687 (0.062%), neg=0, invalid=762
0033: dt=129.472000, rms=0.687 (0.084%), neg=0, invalid=762
0034: dt=129.472000, rms=0.686 (0.090%), neg=0, invalid=762
0035: dt=129.472000, rms=0.686 (0.101%), neg=0, invalid=762
0036: dt=129.472000, rms=0.685 (0.084%), neg=0, invalid=762
0037: dt=129.472000, rms=0.684 (0.083%), neg=0, invalid=762
0038: dt=517.888000, rms=0.684 (0.027%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.689, neg=0, invalid=762
0039: dt=107.506562, rms=0.684 (0.654%), neg=0, invalid=762
0040: dt=331.776000, rms=0.670 (2.104%), neg=0, invalid=762
0041: dt=46.753247, rms=0.665 (0.733%), neg=0, invalid=762
0042: dt=63.072464, rms=0.664 (0.102%), neg=0, invalid=762
0043: dt=63.072464, rms=0.663 (0.248%), neg=0, invalid=762
0044: dt=63.072464, rms=0.660 (0.400%), neg=0, invalid=762
0045: dt=63.072464, rms=0.657 (0.490%), neg=0, invalid=762
0046: dt=63.072464, rms=0.653 (0.528%), neg=0, invalid=762
0047: dt=63.072464, rms=0.650 (0.546%), neg=0, invalid=762
0048: dt=63.072464, rms=0.646 (0.520%), neg=0, invalid=762
0049: dt=63.072464, rms=0.643 (0.458%), neg=0, invalid=762
0050: dt=63.072464, rms=0.641 (0.391%), neg=0, invalid=762
0051: dt=63.072464, rms=0.639 (0.341%), neg=0, invalid=762
0052: dt=63.072464, rms=0.637 (0.334%), neg=0, invalid=762
0053: dt=63.072464, rms=0.635 (0.325%), neg=0, invalid=762
0054: dt=63.072464, rms=0.633 (0.273%), neg=0, invalid=762
0055: dt=63.072464, rms=0.631 (0.228%), neg=0, invalid=762
0056: dt=63.072464, rms=0.630 (0.183%), neg=0, invalid=762
0057: dt=63.072464, rms=0.629 (0.184%), neg=0, invalid=762
0058: dt=63.072464, rms=0.628 (0.213%), neg=0, invalid=762
0059: dt=63.072464, rms=0.626 (0.211%), neg=0, invalid=762
0060: dt=63.072464, rms=0.625 (0.154%), neg=0, invalid=762
0061: dt=63.072464, rms=0.625 (0.119%), neg=0, invalid=762
0062: dt=63.072464, rms=0.624 (0.155%), neg=0, invalid=762
0063: dt=63.072464, rms=0.623 (0.156%), neg=0, invalid=762
0064: dt=63.072464, rms=0.622 (0.129%), neg=0, invalid=762
0065: dt=63.072464, rms=0.621 (0.091%), neg=0, invalid=762
0066: dt=63.072464, rms=0.621 (0.074%), neg=0, invalid=762
0067: dt=248.832000, rms=0.620 (0.085%), neg=0, invalid=762
0068: dt=0.000000, rms=0.620 (-0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.621, neg=0, invalid=762
0069: dt=96.000000, rms=0.619 (0.355%), neg=0, invalid=762
0070: dt=103.680000, rms=0.618 (0.166%), neg=0, invalid=762
0071: dt=103.680000, rms=0.617 (0.026%), neg=0, invalid=762
0072: dt=103.680000, rms=0.617 (0.147%), neg=0, invalid=762
0073: dt=103.680000, rms=0.617 (-0.008%), neg=0, invalid=762
0074: dt=82.944000, rms=0.616 (0.039%), neg=0, invalid=762
0075: dt=36.288000, rms=0.616 (0.010%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.644, neg=0, invalid=762
0076: dt=2.800000, rms=0.643 (0.115%), neg=0, invalid=762
0077: dt=2.400000, rms=0.643 (0.008%), neg=0, invalid=762
0078: dt=2.400000, rms=0.643 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.644, neg=0, invalid=762
0079: dt=2.800000, rms=0.643 (0.102%), neg=0, invalid=762
0080: dt=0.700000, rms=0.643 (0.000%), neg=0, invalid=762
0081: dt=0.700000, rms=0.643 (0.000%), neg=0, invalid=762
0082: dt=0.700000, rms=0.643 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.714, neg=0, invalid=762
0083: dt=6.127536, rms=0.689 (3.536%), neg=0, invalid=762
0084: dt=5.458333, rms=0.686 (0.386%), neg=0, invalid=762
0085: dt=2.304000, rms=0.686 (0.016%), neg=0, invalid=762
0086: dt=2.304000, rms=0.686 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.687, neg=0, invalid=762
0087: dt=0.000000, rms=0.686 (0.083%), neg=0, invalid=762
0088: dt=0.000000, rms=0.686 (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=0.731, neg=0, invalid=762
0089: dt=0.320000, rms=0.730 (0.102%), neg=0, invalid=762
0090: dt=0.384000, rms=0.730 (0.026%), neg=0, invalid=762
0091: dt=0.384000, rms=0.730 (0.045%), neg=0, invalid=762
0092: dt=0.384000, rms=0.730 (0.037%), neg=0, invalid=762
0093: dt=0.384000, rms=0.729 (0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.730, neg=0, invalid=762
0094: dt=2.704545, rms=0.723 (0.921%), neg=0, invalid=762
0095: dt=0.000000, rms=0.723 (-0.002%), neg=0, invalid=762
0096: dt=0.100000, rms=0.723 (-0.009%), 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=0.686, neg=0, invalid=762
0097: dt=0.764706, rms=0.670 (2.398%), neg=0, invalid=762
0098: dt=0.064000, rms=0.669 (0.095%), neg=0, invalid=762
0099: dt=0.064000, rms=0.669 (-0.057%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.670, neg=0, invalid=762
0100: dt=0.028000, rms=0.669 (0.105%), neg=0, invalid=762
0101: dt=0.007000, rms=0.669 (0.002%), neg=0, invalid=762
0102: dt=0.007000, rms=0.669 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.13138 (25)
Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (1710 voxels, overlap=0.521)
Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (1710 voxels, peak = 26), gca=26.5
gca peak = 0.15565 (16)
mri peak = 0.12247 (28)
Right_Lateral_Ventricle (43): linear fit = 1.64 x + 0.0 (971 voxels, overlap=0.315)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (971 voxels, peak = 26), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.08503 (96)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1149 voxels, overlap=0.999)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1149 voxels, peak = 96), gca=95.5
gca peak = 0.20183 (93)
mri peak = 0.07685 (95)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (1038 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (1038 voxels, peak = 92), gca=91.6
gca peak = 0.21683 (55)
mri peak = 0.06307 (64)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1000 voxels, overlap=0.056)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1000 voxels, peak = 64), gca=63.5
gca peak = 0.30730 (58)
mri peak = 0.07783 (70)
Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (713 voxels, overlap=0.073)
Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (713 voxels, peak = 69), gca=68.7
gca peak = 0.11430 (101)
mri peak = 0.13784 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (81849 voxels, overlap=0.549)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (81849 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.12460 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (80133 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (80133 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.05481 (67)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (32372 voxels, overlap=0.285)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (32372 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.05294 (69)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (33433 voxels, overlap=0.385)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (33433 voxels, peak = 68), gca=67.6
gca peak = 0.14161 (67)
mri peak = 0.12225 (83)
Right_Caudate (50): linear fit = 1.23 x + 0.0 (1235 voxels, overlap=0.011)
Right_Caudate (50): linear fit = 1.23 x + 0.0 (1235 voxels, peak = 82), gca=82.1
gca peak = 0.15243 (71)
mri peak = 0.11103 (84)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1424 voxels, overlap=0.256)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1424 voxels, peak = 80), gca=79.9
gca peak = 0.13336 (57)
mri peak = 0.05016 (70)
Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (27532 voxels, overlap=0.033)
Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (27532 voxels, peak = 70), gca=70.4
gca peak = 0.13252 (56)
mri peak = 0.04599 (70)
Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (28138 voxels, overlap=0.036)
Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (28138 voxels, peak = 69), gca=69.2
gca peak = 0.18181 (84)
mri peak = 0.11169 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (11582 voxels, overlap=0.001)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (11582 voxels, peak = 91), gca=91.1
gca peak = 0.20573 (83)
mri peak = 0.10915 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (10245 voxels, overlap=0.054)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (10245 voxels, peak = 91), gca=90.9
gca peak = 0.21969 (57)
mri peak = 0.07977 (73)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (525 voxels, overlap=0.049)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (525 voxels, peak = 70), gca=69.8
gca peak = 0.39313 (56)
mri peak = 0.09781 (69)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (481 voxels, overlap=0.021)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (481 voxels, peak = 67), gca=67.5
gca peak = 0.14181 (85)
mri peak = 0.07576 (96)
Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (6970 voxels, overlap=0.627)
Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (6970 voxels, peak = 92), gca=92.2
gca peak = 0.11978 (83)
mri peak = 0.06869 (94)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5774 voxels, overlap=0.565)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5774 voxels, peak = 93), gca=92.5
gca peak = 0.13399 (79)
mri peak = 0.07170 (84)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (3026 voxels, overlap=0.489)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (3026 voxels, peak = 87), gca=86.5
gca peak = 0.14159 (79)
mri peak = 0.08020 (89)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (3003 voxels, overlap=0.453)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (3003 voxels, peak = 90), gca=90.5
gca peak = 0.10025 (80)
mri peak = 0.09934 (90)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (13924 voxels, overlap=0.108)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (13924 voxels, peak = 89), gca=89.2
gca peak = 0.13281 (86)
mri peak = 0.08728 (92)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1743 voxels, overlap=0.459)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1743 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.08333 (94)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1911 voxels, overlap=0.620)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1911 voxels, peak = 97), gca=96.6
gca peak = 0.20494 (23)
mri peak = 0.05469 (26)
gca peak = 0.15061 (21)
mri peak = 0.12830 (28)
Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (472 voxels, overlap=0.308)
Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (472 voxels, peak = 27), gca=27.4
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 1.18 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.38 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=0.657, neg=0, invalid=762
0103: dt=114.010215, rms=0.644 (2.008%), neg=0, invalid=762
0104: dt=295.936000, rms=0.640 (0.612%), neg=0, invalid=762
0105: dt=295.936000, rms=0.636 (0.578%), neg=0, invalid=762
0106: dt=92.480000, rms=0.635 (0.131%), neg=0, invalid=762
0107: dt=517.888000, rms=0.634 (0.192%), neg=0, invalid=762
0108: dt=295.936000, rms=0.632 (0.253%), neg=0, invalid=762
0109: dt=73.984000, rms=0.632 (0.066%), neg=0, invalid=762
0110: dt=129.472000, rms=0.632 (0.010%), neg=0, invalid=762
0111: dt=129.472000, rms=0.632 (0.044%), neg=0, invalid=762
0112: dt=129.472000, rms=0.631 (0.079%), neg=0, invalid=762
0113: dt=129.472000, rms=0.631 (0.103%), neg=0, invalid=762
0114: dt=129.472000, rms=0.630 (0.117%), neg=0, invalid=762
0115: dt=129.472000, rms=0.629 (0.117%), neg=0, invalid=762
0116: dt=129.472000, rms=0.628 (0.118%), neg=0, invalid=762
0117: dt=129.472000, rms=0.628 (0.113%), neg=0, invalid=762
0118: dt=129.472000, rms=0.627 (0.104%), neg=0, invalid=762
0119: dt=129.472000, rms=0.626 (0.094%), neg=0, invalid=762
0120: dt=129.472000, rms=0.626 (0.086%), neg=0, invalid=762
0121: dt=129.472000, rms=0.625 (0.082%), neg=0, invalid=762
0122: dt=129.472000, rms=0.625 (0.080%), neg=0, invalid=762
0123: dt=129.472000, rms=0.624 (0.075%), neg=0, invalid=762
0124: dt=129.472000, rms=0.624 (0.078%), neg=0, invalid=762
0125: dt=129.472000, rms=0.623 (0.072%), neg=0, invalid=762
0126: dt=129.472000, rms=0.623 (0.070%), neg=0, invalid=762
0127: dt=129.472000, rms=0.623 (0.073%), neg=0, invalid=762
0128: dt=129.472000, rms=0.622 (0.071%), neg=0, invalid=762
0129: dt=129.472000, rms=0.622 (0.065%), neg=0, invalid=762
0130: dt=129.472000, rms=0.621 (0.058%), neg=0, invalid=762
0131: dt=129.472000, rms=0.621 (0.052%), neg=0, invalid=762
0132: dt=129.472000, rms=0.621 (0.046%), neg=0, invalid=762
0133: dt=129.472000, rms=0.620 (0.050%), neg=0, invalid=762
0134: dt=129.472000, rms=0.620 (0.049%), neg=0, invalid=762
0135: dt=129.472000, rms=0.620 (0.047%), neg=0, invalid=762
0136: dt=129.472000, rms=0.620 (0.045%), neg=0, invalid=762
0137: dt=129.472000, rms=0.619 (0.043%), neg=0, invalid=762
0138: dt=129.472000, rms=0.619 (0.047%), neg=0, invalid=762
0139: dt=129.472000, rms=0.619 (0.045%), neg=0, invalid=762
0140: dt=129.472000, rms=0.618 (0.043%), neg=0, invalid=762
0141: dt=129.472000, rms=0.618 (0.040%), neg=0, invalid=762
0142: dt=129.472000, rms=0.618 (0.038%), neg=0, invalid=762
0143: dt=129.472000, rms=0.618 (0.039%), neg=0, invalid=762
0144: dt=129.472000, rms=0.617 (0.038%), neg=0, invalid=762
0145: dt=129.472000, rms=0.617 (0.040%), neg=0, invalid=762
0146: dt=129.472000, rms=0.617 (0.036%), neg=0, invalid=762
0147: dt=129.472000, rms=0.617 (0.032%), neg=0, invalid=762
0148: dt=129.472000, rms=0.617 (0.032%), neg=0, invalid=762
0149: dt=129.472000, rms=0.616 (0.034%), neg=0, invalid=762
0150: dt=129.472000, rms=0.616 (0.037%), neg=0, invalid=762
0151: dt=129.472000, rms=0.616 (0.036%), neg=0, invalid=762
0152: dt=129.472000, rms=0.616 (0.034%), neg=0, invalid=762
0153: dt=129.472000, rms=0.616 (0.030%), neg=0, invalid=762
0154: dt=129.472000, rms=0.615 (0.029%), neg=0, invalid=762
0155: dt=129.472000, rms=0.615 (0.025%), neg=0, invalid=762
0156: dt=129.472000, rms=0.615 (0.025%), neg=0, invalid=762
0157: dt=129.472000, rms=0.615 (0.025%), neg=0, invalid=762
0158: dt=129.472000, rms=0.615 (0.026%), neg=0, invalid=762
0159: dt=129.472000, rms=0.615 (0.025%), neg=0, invalid=762
0160: dt=129.472000, rms=0.614 (0.023%), neg=0, invalid=762
0161: dt=129.472000, rms=0.614 (0.023%), neg=0, invalid=762
0162: dt=5918.720000, rms=0.614 (0.051%), neg=0, invalid=762
0163: dt=110.976000, rms=0.614 (0.040%), neg=0, invalid=762
0164: dt=110.976000, rms=0.614 (0.004%), neg=0, invalid=762
0165: dt=110.976000, rms=0.614 (0.000%), neg=0, invalid=762
0166: dt=110.976000, rms=0.614 (0.004%), neg=0, invalid=762
0167: dt=110.976000, rms=0.614 (0.004%), neg=0, invalid=762
0168: dt=110.976000, rms=0.614 (0.006%), neg=0, invalid=762
0169: dt=110.976000, rms=0.614 (0.006%), neg=0, invalid=762
0170: dt=517.888000, rms=0.614 (0.010%), neg=0, invalid=762
0171: dt=129.472000, rms=0.613 (0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.614, neg=0, invalid=762
0172: dt=295.936000, rms=0.612 (0.215%), neg=0, invalid=762
0173: dt=129.472000, rms=0.612 (0.026%), neg=0, invalid=762
0174: dt=129.472000, rms=0.612 (0.009%), neg=0, invalid=762
0175: dt=129.472000, rms=0.612 (0.021%), neg=0, invalid=762
0176: dt=129.472000, rms=0.612 (0.025%), neg=0, invalid=762
0177: dt=129.472000, rms=0.612 (0.028%), neg=0, invalid=762
0178: dt=129.472000, rms=0.612 (0.026%), neg=0, invalid=762
0179: dt=129.472000, rms=0.611 (0.021%), neg=0, invalid=762
0180: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762
0181: dt=129.472000, rms=0.611 (0.021%), neg=0, invalid=762
0182: dt=887.808000, rms=0.611 (0.020%), neg=0, invalid=762
0183: dt=887.808000, rms=0.611 (-0.030%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.612, neg=0, invalid=762
0184: dt=124.416000, rms=0.609 (0.539%), neg=0, invalid=762
0185: dt=145.152000, rms=0.604 (0.812%), neg=0, invalid=762
0186: dt=93.192982, rms=0.602 (0.338%), neg=0, invalid=762
0187: dt=124.416000, rms=0.600 (0.390%), neg=0, invalid=762
0188: dt=77.432099, rms=0.598 (0.351%), neg=0, invalid=762
0189: dt=103.680000, rms=0.596 (0.258%), neg=0, invalid=762
0190: dt=103.200000, rms=0.594 (0.296%), neg=0, invalid=762
0191: dt=71.929204, rms=0.593 (0.201%), neg=0, invalid=762
0192: dt=145.152000, rms=0.591 (0.291%), neg=0, invalid=762
0193: dt=64.000000, rms=0.590 (0.183%), neg=0, invalid=762
0194: dt=145.152000, rms=0.589 (0.262%), neg=0, invalid=762
0195: dt=69.232704, rms=0.588 (0.138%), neg=0, invalid=762
0196: dt=145.152000, rms=0.587 (0.231%), neg=0, invalid=762
0197: dt=36.288000, rms=0.586 (0.109%), neg=0, invalid=762
0198: dt=414.720000, rms=0.584 (0.400%), neg=0, invalid=762
0199: dt=36.288000, rms=0.582 (0.314%), neg=0, invalid=762
0200: dt=145.152000, rms=0.581 (0.200%), neg=0, invalid=762
0201: dt=36.288000, rms=0.580 (0.057%), neg=0, invalid=762
0202: dt=414.720000, rms=0.579 (0.233%), neg=0, invalid=762
0203: dt=36.288000, rms=0.578 (0.256%), neg=0, invalid=762
0204: dt=145.152000, rms=0.576 (0.185%), neg=0, invalid=762
0205: dt=36.288000, rms=0.576 (0.029%), neg=0, invalid=762
0206: dt=36.288000, rms=0.576 (0.036%), neg=0, invalid=762
0207: dt=36.288000, rms=0.576 (0.056%), neg=0, invalid=762
0208: dt=36.288000, rms=0.575 (0.087%), neg=0, invalid=762
0209: dt=36.288000, rms=0.575 (0.121%), neg=0, invalid=762
0210: dt=36.288000, rms=0.574 (0.138%), neg=0, invalid=762
0211: dt=36.288000, rms=0.573 (0.145%), neg=0, invalid=762
0212: dt=36.288000, rms=0.572 (0.151%), neg=0, invalid=762
0213: dt=36.288000, rms=0.571 (0.152%), neg=0, invalid=762
0214: dt=36.288000, rms=0.570 (0.148%), neg=0, invalid=762
0215: dt=36.288000, rms=0.569 (0.152%), neg=0, invalid=762
0216: dt=36.288000, rms=0.569 (0.151%), neg=0, invalid=762
0217: dt=36.288000, rms=0.568 (0.142%), neg=0, invalid=762
0218: dt=36.288000, rms=0.567 (0.133%), neg=0, invalid=762
0219: dt=36.288000, rms=0.566 (0.127%), neg=0, invalid=762
0220: dt=36.288000, rms=0.566 (0.120%), neg=0, invalid=762
0221: dt=36.288000, rms=0.565 (0.112%), neg=0, invalid=762
0222: dt=36.288000, rms=0.564 (0.109%), neg=0, invalid=762
0223: dt=36.288000, rms=0.564 (0.104%), neg=0, invalid=762
0224: dt=36.288000, rms=0.563 (0.099%), neg=0, invalid=762
0225: dt=36.288000, rms=0.563 (0.096%), neg=0, invalid=762
0226: dt=36.288000, rms=0.562 (0.089%), neg=0, invalid=762
0227: dt=36.288000, rms=0.562 (0.095%), neg=0, invalid=762
0228: dt=36.288000, rms=0.561 (0.088%), neg=0, invalid=762
0229: dt=36.288000, rms=0.561 (0.087%), neg=0, invalid=762
0230: dt=36.288000, rms=0.560 (0.081%), neg=0, invalid=762
0231: dt=36.288000, rms=0.560 (0.084%), neg=0, invalid=762
0232: dt=36.288000, rms=0.559 (0.078%), neg=0, invalid=762
0233: dt=36.288000, rms=0.559 (0.080%), neg=0, invalid=762
0234: dt=36.288000, rms=0.558 (0.078%), neg=0, invalid=762
0235: dt=36.288000, rms=0.558 (0.075%), neg=0, invalid=762
0236: dt=36.288000, rms=0.558 (0.009%), neg=0, invalid=762
0237: dt=36.288000, rms=0.558 (0.015%), neg=0, invalid=762
0238: dt=36.288000, rms=0.558 (0.019%), neg=0, invalid=762
0239: dt=36.288000, rms=0.558 (0.023%), neg=0, invalid=762
0240: dt=9.072000, rms=0.558 (0.001%), neg=0, invalid=762
0241: dt=0.567000, rms=0.558 (0.001%), neg=0, invalid=762
0242: dt=0.567000, rms=0.558 (0.000%), neg=0, invalid=762
0243: dt=0.141750, rms=0.558 (0.000%), neg=0, invalid=762
0244: dt=0.002215, rms=0.558 (0.000%), neg=0, invalid=762
0245: dt=0.000277, rms=0.558 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.558, neg=0, invalid=762
0246: dt=145.152000, rms=0.555 (0.526%), neg=0, invalid=762
0247: dt=103.680000, rms=0.555 (0.093%), neg=0, invalid=762
0248: dt=103.680000, rms=0.554 (0.058%), neg=0, invalid=762
0249: dt=82.944000, rms=0.554 (0.083%), neg=0, invalid=762
0250: dt=36.288000, rms=0.554 (0.017%), neg=0, invalid=762
0251: dt=36.288000, rms=0.554 (0.026%), neg=0, invalid=762
0252: dt=36.288000, rms=0.553 (0.034%), neg=0, invalid=762
0253: dt=36.288000, rms=0.553 (0.049%), neg=0, invalid=762
0254: dt=36.288000, rms=0.553 (0.055%), neg=0, invalid=762
0255: dt=36.288000, rms=0.552 (0.067%), neg=0, invalid=762
0256: dt=36.288000, rms=0.552 (0.066%), neg=0, invalid=762
0257: dt=36.288000, rms=0.552 (0.063%), neg=0, invalid=762
0258: dt=36.288000, rms=0.551 (0.055%), neg=0, invalid=762
0259: dt=36.288000, rms=0.551 (0.060%), neg=0, invalid=762
0260: dt=36.288000, rms=0.551 (0.059%), neg=0, invalid=762
0261: dt=36.288000, rms=0.550 (0.062%), neg=0, invalid=762
0262: dt=36.288000, rms=0.550 (0.062%), neg=0, invalid=762
0263: dt=36.288000, rms=0.550 (0.055%), neg=0, invalid=762
0264: dt=36.288000, rms=0.549 (0.055%), neg=0, invalid=762
0265: dt=36.288000, rms=0.549 (0.054%), neg=0, invalid=762
0266: dt=36.288000, rms=0.549 (0.051%), neg=0, invalid=762
0267: dt=36.288000, rms=0.549 (0.050%), neg=0, invalid=762
0268: dt=36.288000, rms=0.548 (0.049%), neg=0, invalid=762
0269: dt=36.288000, rms=0.548 (0.046%), neg=0, invalid=762
0270: dt=36.288000, rms=0.548 (0.046%), neg=0, invalid=762
0271: dt=36.288000, rms=0.548 (0.048%), neg=0, invalid=762
0272: dt=36.288000, rms=0.547 (0.048%), neg=0, invalid=762
0273: dt=36.288000, rms=0.547 (0.044%), neg=0, invalid=762
0274: dt=36.288000, rms=0.547 (0.041%), neg=0, invalid=762
0275: dt=36.288000, rms=0.547 (0.039%), neg=0, invalid=762
0276: dt=36.288000, rms=0.546 (0.037%), neg=0, invalid=762
0277: dt=36.288000, rms=0.546 (0.039%), neg=0, invalid=762
0278: dt=36.288000, rms=0.546 (0.040%), neg=0, invalid=762
0279: dt=36.288000, rms=0.546 (0.041%), neg=0, invalid=762
0280: dt=36.288000, rms=0.546 (0.037%), neg=0, invalid=762
0281: dt=36.288000, rms=0.545 (0.039%), neg=0, invalid=762
0282: dt=36.288000, rms=0.545 (0.035%), neg=0, invalid=762
0283: dt=36.288000, rms=0.545 (0.033%), neg=0, invalid=762
0284: dt=36.288000, rms=0.545 (0.030%), neg=0, invalid=762
0285: dt=36.288000, rms=0.545 (0.032%), neg=0, invalid=762
0286: dt=36.288000, rms=0.544 (0.034%), neg=0, invalid=762
0287: dt=36.288000, rms=0.544 (0.031%), neg=0, invalid=762
0288: dt=36.288000, rms=0.544 (0.030%), neg=0, invalid=762
0289: dt=36.288000, rms=0.544 (0.031%), neg=0, invalid=762
0290: dt=36.288000, rms=0.544 (0.030%), neg=0, invalid=762
0291: dt=36.288000, rms=0.544 (0.030%), neg=0, invalid=762
0292: dt=36.288000, rms=0.543 (0.031%), neg=0, invalid=762
0293: dt=36.288000, rms=0.543 (0.030%), neg=0, invalid=762
0294: dt=36.288000, rms=0.543 (0.027%), neg=0, invalid=762
0295: dt=36.288000, rms=0.543 (0.029%), neg=0, invalid=762
0296: dt=36.288000, rms=0.543 (0.030%), neg=0, invalid=762
0297: dt=36.288000, rms=0.543 (0.029%), neg=0, invalid=762
0298: dt=36.288000, rms=0.543 (0.030%), neg=0, invalid=762
0299: dt=36.288000, rms=0.542 (0.026%), neg=0, invalid=762
0300: dt=36.288000, rms=0.542 (0.027%), neg=0, invalid=762
0301: dt=36.288000, rms=0.542 (0.027%), neg=0, invalid=762
0302: dt=36.288000, rms=0.542 (0.025%), neg=0, invalid=762
0303: dt=36.288000, rms=0.542 (0.025%), neg=0, invalid=762
0304: dt=36.288000, rms=0.542 (0.026%), neg=0, invalid=762
0305: dt=36.288000, rms=0.542 (0.026%), neg=0, invalid=762
0306: dt=36.288000, rms=0.541 (0.026%), neg=0, invalid=762
0307: dt=36.288000, rms=0.541 (0.022%), neg=0, invalid=762
0308: dt=36.288000, rms=0.541 (0.022%), neg=0, invalid=762
0309: dt=36.288000, rms=0.541 (0.022%), neg=0, invalid=762
0310: dt=580.608000, rms=0.541 (0.027%), neg=0, invalid=762
0311: dt=31.104000, rms=0.541 (0.005%), neg=0, invalid=762
0312: dt=31.104000, rms=0.541 (0.004%), neg=0, invalid=762
0313: dt=31.104000, 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
0314: dt=25.600000, rms=0.548 (0.231%), neg=0, invalid=762
0315: dt=44.800000, rms=0.546 (0.321%), neg=0, invalid=762
0316: dt=44.800000, rms=0.544 (0.419%), neg=0, invalid=762
0317: dt=44.800000, rms=0.541 (0.434%), neg=0, invalid=762
0318: dt=32.000000, rms=0.540 (0.220%), neg=0, invalid=762
0319: dt=2.800000, rms=0.540 (0.041%), neg=0, invalid=762
0320: dt=2.800000, rms=0.540 (0.028%), neg=0, invalid=762
0321: dt=0.700000, rms=0.540 (0.008%), neg=0, invalid=762
0322: dt=0.043750, rms=0.540 (0.000%), neg=0, invalid=762
0323: dt=0.010937, rms=0.540 (0.000%), neg=0, invalid=762
0324: dt=0.010937, rms=0.540 (0.000%), neg=0, invalid=762
0325: dt=0.005469, rms=0.540 (0.000%), neg=0, invalid=762
0326: dt=0.002734, rms=0.540 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.540, neg=0, invalid=762
0327: dt=71.402985, rms=0.535 (0.879%), neg=0, invalid=762
0328: dt=25.600000, rms=0.534 (0.265%), neg=0, invalid=762
0329: dt=44.800000, rms=0.533 (0.294%), neg=0, invalid=762
0330: dt=25.600000, rms=0.532 (0.107%), neg=0, invalid=762
0331: dt=44.800000, rms=0.531 (0.249%), neg=0, invalid=762
0332: dt=25.600000, rms=0.530 (0.081%), neg=0, invalid=762
0333: dt=44.800000, rms=0.529 (0.220%), neg=0, invalid=762
0334: dt=25.600000, rms=0.529 (0.072%), neg=0, invalid=762
0335: dt=44.800000, rms=0.528 (0.210%), neg=0, invalid=762
0336: dt=25.600000, rms=0.527 (0.069%), neg=0, invalid=762
0337: dt=44.800000, rms=0.526 (0.186%), neg=0, invalid=762
0338: dt=19.200000, rms=0.526 (0.054%), neg=0, invalid=762
0339: dt=179.200000, rms=0.524 (0.425%), neg=0, invalid=762
0340: dt=11.200000, rms=0.523 (0.142%), neg=0, invalid=762
0341: dt=32.000000, rms=0.522 (0.086%), neg=0, invalid=762
0342: dt=32.000000, rms=0.522 (0.077%), neg=0, invalid=762
0343: dt=25.600000, rms=0.522 (0.063%), neg=0, invalid=762
0344: dt=38.400000, rms=0.521 (0.072%), neg=0, invalid=762
0345: dt=25.600000, rms=0.521 (0.065%), neg=0, invalid=762
0346: dt=32.000000, rms=0.521 (0.054%), neg=0, invalid=762
0347: dt=32.000000, rms=0.520 (0.064%), neg=0, invalid=762
0348: dt=25.600000, rms=0.520 (0.053%), neg=0, invalid=762
0349: dt=32.000000, rms=0.520 (0.055%), neg=0, invalid=762
0350: dt=25.600000, rms=0.520 (0.052%), neg=0, invalid=762
0351: dt=32.000000, rms=0.519 (0.055%), neg=0, invalid=762
0352: dt=25.600000, rms=0.519 (0.040%), neg=0, invalid=762
0353: dt=25.600000, rms=0.519 (0.053%), neg=0, invalid=762
0354: dt=25.600000, rms=0.518 (0.083%), neg=0, invalid=762
0355: dt=25.600000, rms=0.518 (0.103%), neg=0, invalid=762
0356: dt=25.600000, rms=0.517 (0.142%), neg=0, invalid=762
0357: dt=25.600000, rms=0.516 (0.159%), neg=0, invalid=762
0358: dt=25.600000, rms=0.515 (0.167%), neg=0, invalid=762
0359: dt=25.600000, rms=0.515 (0.173%), neg=0, invalid=762
0360: dt=25.600000, rms=0.514 (0.186%), neg=0, invalid=762
0361: dt=25.600000, rms=0.513 (0.179%), neg=0, invalid=762
0362: dt=25.600000, rms=0.512 (0.193%), neg=0, invalid=762
0363: dt=25.600000, rms=0.511 (0.177%), neg=0, invalid=762
0364: dt=25.600000, rms=0.510 (0.169%), neg=0, invalid=762
0365: dt=25.600000, rms=0.509 (0.160%), neg=0, invalid=762
0366: dt=25.600000, rms=0.508 (0.157%), neg=0, invalid=762
0367: dt=25.600000, rms=0.508 (0.126%), neg=0, invalid=762
0368: dt=25.600000, rms=0.507 (0.124%), neg=0, invalid=762
0369: dt=25.600000, rms=0.506 (0.121%), neg=0, invalid=762
0370: dt=25.600000, rms=0.506 (0.115%), neg=0, invalid=762
0371: dt=25.600000, rms=0.505 (0.095%), neg=0, invalid=762
0372: dt=25.600000, rms=0.505 (0.082%), neg=0, invalid=762
0373: dt=25.600000, rms=0.505 (0.082%), neg=0, invalid=762
0374: dt=25.600000, rms=0.504 (0.076%), neg=0, invalid=762
0375: dt=25.600000, rms=0.504 (0.057%), neg=0, invalid=762
0376: dt=25.600000, rms=0.503 (0.077%), neg=0, invalid=762
0377: dt=25.600000, rms=0.503 (0.069%), neg=0, invalid=762
0378: dt=25.600000, rms=0.503 (0.052%), neg=0, invalid=762
0379: dt=25.600000, rms=0.503 (0.045%), neg=0, invalid=762
0380: dt=25.600000, rms=0.502 (0.046%), neg=0, invalid=762
0381: dt=25.600000, rms=0.502 (0.047%), neg=0, invalid=762
0382: dt=25.600000, rms=0.502 (0.037%), neg=0, invalid=762
0383: dt=25.600000, rms=0.502 (0.039%), neg=0, invalid=762
0384: dt=25.600000, rms=0.502 (0.047%), neg=0, invalid=762
0385: dt=25.600000, rms=0.501 (0.052%), neg=0, invalid=762
0386: dt=25.600000, rms=0.501 (0.033%), neg=0, invalid=762
0387: dt=25.600000, rms=0.501 (0.038%), neg=0, invalid=762
0388: dt=25.600000, rms=0.501 (0.034%), neg=0, invalid=762
0389: dt=25.600000, rms=0.501 (0.036%), neg=0, invalid=762
0390: dt=25.600000, rms=0.500 (0.032%), neg=0, invalid=762
0391: dt=25.600000, rms=0.500 (0.025%), neg=0, invalid=762
0392: dt=25.600000, rms=0.500 (0.023%), neg=0, invalid=762
0393: dt=32.000000, rms=0.500 (0.010%), neg=0, invalid=762
0394: dt=32.000000, rms=0.500 (-0.007%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0395: dt=0.000000, rms=0.519 (0.070%), neg=0, invalid=762
0396: dt=0.000000, rms=0.519 (0.000%), neg=0, invalid=762
0397: dt=0.150000, rms=0.519 (-0.022%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0398: dt=0.000000, rms=0.519 (0.070%), neg=0, invalid=762
0399: dt=0.000000, rms=0.519 (0.000%), neg=0, invalid=762
0400: dt=0.150000, rms=0.519 (-0.021%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.558, neg=0, invalid=762
0401: dt=1.024000, rms=0.556 (0.405%), neg=0, invalid=762
0402: dt=0.096000, rms=0.556 (0.003%), neg=0, invalid=762
0403: dt=0.096000, rms=0.556 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.556, neg=0, invalid=762
0404: dt=0.448000, rms=0.555 (0.131%), neg=0, invalid=762
0405: dt=0.256000, rms=0.555 (0.013%), neg=0, invalid=762
0406: dt=0.256000, rms=0.555 (-0.005%), 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=0.509, neg=0, invalid=762
0407: dt=0.448000, rms=0.496 (2.500%), neg=0, invalid=762
0408: dt=0.448000, rms=0.493 (0.476%), neg=0, invalid=762
0409: dt=0.448000, rms=0.492 (0.267%), neg=0, invalid=762
0410: dt=0.625000, rms=0.491 (0.227%), neg=0, invalid=762
0411: dt=0.448000, rms=0.491 (0.102%), neg=0, invalid=762
0412: dt=0.448000, rms=0.490 (0.074%), neg=0, invalid=762
0413: dt=0.448000, rms=0.490 (0.062%), neg=0, invalid=762
0414: dt=0.448000, rms=0.490 (0.048%), neg=0, invalid=762
0415: dt=0.448000, rms=0.489 (0.039%), neg=0, invalid=762
0416: dt=0.448000, rms=0.489 (0.069%), neg=0, invalid=762
0417: dt=0.448000, rms=0.489 (0.080%), neg=0, invalid=762
0418: dt=0.448000, rms=0.488 (0.075%), neg=0, invalid=762
0419: dt=0.448000, rms=0.488 (0.065%), neg=0, invalid=762
0420: dt=0.448000, rms=0.488 (0.040%), neg=0, invalid=762
0421: dt=0.448000, rms=0.488 (0.023%), neg=0, invalid=762
0422: dt=0.448000, rms=0.488 (0.002%), neg=0, invalid=762
0423: dt=0.000000, rms=0.488 (0.002%), neg=0, invalid=762
0424: dt=0.050000, rms=0.488 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.488, neg=0, invalid=762
0425: dt=0.448000, rms=0.482 (1.203%), neg=0, invalid=762
0426: dt=0.448000, rms=0.481 (0.182%), neg=0, invalid=762
0427: dt=0.448000, rms=0.481 (0.076%), neg=0, invalid=762
0428: dt=0.448000, rms=0.481 (0.020%), neg=0, invalid=762
0429: dt=0.448000, rms=0.481 (0.011%), neg=0, invalid=762
0430: dt=0.448000, rms=0.481 (0.008%), neg=0, invalid=762
0431: dt=0.448000, rms=0.481 (-0.002%), 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=0.479, neg=0, invalid=762
0432: dt=0.000000, rms=0.479 (0.089%), neg=0, invalid=762
0433: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
0434: dt=129.472000, rms=0.478 (0.126%), neg=0, invalid=762
0435: dt=129.472000, rms=0.478 (0.020%), neg=0, invalid=762
0436: dt=129.472000, rms=0.478 (0.001%), neg=0, invalid=762
0437: dt=129.472000, rms=0.478 (0.033%), neg=0, invalid=762
0438: dt=129.472000, rms=0.478 (0.016%), neg=0, invalid=762
0439: dt=129.472000, rms=0.478 (0.021%), neg=0, invalid=762
0440: dt=129.472000, rms=0.478 (0.005%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.478, neg=0, invalid=762
0441: dt=9.072000, rms=0.478 (0.091%), neg=0, invalid=762
0442: dt=5.184000, rms=0.478 (0.002%), neg=0, invalid=762
0443: dt=5.184000, rms=0.478 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.478, neg=0, invalid=762
0444: dt=145.152000, rms=0.477 (0.368%), neg=0, invalid=762
0445: dt=36.288000, rms=0.476 (0.076%), neg=0, invalid=762
0446: dt=36.288000, rms=0.476 (0.034%), neg=0, invalid=762
0447: dt=36.288000, rms=0.476 (0.060%), neg=0, invalid=762
0448: dt=36.288000, rms=0.475 (0.084%), neg=0, invalid=762
0449: dt=36.288000, rms=0.475 (0.095%), neg=0, invalid=762
0450: dt=36.288000, rms=0.474 (0.100%), neg=0, invalid=762
0451: dt=36.288000, rms=0.474 (0.093%), neg=0, invalid=762
0452: dt=36.288000, rms=0.474 (0.086%), neg=0, invalid=762
0453: dt=248.832000, rms=0.473 (0.049%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.474, neg=0, invalid=762
0454: dt=11.200000, rms=0.473 (0.219%), neg=0, invalid=762
0455: dt=11.200000, rms=0.473 (0.073%), neg=0, invalid=762
0456: dt=11.200000, rms=0.472 (0.043%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0457: dt=11.200000, rms=0.472 (0.001%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0458: dt=11.200000, rms=0.472 (-0.066%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.473, neg=0, invalid=762
0459: dt=54.681992, rms=0.467 (1.206%), neg=0, invalid=762
0460: dt=25.600000, rms=0.466 (0.311%), neg=0, invalid=762
0461: dt=44.800000, rms=0.465 (0.248%), neg=0, invalid=762
0462: dt=44.800000, rms=0.465 (-0.074%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.467, neg=0, invalid=762
0463: dt=10.971429, rms=0.464 (0.534%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0464: dt=24.406780, rms=0.462 (0.450%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
0465: dt=11.520000, rms=0.462 (0.073%), neg=0, invalid=762
0466: dt=11.520000, rms=0.461 (0.158%), neg=0, invalid=762
0467: dt=11.520000, rms=0.460 (0.126%), neg=0, invalid=762
0468: dt=11.520000, rms=0.460 (0.088%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0469: dt=11.520000, rms=0.460 (0.063%), neg=0, invalid=762
0470: dt=13.824000, rms=0.459 (0.051%), neg=0, invalid=762
0471: dt=13.824000, rms=0.460 (-0.053%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0472: dt=17.050193, rms=0.455 (1.007%), neg=0, invalid=762
0473: dt=13.122302, rms=0.454 (0.280%), neg=0, invalid=762
0474: dt=13.263158, rms=0.453 (0.191%), neg=0, invalid=762
0475: dt=13.263158, rms=0.453 (0.115%), neg=0, invalid=762
0476: dt=13.263158, rms=0.452 (0.170%), neg=0, invalid=762
0477: dt=13.263158, rms=0.451 (0.124%), neg=0, invalid=762
0478: dt=13.263158, rms=0.451 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0479: dt=13.263158, rms=0.450 (0.178%), neg=0, invalid=762
0480: dt=13.263158, rms=0.449 (0.199%), neg=0, invalid=762
0481: dt=13.263158, rms=0.448 (0.160%), neg=0, invalid=762
0482: dt=13.263158, rms=0.447 (0.166%), neg=0, invalid=762
0483: dt=13.263158, rms=0.447 (0.122%), neg=0, invalid=762
0484: dt=13.263158, rms=0.446 (0.102%), neg=0, invalid=762
0485: dt=9.333333, rms=0.446 (0.044%), neg=0, invalid=762
0486: dt=9.333333, rms=0.446 (0.021%), neg=0, invalid=762
0487: dt=9.333333, rms=0.446 (-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=0.451, neg=0, invalid=762
0488: dt=0.000000, rms=0.451 (0.089%), neg=0, invalid=762
0489: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.451, neg=0, invalid=762
0490: dt=0.000000, rms=0.451 (0.089%), neg=0, invalid=762
0491: dt=0.000000, rms=0.451 (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=0.443, neg=0, invalid=762
iter 0, gcam->neg = 294
after 14 iterations, nbhd size=1, neg = 0
0492: dt=2.058065, rms=0.420 (5.203%), neg=0, invalid=762
0493: dt=0.064000, rms=0.420 (0.043%), neg=0, invalid=762
0494: dt=0.064000, rms=0.420 (-0.034%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0495: dt=0.096000, rms=0.420 (0.204%), neg=0, invalid=762
0496: dt=0.007000, rms=0.420 (-0.003%), 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=0.408, neg=0, invalid=762
0497: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0498: dt=8.092000, rms=0.408 (0.000%), neg=0, invalid=762
0499: dt=3.468000, rms=0.408 (0.000%), neg=0, invalid=762
0500: dt=3.468000, rms=0.408 (-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=0.408, neg=0, invalid=762
0501: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0502: dt=36.288000, rms=0.408 (0.023%), neg=0, invalid=762
0503: dt=82.944000, rms=0.408 (0.015%), neg=0, invalid=762
0504: dt=82.944000, rms=0.408 (0.031%), neg=0, invalid=762
0505: dt=82.944000, rms=0.408 (0.030%), neg=0, invalid=762
0506: dt=82.944000, rms=0.408 (0.015%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0507: dt=2.800000, rms=0.408 (0.008%), neg=0, invalid=762
0508: dt=0.700000, rms=0.408 (0.001%), neg=0, invalid=762
0509: dt=0.700000, rms=0.408 (0.000%), neg=0, invalid=762
0510: dt=0.700000, rms=0.408 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0511: dt=118.153846, rms=0.405 (0.716%), neg=0, invalid=762
0512: dt=25.128834, rms=0.405 (0.164%), neg=0, invalid=762
0513: dt=25.128834, rms=0.404 (0.054%), neg=0, invalid=762
0514: dt=25.128834, rms=0.404 (0.063%), neg=0, invalid=762
0515: dt=25.128834, rms=0.404 (0.092%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0516: dt=25.128834, rms=0.403 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0517: dt=25.128834, rms=0.403 (0.146%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0518: dt=25.128834, rms=0.402 (0.135%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0519: dt=25.128834, rms=0.402 (0.111%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0520: dt=25.128834, rms=0.401 (0.089%), neg=0, invalid=762
0521: dt=32.000000, rms=0.401 (0.004%), neg=0, invalid=762
0522: dt=32.000000, rms=0.401 (0.010%), neg=0, invalid=762
0523: dt=32.000000, rms=0.401 (0.015%), neg=0, invalid=762
0524: dt=32.000000, rms=0.401 (0.019%), neg=0, invalid=762
0525: dt=32.000000, rms=0.401 (0.028%), neg=0, invalid=762
0526: dt=32.000000, rms=0.401 (0.034%), neg=0, invalid=762
0527: dt=32.000000, rms=0.401 (0.037%), neg=0, invalid=762
0528: dt=32.000000, rms=0.401 (0.039%), neg=0, invalid=762
0529: dt=32.000000, rms=0.400 (0.045%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0530: dt=32.000000, rms=0.400 (0.047%), neg=0, invalid=762
0531: dt=32.000000, rms=0.400 (0.051%), neg=0, invalid=762
0532: dt=32.000000, rms=0.400 (0.051%), neg=0, invalid=762
0533: dt=32.000000, rms=0.400 (0.050%), neg=0, invalid=762
0534: dt=32.000000, rms=0.399 (0.046%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.403, neg=0, invalid=762
0535: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.403, neg=0, invalid=762
0536: dt=2.500000, rms=0.403 (0.009%), neg=0, invalid=762
0537: dt=1.008000, rms=0.403 (0.002%), neg=0, invalid=762
0538: dt=1.008000, rms=0.403 (0.001%), neg=0, invalid=762
0539: dt=1.008000, rms=0.403 (-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=0.409, neg=0, invalid=762
0540: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0541: dt=0.000000, rms=0.409 (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=0.398, neg=0, invalid=762
iter 0, gcam->neg = 302
after 12 iterations, nbhd size=1, neg = 0
0542: dt=1.280000, rms=0.390 (2.054%), neg=0, invalid=762
0543: dt=0.000016, rms=0.390 (0.000%), neg=0, invalid=762
0544: dt=0.000016, rms=0.390 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.390, neg=0, invalid=762
0545: dt=0.112000, rms=0.390 (0.093%), neg=0, invalid=762
0546: dt=0.112000, rms=0.390 (0.044%), neg=0, invalid=762
0547: dt=0.112000, rms=0.390 (0.031%), neg=0, invalid=762
0548: dt=0.112000, rms=0.390 (-0.005%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 43 minutes and 20 seconds.
mri_ca_register utimesec    10703.778778
mri_ca_register stimesec    8.002783
mri_ca_register ru_maxrss   1343492
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4706057
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63520
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    5247
mri_ca_register ru_nivcsw   17112
FSRUNTIME@ mri_ca_register  2.7221 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 22:39:34 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-112
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-6.0.0/0050233/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 8.14
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 = 0.12168 (25)
Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (2640 voxels, overlap=0.587)
Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (2640 voxels, peak = 24), gca=24.5
gca peak = 0.17677 (13)
mri peak = 0.11386 (27)
Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (1069 voxels, overlap=0.335)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1069 voxels, peak = 24), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.12054 (97)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (813 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (813 voxels, peak = 96), gca=96.4
gca peak = 0.16930 (96)
mri peak = 0.11935 (97)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (860 voxels, overlap=0.982)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (860 voxels, peak = 97), gca=97.4
gca peak = 0.24553 (55)
mri peak = 0.09693 (70)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1238 voxels, overlap=0.069)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1238 voxels, peak = 66), gca=66.3
gca peak = 0.30264 (59)
mri peak = 0.09545 (72)
Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1344 voxels, overlap=0.022)
Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1344 voxels, peak = 71), gca=70.5
gca peak = 0.07580 (103)
mri peak = 0.15089 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (56494 voxels, overlap=0.597)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (56494 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.13087 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55987 voxels, overlap=0.658)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55987 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.05670 (67)
Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (42289 voxels, overlap=0.447)
Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (42289 voxels, peak = 68), gca=67.6
gca peak = 0.11620 (58)
mri peak = 0.05614 (69)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (40837 voxels, overlap=0.432)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (40837 voxels, peak = 68), gca=67.6
gca peak = 0.30970 (66)
mri peak = 0.14516 (82)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1178 voxels, overlap=0.018)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1178 voxels, peak = 80), gca=79.5
gca peak = 0.15280 (69)
mri peak = 0.13355 (82)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1228 voxels, overlap=0.314)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1228 voxels, peak = 78), gca=77.6
gca peak = 0.13902 (56)
mri peak = 0.05616 (70)
Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (32194 voxels, overlap=0.076)
Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (32194 voxels, peak = 71), gca=70.8
gca peak = 0.14777 (55)
mri peak = 0.05392 (70)
Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (31571 voxels, overlap=0.086)
Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (31571 voxels, peak = 70), gca=69.6
gca peak = 0.16765 (84)
mri peak = 0.15844 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8035 voxels, overlap=0.087)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8035 voxels, peak = 91), gca=91.1
gca peak = 0.18739 (84)
mri peak = 0.16666 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7322 voxels, overlap=0.138)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7322 voxels, peak = 91), gca=91.1
gca peak = 0.29869 (57)
mri peak = 0.08856 (71)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (730 voxels, overlap=0.057)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (730 voxels, peak = 69), gca=69.3
gca peak = 0.33601 (57)
mri peak = 0.07196 (66)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (806 voxels, overlap=0.053)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (806 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.07839 (94)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5334 voxels, overlap=0.671)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5334 voxels, peak = 96), gca=95.9
gca peak = 0.11793 (83)
mri peak = 0.07767 (94)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5076 voxels, overlap=0.378)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5076 voxels, peak = 93), gca=92.5
gca peak = 0.08324 (81)
mri peak = 0.08716 (86)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2625 voxels, overlap=0.500)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2625 voxels, peak = 89), gca=88.7
gca peak = 0.10360 (77)
mri peak = 0.09820 (87)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (2841 voxels, overlap=0.321)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (2841 voxels, peak = 86), gca=85.9
gca peak = 0.08424 (78)
mri peak = 0.10012 (90)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13531 voxels, overlap=0.277)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13531 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.07861 (99)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1729 voxels, overlap=0.391)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1729 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.08166 (96)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1727 voxels, overlap=0.724)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1727 voxels, peak = 95), gca=95.3
gca peak = 0.14975 (24)
mri peak = 0.14713 (30)
gca peak = 0.19357 (14)
mri peak = 0.17040 (27)
Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (220 voxels, overlap=0.178)
Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (220 voxels, peak = 25), gca=24.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.19 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 1.36 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.13931 (25)
mri peak = 0.12168 (25)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2640 voxels, overlap=0.842)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2640 voxels, peak = 26), gca=25.6
gca peak = 0.13758 (19)
mri peak = 0.11386 (27)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (1069 voxels, overlap=0.687)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (1069 voxels, peak = 23), gca=22.5
gca peak = 0.25970 (97)
mri peak = 0.12054 (97)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (813 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (813 voxels, peak = 97), gca=96.5
gca peak = 0.16279 (96)
mri peak = 0.11935 (97)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (860 voxels, overlap=1.000)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (860 voxels, peak = 96), gca=95.5
gca peak = 0.28157 (67)
mri peak = 0.09693 (70)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1238 voxels, overlap=1.006)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1238 voxels, peak = 68), gca=68.0
gca peak = 0.28883 (67)
mri peak = 0.09545 (72)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, overlap=1.006)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, peak = 67), gca=67.0
gca peak = 0.07767 (104)
mri peak = 0.15089 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (56494 voxels, overlap=0.662)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (56494 voxels, peak = 104), gca=104.0
gca peak = 0.07714 (104)
mri peak = 0.13087 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55987 voxels, overlap=0.658)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55987 voxels, peak = 104), gca=104.0
gca peak = 0.08240 (66)
mri peak = 0.05670 (67)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (42289 voxels, overlap=0.936)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (42289 voxels, peak = 65), gca=65.0
gca peak = 0.09795 (68)
mri peak = 0.05614 (69)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40837 voxels, overlap=0.946)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40837 voxels, peak = 67), gca=67.0
gca peak = 0.21545 (80)
mri peak = 0.14516 (82)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1178 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1178 voxels, peak = 81), gca=81.2
gca peak = 0.16641 (87)
mri peak = 0.13355 (82)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1228 voxels, overlap=0.999)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1228 voxels, peak = 86), gca=85.7
gca peak = 0.11411 (70)
mri peak = 0.05616 (70)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (32194 voxels, overlap=0.993)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (32194 voxels, peak = 70), gca=70.0
gca peak = 0.12268 (69)
mri peak = 0.05392 (70)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (31571 voxels, overlap=0.991)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (31571 voxels, peak = 68), gca=68.0
gca peak = 0.15503 (91)
mri peak = 0.15844 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8035 voxels, overlap=0.847)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8035 voxels, peak = 91), gca=90.5
gca peak = 0.14985 (91)
mri peak = 0.16666 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7322 voxels, overlap=0.849)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7322 voxels, peak = 91), gca=90.5
gca peak = 0.28303 (69)
mri peak = 0.08856 (71)
Left_Amygdala (18): linear fit = 1.03 x + 0.0 (730 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.03 x + 0.0 (730 voxels, peak = 71), gca=71.4
gca peak = 0.29009 (68)
mri peak = 0.07196 (66)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (806 voxels, overlap=1.011)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (806 voxels, peak = 67), gca=67.0
gca peak = 0.11239 (94)
mri peak = 0.07839 (94)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5334 voxels, overlap=0.910)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5334 voxels, peak = 94), gca=93.5
gca peak = 0.10424 (90)
mri peak = 0.07767 (94)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5076 voxels, overlap=0.938)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5076 voxels, peak = 90), gca=90.4
gca peak = 0.07727 (85)
mri peak = 0.08716 (86)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2625 voxels, overlap=0.851)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2625 voxels, peak = 85), gca=85.0
gca peak = 0.09434 (84)
mri peak = 0.09820 (87)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2841 voxels, overlap=0.823)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2841 voxels, peak = 83), gca=82.7
gca peak = 0.07242 (90)
mri peak = 0.10012 (90)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (13531 voxels, overlap=0.681)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (13531 voxels, peak = 90), gca=89.6
gca peak = 0.12268 (92)
mri peak = 0.07861 (99)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1729 voxels, overlap=0.810)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1729 voxels, peak = 93), gca=93.4
gca peak = 0.14011 (95)
mri peak = 0.08166 (96)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1727 voxels, overlap=0.922)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1727 voxels, peak = 95), gca=95.0
gca peak = 0.12335 (35)
mri peak = 0.14713 (30)
gca peak = 0.14598 (22)
mri peak = 0.17040 (27)
Fourth_Ventricle (15): linear fit = 1.29 x + 0.0 (220 voxels, overlap=0.427)
Fourth_Ventricle (15): linear fit = 1.29 x + 0.0 (220 voxels, peak = 28), gca=28.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.13617 (32)
gca peak Left_Thalamus = 0.36646 (102)
gca peak Third_Ventricle = 0.12335 (35)
gca peak CSF = 0.18746 (49)
gca peak Left_Accumbens_area = 0.64704 (70)
gca peak Left_undetermined = 0.96707 (28)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12577 (35)
gca peak Right_Inf_Lat_Vent = 0.24202 (28)
gca peak Right_Accumbens_area = 0.29896 (78)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14507 (37)
gca peak Fifth_Ventricle = 0.75707 (42)
gca peak WM_hypointensities = 0.07901 (76)
gca peak non_WM_hypointensities = 0.09318 (44)
gca peak Optic_Chiasm = 0.68739 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.17 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
88835 voxels changed in iteration 0 of unlikely voxel relabeling
314 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
59035 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
419 hippocampal voxels changed.
2 amygdala voxels changed.
pass 1: 81893 changed. image ll: -2.159, PF=0.500
pass 2: 22048 changed. image ll: -2.159, PF=0.500
pass 3: 6277 changed.
pass 4: 2208 changed.
66096 voxels changed in iteration 0 of unlikely voxel relabeling
509 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8949 voxels changed in iteration 0 of unlikely voxel relabeling
215 voxels changed in iteration 1 of unlikely voxel relabeling
7 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7570 voxels changed in iteration 0 of unlikely voxel relabeling
94 voxels changed in iteration 1 of unlikely voxel relabeling
7 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5212 voxels changed in iteration 0 of unlikely voxel relabeling
29 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    4306.218355
mri_ca_label stimesec    9.648533
mri_ca_label ru_maxrss   2111296
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   714332
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63512
mri_ca_label ru_oublock  552
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    262
mri_ca_label ru_nivcsw   5661
auto-labeling took 71 minutes and 11 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/transforms/cc_up.lta 0050233 

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-6.0.0/0050233/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/norm.mgz
37820 voxels in left wm, 39516 in right wm, xrange [125, 132]
searching rotation angles z=[-6  8], y=[-7  7]

searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.8  global minimum found at slice 128.1, rotations (-0.15, 1.06)
final transformation (x=128.1, yr=-0.146, zr=1.064):
 0.99982  -0.01857  -0.00255   1.80444;
 0.01857   0.99983  -0.00005   38.64099;
 0.00255   0.00000   1.00000   25.67359;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 87 102
eigenvectors:
 0.00019  -0.01053   0.99994;
-0.07258  -0.99731  -0.01049;
 0.99736  -0.07258  -0.00095;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.7 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 23:51:26 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 23:51:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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...
553 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 73 (73), valley at 34 (34)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 73 (73), valley at 33 (33)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 6 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 23:54:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1993113 voxels in mask (pct= 11.88)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 23:54:35 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): 103.8 +- 6.9 [79.0 --> 125.0]
GM (74.0) : 72.8 +- 9.8 [30.0 --> 95.0]
setting bottom of white matter range to 82.5
setting top of gray matter range to 92.3
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...
10490 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4881 filled
3320 bright non-wm voxels segmented.
5447 diagonally connected voxels added...
white matter segmentation took 1.7 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.46 minutes
reading wm segmentation from wm.seg.mgz...
127 voxels added to wm to prevent paths from MTL structures to cortex
2702 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 47571 voxels turned on, 71719 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  27 found -  27 modified     |    TOTAL:  27
pass   2 (xy+):   0 found -  27 modified     |    TOTAL:  27
pass   1 (xy-):  29 found -  29 modified     |    TOTAL:  56
pass   2 (xy-):   0 found -  29 modified     |    TOTAL:  56
pass   1 (yz+):  24 found -  24 modified     |    TOTAL:  80
pass   2 (yz+):   0 found -  24 modified     |    TOTAL:  80
pass   1 (yz-):  17 found -  17 modified     |    TOTAL:  97
pass   2 (yz-):   0 found -  17 modified     |    TOTAL:  97
pass   1 (xz+):  16 found -  16 modified     |    TOTAL: 113
pass   2 (xz+):   0 found -  16 modified     |    TOTAL: 113
pass   1 (xz-):  24 found -  24 modified     |    TOTAL: 137
pass   2 (xz-):   0 found -  24 modified     |    TOTAL: 137
Iteration Number : 1
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  16
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  16
pass   1 (+++):  25 found -  25 modified     |    TOTAL:  41
pass   2 (+++):   0 found -  25 modified     |    TOTAL:  41
pass   1 (+++):  34 found -  34 modified     |    TOTAL:  75
pass   2 (+++):   0 found -  34 modified     |    TOTAL:  75
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  91
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  91
Iteration Number : 1
pass   1 (++): 203 found - 203 modified     |    TOTAL: 203
pass   2 (++):   0 found - 203 modified     |    TOTAL: 203
pass   1 (+-): 234 found - 234 modified     |    TOTAL: 437
pass   2 (+-):   0 found - 234 modified     |    TOTAL: 437
pass   1 (--): 198 found - 198 modified     |    TOTAL: 635
pass   2 (--):   0 found - 198 modified     |    TOTAL: 635
pass   1 (-+): 183 found - 183 modified     |    TOTAL: 818
pass   2 (-+):   0 found - 183 modified     |    TOTAL: 818
Iteration Number : 2
pass   1 (xy+):   8 found -   8 modified     |    TOTAL:   8
pass   2 (xy+):   0 found -   8 modified     |    TOTAL:   8
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  13
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  13
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:  17
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:  17
pass   1 (yz-):   7 found -   7 modified     |    TOTAL:  24
pass   2 (yz-):   0 found -   7 modified     |    TOTAL:  24
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  28
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  28
pass   1 (xz-):   5 found -   5 modified     |    TOTAL:  33
pass   2 (xz-):   0 found -   5 modified     |    TOTAL:  33
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (--):   1 found -   1 modified     |    TOTAL:   6
pass   2 (--):   0 found -   1 modified     |    TOTAL:   6
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   8
Iteration Number : 3
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-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   4
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 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 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

Total Number of Modified Voxels = 1096 (out of 673728: 0.162677)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 23:56:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

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

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 0.98047  -0.00876   0.03639  -3.27762;
 0.00146   1.02783   0.24341  -12.74147;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 0.98047  -0.00876   0.03639  -3.27762;
 0.00146   1.02783   0.24341  -12.74147;
-0.03990  -0.21125   0.92319   35.43819;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2602 (min = 350, max = 1400), aspect = 1.21 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 125, 154), TAL = (1.0, 26.0, 3.0)
talairach voxel to voxel transform
 1.01828   0.00041  -0.04025   4.76899;
-0.01126   0.92290  -0.24289   20.32977;
 0.04143   0.21120   1.02588  -33.52858;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  125,  154) --> (1.0, 26.0, 3.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (1.00, 26.00, 3.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, 26.00, 3.00) SRC: (109.61, 97.06, 155.37)
search lh wm seed point around talairach space (-17.00, 26.00, 3.00), SRC: (146.27, 96.66, 156.87)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 23:57:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 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 = 6 (out of 329121: 0.001823)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 30: 2620 vertices, 2787 faces
slice 40: 9682 vertices, 10017 faces
slice 50: 21511 vertices, 21964 faces
slice 60: 34678 vertices, 35145 faces
slice 70: 49059 vertices, 49497 faces
slice 80: 62801 vertices, 63243 faces
slice 90: 76284 vertices, 76720 faces
slice 100: 89966 vertices, 90424 faces
slice 110: 102803 vertices, 103285 faces
slice 120: 115761 vertices, 116276 faces
slice 130: 128075 vertices, 128599 faces
slice 140: 139909 vertices, 140338 faces
slice 150: 150742 vertices, 151195 faces
slice 160: 160785 vertices, 161200 faces
slice 170: 168461 vertices, 168806 faces
slice 180: 175806 vertices, 176120 faces
slice 190: 181383 vertices, 181657 faces
slice 200: 184253 vertices, 184370 faces
slice 210: 184472 vertices, 184558 faces
slice 220: 184472 vertices, 184558 faces
slice 230: 184472 vertices, 184558 faces
slice 240: 184472 vertices, 184558 faces
slice 250: 184472 vertices, 184558 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...
   184472 voxel in cpt #1: X=-86 [v=184472,e=553674,f=369116] located at (-28.907064, -24.499365, 30.371927)
For the whole surface: X=-86 [v=184472,e=553674,f=369116]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 23:57:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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


Iteration Number : 1
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   9
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:  10
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  12
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  12
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  13
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  13
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   3 found -   3 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   3 modified     |    TOTAL:   5
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 = 18 (out of 322332: 0.005584)
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 30: 1219 vertices, 1327 faces
slice 40: 7307 vertices, 7552 faces
slice 50: 17859 vertices, 18321 faces
slice 60: 31083 vertices, 31556 faces
slice 70: 44781 vertices, 45316 faces
slice 80: 59106 vertices, 59529 faces
slice 90: 72520 vertices, 72980 faces
slice 100: 86656 vertices, 87134 faces
slice 110: 99891 vertices, 100333 faces
slice 120: 112885 vertices, 113378 faces
slice 130: 125633 vertices, 126126 faces
slice 140: 137904 vertices, 138314 faces
slice 150: 149115 vertices, 149576 faces
slice 160: 159632 vertices, 160023 faces
slice 170: 167574 vertices, 167896 faces
slice 180: 174913 vertices, 175219 faces
slice 190: 181045 vertices, 181303 faces
slice 200: 184675 vertices, 184773 faces
slice 210: 184912 vertices, 184970 faces
slice 220: 184912 vertices, 184970 faces
slice 230: 184912 vertices, 184970 faces
slice 240: 184912 vertices, 184970 faces
slice 250: 184912 vertices, 184970 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...
   184912 voxel in cpt #1: X=-58 [v=184912,e=554910,f=369940] located at (28.180134, -22.079266, 30.957666)
For the whole surface: X=-58 [v=184912,e=554910,f=369940]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 23:57:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 23:57:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

Waiting for PID 32558 of (32558 32561) to complete...
Waiting for PID 32561 of (32558 32561) 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 (32558 32561) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 23:57:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 23:57:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

Waiting for PID 32604 of (32604 32607) to complete...
Waiting for PID 32607 of (32604 32607) 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 = 51.3 mm, total surface area = 96035 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.158 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.089 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.057 (target=0.015)   
step 030: RMS=0.051 (target=0.015)   
step 035: RMS=0.045 (target=0.015)   
step 040: RMS=0.043 (target=0.015)   
step 045: RMS=0.042 (target=0.015)   
step 050: RMS=0.040 (target=0.015)   
step 055: RMS=0.039 (target=0.015)   
step 060: RMS=0.039 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    51.733135
mris_inflate stimesec    0.149977
mris_inflate ru_maxrss   268388
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   38417
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12984
mris_inflate ru_oublock  13000
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    3884
mris_inflate ru_nivcsw   3853

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 50.8 mm, total surface area = 96166 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.087 (target=0.015)   
step 015: RMS=0.073 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.050 (target=0.015)   
step 035: RMS=0.045 (target=0.015)   
step 040: RMS=0.043 (target=0.015)   
step 045: RMS=0.039 (target=0.015)   
step 050: RMS=0.038 (target=0.015)   
step 055: RMS=0.038 (target=0.015)   
step 060: RMS=0.037 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    52.294050
mris_inflate stimesec    0.121981
mris_inflate ru_maxrss   268772
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   38512
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  13024
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2561
mris_inflate ru_nivcsw   4925
PIDs (32604 32607) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 23:58:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 23:58:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

Waiting for PID 325 of (325 329) to complete...
Waiting for PID 329 of (325 329) 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 0.85 +- 0.53 (0.00-->7.20) (max @ vno 138494 --> 139565)
face area 0.02 +- 0.03 (-0.17-->0.56)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.266...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.221, avgs=0
005/300: dt: 0.9000, rms radial error=176.958, avgs=0
010/300: dt: 0.9000, rms radial error=176.394, avgs=0
015/300: dt: 0.9000, rms radial error=175.652, avgs=0
020/300: dt: 0.9000, rms radial error=174.811, avgs=0
025/300: dt: 0.9000, rms radial error=173.910, avgs=0
030/300: dt: 0.9000, rms radial error=172.979, avgs=0
035/300: dt: 0.9000, rms radial error=172.033, avgs=0
040/300: dt: 0.9000, rms radial error=171.081, avgs=0
045/300: dt: 0.9000, rms radial error=170.126, avgs=0
050/300: dt: 0.9000, rms radial error=169.172, avgs=0
055/300: dt: 0.9000, rms radial error=168.222, avgs=0
060/300: dt: 0.9000, rms radial error=167.275, avgs=0
065/300: dt: 0.9000, rms radial error=166.333, avgs=0
070/300: dt: 0.9000, rms radial error=165.396, avgs=0
075/300: dt: 0.9000, rms radial error=164.466, avgs=0
080/300: dt: 0.9000, rms radial error=163.541, avgs=0
085/300: dt: 0.9000, rms radial error=162.622, avgs=0
090/300: dt: 0.9000, rms radial error=161.707, avgs=0
095/300: dt: 0.9000, rms radial error=160.797, avgs=0
100/300: dt: 0.9000, rms radial error=159.893, avgs=0
105/300: dt: 0.9000, rms radial error=158.995, avgs=0
110/300: dt: 0.9000, rms radial error=158.101, avgs=0
115/300: dt: 0.9000, rms radial error=157.212, avgs=0
120/300: dt: 0.9000, rms radial error=156.329, avgs=0
125/300: dt: 0.9000, rms radial error=155.450, avgs=0
130/300: dt: 0.9000, rms radial error=154.577, avgs=0
135/300: dt: 0.9000, rms radial error=153.708, avgs=0
140/300: dt: 0.9000, rms radial error=152.844, avgs=0
145/300: dt: 0.9000, rms radial error=151.985, avgs=0
150/300: dt: 0.9000, rms radial error=151.130, avgs=0
155/300: dt: 0.9000, rms radial error=150.280, avgs=0
160/300: dt: 0.9000, rms radial error=149.435, avgs=0
165/300: dt: 0.9000, rms radial error=148.595, avgs=0
170/300: dt: 0.9000, rms radial error=147.760, avgs=0
175/300: dt: 0.9000, rms radial error=146.928, avgs=0
180/300: dt: 0.9000, rms radial error=146.102, avgs=0
185/300: dt: 0.9000, rms radial error=145.280, avgs=0
190/300: dt: 0.9000, rms radial error=144.463, avgs=0
195/300: dt: 0.9000, rms radial error=143.650, avgs=0
200/300: dt: 0.9000, rms radial error=142.842, avgs=0
205/300: dt: 0.9000, rms radial error=142.038, avgs=0
210/300: dt: 0.9000, rms radial error=141.239, avgs=0
215/300: dt: 0.9000, rms radial error=140.444, avgs=0
220/300: dt: 0.9000, rms radial error=139.653, avgs=0
225/300: dt: 0.9000, rms radial error=138.867, avgs=0
230/300: dt: 0.9000, rms radial error=138.085, avgs=0
235/300: dt: 0.9000, rms radial error=137.308, avgs=0
240/300: dt: 0.9000, rms radial error=136.535, avgs=0
245/300: dt: 0.9000, rms radial error=135.766, avgs=0
250/300: dt: 0.9000, rms radial error=135.002, avgs=0
255/300: dt: 0.9000, rms radial error=134.242, avgs=0
260/300: dt: 0.9000, rms radial error=133.486, avgs=0
265/300: dt: 0.9000, rms radial error=132.735, avgs=0
270/300: dt: 0.9000, rms radial error=131.988, avgs=0
275/300: dt: 0.9000, rms radial error=131.244, avgs=0
280/300: dt: 0.9000, rms radial error=130.505, avgs=0
285/300: dt: 0.9000, rms radial error=129.770, avgs=0
290/300: dt: 0.9000, rms radial error=129.040, avgs=0
295/300: dt: 0.9000, rms radial error=128.313, avgs=0
300/300: dt: 0.9000, rms radial error=127.590, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 22620.22
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 4188.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
epoch 3 (K=160.0), pass 1, starting sse = 517.25
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00398
epoch 4 (K=640.0), pass 1, starting sse = 40.54
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/10 = 0.00607
final distance error %30.01
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    292.708501
mris_sphere stimesec    0.238963
mris_sphere ru_maxrss   268576
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   37955
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  12984
mris_sphere ru_oublock  13024
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    11097
mris_sphere ru_nivcsw   23157
FSRUNTIME@ mris_sphere  0.0814 hours 1 threads

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.85 +- 0.53 (0.00-->6.52) (max @ vno 83175 --> 84714)
face area 0.02 +- 0.03 (-0.20-->0.68)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.269...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.032, avgs=0
005/300: dt: 0.9000, rms radial error=176.771, avgs=0
010/300: dt: 0.9000, rms radial error=176.209, avgs=0
015/300: dt: 0.9000, rms radial error=175.472, avgs=0
020/300: dt: 0.9000, rms radial error=174.633, avgs=0
025/300: dt: 0.9000, rms radial error=173.737, avgs=0
030/300: dt: 0.9000, rms radial error=172.810, avgs=0
035/300: dt: 0.9000, rms radial error=171.866, avgs=0
040/300: dt: 0.9000, rms radial error=170.916, avgs=0
045/300: dt: 0.9000, rms radial error=169.963, avgs=0
050/300: dt: 0.9000, rms radial error=169.012, avgs=0
055/300: dt: 0.9000, rms radial error=168.064, avgs=0
060/300: dt: 0.9000, rms radial error=167.121, avgs=0
065/300: dt: 0.9000, rms radial error=166.181, avgs=0
070/300: dt: 0.9000, rms radial error=165.247, avgs=0
075/300: dt: 0.9000, rms radial error=164.318, avgs=0
080/300: dt: 0.9000, rms radial error=163.394, avgs=0
085/300: dt: 0.9000, rms radial error=162.475, avgs=0
090/300: dt: 0.9000, rms radial error=161.562, avgs=0
095/300: dt: 0.9000, rms radial error=160.654, avgs=0
100/300: dt: 0.9000, rms radial error=159.751, avgs=0
105/300: dt: 0.9000, rms radial error=158.853, avgs=0
110/300: dt: 0.9000, rms radial error=157.961, avgs=0
115/300: dt: 0.9000, rms radial error=157.073, avgs=0
120/300: dt: 0.9000, rms radial error=156.191, avgs=0
125/300: dt: 0.9000, rms radial error=155.313, avgs=0
130/300: dt: 0.9000, rms radial error=154.440, avgs=0
135/300: dt: 0.9000, rms radial error=153.572, avgs=0
140/300: dt: 0.9000, rms radial error=152.710, avgs=0
145/300: dt: 0.9000, rms radial error=151.853, avgs=0
150/300: dt: 0.9000, rms radial error=151.000, avgs=0
155/300: dt: 0.9000, rms radial error=150.153, avgs=0
160/300: dt: 0.9000, rms radial error=149.309, avgs=0
165/300: dt: 0.9000, rms radial error=148.471, avgs=0
170/300: dt: 0.9000, rms radial error=147.637, avgs=0
175/300: dt: 0.9000, rms radial error=146.807, avgs=0
180/300: dt: 0.9000, rms radial error=145.982, avgs=0
185/300: dt: 0.9000, rms radial error=145.162, avgs=0
190/300: dt: 0.9000, rms radial error=144.346, avgs=0
195/300: dt: 0.9000, rms radial error=143.534, avgs=0
200/300: dt: 0.9000, rms radial error=142.727, avgs=0
205/300: dt: 0.9000, rms radial error=141.925, avgs=0
210/300: dt: 0.9000, rms radial error=141.126, avgs=0
215/300: dt: 0.9000, rms radial error=140.333, avgs=0
220/300: dt: 0.9000, rms radial error=139.543, avgs=0
225/300: dt: 0.9000, rms radial error=138.758, avgs=0
230/300: dt: 0.9000, rms radial error=137.977, avgs=0
235/300: dt: 0.9000, rms radial error=137.201, avgs=0
240/300: dt: 0.9000, rms radial error=136.429, avgs=0
245/300: dt: 0.9000, rms radial error=135.661, avgs=0
250/300: dt: 0.9000, rms radial error=134.898, avgs=0
255/300: dt: 0.9000, rms radial error=134.139, avgs=0
260/300: dt: 0.9000, rms radial error=133.384, avgs=0
265/300: dt: 0.9000, rms radial error=132.633, avgs=0
270/300: dt: 0.9000, rms radial error=131.886, avgs=0
275/300: dt: 0.9000, rms radial error=131.144, avgs=0
280/300: dt: 0.9000, rms radial error=130.405, avgs=0
285/300: dt: 0.9000, rms radial error=129.671, avgs=0
290/300: dt: 0.9000, rms radial error=128.941, avgs=0
295/300: dt: 0.9000, rms radial error=128.214, avgs=0
300/300: dt: 0.9000, rms radial error=127.492, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 22597.61
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 2 (K=40.0), pass 1, starting sse = 4146.65
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00000
epoch 3 (K=160.0), pass 1, starting sse = 495.11
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00369
epoch 4 (K=640.0), pass 1, starting sse = 37.07
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00729
final distance error %29.73
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    297.011847
mris_sphere stimesec    0.224965
mris_sphere ru_maxrss   268980
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   38061
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  13008
mris_sphere ru_oublock  13048
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    12940
mris_sphere ru_nivcsw   22772
FSRUNTIME@ mris_sphere  0.0822 hours 1 threads
PIDs (325 329) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 00:03:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 00:03:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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


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

#@# Fix Topology lh Sun Oct  8 00:03:42 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050233 lh 

#@# Fix Topology rh Sun Oct  8 00:03:42 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050233 rh 

Waiting for PID 915 of (915 918) to complete...
Waiting for PID 918 of (915 918) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050233 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=-86 (nv=184472, nf=369116, ne=553674, g=44)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
8699 ambiguous faces found in tessellation
segmenting defects...
31 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 8 into 3
30 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4511  (-4.7255)
      -vertex     loglikelihood: -6.0298  (-3.0149)
      -normal dot loglikelihood: -3.6079  (-3.6079)
      -quad curv  loglikelihood: -6.4614  (-3.2307)
      Total Loglikelihood : -25.5502

CORRECTING DEFECT 0 (vertices=56, convex hull=64, v0=22416)
After retessellation of defect 0 (v0=22416), euler #=-23 (179461,536989,357505) : difference with theory (-27) = -4 

CORRECTING DEFECT 1 (vertices=47, convex hull=79, v0=26101)
After retessellation of defect 1 (v0=26101), euler #=-22 (179487,537099,357590) : difference with theory (-26) = -4 

CORRECTING DEFECT 2 (vertices=26, convex hull=43, v0=62801)
After retessellation of defect 2 (v0=62801), euler #=-21 (179499,537150,357630) : difference with theory (-25) = -4 

CORRECTING DEFECT 3 (vertices=2341, convex hull=1101, v0=75990)
XL defect detected...
After retessellation of defect 3 (v0=75990), euler #=-24 (179772,538589,358793) : difference with theory (-24) = 0 

CORRECTING DEFECT 4 (vertices=11, convex hull=16, v0=81346)
After retessellation of defect 4 (v0=81346), euler #=-23 (179773,538595,358799) : difference with theory (-23) = 0 

CORRECTING DEFECT 5 (vertices=25, convex hull=57, v0=84016)
After retessellation of defect 5 (v0=84016), euler #=-22 (179783,538649,358844) : difference with theory (-22) = 0 

CORRECTING DEFECT 6 (vertices=44, convex hull=28, v0=92224)
After retessellation of defect 6 (v0=92224), euler #=-21 (179791,538684,358872) : difference with theory (-21) = 0 

CORRECTING DEFECT 7 (vertices=20, convex hull=47, v0=100882)
After retessellation of defect 7 (v0=100882), euler #=-20 (179801,538728,358907) : difference with theory (-20) = 0 

CORRECTING DEFECT 8 (vertices=39, convex hull=26, v0=114444)
After retessellation of defect 8 (v0=114444), euler #=-19 (179807,538752,358926) : difference with theory (-19) = 0 

CORRECTING DEFECT 9 (vertices=6, convex hull=28, v0=115474)
After retessellation of defect 9 (v0=115474), euler #=-18 (179810,538768,358940) : difference with theory (-18) = 0 

CORRECTING DEFECT 10 (vertices=39, convex hull=60, v0=115741)
After retessellation of defect 10 (v0=115741), euler #=-17 (179830,538855,359008) : difference with theory (-17) = 0 

CORRECTING DEFECT 11 (vertices=9, convex hull=23, v0=119958)
After retessellation of defect 11 (v0=119958), euler #=-16 (179833,538869,359020) : difference with theory (-16) = 0 

CORRECTING DEFECT 12 (vertices=170, convex hull=54, v0=121657)
After retessellation of defect 12 (v0=121657), euler #=-15 (179847,538931,359069) : difference with theory (-15) = 0 

CORRECTING DEFECT 13 (vertices=50, convex hull=63, v0=128915)
After retessellation of defect 13 (v0=128915), euler #=-14 (179859,538994,359121) : difference with theory (-14) = 0 

CORRECTING DEFECT 14 (vertices=206, convex hull=89, v0=128955)
After retessellation of defect 14 (v0=128955), euler #=-13 (179871,539063,359179) : difference with theory (-13) = 0 

CORRECTING DEFECT 15 (vertices=89, convex hull=68, v0=130091)
After retessellation of defect 15 (v0=130091), euler #=-12 (179886,539134,359236) : difference with theory (-12) = 0 

CORRECTING DEFECT 16 (vertices=738, convex hull=261, v0=134991)
After retessellation of defect 16 (v0=134991), euler #=-11 (179953,539462,359498) : difference with theory (-11) = 0 

CORRECTING DEFECT 17 (vertices=63, convex hull=69, v0=137758)
After retessellation of defect 17 (v0=137758), euler #=-10 (179972,539543,359561) : difference with theory (-10) = 0 

CORRECTING DEFECT 18 (vertices=9, convex hull=19, v0=139459)
After retessellation of defect 18 (v0=139459), euler #=-9 (179973,539555,359573) : difference with theory (-9) = 0 

CORRECTING DEFECT 19 (vertices=45, convex hull=52, v0=139512)
After retessellation of defect 19 (v0=139512), euler #=-8 (179989,539623,359626) : difference with theory (-8) = 0 

CORRECTING DEFECT 20 (vertices=234, convex hull=240, v0=139840)
After retessellation of defect 20 (v0=139840), euler #=-7 (180061,539951,359883) : difference with theory (-7) = 0 

CORRECTING DEFECT 21 (vertices=296, convex hull=62, v0=141649)
After retessellation of defect 21 (v0=141649), euler #=-6 (180082,540044,359956) : difference with theory (-6) = 0 

CORRECTING DEFECT 22 (vertices=35, convex hull=82, v0=143759)
After retessellation of defect 22 (v0=143759), euler #=-5 (180095,540114,360014) : difference with theory (-5) = 0 

CORRECTING DEFECT 23 (vertices=82, convex hull=44, v0=146140)
After retessellation of defect 23 (v0=146140), euler #=-4 (180108,540171,360059) : difference with theory (-4) = 0 

CORRECTING DEFECT 24 (vertices=60, convex hull=89, v0=160982)
After retessellation of defect 24 (v0=160982), euler #=-3 (180141,540314,360170) : difference with theory (-3) = 0 

CORRECTING DEFECT 25 (vertices=168, convex hull=156, v0=161588)
After retessellation of defect 25 (v0=161588), euler #=-2 (180184,540513,360327) : difference with theory (-2) = 0 

CORRECTING DEFECT 26 (vertices=21, convex hull=31, v0=169202)
After retessellation of defect 26 (v0=169202), euler #=-1 (180186,540529,360342) : difference with theory (-1) = 0 

CORRECTING DEFECT 27 (vertices=17, convex hull=23, v0=178673)
After retessellation of defect 27 (v0=178673), euler #=0 (180189,540545,360356) : difference with theory (0) = 0 

CORRECTING DEFECT 28 (vertices=63, convex hull=28, v0=184322)
After retessellation of defect 28 (v0=184322), euler #=1 (180194,540567,360374) : difference with theory (1) = 0 

CORRECTING DEFECT 29 (vertices=6, convex hull=28, v0=184408)
After retessellation of defect 29 (v0=184408), euler #=2 (180195,540579,360386) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.24 (0.04-->11.81) (max @ vno 85966 --> 89945)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.24 (0.04-->11.81) (max @ vno 85966 --> 89945)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
127 mutations (36.5%), 221 crossovers (63.5%), 829 vertices were eliminated
building final representation...
4277 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=180195, nf=360386, ne=540579, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 53.4 minutes
0 defective edges
removing intersecting faces
000: 489 intersecting
001: 31 intersecting
002: 10 intersecting
mris_fix_topology utimesec    3202.411159
mris_fix_topology stimesec    2.957550
mris_fix_topology ru_maxrss   595340
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   65006
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  12984
mris_fix_topology ru_oublock  17208
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    849
mris_fix_topology ru_nivcsw   6016
FSRUNTIME@ mris_fix_topology lh  0.8900 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050233 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=-58 (nv=184912, nf=369940, ne=554910, g=30)
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...
6468 ambiguous faces found in tessellation
segmenting defects...
34 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
34 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5709  (-4.7854)
      -vertex     loglikelihood: -6.0453  (-3.0226)
      -normal dot loglikelihood: -3.5837  (-3.5837)
      -quad curv  loglikelihood: -5.9211  (-2.9605)
      Total Loglikelihood : -25.1210

CORRECTING DEFECT 0 (vertices=41, convex hull=100, v0=2433)
After retessellation of defect 0 (v0=2433), euler #=-26 (181076,541987,360885) : difference with theory (-31) = -5 

CORRECTING DEFECT 1 (vertices=16, convex hull=33, v0=12503)
After retessellation of defect 1 (v0=12503), euler #=-25 (181078,542006,360903) : difference with theory (-30) = -5 

CORRECTING DEFECT 2 (vertices=63, convex hull=67, v0=41310)
After retessellation of defect 2 (v0=41310), euler #=-24 (181086,542055,360945) : difference with theory (-29) = -5 

CORRECTING DEFECT 3 (vertices=47, convex hull=88, v0=66650)
After retessellation of defect 3 (v0=66650), euler #=-23 (181095,542120,361002) : difference with theory (-28) = -5 

CORRECTING DEFECT 4 (vertices=28, convex hull=40, v0=71160)
After retessellation of defect 4 (v0=71160), euler #=-22 (181107,542171,361042) : difference with theory (-27) = -5 

CORRECTING DEFECT 5 (vertices=79, convex hull=109, v0=74831)
After retessellation of defect 5 (v0=74831), euler #=-21 (181149,542347,361177) : difference with theory (-26) = -5 

CORRECTING DEFECT 6 (vertices=21, convex hull=54, v0=75192)
After retessellation of defect 6 (v0=75192), euler #=-20 (181159,542398,361219) : difference with theory (-25) = -5 

CORRECTING DEFECT 7 (vertices=5, convex hull=14, v0=75366)
After retessellation of defect 7 (v0=75366), euler #=-19 (181159,542400,361222) : difference with theory (-24) = -5 

CORRECTING DEFECT 8 (vertices=22, convex hull=28, v0=77892)
After retessellation of defect 8 (v0=77892), euler #=-18 (181164,542424,361242) : difference with theory (-23) = -5 

CORRECTING DEFECT 9 (vertices=26, convex hull=43, v0=80051)
After retessellation of defect 9 (v0=80051), euler #=-17 (181174,542467,361276) : difference with theory (-22) = -5 

CORRECTING DEFECT 10 (vertices=125, convex hull=88, v0=81686)
After retessellation of defect 10 (v0=81686), euler #=-16 (181206,542604,361382) : difference with theory (-21) = -5 

CORRECTING DEFECT 11 (vertices=22, convex hull=39, v0=83455)
After retessellation of defect 11 (v0=83455), euler #=-15 (181210,542628,361403) : difference with theory (-20) = -5 

CORRECTING DEFECT 12 (vertices=35, convex hull=39, v0=83710)
After retessellation of defect 12 (v0=83710), euler #=-14 (181216,542663,361433) : difference with theory (-19) = -5 

CORRECTING DEFECT 13 (vertices=1476, convex hull=770, v0=95501)
XL defect detected...
After retessellation of defect 13 (v0=95501), euler #=-18 (181648,544378,362712) : difference with theory (-18) = 0 

CORRECTING DEFECT 14 (vertices=154, convex hull=44, v0=96468)
After retessellation of defect 14 (v0=96468), euler #=-17 (181656,544416,362743) : difference with theory (-17) = 0 

CORRECTING DEFECT 15 (vertices=197, convex hull=234, v0=103739)
After retessellation of defect 15 (v0=103739), euler #=-16 (181760,544844,363068) : difference with theory (-16) = 0 

CORRECTING DEFECT 16 (vertices=10, convex hull=22, v0=105770)
After retessellation of defect 16 (v0=105770), euler #=-15 (181761,544853,363077) : difference with theory (-15) = 0 

CORRECTING DEFECT 17 (vertices=30, convex hull=52, v0=112651)
After retessellation of defect 17 (v0=112651), euler #=-14 (181776,544918,363128) : difference with theory (-14) = 0 

CORRECTING DEFECT 18 (vertices=24, convex hull=30, v0=116081)
After retessellation of defect 18 (v0=116081), euler #=-13 (181782,544946,363151) : difference with theory (-13) = 0 

CORRECTING DEFECT 19 (vertices=127, convex hull=48, v0=117823)
After retessellation of defect 19 (v0=117823), euler #=-12 (181802,545029,363215) : difference with theory (-12) = 0 

CORRECTING DEFECT 20 (vertices=26, convex hull=37, v0=130651)
After retessellation of defect 20 (v0=130651), euler #=-11 (181808,545059,363240) : difference with theory (-11) = 0 

CORRECTING DEFECT 21 (vertices=19, convex hull=48, v0=133030)
After retessellation of defect 21 (v0=133030), euler #=-10 (181823,545122,363289) : difference with theory (-10) = 0 

CORRECTING DEFECT 22 (vertices=600, convex hull=268, v0=133183)
After retessellation of defect 22 (v0=133183), euler #=-9 (181924,545563,363630) : difference with theory (-9) = 0 

CORRECTING DEFECT 23 (vertices=21, convex hull=28, v0=134473)
After retessellation of defect 23 (v0=134473), euler #=-8 (181932,545595,363655) : difference with theory (-8) = 0 

CORRECTING DEFECT 24 (vertices=13, convex hull=23, v0=137521)
After retessellation of defect 24 (v0=137521), euler #=-7 (181935,545610,363668) : difference with theory (-7) = 0 

CORRECTING DEFECT 25 (vertices=51, convex hull=32, v0=138692)
After retessellation of defect 25 (v0=138692), euler #=-6 (181943,545645,363696) : difference with theory (-6) = 0 

CORRECTING DEFECT 26 (vertices=53, convex hull=40, v0=140960)
After retessellation of defect 26 (v0=140960), euler #=-5 (181952,545686,363729) : difference with theory (-5) = 0 

CORRECTING DEFECT 27 (vertices=24, convex hull=25, v0=145183)
After retessellation of defect 27 (v0=145183), euler #=-4 (181952,545692,363736) : difference with theory (-4) = 0 

CORRECTING DEFECT 28 (vertices=117, convex hull=68, v0=146399)
After retessellation of defect 28 (v0=146399), euler #=-3 (181978,545798,363817) : difference with theory (-3) = 0 

CORRECTING DEFECT 29 (vertices=140, convex hull=36, v0=153284)
After retessellation of defect 29 (v0=153284), euler #=-2 (181982,545827,363843) : difference with theory (-2) = 0 

CORRECTING DEFECT 30 (vertices=182, convex hull=155, v0=162919)
After retessellation of defect 30 (v0=162919), euler #=-1 (182062,546142,364079) : difference with theory (-1) = 0 

CORRECTING DEFECT 31 (vertices=29, convex hull=64, v0=168417)
After retessellation of defect 31 (v0=168417), euler #=0 (182076,546207,364131) : difference with theory (0) = 0 

CORRECTING DEFECT 32 (vertices=12, convex hull=31, v0=182066)
After retessellation of defect 32 (v0=182066), euler #=1 (182077,546220,364144) : difference with theory (1) = 0 

CORRECTING DEFECT 33 (vertices=7, convex hull=20, v0=182500)
After retessellation of defect 33 (v0=182500), euler #=2 (182078,546228,364152) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.01-->9.48) (max @ vno 101389 --> 112223)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.01-->9.48) (max @ vno 101389 --> 112223)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
119 mutations (36.0%), 212 crossovers (64.0%), 216 vertices were eliminated
building final representation...
2834 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=182078, nf=364152, ne=546228, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 26.3 minutes
0 defective edges
removing intersecting faces
000: 275 intersecting
001: 16 intersecting
mris_fix_topology utimesec    1579.457885
mris_fix_topology stimesec    0.234964
mris_fix_topology ru_maxrss   584204
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   62400
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  24528
mris_fix_topology ru_oublock  17336
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    645
mris_fix_topology ru_nivcsw   3525
FSRUNTIME@ mris_fix_topology rh  0.4386 hours 1 threads
PIDs (915 918) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 180195 - 540579 + 360386 = 2 --> 0 holes
      F =2V-4:          360386 = 360390-4 (0)
      2E=3F:            1081158 = 1081158 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 182078 - 546228 + 364152 = 2 --> 0 holes
      F =2V-4:          364152 = 364156-4 (0)
      2E=3F:            1092456 = 1092456 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 124 intersecting
001: 30 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 31 intersecting
001: 3 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:57:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050233 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:57:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050233 rh 

Waiting for PID 4780 of (4780 4783) to complete...
Waiting for PID 4783 of (4780 4783) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050233 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-6.0.0/0050233/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
36952 bright wm thresholded.
3455 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.orig...
computing class statistics...
border white:    328104 voxels (1.96%)
border gray      385806 voxels (2.30%)
WM (102.0): 101.4 +- 7.7 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 9.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.6 (was 70)
setting MAX_BORDER_WHITE to 114.7 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 54.1 (was 40)
setting MAX_GRAY to 99.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.04-->4.28) (max @ vno 88648 --> 179527)
face area 0.28 +- 0.12 (0.00-->4.87)
mean absolute distance = 0.66 +- 0.81
4859 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=107+-5.2,    GM=73+-6.1
mean inside = 97.4, mean outside = 79.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=83.4, 77 (77) missing vertices, mean dist 0.3 [0.5 (%36.2)->0.7 (%63.8))]
%71 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.04-->5.70) (max @ vno 85922 --> 179527)
face area 0.28 +- 0.13 (0.00-->4.23)
mean absolute distance = 0.32 +- 0.45
4360 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4029824.2, rms=9.697
001: dt: 0.5000, sse=2314079.8, rms=6.767 (30.213%)
002: dt: 0.5000, sse=1592242.0, rms=5.034 (25.613%)
003: dt: 0.5000, sse=1284937.8, rms=4.038 (19.784%)
004: dt: 0.5000, sse=1127244.0, rms=3.470 (14.078%)
005: dt: 0.5000, sse=1073084.6, rms=3.235 (6.753%)
006: dt: 0.5000, sse=1046369.9, rms=3.106 (3.998%)
rms = 3.08, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=1039714.2, rms=3.079 (0.876%)
008: dt: 0.2500, sse=852217.8, rms=1.907 (38.072%)
009: dt: 0.2500, sse=816320.9, rms=1.612 (15.454%)
010: dt: 0.2500, sse=811236.1, rms=1.539 (4.517%)
rms = 1.50, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=805344.8, rms=1.497 (2.745%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=800996.4, rms=1.457 (2.677%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=87.0, 58 (17) missing vertices, mean dist -0.2 [0.3 (%80.3)->0.2 (%19.7))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.08-->5.99) (max @ vno 85922 --> 179527)
face area 0.35 +- 0.16 (0.00-->6.04)
mean absolute distance = 0.20 +- 0.30
4423 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1708067.5, rms=4.795
013: dt: 0.5000, sse=1205690.9, rms=2.893 (39.670%)
rms = 2.88, time step reduction 1 of 3 to 0.250...
014: dt: 0.5000, sse=1192795.5, rms=2.882 (0.389%)
015: dt: 0.2500, sse=996474.1, rms=1.599 (44.523%)
016: dt: 0.2500, sse=971148.9, rms=1.344 (15.939%)
017: dt: 0.2500, sse=967804.8, rms=1.279 (4.857%)
rms = 1.24, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=964092.1, rms=1.240 (3.042%)
rms = 1.21, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=960215.5, rms=1.207 (2.642%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=89.3, 50 (7) missing vertices, mean dist -0.1 [0.2 (%75.4)->0.2 (%24.6))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.08-->5.94) (max @ vno 85922 --> 179527)
face area 0.33 +- 0.15 (0.00-->6.08)
mean absolute distance = 0.16 +- 0.25
3585 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1186992.9, rms=2.977
020: dt: 0.5000, sse=1094568.0, rms=2.442 (17.985%)
rms = 2.75, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=972313.7, rms=1.612 (33.962%)
022: dt: 0.2500, sse=932452.7, rms=1.227 (23.931%)
023: dt: 0.2500, sse=923738.2, rms=1.125 (8.310%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=923194.5, rms=1.120 (0.384%)
rms = 1.09, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=921482.7, rms=1.086 (3.086%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=89.9, 61 (4) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))]
%92 local maxima, % 4 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-6.0.0/0050233/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=928641.2, rms=1.296
rms = 1.39, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=900002.6, rms=0.948 (26.873%)
027: dt: 0.2500, sse=892159.9, rms=0.808 (14.734%)
rms = 0.83, time step reduction 2 of 3 to 0.125...
rms = 0.81, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=890985.6, rms=0.807 (0.130%)
positioning took 0.6 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7224 vertices
erasing segment 1 (vno[0] = 79410)
erasing segment 2 (vno[0] = 114365)
erasing segment 3 (vno[0] = 117684)
erasing segment 4 (vno[0] = 118768)
erasing segment 5 (vno[0] = 125893)
erasing segment 6 (vno[0] = 133097)
erasing segment 7 (vno[0] = 134233)
erasing segment 8 (vno[0] = 135207)
erasing segment 9 (vno[0] = 135236)
erasing segment 10 (vno[0] = 162491)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.area
vertex spacing 0.89 +- 0.24 (0.04-->5.96) (max @ vno 85922 --> 179527)
face area 0.33 +- 0.15 (0.00-->6.07)
refinement took 6.3 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050233 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-6.0.0/0050233/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
36952 bright wm thresholded.
3455 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.orig...
computing class statistics...
border white:    328104 voxels (1.96%)
border gray      385806 voxels (2.30%)
WM (102.0): 101.4 +- 7.7 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 9.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.6 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 54.1 (was 40)
setting MAX_GRAY to 98.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->4.29) (max @ vno 101389 --> 112223)
face area 0.28 +- 0.12 (0.00-->3.05)
mean absolute distance = 0.65 +- 0.81
5159 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=106+-4.3,    GM=73+-6.1
mean inside = 97.3, mean outside = 79.2
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=83.5, 47 (47) missing vertices, mean dist 0.3 [0.5 (%37.6)->0.7 (%62.4))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.24 (0.08-->5.54) (max @ vno 95005 --> 93693)
face area 0.28 +- 0.12 (0.00-->3.43)
mean absolute distance = 0.31 +- 0.45
4481 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4055505.8, rms=9.687
001: dt: 0.5000, sse=2340030.8, rms=6.782 (29.994%)
002: dt: 0.5000, sse=1623094.6, rms=5.080 (25.098%)
003: dt: 0.5000, sse=1297008.6, rms=4.079 (19.694%)
004: dt: 0.5000, sse=1141762.1, rms=3.499 (14.224%)
005: dt: 0.5000, sse=1093586.8, rms=3.274 (6.415%)
006: dt: 0.5000, sse=1062620.8, rms=3.139 (4.140%)
rms = 3.12, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=1062988.5, rms=3.123 (0.500%)
008: dt: 0.2500, sse=861932.2, rms=1.935 (38.047%)
009: dt: 0.2500, sse=827096.2, rms=1.644 (15.013%)
010: dt: 0.2500, sse=819359.7, rms=1.573 (4.321%)
rms = 1.53, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=814401.9, rms=1.534 (2.509%)
rms = 1.50, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=812147.6, rms=1.495 (2.510%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=87.0, 76 (12) missing vertices, mean dist -0.2 [0.3 (%79.6)->0.2 (%20.4))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.08-->5.54) (max @ vno 95005 --> 93693)
face area 0.35 +- 0.15 (0.00-->4.82)
mean absolute distance = 0.20 +- 0.29
4065 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1685823.6, rms=4.683
013: dt: 0.5000, sse=1209247.8, rms=2.901 (38.054%)
rms = 2.92, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=1090534.9, rms=2.240 (22.768%)
015: dt: 0.2500, sse=1015744.9, rms=1.689 (24.616%)
016: dt: 0.2500, sse=989295.8, rms=1.441 (14.666%)
017: dt: 0.2500, sse=981506.1, rms=1.344 (6.758%)
018: dt: 0.2500, sse=975473.7, rms=1.286 (4.270%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=972961.4, rms=1.269 (1.387%)
rms = 1.24, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=969606.4, rms=1.235 (2.631%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=89.2, 93 (3) missing vertices, mean dist -0.1 [0.2 (%74.9)->0.2 (%25.1))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.04-->5.76) (max @ vno 95005 --> 93693)
face area 0.33 +- 0.15 (0.00-->4.77)
mean absolute distance = 0.16 +- 0.24
4409 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1178221.8, rms=2.890
021: dt: 0.5000, sse=1108359.1, rms=2.447 (15.307%)
rms = 2.77, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=982076.4, rms=1.617 (33.946%)
023: dt: 0.2500, sse=944514.1, rms=1.238 (23.404%)
024: dt: 0.2500, sse=932213.1, rms=1.133 (8.490%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=931614.0, rms=1.132 (0.098%)
rms = 1.09, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=927641.2, rms=1.092 (3.519%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=89.8, 116 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))]
%92 local maxima, % 4 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-6.0.0/0050233/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=935403.8, rms=1.320
rms = 1.44, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=906958.5, rms=0.960 (27.278%)
028: dt: 0.2500, sse=900912.4, rms=0.820 (14.556%)
rms = 0.85, time step reduction 2 of 3 to 0.125...
rms = 0.82, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=898255.7, rms=0.816 (0.480%)
positioning took 0.6 minutes
generating cortex label...
17 non-cortical segments detected
only using segment with 8411 vertices
erasing segment 1 (vno[0] = 93280)
erasing segment 2 (vno[0] = 100234)
erasing segment 3 (vno[0] = 114037)
erasing segment 4 (vno[0] = 120147)
erasing segment 5 (vno[0] = 126720)
erasing segment 6 (vno[0] = 126744)
erasing segment 7 (vno[0] = 128046)
erasing segment 8 (vno[0] = 131726)
erasing segment 9 (vno[0] = 132872)
erasing segment 10 (vno[0] = 133840)
erasing segment 11 (vno[0] = 133910)
erasing segment 12 (vno[0] = 134754)
erasing segment 13 (vno[0] = 134985)
erasing segment 14 (vno[0] = 135921)
erasing segment 15 (vno[0] = 138158)
erasing segment 16 (vno[0] = 142279)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.area
vertex spacing 0.89 +- 0.24 (0.03-->5.76) (max @ vno 93693 --> 95005)
face area 0.33 +- 0.15 (0.00-->4.77)
refinement took 6.6 minutes
PIDs (4780 4783) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 01:03:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 01:03:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

Waiting for PID 5936 of (5936 5939) to complete...
Waiting for PID 5939 of (5936 5939) 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 (5936 5939) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 01:04:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 01:04:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 5986 of (5986 5989) to complete...
Waiting for PID 5989 of (5986 5989) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 51.6 mm, total surface area = 108268 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.043 (target=0.015)   
step 035: RMS=0.035 (target=0.015)   
step 040: RMS=0.030 (target=0.015)   
step 045: RMS=0.026 (target=0.015)   
step 050: RMS=0.023 (target=0.015)   
step 055: RMS=0.021 (target=0.015)   
step 060: RMS=0.020 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    51.575159
mris_inflate stimesec    0.119981
mris_inflate ru_maxrss   262328
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   37541
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12680
mris_inflate ru_oublock  14104
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2118
mris_inflate ru_nivcsw   3780

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 51.0 mm, total surface area = 109136 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.179 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.043 (target=0.015)   
step 035: RMS=0.037 (target=0.015)   
step 040: RMS=0.031 (target=0.015)   
step 045: RMS=0.027 (target=0.015)   
step 050: RMS=0.025 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    52.060085
mris_inflate stimesec    0.112982
mris_inflate ru_maxrss   264884
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   38185
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12808
mris_inflate ru_oublock  14248
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2434
mris_inflate ru_nivcsw   3795
PIDs (5986 5989) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 01:04:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 01:04:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 6088 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6091 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6094 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6097 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6100 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6103 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6106 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6109 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6112 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6115 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6118 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...
Waiting for PID 6122 of (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 1.139*4pi (14.310) --> 0 handles
ICI = 197.2, FI = 2405.3, variation=36753.386
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
249 vertices thresholded to be in k1 ~ [-0.22 0.22], k2 ~ [-0.08 0.04]
total integrated curvature = 0.567*4pi (7.124) --> 0 handles
ICI = 1.6, FI = 11.8, variation=193.193
186 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
203 vertices thresholded to be in [-0.13 0.11]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = -1.792*4pi (-22.524) --> 3 handles
ICI = 198.6, FI = 2543.7, variation=38545.592
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
256 vertices thresholded to be in k1 ~ [-0.21 0.33], k2 ~ [-0.10 0.04]
total integrated curvature = 0.492*4pi (6.177) --> 1 handles
ICI = 1.6, FI = 13.0, variation=210.062
163 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
181 vertices thresholded to be in [-0.12 0.17]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.023
done.
PIDs (6088 6091 6094 6097 6100 6103 6106 6109 6112 6115 6118 6122) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 01:06:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050233 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      [ 0050233/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                      [ 330 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.595019
WARN:    S explicit min:                          0.000000	vertex = 143

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 01:06:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050233 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      [ 0050233/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                      [ 349 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.331104
WARN:    S explicit min:                          0.000000	vertex = 627
#--------------------------------------------
#@# Sphere lh Sun Oct  8 01:06:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 01:06:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 6277 of (6277 6280) to complete...
Waiting for PID 6280 of (6277 6280) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0.249...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.78
pass 1: epoch 2 of 3 starting distance error %19.78
unfolding complete - removing small folds...
starting distance error %19.71
removing remaining folds...
final distance error %19.72
MRISunfold() return, current seed 1234
-01: dt=0.0000, 157 negative triangles
175: dt=0.9900, 157 negative triangles
176: dt=0.9900, 62 negative triangles
177: dt=0.9900, 42 negative triangles
178: dt=0.9900, 31 negative triangles
179: dt=0.9900, 25 negative triangles
180: dt=0.9900, 22 negative triangles
181: dt=0.9900, 18 negative triangles
182: dt=0.9900, 19 negative triangles
183: dt=0.9900, 20 negative triangles
184: dt=0.9900, 11 negative triangles
185: dt=0.9900, 14 negative triangles
186: dt=0.9900, 6 negative triangles
187: dt=0.9900, 3 negative triangles
188: dt=0.9900, 5 negative triangles
189: dt=0.9900, 2 negative triangles
190: dt=0.9900, 2 negative triangles
191: dt=0.9900, 3 negative triangles
192: dt=0.9900, 1 negative triangles
193: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.09 hours
mris_sphere utimesec    3943.729461
mris_sphere stimesec    1.956702
mris_sphere ru_maxrss   368284
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   64193
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12712
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    141472
mris_sphere ru_nivcsw   307760
FSRUNTIME@ mris_sphere  1.0884 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0.251...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.34
pass 1: epoch 2 of 3 starting distance error %20.29
unfolding complete - removing small folds...
starting distance error %20.24
removing remaining folds...
final distance error %20.26
MRISunfold() return, current seed 1234
-01: dt=0.0000, 196 negative triangles
167: dt=0.9900, 196 negative triangles
168: dt=0.9900, 110 negative triangles
169: dt=0.9900, 83 negative triangles
170: dt=0.9900, 73 negative triangles
171: dt=0.9900, 60 negative triangles
172: dt=0.9900, 57 negative triangles
173: dt=0.9900, 59 negative triangles
174: dt=0.9900, 44 negative triangles
175: dt=0.9900, 40 negative triangles
176: dt=0.9900, 44 negative triangles
177: dt=0.9900, 36 negative triangles
178: dt=0.9900, 41 negative triangles
179: dt=0.9900, 36 negative triangles
180: dt=0.9900, 38 negative triangles
181: dt=0.9900, 27 negative triangles
182: dt=0.9900, 33 negative triangles
183: dt=0.9900, 34 negative triangles
184: dt=0.9900, 27 negative triangles
185: dt=0.9900, 30 negative triangles
186: dt=0.9900, 21 negative triangles
187: dt=0.9900, 9 negative triangles
188: dt=0.9900, 12 negative triangles
189: dt=0.9900, 11 negative triangles
190: dt=0.9900, 9 negative triangles
191: dt=0.9900, 8 negative triangles
192: dt=0.9900, 6 negative triangles
193: dt=0.9900, 3 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.08 hours
mris_sphere utimesec    3890.321581
mris_sphere stimesec    1.976699
mris_sphere ru_maxrss   373360
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   65440
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12848
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    143804
mris_sphere ru_nivcsw   306032
FSRUNTIME@ mris_sphere  1.0802 hours 1 threads
PIDs (6277 6280) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 02:12:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 02:12:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 9394 of (9394 9397) to complete...
Waiting for PID 9397 of (9394 9397) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 5.702
curvature mean = 0.028, std = 0.820
curvature mean = 0.025, std = 0.837
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 460143.2, tmin=1.3493
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 392506.6, tmin=2.7271
  d=16.00 min @ (-4.00, 0.00, 0.00) sse = 366004.1, tmin=4.1262
  d=4.00 min @ (0.00, 0.00, 1.00) sse = 365795.8, tmin=6.9383
  d=2.00 min @ (0.00, 0.00, -0.50) sse = 365569.5, tmin=8.3470
  d=0.50 min @ (0.00, 0.12, 0.12) sse = 365566.8, tmin=11.1780
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done  11.18 min
curvature mean = 0.007, std = 0.816
curvature mean = 0.009, std = 0.934
curvature mean = 0.003, std = 0.822
curvature mean = 0.004, std = 0.973
curvature mean = 0.000, std = 0.822
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.024, std = 0.306
curvature mean = 0.040, std = 0.243
curvature mean = 0.074, std = 0.295
curvature mean = 0.036, std = 0.299
curvature mean = 0.042, std = 0.478
curvature mean = 0.036, std = 0.325
curvature mean = 0.024, std = 0.627
curvature mean = 0.036, std = 0.334
curvature mean = 0.009, std = 0.747
MRISregister() return, current seed 0
-01: dt=0.0000, 61 negative triangles
134: dt=0.9900, 61 negative triangles
expanding nbhd size to 1
135: dt=0.9900, 65 negative triangles
136: dt=0.9900, 52 negative triangles
137: dt=0.9900, 48 negative triangles
138: dt=0.9900, 45 negative triangles
139: dt=0.9900, 39 negative triangles
140: dt=0.9900, 38 negative triangles
141: dt=0.9900, 34 negative triangles
142: dt=0.9900, 26 negative triangles
143: dt=0.9900, 25 negative triangles
144: dt=0.9900, 25 negative triangles
145: dt=0.9900, 24 negative triangles
146: dt=0.9900, 24 negative triangles
147: dt=0.9900, 22 negative triangles
148: dt=0.9900, 21 negative triangles
149: dt=0.9900, 20 negative triangles
150: dt=0.9900, 20 negative triangles
151: dt=0.9900, 18 negative triangles
152: dt=0.9900, 20 negative triangles
153: dt=0.9900, 18 negative triangles
154: dt=0.9900, 16 negative triangles
155: dt=0.9900, 15 negative triangles
156: dt=0.9900, 13 negative triangles
157: dt=0.9900, 8 negative triangles
158: dt=0.9900, 8 negative triangles
159: dt=0.9900, 9 negative triangles
160: dt=0.9900, 7 negative triangles
161: dt=0.9900, 5 negative triangles
162: dt=0.9900, 5 negative triangles
163: dt=0.9900, 6 negative triangles
164: dt=0.9900, 6 negative triangles
165: dt=0.9900, 5 negative triangles
166: dt=0.9900, 6 negative triangles
167: dt=0.9900, 6 negative triangles
168: dt=0.9900, 4 negative triangles
169: dt=0.9900, 3 negative triangles
170: dt=0.9900, 3 negative triangles
171: dt=0.9900, 1 negative triangles
172: dt=0.9900, 1 negative triangles
173: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.65 hours
mris_register utimesec    5950.890327
mris_register stimesec    5.899103
mris_register ru_maxrss   319636
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   45244
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  12680
mris_register ru_oublock  12768
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    428073
mris_register ru_nivcsw   275888
FSRUNTIME@ mris_register  1.6541 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 5.661
curvature mean = 0.029, std = 0.815
curvature mean = 0.025, std = 0.835
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 485284.9, tmin=1.3610
  d=32.00 min @ (-8.00, -8.00, 0.00) sse = 417929.1, tmin=2.7538
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 408973.0, tmin=4.1652
  d=8.00 min @ (2.00, 0.00, 0.00) sse = 405101.7, tmin=5.5876
  d=4.00 min @ (0.00, 1.00, 0.00) sse = 404682.6, tmin=7.0193
  d=2.00 min @ (0.00, -0.50, 0.50) sse = 404624.8, tmin=8.4498
  d=1.00 min @ (0.00, 0.25, -0.25) sse = 404527.4, tmin=9.8864
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 404497.5, tmin=11.3447
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done  11.34 min
curvature mean = 0.014, std = 0.814
curvature mean = 0.011, std = 0.933
curvature mean = 0.010, std = 0.819
curvature mean = 0.005, std = 0.972
curvature mean = 0.007, std = 0.816
curvature mean = 0.001, std = 0.988
2 Reading smoothwm
curvature mean = -0.024, std = 0.474
curvature mean = 0.036, std = 0.239
curvature mean = 0.049, std = 0.191
curvature mean = 0.031, std = 0.295
curvature mean = 0.029, std = 0.309
curvature mean = 0.030, std = 0.322
curvature mean = 0.017, std = 0.412
curvature mean = 0.030, std = 0.334
curvature mean = 0.007, std = 0.506
MRISregister() return, current seed 0
-01: dt=0.0000, 83 negative triangles
131: dt=0.9900, 83 negative triangles
132: dt=0.9900, 63 negative triangles
133: dt=0.9900, 63 negative triangles
134: dt=0.9900, 49 negative triangles
135: dt=0.9900, 45 negative triangles
136: dt=0.9900, 44 negative triangles
137: dt=0.9900, 40 negative triangles
138: dt=0.9900, 36 negative triangles
139: dt=0.9900, 40 negative triangles
140: dt=0.9900, 30 negative triangles
141: dt=0.9900, 30 negative triangles
142: dt=0.9900, 28 negative triangles
143: dt=0.9900, 19 negative triangles
144: dt=0.9900, 26 negative triangles
145: dt=0.9900, 21 negative triangles
146: dt=0.9900, 19 negative triangles
147: dt=0.9900, 18 negative triangles
148: dt=0.9900, 23 negative triangles
149: dt=0.9900, 16 negative triangles
150: dt=0.9900, 11 negative triangles
151: dt=0.9900, 8 negative triangles
152: dt=0.9900, 15 negative triangles
153: dt=0.9900, 8 negative triangles
154: dt=0.9900, 7 negative triangles
155: dt=0.9900, 5 negative triangles
156: dt=0.9900, 3 negative triangles
157: dt=0.9900, 4 negative triangles
158: dt=0.9900, 3 negative triangles
159: dt=0.9900, 3 negative triangles
160: dt=0.9900, 3 negative triangles
161: dt=0.9900, 1 negative triangles
162: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.78 hours
mris_register utimesec    6698.134728
mris_register stimesec    6.318039
mris_register ru_maxrss   318680
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   44478
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  12808
mris_register ru_oublock  12912
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    453870
mris_register ru_nivcsw   264507
FSRUNTIME@ mris_register  1.7821 hours 1 threads
PIDs (9394 9397) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 03:59:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 03:59:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

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

Waiting for PID 15902 of (15902 15905) to complete...
Waiting for PID 15905 of (15902 15905) 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 (15902 15905) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 03:59:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 03:59:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 15950 of (15950 15953) to complete...
Waiting for PID 15953 of (15950 15953) 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 (15950 15953) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 03:59:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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 03:59:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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 15999 of (15999 16002) to complete...
Waiting for PID 16002 of (15999 16002) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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...
2027 labels changed using aseg
relabeling using gibbs priors...
000:   3962 changed, 180195 examined...
001:    921 changed, 16498 examined...
002:    223 changed, 5173 examined...
003:     78 changed, 1355 examined...
004:     40 changed, 461 examined...
005:     29 changed, 238 examined...
006:     16 changed, 159 examined...
007:      7 changed, 93 examined...
008:      5 changed, 36 examined...
009:      3 changed, 32 examined...
010:      2 changed, 14 examined...
011:      0 changed, 9 examined...
330 labels changed using aseg
000: 139 total segments, 95 labels (544 vertices) changed
001: 45 total segments, 4 labels (19 vertices) changed
002: 41 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2178 vertices marked for relabeling...
2178 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 19 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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...
1859 labels changed using aseg
relabeling using gibbs priors...
000:   3535 changed, 182078 examined...
001:    784 changed, 14891 examined...
002:    199 changed, 4406 examined...
003:     63 changed, 1180 examined...
004:     24 changed, 388 examined...
005:      8 changed, 154 examined...
006:      2 changed, 51 examined...
007:      0 changed, 14 examined...
155 labels changed using aseg
000: 121 total segments, 83 labels (375 vertices) changed
001: 41 total segments, 3 labels (16 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2192 vertices marked for relabeling...
2192 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 18 seconds.
PIDs (15999 16002) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 03:59:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050233 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 03:59:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050233 rh 

Waiting for PID 16056 of (16056 16059) to complete...
Waiting for PID 16059 of (16056 16059) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050233 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-6.0.0/0050233/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
36952 bright wm thresholded.
3455 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.orig...
computing class statistics...
border white:    328104 voxels (1.96%)
border gray      385806 voxels (2.30%)
WM (102.0): 101.4 +- 7.7 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 9.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.6 (was 70)
setting MAX_BORDER_WHITE to 114.7 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 54.1 (was 40)
setting MAX_GRAY to 99.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=107+-5.2,    GM=73+-6.1
mean inside = 97.4, mean outside = 79.3
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.24 (0.04-->5.96) (max @ vno 85922 --> 179527)
face area 0.33 +- 0.15 (0.00-->6.05)
mean absolute distance = 0.59 +- 0.77
3188 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 30 points - only 0.00% unknown
deleting segment 1 with 31 points - only 0.00% unknown
deleting segment 2 with 62 points - only 0.00% unknown
deleting segment 6 with 20 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 107 points - only 0.00% unknown
deleting segment 10 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
deleting segment 15 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
mean border=83.2, 102 (102) missing vertices, mean dist 0.4 [0.9 (%10.3)->0.6 (%89.7))]
%68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.08-->6.17) (max @ vno 85922 --> 179527)
face area 0.33 +- 0.15 (0.00-->5.64)
mean absolute distance = 0.32 +- 0.44
3591 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3119893.2, rms=8.041
001: dt: 0.5000, sse=1564065.1, rms=4.488 (44.188%)
002: dt: 0.5000, sse=1189858.8, rms=3.093 (31.077%)
003: dt: 0.5000, sse=1151184.8, rms=2.924 (5.482%)
004: dt: 0.5000, sse=1107375.0, rms=2.716 (7.103%)
rms = 2.90, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=987648.0, rms=1.921 (29.251%)
006: dt: 0.2500, sse=947278.2, rms=1.558 (18.889%)
007: dt: 0.2500, sse=936625.8, rms=1.454 (6.723%)
rms = 1.43, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=938703.4, rms=1.428 (1.767%)
rms = 1.39, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=931791.8, rms=1.394 (2.412%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 24 points - only 0.00% unknown
deleting segment 1 with 19 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 57 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 33 points - only 0.00% unknown
deleting segment 9 with 9 points - only 0.00% unknown
deleting segment 10 with 10 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
mean border=86.9, 54 (16) missing vertices, mean dist -0.2 [0.3 (%81.0)->0.2 (%19.0))]
%84 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.06-->5.98) (max @ vno 85922 --> 179527)
face area 0.35 +- 0.17 (0.00-->6.44)
mean absolute distance = 0.21 +- 0.30
4462 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1717622.2, rms=4.784
010: dt: 0.5000, sse=1197953.9, rms=2.821 (41.032%)
011: dt: 0.5000, sse=1184749.1, rms=2.763 (2.044%)
rms = 2.81, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=1045754.4, rms=1.877 (32.062%)
013: dt: 0.2500, sse=984036.4, rms=1.314 (30.034%)
014: dt: 0.2500, sse=972861.2, rms=1.201 (8.545%)
rms = 1.18, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=972069.6, rms=1.179 (1.886%)
rms = 1.15, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=970497.6, rms=1.145 (2.836%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 24 points - only 0.00% unknown
deleting segment 2 with 56 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 28 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 74 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 14 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
mean border=89.2, 51 (9) missing vertices, mean dist -0.1 [0.2 (%75.8)->0.2 (%24.2))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.09-->6.04) (max @ vno 85922 --> 179527)
face area 0.34 +- 0.16 (0.00-->6.37)
mean absolute distance = 0.16 +- 0.25
3591 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1199380.4, rms=2.993
017: dt: 0.5000, sse=1100960.4, rms=2.426 (18.953%)
rms = 2.71, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=978631.6, rms=1.593 (34.340%)
019: dt: 0.2500, sse=938474.4, rms=1.189 (25.366%)
020: dt: 0.2500, sse=932320.4, rms=1.084 (8.843%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=928931.3, rms=1.081 (0.286%)
rms = 1.05, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=926202.7, rms=1.045 (3.276%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 24 points - only 0.00% unknown
deleting segment 1 with 24 points - only 0.00% unknown
deleting segment 2 with 57 points - only 0.00% unknown
deleting segment 3 with 28 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 90 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 14 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
mean border=89.9, 69 (8) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))]
%93 local maxima, % 4 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-6.0.0/0050233/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=933553.2, rms=1.281
rms = 1.38, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=906368.2, rms=0.924 (27.889%)
024: dt: 0.2500, sse=897281.9, rms=0.776 (16.018%)
rms = 0.80, time step reduction 2 of 3 to 0.125...
rms = 0.78, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=896470.7, rms=0.775 (0.081%)
positioning took 0.6 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7207 vertices
erasing segment 1 (vno[0] = 97541)
erasing segment 2 (vno[0] = 114365)
erasing segment 3 (vno[0] = 117684)
erasing segment 4 (vno[0] = 125893)
erasing segment 5 (vno[0] = 133097)
erasing segment 6 (vno[0] = 134233)
erasing segment 7 (vno[0] = 135207)
erasing segment 8 (vno[0] = 135236)
erasing segment 9 (vno[0] = 162491)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.04-->6.04) (max @ vno 85922 --> 179527)
face area 0.33 +- 0.16 (0.00-->6.33)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.0, 125 (125) missing vertices, mean dist 1.6 [0.3 (%0.0)->2.7 (%100.0))]
%13 local maxima, %44 large gradients and %39 min vals, 253 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=29009356.0, rms=28.423
001: dt: 0.0500, sse=25372630.0, rms=26.523 (6.684%)
002: dt: 0.0500, sse=22791438.0, rms=25.087 (5.413%)
003: dt: 0.0500, sse=20838226.0, rms=23.944 (4.559%)
004: dt: 0.0500, sse=19283424.0, rms=22.993 (3.972%)
005: dt: 0.0500, sse=17998314.0, rms=22.176 (3.553%)
006: dt: 0.0500, sse=16904550.0, rms=21.456 (3.246%)
007: dt: 0.0500, sse=15953797.0, rms=20.810 (3.011%)
008: dt: 0.0500, sse=15115262.0, rms=20.223 (2.821%)
009: dt: 0.0500, sse=14365622.0, rms=19.683 (2.669%)
010: dt: 0.0500, sse=13688945.0, rms=19.183 (2.541%)
positioning took 1.2 minutes
mean border=61.8, 87 (59) missing vertices, mean dist 1.4 [0.2 (%0.0)->2.2 (%100.0))]
%14 local maxima, %44 large gradients and %38 min vals, 242 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=14573724.0, rms=19.837
011: dt: 0.0500, sse=13954769.0, rms=19.384 (2.285%)
012: dt: 0.0500, sse=13388903.0, rms=18.960 (2.187%)
013: dt: 0.0500, sse=12869364.0, rms=18.562 (2.098%)
014: dt: 0.0500, sse=12390848.0, rms=18.188 (2.016%)
015: dt: 0.0500, sse=11949099.0, rms=17.836 (1.938%)
016: dt: 0.0500, sse=11540220.0, rms=17.503 (1.865%)
017: dt: 0.0500, sse=11161402.0, rms=17.189 (1.794%)
018: dt: 0.0500, sse=10809774.0, rms=16.892 (1.727%)
019: dt: 0.0500, sse=10482347.0, rms=16.611 (1.665%)
020: dt: 0.0500, sse=10176963.0, rms=16.344 (1.606%)
positioning took 1.2 minutes
mean border=61.7, 102 (41) missing vertices, mean dist 1.2 [0.1 (%0.4)->1.9 (%99.6))]
%15 local maxima, %44 large gradients and %38 min vals, 205 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=10293806.0, rms=16.455
021: dt: 0.0500, sse=10003542.0, rms=16.199 (1.555%)
022: dt: 0.0500, sse=9731914.0, rms=15.956 (1.502%)
023: dt: 0.0500, sse=9475976.0, rms=15.723 (1.459%)
024: dt: 0.0500, sse=9235338.0, rms=15.501 (1.413%)
025: dt: 0.0500, sse=9008258.0, rms=15.288 (1.372%)
026: dt: 0.0500, sse=8793337.0, rms=15.084 (1.336%)
027: dt: 0.0500, sse=8588277.0, rms=14.886 (1.309%)
028: dt: 0.0500, sse=8391053.0, rms=14.694 (1.294%)
029: dt: 0.0500, sse=8200665.0, rms=14.506 (1.282%)
030: dt: 0.0500, sse=8016489.0, rms=14.321 (1.273%)
positioning took 1.2 minutes
mean border=61.6, 142 (36) missing vertices, mean dist 1.0 [0.1 (%4.6)->1.7 (%95.4))]
%15 local maxima, %44 large gradients and %38 min vals, 217 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=8105460.5, rms=14.413
031: dt: 0.5000, sse=6747732.5, rms=12.981 (9.940%)
032: dt: 0.5000, sse=5697461.0, rms=11.747 (9.503%)
033: dt: 0.5000, sse=4812393.5, rms=10.598 (9.782%)
034: dt: 0.5000, sse=4068180.8, rms=9.520 (10.172%)
035: dt: 0.5000, sse=3424856.2, rms=8.480 (10.921%)
036: dt: 0.5000, sse=2878102.0, rms=7.482 (11.771%)
037: dt: 0.5000, sse=2416704.0, rms=6.527 (12.766%)
038: dt: 0.5000, sse=2084203.4, rms=5.738 (12.083%)
039: dt: 0.5000, sse=1872962.1, rms=5.179 (9.743%)
040: dt: 0.5000, sse=1756418.2, rms=4.840 (6.552%)
041: dt: 0.5000, sse=1688197.2, rms=4.633 (4.278%)
042: dt: 0.5000, sse=1656377.9, rms=4.529 (2.241%)
043: dt: 0.5000, sse=1631159.2, rms=4.450 (1.745%)
rms = 4.41, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1620270.8, rms=4.411 (0.877%)
045: dt: 0.2500, sse=1471820.4, rms=3.836 (13.033%)
046: dt: 0.2500, sse=1430725.9, rms=3.676 (4.176%)
rms = 3.67, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1430856.8, rms=3.672 (0.099%)
048: dt: 0.1250, sse=1406990.9, rms=3.570 (2.778%)
rms = 3.55, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1403322.1, rms=3.555 (0.431%)
positioning took 3.2 minutes
mean border=60.5, 3047 (11) missing vertices, mean dist 0.1 [0.2 (%45.7)->0.4 (%54.3))]
%28 local maxima, %32 large gradients and %34 min vals, 131 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=1786160.2, rms=4.117
050: dt: 0.5000, sse=1718985.1, rms=3.885 (5.633%)
rms = 3.85, time step reduction 1 of 3 to 0.250...
051: dt: 0.5000, sse=1700512.6, rms=3.855 (0.767%)
052: dt: 0.2500, sse=1544586.0, rms=3.139 (18.569%)
053: dt: 0.2500, sse=1506669.6, rms=2.960 (5.708%)
rms = 2.93, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1501795.0, rms=2.933 (0.902%)
055: dt: 0.1250, sse=1472804.0, rms=2.776 (5.355%)
rms = 2.75, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1467035.1, rms=2.747 (1.040%)
positioning took 1.4 minutes
mean border=59.5, 3313 (7) missing vertices, mean dist 0.1 [0.1 (%41.9)->0.3 (%58.1))]
%44 local maxima, %18 large gradients and %33 min vals, 116 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=1550671.9, rms=3.157
rms = 3.58, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1496416.6, rms=2.887 (8.547%)
058: dt: 0.2500, sse=1481820.4, rms=2.812 (2.602%)
rms = 2.82, time step reduction 2 of 3 to 0.125...
rms = 2.78, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1476129.9, rms=2.780 (1.140%)
positioning took 0.9 minutes
mean border=59.0, 6286 (6) missing vertices, mean dist 0.0 [0.2 (%45.7)->0.2 (%54.3))]
%47 local maxima, %14 large gradients and %32 min vals, 115 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-6.0.0/0050233/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1501083.4, rms=2.914
rms = 3.27, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1475210.5, rms=2.777 (4.719%)
061: dt: 0.2500, sse=1459936.2, rms=2.712 (2.330%)
rms = 2.71, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1456978.5, rms=2.706 (0.204%)
063: dt: 0.1250, sse=1437149.5, rms=2.594 (4.144%)
rms = 2.57, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1431250.6, rms=2.567 (1.052%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.area.pial
vertex spacing 1.00 +- 0.43 (0.07-->9.48) (max @ vno 85922 --> 179527)
face area 0.40 +- 0.31 (0.00-->7.51)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 180195 vertices processed
25000 of 180195 vertices processed
50000 of 180195 vertices processed
75000 of 180195 vertices processed
100000 of 180195 vertices processed
125000 of 180195 vertices processed
150000 of 180195 vertices processed
175000 of 180195 vertices processed
0 of 180195 vertices processed
25000 of 180195 vertices processed
50000 of 180195 vertices processed
75000 of 180195 vertices processed
100000 of 180195 vertices processed
125000 of 180195 vertices processed
150000 of 180195 vertices processed
175000 of 180195 vertices processed
thickness calculation complete, 254:529 truncations.
41719 vertices at 0 distance
129122 vertices at 1 distance
112852 vertices at 2 distance
44918 vertices at 3 distance
13632 vertices at 4 distance
4161 vertices at 5 distance
1310 vertices at 6 distance
389 vertices at 7 distance
155 vertices at 8 distance
83 vertices at 9 distance
52 vertices at 10 distance
42 vertices at 11 distance
24 vertices at 12 distance
21 vertices at 13 distance
32 vertices at 14 distance
22 vertices at 15 distance
17 vertices at 16 distance
10 vertices at 17 distance
17 vertices at 18 distance
18 vertices at 19 distance
12 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.thickness
positioning took 19.3 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050233 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-6.0.0/0050233/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
36952 bright wm thresholded.
3455 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.orig...
computing class statistics...
border white:    328104 voxels (1.96%)
border gray      385806 voxels (2.30%)
WM (102.0): 101.4 +- 7.7 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 9.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.6 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 54.1 (was 40)
setting MAX_GRAY to 98.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=73+-6.1
mean inside = 97.3, mean outside = 79.2
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 0.89 +- 0.24 (0.03-->5.76) (max @ vno 93693 --> 95005)
face area 0.33 +- 0.15 (0.00-->4.75)
mean absolute distance = 0.59 +- 0.76
3509 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 16 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 71 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 40 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
deleting segment 11 with 35 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
mean border=83.2, 127 (127) missing vertices, mean dist 0.4 [0.8 (%10.5)->0.6 (%89.5))]
%69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.09-->5.76) (max @ vno 95005 --> 93693)
face area 0.33 +- 0.15 (0.00-->4.77)
mean absolute distance = 0.31 +- 0.44
3739 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3075875.5, rms=7.924
001: dt: 0.5000, sse=1567961.5, rms=4.465 (43.649%)
002: dt: 0.5000, sse=1200124.2, rms=3.110 (30.344%)
003: dt: 0.5000, sse=1164630.9, rms=2.957 (4.922%)
004: dt: 0.5000, sse=1118874.2, rms=2.741 (7.308%)
rms = 2.94, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=996022.8, rms=1.941 (29.186%)
006: dt: 0.2500, sse=955292.6, rms=1.585 (18.362%)
007: dt: 0.2500, sse=945425.2, rms=1.483 (6.433%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=943502.1, rms=1.458 (1.663%)
rms = 1.42, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=940200.2, rms=1.424 (2.300%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 54 points - only 0.00% unknown
deleting segment 2 with 22 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 22 points - only 0.00% unknown
mean border=86.9, 77 (30) missing vertices, mean dist -0.2 [0.3 (%80.7)->0.2 (%19.3))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.09-->5.94) (max @ vno 95005 --> 93693)
face area 0.35 +- 0.16 (0.00-->5.34)
mean absolute distance = 0.20 +- 0.29
3994 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1702831.6, rms=4.700
010: dt: 0.5000, sse=1211428.0, rms=2.834 (39.705%)
rms = 2.80, time step reduction 1 of 3 to 0.250...
011: dt: 0.5000, sse=1204084.8, rms=2.801 (1.144%)
012: dt: 0.2500, sse=1010502.9, rms=1.508 (46.165%)
013: dt: 0.2500, sse=986470.8, rms=1.255 (16.794%)
rms = 1.21, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=983018.6, rms=1.207 (3.812%)
015: dt: 0.1250, sse=977287.5, rms=1.156 (4.205%)
rms = 1.16, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=977467.7, rms=1.157 (-0.044%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 0.00% unknown
deleting segment 1 with 57 points - only 0.00% unknown
deleting segment 2 with 24 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 27 points - only 0.00% unknown
mean border=89.1, 80 (19) missing vertices, mean dist -0.1 [0.2 (%75.7)->0.2 (%24.3))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.03-->5.95) (max @ vno 95005 --> 93693)
face area 0.34 +- 0.16 (0.00-->4.99)
mean absolute distance = 0.16 +- 0.25
3314 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1189398.1, rms=2.911
017: dt: 0.5000, sse=1112542.5, rms=2.427 (16.623%)
rms = 2.72, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=986156.8, rms=1.590 (34.507%)
019: dt: 0.2500, sse=946469.6, rms=1.196 (24.775%)
020: dt: 0.2500, sse=937298.4, rms=1.091 (8.788%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
rms = 1.07, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=935165.0, rms=1.071 (1.804%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 0.00% unknown
deleting segment 1 with 68 points - only 0.00% unknown
deleting segment 2 with 27 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 24 points - only 0.00% unknown
mean border=89.8, 97 (17) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))]
%92 local maxima, % 4 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-6.0.0/0050233/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=942751.6, rms=1.305
rms = 1.50, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=914211.1, rms=0.933 (28.543%)
023: dt: 0.2500, sse=919878.2, rms=0.802 (13.977%)
rms = 0.82, time step reduction 2 of 3 to 0.125...
rms = 0.79, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=904975.7, rms=0.795 (0.925%)
positioning took 0.6 minutes
generating cortex label...
18 non-cortical segments detected
only using segment with 8414 vertices
erasing segment 1 (vno[0] = 82785)
erasing segment 2 (vno[0] = 93280)
erasing segment 3 (vno[0] = 99047)
erasing segment 4 (vno[0] = 114037)
erasing segment 5 (vno[0] = 126720)
erasing segment 6 (vno[0] = 126744)
erasing segment 7 (vno[0] = 128046)
erasing segment 8 (vno[0] = 131728)
erasing segment 9 (vno[0] = 132872)
erasing segment 10 (vno[0] = 133840)
erasing segment 11 (vno[0] = 133910)
erasing segment 12 (vno[0] = 134754)
erasing segment 13 (vno[0] = 134985)
erasing segment 14 (vno[0] = 135921)
erasing segment 15 (vno[0] = 138158)
erasing segment 16 (vno[0] = 142279)
erasing segment 17 (vno[0] = 161318)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.03-->6.00) (max @ vno 93693 --> 95005)
face area 0.33 +- 0.16 (0.00-->4.96)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.1, 138 (138) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.8 (%100.0))]
%12 local maxima, %42 large gradients and %42 min vals, 191 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=28891258.0, rms=28.276
001: dt: 0.0500, sse=25251914.0, rms=26.376 (6.719%)
002: dt: 0.0500, sse=22665218.0, rms=24.937 (5.453%)
003: dt: 0.0500, sse=20709580.0, rms=23.792 (4.592%)
004: dt: 0.0500, sse=19154064.0, rms=22.840 (4.001%)
005: dt: 0.0500, sse=17868768.0, rms=22.022 (3.580%)
006: dt: 0.0500, sse=16777522.0, rms=21.303 (3.265%)
007: dt: 0.0500, sse=15829007.0, rms=20.658 (3.029%)
008: dt: 0.0500, sse=14991434.0, rms=20.071 (2.842%)
009: dt: 0.0500, sse=14243562.0, rms=19.532 (2.687%)
010: dt: 0.0500, sse=13568784.0, rms=19.032 (2.558%)
positioning took 1.3 minutes
mean border=61.9, 109 (67) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.3 (%100.0))]
%13 local maxima, %42 large gradients and %41 min vals, 180 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=14458717.0, rms=19.691
011: dt: 0.0500, sse=13841759.0, rms=19.239 (2.298%)
012: dt: 0.0500, sse=13278549.0, rms=18.816 (2.197%)
013: dt: 0.0500, sse=12761413.0, rms=18.419 (2.108%)
014: dt: 0.0500, sse=12285202.0, rms=18.046 (2.025%)
015: dt: 0.0500, sse=11846629.0, rms=17.696 (1.943%)
016: dt: 0.0500, sse=11441323.0, rms=17.365 (1.867%)
017: dt: 0.0500, sse=11066387.0, rms=17.054 (1.793%)
018: dt: 0.0500, sse=10718978.0, rms=16.760 (1.723%)
019: dt: 0.0500, sse=10396102.0, rms=16.482 (1.658%)
020: dt: 0.0500, sse=10095702.0, rms=16.219 (1.595%)
positioning took 1.3 minutes
mean border=61.8, 106 (48) missing vertices, mean dist 1.1 [0.1 (%0.5)->2.0 (%99.5))]
%14 local maxima, %42 large gradients and %41 min vals, 199 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=10237576.0, rms=16.353
021: dt: 0.0500, sse=9951591.0, rms=16.100 (1.543%)
022: dt: 0.0500, sse=9684792.0, rms=15.861 (1.485%)
023: dt: 0.0500, sse=9434093.0, rms=15.633 (1.438%)
024: dt: 0.0500, sse=9198970.0, rms=15.416 (1.388%)
025: dt: 0.0500, sse=8977746.0, rms=15.209 (1.343%)
026: dt: 0.0500, sse=8768385.0, rms=15.010 (1.307%)
027: dt: 0.0500, sse=8569107.0, rms=14.819 (1.277%)
028: dt: 0.0500, sse=8377759.0, rms=14.632 (1.259%)
029: dt: 0.0500, sse=8193225.0, rms=14.450 (1.246%)
030: dt: 0.0500, sse=8014741.5, rms=14.271 (1.236%)
positioning took 1.3 minutes
mean border=61.7, 121 (34) missing vertices, mean dist 1.0 [0.1 (%5.0)->1.7 (%95.0))]
%14 local maxima, %42 large gradients and %40 min vals, 163 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=8124087.0, rms=14.384
031: dt: 0.5000, sse=6798548.5, rms=12.992 (9.673%)
032: dt: 0.5000, sse=5768933.0, rms=11.793 (9.234%)
033: dt: 0.5000, sse=4918915.0, rms=10.702 (9.250%)
034: dt: 0.5000, sse=4202280.0, rms=9.683 (9.523%)
035: dt: 0.5000, sse=3578641.5, rms=8.700 (10.144%)
036: dt: 0.5000, sse=3036239.0, rms=7.745 (10.980%)
037: dt: 0.5000, sse=2567245.0, rms=6.817 (11.986%)
038: dt: 0.5000, sse=2218557.2, rms=6.032 (11.506%)
039: dt: 0.5000, sse=1980379.8, rms=5.436 (9.894%)
040: dt: 0.5000, sse=1842393.8, rms=5.054 (7.022%)
041: dt: 0.5000, sse=1758488.9, rms=4.811 (4.808%)
042: dt: 0.5000, sse=1718550.1, rms=4.686 (2.588%)
043: dt: 0.5000, sse=1691715.5, rms=4.604 (1.757%)
044: dt: 0.5000, sse=1676238.1, rms=4.552 (1.124%)
rms = 4.52, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1665144.1, rms=4.519 (0.736%)
046: dt: 0.2500, sse=1523557.1, rms=3.985 (11.822%)
047: dt: 0.2500, sse=1482610.2, rms=3.834 (3.787%)
rms = 3.83, time step reduction 2 of 3 to 0.125...
rms = 3.79, time step reduction 3 of 3 to 0.062...
048: dt: 0.1250, sse=1472126.8, rms=3.791 (1.118%)
positioning took 3.2 minutes
mean border=60.6, 3254 (16) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))]
%26 local maxima, %32 large gradients and %37 min vals, 98 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=1864015.6, rms=4.321
049: dt: 0.5000, sse=1795267.0, rms=4.099 (5.144%)
050: dt: 0.5000, sse=1765559.2, rms=4.027 (1.746%)
rms = 4.20, time step reduction 1 of 3 to 0.250...
051: dt: 0.2500, sse=1624143.6, rms=3.430 (14.812%)
052: dt: 0.2500, sse=1590421.2, rms=3.265 (4.836%)
rms = 3.26, time step reduction 2 of 3 to 0.125...
053: dt: 0.2500, sse=1589173.4, rms=3.258 (0.194%)
054: dt: 0.1250, sse=1560133.1, rms=3.116 (4.353%)
rms = 3.09, time step reduction 3 of 3 to 0.062...
055: dt: 0.1250, sse=1554977.1, rms=3.093 (0.746%)
positioning took 1.6 minutes
mean border=59.8, 3467 (11) missing vertices, mean dist 0.1 [0.1 (%43.2)->0.3 (%56.8))]
%41 local maxima, %18 large gradients and %36 min vals, 101 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=1629673.1, rms=3.438
rms = 3.80, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1580770.6, rms=3.218 (6.375%)
057: dt: 0.2500, sse=1566628.2, rms=3.156 (1.926%)
rms = 3.17, time step reduction 2 of 3 to 0.125...
rms = 3.13, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1561001.8, rms=3.128 (0.892%)
positioning took 0.9 minutes
mean border=59.2, 7073 (10) missing vertices, mean dist 0.0 [0.1 (%45.3)->0.2 (%54.7))]
%44 local maxima, %14 large gradients and %34 min vals, 100 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-6.0.0/0050233/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1583725.2, rms=3.235
rms = 3.52, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1555524.8, rms=3.103 (4.090%)
060: dt: 0.2500, sse=1534346.6, rms=3.021 (2.648%)
rms = 3.00, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1528381.9, rms=3.002 (0.623%)
062: dt: 0.1250, sse=1504307.5, rms=2.881 (4.033%)
rms = 2.85, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1496912.1, rms=2.848 (1.155%)
positioning took 1.3 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.area.pial
vertex spacing 1.00 +- 0.43 (0.04-->7.35) (max @ vno 77190 --> 78506)
face area 0.40 +- 0.31 (0.00-->6.46)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 182078 vertices processed
25000 of 182078 vertices processed
50000 of 182078 vertices processed
75000 of 182078 vertices processed
100000 of 182078 vertices processed
125000 of 182078 vertices processed
150000 of 182078 vertices processed
175000 of 182078 vertices processed
0 of 182078 vertices processed
25000 of 182078 vertices processed
50000 of 182078 vertices processed
75000 of 182078 vertices processed
100000 of 182078 vertices processed
125000 of 182078 vertices processed
150000 of 182078 vertices processed
175000 of 182078 vertices processed
thickness calculation complete, 413:865 truncations.
42073 vertices at 0 distance
128388 vertices at 1 distance
112321 vertices at 2 distance
46527 vertices at 3 distance
14593 vertices at 4 distance
4356 vertices at 5 distance
1348 vertices at 6 distance
487 vertices at 7 distance
180 vertices at 8 distance
117 vertices at 9 distance
84 vertices at 10 distance
52 vertices at 11 distance
47 vertices at 12 distance
41 vertices at 13 distance
35 vertices at 14 distance
18 vertices at 15 distance
17 vertices at 16 distance
18 vertices at 17 distance
13 vertices at 18 distance
20 vertices at 19 distance
19 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.thickness
positioning took 19.6 minutes
PIDs (16056 16059) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 04:19:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/lh.cortex.label
Total face volume 335316
Total vertex volume 331805 (mask=0)
#@# 0050233 lh 331805
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 04:19:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/rh.cortex.label
Total face volume 336476
Total vertex volume 332585 (mask=0)
#@# 0050233 rh 332585
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 04:19:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 

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 = 170
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/ribbon.mgz
mris_volmask took 27.21 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 04:46:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 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 0050233 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 04:46:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 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 0050233 rh pial 

Waiting for PID 18142 of (18142 18161 18165 18168) to complete...
Waiting for PID 18161 of (18142 18161 18165 18168) to complete...
Waiting for PID 18165 of (18142 18161 18165 18168) to complete...
Waiting for PID 18168 of (18142 18161 18165 18168) 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 0050233 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 335316
Total vertex volume 331805 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1779   1289   3166  2.634 0.340     0.104     0.018       11     1.4  bankssts
 1683   1112   3352  2.619 0.761     0.141     0.033       35     2.3  caudalanteriorcingulate
 4948   3262   9305  2.593 0.495     0.113     0.019       53     3.6  caudalmiddlefrontal
 3112   1953   4250  2.098 0.514     0.141     0.034       44     4.4  cuneus
  892    614   2271  2.994 0.799     0.121     0.030        9     1.2  entorhinal
 6629   4415  14088  2.830 0.511     0.123     0.025       86     6.6  fusiform
 8781   5851  16298  2.617 0.450     0.128     0.025      122     8.3  inferiorparietal
 7248   4905  15876  2.891 0.602     0.130     0.031      114     8.8  inferiortemporal
 2022   1254   3443  2.590 0.784     0.129     0.034       32     2.4  isthmuscingulate
10633   6749  17603  2.289 0.572     0.142     0.036      162    15.2  lateraloccipital
 4440   2971   9304  2.818 0.645     0.143     0.036       76     6.2  lateralorbitofrontal
 6269   4016   9820  2.265 0.638     0.140     0.033       93     8.1  lingual
 3176   2143   5934  2.442 0.692     0.114     0.027       45     3.1  medialorbitofrontal
 6301   4299  14807  2.879 0.523     0.129     0.025       96     6.5  middletemporal
 1059    663   2087  2.805 0.791     0.089     0.019        8     0.7  parahippocampal
 2855   1842   5142  2.583 0.510     0.105     0.019       21     2.1  paracentral
 3129   2087   6596  2.811 0.440     0.120     0.021       38     2.6  parsopercularis
 1276    837   3101  2.946 0.475     0.149     0.037       23     1.7  parsorbitalis
 2529   1684   5120  2.627 0.442     0.111     0.019       27     1.9  parstriangularis
 2591   1785   2616  1.738 0.513     0.138     0.032       26     3.4  pericalcarine
 8085   5092  12313  2.162 0.570     0.116     0.025       92     8.0  postcentral
 2599   1726   5356  2.820 0.765     0.136     0.027       44     2.7  posteriorcingulate
 9756   6157  18236  2.682 0.487     0.106     0.023       94     9.8  precentral
 8213   5518  14893  2.593 0.458     0.126     0.025      108     8.5  precuneus
 1940   1264   3949  2.784 0.659     0.145     0.037       42     3.0  rostralanteriorcingulate
10910   7360  21042  2.473 0.496     0.138     0.031      195    14.2  rostralmiddlefrontal
13595   9117  28774  2.811 0.554     0.120     0.024      154    12.7  superiorfrontal
10823   7098  19196  2.407 0.463     0.121     0.022      132     9.1  superiorparietal
 8978   5985  20119  2.980 0.559     0.112     0.021       99     7.5  superiortemporal
 9712   6553  18880  2.593 0.450     0.125     0.023      130     8.7  supramarginal
  492    322   1258  2.752 0.697     0.174     0.067       14     1.4  frontalpole
  845    574   3081  3.634 0.778     0.129     0.027        9     1.0  temporalpole
 1234    658   2075  2.691 0.448     0.102     0.030       13     1.6  transversetemporal
 4126   2727   8426  3.142 0.592     0.115     0.034       49     5.4  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 0050233 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 335316
Total vertex volume 331805 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1779   1111   3166  2.634 0.340     0.120     0.033       22     2.5  bankssts
 1683   1397   3352  2.619 0.761     0.170     0.051       33     4.6  caudalanteriorcingulate
 4948   3843   9305  2.593 0.495     0.130     0.026       62     5.7  caudalmiddlefrontal
 3112   2196   4250  2.098 0.514     0.134     0.034       50     4.5  cuneus
  892    841   2271  2.994 0.799     0.158     0.036       21     1.4  entorhinal
 6629   5504  14088  2.830 0.511     0.142     0.034       99    10.5  fusiform
 8781   6547  16298  2.617 0.450     0.137     0.032      134    11.8  inferiorparietal
 7248   6033  15876  2.891 0.602     0.144     0.037       96    12.1  inferiortemporal
 2022   1422   3443  2.590 0.784     0.141     0.038       48     3.1  isthmuscingulate
10633   8369  17603  2.289 0.572     0.145     0.035      149    16.6  lateraloccipital
 4440   3562   9304  2.818 0.645     0.159     0.041       83     8.4  lateralorbitofrontal
 6269   4853   9820  2.265 0.638     0.140     0.034       83     9.8  lingual
 3176   2734   5934  2.442 0.692     0.147     0.033       43     4.5  medialorbitofrontal
 6301   5888  14807  2.879 0.523     0.155     0.032       83     9.0  middletemporal
 1059    873   2087  2.805 0.791     0.136     0.032       12     1.7  parahippocampal
 2855   2097   5142  2.583 0.510     0.118     0.025       29     3.1  paracentral
 3129   2580   6596  2.811 0.440     0.142     0.030       41     4.1  parsopercularis
 1276   1244   3101  2.946 0.475     0.167     0.033       16     1.9  parsorbitalis
 2529   2123   5120  2.627 0.442     0.138     0.027       30     3.1  parstriangularis
 2591   1362   2616  1.738 0.513     0.103     0.027       54     2.9  pericalcarine
 8085   6292  12313  2.162 0.570     0.127     0.027       79     9.2  postcentral
 2599   2057   5356  2.820 0.765     0.157     0.041       68     4.7  posteriorcingulate
 9756   7257  18236  2.682 0.487     0.117     0.023      112    10.1  precentral
 8213   5954  14893  2.593 0.458     0.132     0.032      108    11.2  precuneus
 1940   1633   3949  2.784 0.659     0.159     0.080       45     9.7  rostralanteriorcingulate
10910   9350  21042  2.473 0.496     0.158     0.033      192    16.3  rostralmiddlefrontal
13595  10839  28774  2.811 0.554     0.135     0.030      176    17.1  superiorfrontal
10823   8639  19196  2.407 0.463     0.139     0.030      153    15.6  superiorparietal
 8978   7255  20119  2.980 0.559     0.137     0.032      128    12.6  superiortemporal
 9712   7941  18880  2.593 0.450     0.141     0.030      139    12.7  supramarginal
  492    530   1258  2.752 0.697     0.166     0.030        4     0.6  frontalpole
  845   1110   3081  3.634 0.778     0.208     0.043       16     2.0  temporalpole
 1234    953   2075  2.691 0.448     0.125     0.033       10     1.7  transversetemporal
 4126   2630   8426  3.142 0.592     0.138     0.047       96     8.9  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 0050233 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 336476
Total vertex volume 332585 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1658   1194   3238  2.874 0.420     0.120     0.021       15     1.4  bankssts
 1976   1300   3856  2.578 0.663     0.128     0.027       30     2.0  caudalanteriorcingulate
 4830   3265  10365  2.768 0.492     0.119     0.022       55     4.1  caudalmiddlefrontal
 3412   2122   4461  2.008 0.495     0.147     0.033       54     4.7  cuneus
  750    494   2060  3.142 1.059     0.132     0.053       10     1.3  entorhinal
 6506   4230  13320  2.805 0.581     0.124     0.030       86     8.2  fusiform
11990   8071  22943  2.548 0.484     0.129     0.026      177    13.3  inferiorparietal
 6941   4648  14839  2.795 0.587     0.125     0.029      111     7.7  inferiortemporal
 1632   1066   3011  2.424 0.811     0.129     0.027       25     1.6  isthmuscingulate
 9912   6391  16738  2.269 0.548     0.137     0.031      143    11.9  lateraloccipital
 4074   2688   8409  2.906 0.610     0.136     0.041       79     6.0  lateralorbitofrontal
 7174   4528  11136  2.299 0.663     0.144     0.038      112    10.9  lingual
 3327   2215   6322  2.560 0.632     0.136     0.037      110     5.3  medialorbitofrontal
 7178   4910  16975  2.946 0.588     0.129     0.026      118     7.2  middletemporal
 1266    802   2514  2.673 0.632     0.102     0.036       22     1.8  parahippocampal
 3229   2140   5599  2.451 0.464     0.104     0.017       26     2.2  paracentral
 3029   2071   6308  2.845 0.457     0.115     0.019       33     2.3  parsopercularis
 1431    940   3400  2.881 0.590     0.142     0.026       25     1.6  parsorbitalis
 3272   2156   6679  2.754 0.508     0.129     0.027       53     3.5  parstriangularis
 3356   2182   3600  1.853 0.538     0.106     0.021       24     2.9  pericalcarine
 7654   4937  11636  2.122 0.606     0.106     0.021       74     6.4  postcentral
 2627   1739   4901  2.562 0.795     0.134     0.026       40     2.6  posteriorcingulate
 9418   5834  17894  2.748 0.467     0.101     0.018       83     6.9  precentral
 8886   5938  15722  2.517 0.486     0.130     0.027      124    10.1  precuneus
 1341    901   3038  2.841 0.479     0.130     0.025       23     1.3  rostralanteriorcingulate
11242   7591  21448  2.477 0.484     0.137     0.031      187    13.8  rostralmiddlefrontal
12974   8760  27761  2.832 0.514     0.123     0.024      146    12.2  superiorfrontal
10352   6758  17548  2.328 0.463     0.129     0.025      139    10.2  superiorparietal
 7961   5242  18602  3.172 0.562     0.115     0.021       94     6.3  superiortemporal
 7181   4865  13312  2.540 0.459     0.125     0.026      101     7.2  supramarginal
  546    344   1389  2.820 0.546     0.161     0.056       15     1.3  frontalpole
  699    463   2437  4.055 0.622     0.130     0.029        9     0.8  temporalpole
  831    485   1438  2.639 0.458     0.107     0.019        7     0.6  transversetemporal
 4689   3114   9641  2.979 0.731     0.115     0.037      111     5.6  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 0050233 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 336476
Total vertex volume 332585 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1658   1066   3238  2.874 0.420     0.131     0.037       23     2.8  bankssts
 1976   1629   3856  2.578 0.663     0.154     0.041       38     3.4  caudalanteriorcingulate
 4830   4006  10365  2.768 0.492     0.134     0.029       65     5.9  caudalmiddlefrontal
 3412   2445   4461  2.008 0.495     0.139     0.032       46     5.2  cuneus
  750    684   2060  3.142 1.059     0.151     0.035       14     1.2  entorhinal
 6506   5199  13320  2.805 0.581     0.141     0.034       96    10.2  fusiform
11990   9787  22943  2.548 0.484     0.148     0.034      167    18.1  inferiorparietal
 6941   5896  14839  2.795 0.587     0.148     0.036      112    11.5  inferiortemporal
 1632   1344   3011  2.424 0.811     0.151     0.037       33     2.5  isthmuscingulate
 9912   8199  16738  2.269 0.548     0.154     0.035      160    15.8  lateraloccipital
 4074   3175   8409  2.906 0.610     0.160     0.044       83     8.3  lateralorbitofrontal
 7174   5304  11136  2.299 0.663     0.137     0.037      135    11.5  lingual
 3327   2745   6322  2.560 0.632     0.152     0.042       66     6.6  medialorbitofrontal
 7178   6503  16975  2.946 0.588     0.149     0.031       98    10.1  middletemporal
 1266    991   2514  2.673 0.632     0.131     0.038       19     2.5  parahippocampal
 3229   2342   5599  2.451 0.464     0.120     0.023       37     3.4  paracentral
 3029   2390   6308  2.845 0.457     0.133     0.032       34     4.2  parsopercularis
 1431   1393   3400  2.881 0.590     0.167     0.031       18     2.2  parsorbitalis
 3272   2721   6679  2.754 0.508     0.148     0.034       44     4.8  parstriangularis
 3356   1914   3600  1.853 0.538     0.100     0.024       46     3.6  pericalcarine
 7654   6039  11636  2.122 0.606     0.127     0.027       88     9.2  postcentral
 2627   1978   4901  2.562 0.795     0.154     0.040       49     4.8  posteriorcingulate
 9418   6913  17894  2.748 0.467     0.109     0.023       96     9.4  precentral
 8886   6626  15722  2.517 0.486     0.139     0.032      133    13.1  precuneus
 1341   1266   3038  2.841 0.479     0.170     0.042       35     2.4  rostralanteriorcingulate
11242   9541  21448  2.477 0.484     0.157     0.033      154    16.8  rostralmiddlefrontal
12974  10423  27761  2.832 0.514     0.136     0.030      167    17.2  superiorfrontal
10352   8210  17548  2.328 0.463     0.143     0.030      143    13.2  superiorparietal
 7961   6536  18602  3.172 0.562     0.140     0.034      101    12.1  superiortemporal
 7181   5602  13312  2.540 0.459     0.140     0.032      100    10.2  supramarginal
  546    575   1389  2.820 0.546     0.179     0.040        6     0.9  frontalpole
  699    728   2437  4.055 0.622     0.180     0.045       14     1.6  temporalpole
  831    608   1438  2.639 0.458     0.114     0.031        6     1.2  transversetemporal
 4689   3172   9641  2.979 0.731     0.149     0.243      391    46.9  insula
PIDs (18142 18161 18165 18168) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 04:48:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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 04:48:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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 18309 of (18309 18312) to complete...
Waiting for PID 18312 of (18309 18312) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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...
41 labels changed using aseg
relabeling using gibbs priors...
000:  11894 changed, 180195 examined...
001:   2847 changed, 46451 examined...
002:    875 changed, 14713 examined...
003:    349 changed, 4909 examined...
004:    166 changed, 2036 examined...
005:     88 changed, 924 examined...
006:     47 changed, 506 examined...
007:     17 changed, 276 examined...
008:      1 changed, 96 examined...
009:      1 changed, 7 examined...
010:      0 changed, 7 examined...
6 labels changed using aseg
000: 341 total segments, 261 labels (3738 vertices) changed
001: 92 total segments, 13 labels (56 vertices) changed
002: 79 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 62 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1195 vertices marked for relabeling...
1195 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 25 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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...
0 labels changed using aseg
relabeling using gibbs priors...
000:  11592 changed, 182078 examined...
001:   2673 changed, 45544 examined...
002:    817 changed, 14273 examined...
003:    363 changed, 4603 examined...
004:    183 changed, 2028 examined...
005:     87 changed, 1013 examined...
006:     31 changed, 486 examined...
007:     22 changed, 186 examined...
008:     11 changed, 131 examined...
009:      5 changed, 58 examined...
010:      3 changed, 29 examined...
011:      2 changed, 13 examined...
012:      1 changed, 12 examined...
013:      0 changed, 5 examined...
0 labels changed using aseg
000: 272 total segments, 186 labels (4046 vertices) changed
001: 96 total segments, 11 labels (41 vertices) changed
002: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 41 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1481 vertices marked for relabeling...
1481 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 25 seconds.
PIDs (18309 18312) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 04:48:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 04:48:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 rh white 

Waiting for PID 18420 of (18420 18423) to complete...
Waiting for PID 18423 of (18420 18423) 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 0050233 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 335316
Total vertex volume 331805 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1409    942   2665  2.574 0.533     0.161     0.042       28     2.9  G&S_frontomargin
 2446   1585   4821  2.474 0.591     0.141     0.035       43     3.3  G&S_occipital_inf
 2375   1400   4019  2.393 0.498     0.113     0.026       27     2.7  G&S_paracentral
 1939   1261   3934  2.669 0.415     0.129     0.023       27     1.8  G&S_subcentral
 1094    711   2438  2.529 0.626     0.168     0.055       30     2.4  G&S_transv_frontopol
 3101   2086   5923  2.613 0.505     0.119     0.022       40     2.8  G&S_cingul-Ant
 1758   1197   3488  2.882 0.535     0.118     0.027       22     1.9  G&S_cingul-Mid-Ant
 1986   1335   3974  2.846 0.531     0.119     0.023       24     1.8  G&S_cingul-Mid-Post
  921    594   2483  3.268 0.460     0.150     0.040       18     1.4  G_cingul-Post-dorsal
  440    238    832  2.986 0.521     0.127     0.035        7     0.5  G_cingul-Post-ventral
 2852   1763   3936  2.023 0.570     0.148     0.036       43     4.4  G_cuneus
 1681   1077   4193  2.928 0.443     0.126     0.025       28     1.6  G_front_inf-Opercular
  405    254   1142  3.165 0.429     0.155     0.033        9     0.4  G_front_inf-Orbital
 1636   1060   4009  2.784 0.429     0.130     0.024       26     1.5  G_front_inf-Triangul
 6302   4153  14705  2.643 0.514     0.134     0.028      125     6.9  G_front_middle
 8433   5600  21407  3.036 0.535     0.132     0.028      125     9.2  G_front_sup
 1021    667   2354  3.314 0.541     0.119     0.046       16     1.5  G_Ins_lg&S_cent_ins
  967    581   2635  3.423 0.713     0.129     0.047       21     1.9  G_insular_short
 3167   2001   6483  2.607 0.548     0.147     0.036       64     4.6  G_occipital_middle
 1944   1227   3734  2.383 0.569     0.134     0.037       26     2.5  G_occipital_sup
 2614   1653   6270  2.971 0.466     0.129     0.030       45     2.9  G_oc-temp_lat-fusifor
 4934   3057   7708  2.147 0.673     0.148     0.037       83     7.4  G_oc-temp_med-Lingual
 1744   1120   4308  2.962 0.814     0.116     0.030       22     2.0  G_oc-temp_med-Parahip
 2888   1883   7222  2.848 0.651     0.152     0.044       70     4.9  G_orbital
 4105   2676   9641  2.799 0.484     0.144     0.029       82     4.5  G_pariet_inf-Angular
 4239   2829   9547  2.699 0.485     0.134     0.025       70     4.1  G_pariet_inf-Supramar
 3669   2371   8295  2.595 0.465     0.131     0.025       66     3.6  G_parietal_sup
 3146   1874   5139  2.243 0.477     0.123     0.029       42     3.6  G_postcentral
 3930   2276   8830  2.919 0.448     0.108     0.024       45     3.6  G_precentral
 4344   2830   9600  2.712 0.463     0.145     0.032       87     5.6  G_precuneus
 1043    670   2580  2.658 0.800     0.137     0.038       24     1.6  G_rectus
  812    547   1428  2.620 0.863     0.107     0.050        9     1.5  G_subcallosal
 1181    609   2186  2.756 0.462     0.108     0.033       18     1.7  G_temp_sup-G_T_transv
 2968   1964   9231  3.320 0.603     0.141     0.030       53     3.6  G_temp_sup-Lateral
  933    650   2514  3.307 0.522     0.094     0.021        5     0.8  G_temp_sup-Plan_polar
 1615   1094   3205  2.741 0.372     0.096     0.015       12     0.9  G_temp_sup-Plan_tempo
 3915   2549  10280  3.063 0.650     0.144     0.038       89     5.6  G_temporal_inf
 3614   2424  10039  2.990 0.522     0.139     0.029       73     4.3  G_temporal_middle
  366    255    520  2.333 0.345     0.088     0.012        1     0.1  Lat_Fis-ant-Horizont
  507    360    827  2.595 0.464     0.122     0.016        4     0.4  Lat_Fis-ant-Vertical
 1559   1034   2229  2.651 0.343     0.126     0.027       16     1.8  Lat_Fis-post
 2857   1734   4027  2.047 0.530     0.145     0.040       43     4.4  Pole_occipital
 1910   1347   6124  3.265 0.814     0.146     0.036       29     3.0  Pole_temporal
 2964   2065   3563  2.133 0.687     0.137     0.030       31     3.6  S_calcarine
 3652   2437   4240  1.935 0.543     0.096     0.025       27     4.5  S_central
 1547   1088   2438  2.508 0.441     0.103     0.016       10     1.0  S_cingul-Marginalis
  607    408   1101  3.031 0.495     0.103     0.017        3     0.5  S_circular_insula_ant
 1929   1314   3138  2.920 0.444     0.088     0.013        8     1.0  S_circular_insula_inf
 1899   1305   2953  2.855 0.388     0.104     0.016        9     1.4  S_circular_insula_sup
 1417    989   2400  2.805 0.446     0.101     0.018        9     1.1  S_collat_transv_ant
  777    522    860  1.996 0.480     0.124     0.024        6     0.8  S_collat_transv_post
 2782   1912   4108  2.273 0.390     0.110     0.019       24     2.0  S_front_inf
 2211   1510   3064  2.260 0.424     0.119     0.023       20     2.1  S_front_middle
 4487   3088   7460  2.510 0.416     0.110     0.020       40     3.7  S_front_sup
  934    638   1256  2.394 0.298     0.102     0.016        5     0.6  S_interm_prim-Jensen
 4616   3115   6480  2.302 0.383     0.106     0.017       34     2.9  S_intrapariet&P_trans
 1619   1101   2292  2.220 0.493     0.128     0.026       15     1.8  S_oc_middle&Lunatus
 1914   1256   2618  2.326 0.394     0.125     0.020       18     1.6  S_oc_sup&transversal
  755    531   1140  2.455 0.345     0.112     0.019        6     0.5  S_occipital_ant
 1734   1172   2808  2.802 0.415     0.107     0.018       10     1.4  S_oc-temp_lat
 2358   1672   3788  2.534 0.394     0.109     0.017       18     1.6  S_oc-temp_med&Lingual
  447    313    672  2.300 0.347     0.107     0.019        2     0.3  S_orbital_lateral
  635    451    862  2.285 0.495     0.116     0.017        5     0.4  S_orbital_med-olfact
 1823   1230   3314  2.811 0.577     0.144     0.034       26     2.6  S_orbital-H_Shaped
 2715   1835   3984  2.474 0.460     0.103     0.018       20     2.1  S_parieto_occipital
 1874   1155   2098  2.091 0.910     0.142     0.032       41     2.1  S_pericallosal
 4187   2827   6204  2.289 0.444     0.117     0.021       40     3.4  S_postcentral
 2533   1705   4095  2.655 0.315     0.104     0.017       18     1.7  S_precentral-inf-part
 2180   1501   3434  2.556 0.362     0.105     0.016       14     1.4  S_precentral-sup-part
  884    619   1169  2.119 0.367     0.111     0.013        8     0.5  S_suborbital
 1844   1268   2730  2.431 0.328     0.118     0.022       15     1.6  S_subparietal
 2186   1530   3117  2.525 0.343     0.111     0.018       14     1.7  S_temporal_inf
 7697   5305  12580  2.605 0.364     0.107     0.019       60     5.8  S_temporal_sup
  671    476    917  2.368 0.306     0.100     0.011        4     0.3  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050233 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 336476
Total vertex volume 332585 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1045    707   1931  2.490 0.445     0.138     0.039       18     1.8  G&S_frontomargin
 1558   1032   2904  2.371 0.563     0.130     0.028       21     1.8  G&S_occipital_inf
 2161   1283   3564  2.371 0.535     0.111     0.024       24     2.0  G&S_paracentral
 2002   1330   4341  2.814 0.395     0.137     0.031       31     2.4  G&S_subcentral
 1579   1068   3410  2.546 0.492     0.157     0.040       36     2.4  G&S_transv_frontopol
 3883   2624   7360  2.645 0.435     0.119     0.023       50     3.4  G&S_cingul-Ant
 1927   1310   4050  2.947 0.441     0.119     0.024       23     2.0  G&S_cingul-Mid-Ant
 2085   1434   4350  2.824 0.562     0.126     0.028       24     2.2  G&S_cingul-Mid-Post
  821    520   2155  3.022 0.432     0.144     0.034       15     1.1  G_cingul-Post-dorsal
  426    253    945  2.655 0.781     0.122     0.027        7     0.4  G_cingul-Post-ventral
 3193   1972   4265  1.954 0.543     0.143     0.033       51     4.2  G_cuneus
 1677   1112   4379  2.984 0.422     0.123     0.022       26     1.5  G_front_inf-Opercular
  485    302   1236  3.057 0.481     0.141     0.032       10     0.5  G_front_inf-Orbital
 1635   1024   3824  2.886 0.504     0.147     0.035       39     2.2  G_front_inf-Triangul
 6287   4108  15413  2.757 0.523     0.146     0.032      131     8.0  G_front_middle
 8018   5293  20334  2.984 0.509     0.135     0.027      122     8.8  G_front_sup
  747    508   1764  3.060 0.587     0.135     0.038       13     0.9  G_Ins_lg&S_cent_ins
  949    595   2764  3.166 0.814     0.137     0.048       23     1.7  G_insular_short
 3523   2262   7776  2.681 0.484     0.145     0.031       71     4.1  G_occipital_middle
 2111   1316   4174  2.469 0.526     0.145     0.032       36     2.8  G_occipital_sup
 2963   1822   6906  2.883 0.588     0.142     0.039       58     4.7  G_oc-temp_lat-fusifor
 4471   2776   7168  2.189 0.682     0.146     0.041       75     7.3  G_oc-temp_med-Lingual
 1761   1088   4456  2.991 0.928     0.131     0.063       37     4.3  G_oc-temp_med-Parahip
 3100   1987   7683  2.904 0.675     0.147     0.050       84     5.5  G_orbital
 4823   3140  11407  2.724 0.497     0.145     0.035      106     6.8  G_pariet_inf-Angular
 3588   2430   7510  2.646 0.520     0.133     0.027       62     3.8  G_pariet_inf-Supramar
 3460   2231   6786  2.433 0.449     0.135     0.029       62     3.7  G_parietal_sup
 2866   1708   4608  2.138 0.529     0.106     0.021       32     2.4  G_postcentral
 3791   2206   9123  2.975 0.417     0.103     0.020       44     3.0  G_precentral
 3637   2372   7939  2.655 0.411     0.146     0.034       71     4.6  G_precuneus
  904    593   1998  2.428 0.752     0.151     0.054       70     2.4  G_rectus
  678    439   1300  2.587 0.971     0.104     0.048       11     1.0  G_subcallosal
  723    389   1448  2.690 0.466     0.096     0.018        7     0.5  G_temp_sup-G_T_transv
 2828   1817   7925  3.400 0.566     0.138     0.030       51     3.0  G_temp_sup-Lateral
 1287    841   3319  3.500 0.785     0.099     0.042       64     1.4  G_temp_sup-Plan_polar
 1330    876   3010  2.888 0.480     0.097     0.017       12     0.9  G_temp_sup-Plan_tempo
 3776   2480   9607  2.937 0.644     0.144     0.038       83     5.4  G_temporal_inf
 4285   2931  11996  3.057 0.616     0.143     0.034      102     5.5  G_temporal_middle
  634    437    956  2.565 0.393     0.095     0.013        3     0.3  Lat_Fis-ant-Horizont
  467    363    841  2.526 0.450     0.092     0.016        2     0.3  Lat_Fis-ant-Vertical
 1631   1100   2447  2.729 0.420     0.113     0.021       12     1.3  Lat_Fis-post
 4733   2977   7025  2.040 0.554     0.147     0.037       73     6.9  Pole_occipital
 2021   1348   6147  3.342 0.744     0.133     0.029       29     2.2  Pole_temporal
 3598   2317   4434  2.285 0.712     0.116     0.023       31     3.6  S_calcarine
 3630   2433   4182  1.993 0.577     0.088     0.015       16     2.1  S_central
 1929   1286   2848  2.396 0.406     0.093     0.016       13     1.3  S_cingul-Marginalis
  589    400   1008  3.046 0.493     0.101     0.021        3     0.5  S_circular_insula_ant
 1345    896   2268  3.057 0.690     0.082     0.012        4     0.7  S_circular_insula_inf
 1708   1183   2826  2.853 0.400     0.098     0.015        7     1.2  S_circular_insula_sup
 1679   1158   2863  2.789 0.334     0.090     0.012        7     0.8  S_collat_transv_ant
  460    314    506  2.020 0.308     0.120     0.023        3     0.5  S_collat_transv_post
 2691   1829   3988  2.401 0.351     0.115     0.021       22     2.4  S_front_inf
 3329   2342   5256  2.321 0.433     0.127     0.024       34     3.2  S_front_middle
 3562   2506   6056  2.555 0.365     0.100     0.017       25     2.2  S_front_sup
  888    624   1128  2.219 0.327     0.114     0.026        7     0.9  S_interm_prim-Jensen
 4901   3277   6862  2.233 0.401     0.117     0.019       42     4.2  S_intrapariet&P_trans
 1468    999   1838  2.021 0.388     0.114     0.021       14     1.2  S_oc_middle&Lunatus
 1598   1118   2162  2.143 0.394     0.124     0.022       14     1.5  S_oc_sup&transversal
  856    616   1528  2.569 0.394     0.111     0.017        7     0.7  S_occipital_ant
 1531   1047   2270  2.543 0.430     0.104     0.017        8     1.2  S_oc-temp_lat
 2911   2005   4453  2.565 0.440     0.106     0.018       20     2.1  S_oc-temp_med&Lingual
  455    307    615  2.246 0.584     0.126     0.022        4     0.5  S_orbital_lateral
 1029    713   1535  2.562 0.595     0.111     0.021        8     0.7  S_orbital_med-olfact
 1502   1019   2834  2.925 0.480     0.138     0.032       19     2.0  S_orbital-H_Shaped
 3119   2093   4332  2.311 0.485     0.116     0.019       30     2.6  S_parieto_occipital
 2247   1447   2220  1.910 0.687     0.129     0.021       32     1.5  S_pericallosal
 2574   1764   3271  2.090 0.400     0.107     0.018       19     1.8  S_postcentral
 2309   1533   3737  2.765 0.353     0.103     0.016       15     1.6  S_precentral-inf-part
 1878   1293   2766  2.551 0.336     0.100     0.015       10     1.2  S_precentral-sup-part
  358    254    605  2.749 0.683     0.148     0.026        4     0.4  S_suborbital
 2339   1623   3810  2.432 0.453     0.139     0.027       29     3.0  S_subparietal
 1935   1338   2834  2.549 0.436     0.113     0.017       15     1.5  S_temporal_inf
 8578   5916  14319  2.660 0.453     0.113     0.018       76     6.6  S_temporal_sup
  488    340    694  2.792 0.401     0.116     0.014        3     0.3  S_temporal_transverse
PIDs (18420 18423) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 04:49:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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 04:49:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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 18494 of (18494 18497) to complete...
Waiting for PID 18497 of (18494 18497) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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...
1818 labels changed using aseg
relabeling using gibbs priors...
000:   2487 changed, 180195 examined...
001:    587 changed, 11388 examined...
002:    156 changed, 3356 examined...
003:     76 changed, 960 examined...
004:     37 changed, 440 examined...
005:     18 changed, 228 examined...
006:      9 changed, 102 examined...
007:      4 changed, 46 examined...
008:      7 changed, 23 examined...
009:      1 changed, 30 examined...
010:      0 changed, 7 examined...
277 labels changed using aseg
000: 61 total segments, 28 labels (537 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
679 vertices marked for relabeling...
679 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 19 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050233 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...
1735 labels changed using aseg
relabeling using gibbs priors...
000:   2486 changed, 182078 examined...
001:    565 changed, 11584 examined...
002:    128 changed, 3212 examined...
003:     50 changed, 786 examined...
004:     19 changed, 300 examined...
005:     13 changed, 110 examined...
006:      5 changed, 78 examined...
007:      4 changed, 35 examined...
008:      3 changed, 28 examined...
009:      4 changed, 21 examined...
010:      3 changed, 21 examined...
011:      1 changed, 20 examined...
012:      1 changed, 8 examined...
013:      0 changed, 9 examined...
114 labels changed using aseg
000: 68 total segments, 35 labels (162 vertices) changed
001: 35 total segments, 2 labels (17 vertices) changed
002: 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...
1472 vertices marked for relabeling...
1472 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 19 seconds.
PIDs (18494 18497) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 04:50:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 04:50:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 rh white 

Waiting for PID 18563 of (18563 18566) to complete...
Waiting for PID 18566 of (18563 18566) 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 0050233 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 335316
Total vertex volume 331805 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 2549   1697   4919  2.685 0.699     0.133     0.029       43     3.0  caudalanteriorcingulate
 5385   3534  10085  2.590 0.490     0.113     0.020       58     4.1  caudalmiddlefrontal
 4057   2611   5746  2.167 0.506     0.134     0.031       52     5.1  cuneus
  765    519   2024  2.994 0.861     0.118     0.033        9     1.0  entorhinal
 6093   4059  12536  2.814 0.498     0.121     0.024       76     5.6  fusiform
 9270   6205  17394  2.612 0.451     0.129     0.025      132     9.0  inferiorparietal
 7283   4888  16418  2.916 0.617     0.131     0.032      118     9.2  inferiortemporal
 1986   1239   3423  2.592 0.774     0.128     0.033       30     2.3  isthmuscingulate
10672   6794  17912  2.294 0.572     0.142     0.036      162    15.1  lateraloccipital
 4924   3291  10398  2.816 0.660     0.145     0.041       94     7.9  lateralorbitofrontal
 6426   4106  10006  2.252 0.638     0.141     0.033       95     8.5  lingual
 2519   1689   4717  2.436 0.724     0.119     0.028       35     2.7  medialorbitofrontal
 8239   5655  18218  2.824 0.502     0.125     0.024      113     8.1  middletemporal
 1145    727   2251  2.803 0.790     0.092     0.019        8     0.8  parahippocampal
 3420   2217   6326  2.626 0.508     0.106     0.019       26     2.6  paracentral
 2962   1955   6148  2.826 0.432     0.120     0.022       37     2.5  parsopercularis
 1289    835   2823  2.874 0.475     0.132     0.026       18     1.3  parsorbitalis
 3083   2078   6061  2.584 0.442     0.118     0.021       35     2.6  parstriangularis
 2627   1801   2669  1.751 0.510     0.136     0.031       26     3.4  pericalcarine
 9095   5775  14006  2.195 0.577     0.118     0.025      105     9.0  postcentral
 2810   1865   5756  2.829 0.729     0.136     0.027       46     2.9  posteriorcingulate
 9471   5983  17761  2.691 0.484     0.105     0.023       91     9.5  precentral
 8033   5358  14972  2.615 0.469     0.127     0.026      110     8.6  precuneus
 2340   1540   4504  2.697 0.649     0.133     0.033       43     3.1  rostralanteriorcingulate
 7534   5120  14845  2.479 0.520     0.136     0.028      125     9.0  rostralmiddlefrontal
15344  10275  32732  2.752 0.570     0.126     0.027      215    16.4  superiorfrontal
 8674   5700  15183  2.380 0.439     0.118     0.020      103     6.9  superiorparietal
11022   7413  25248  2.995 0.600     0.113     0.022      114     9.6  superiortemporal
 8894   5979  17250  2.602 0.446     0.126     0.023      121     8.2  supramarginal
 1229    650   2054  2.692 0.450     0.102     0.030       14     1.6  transversetemporal
 3508   2320   7422  3.175 0.575     0.112     0.032       43     4.3  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 0050233 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 336476
Total vertex volume 332585 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 2168   1435   4150  2.563 0.672     0.129     0.026       34     2.1  caudalanteriorcingulate
 5053   3415  10789  2.766 0.495     0.120     0.022       57     4.3  caudalmiddlefrontal
 4040   2554   5605  2.061 0.495     0.141     0.031       60     5.1  cuneus
  728    475   1992  3.097 1.048     0.135     0.055       10     1.4  entorhinal
 6045   3940  11991  2.770 0.545     0.123     0.030       79     7.7  fusiform
11753   7913  22468  2.546 0.486     0.131     0.027      177    13.4  inferiorparietal
 7396   4933  16150  2.833 0.618     0.125     0.028      109     8.2  inferiortemporal
 1617   1055   2951  2.434 0.793     0.127     0.027       24     1.5  isthmuscingulate
10049   6470  16993  2.257 0.552     0.139     0.031      149    12.3  lateraloccipital
 4969   3288   9954  2.786 0.670     0.143     0.052      160     9.0  lateralorbitofrontal
 6996   4440  10843  2.284 0.655     0.143     0.038      109    10.5  lingual
 2745   1807   5558  2.551 0.743     0.131     0.039      101     4.6  medialorbitofrontal
 8753   6015  20051  2.919 0.568     0.128     0.026      141     8.7  middletemporal
 1337    851   2659  2.693 0.633     0.103     0.036       23     1.9  parahippocampal
 3386   2229   5901  2.462 0.468     0.106     0.018       29     2.5  paracentral
 3372   2311   7027  2.818 0.460     0.115     0.019       38     2.6  parsopercularis
 1193    787   2843  2.909 0.546     0.133     0.027       18     1.4  parsorbitalis
 3273   2129   6461  2.727 0.531     0.131     0.028       52     3.5  parstriangularis
 3367   2146   3652  1.878 0.543     0.107     0.021       24     3.1  pericalcarine
 8324   5393  12711  2.138 0.610     0.109     0.022       83     7.1  postcentral
 2718   1799   5216  2.602 0.791     0.135     0.027       40     2.9  posteriorcingulate
 9197   5696  17588  2.752 0.457     0.101     0.018       83     6.8  precentral
 9057   6045  16136  2.520 0.494     0.132     0.028      130    10.4  precuneus
 1780   1187   3641  2.781 0.507     0.126     0.025       26     1.7  rostralanteriorcingulate
 8014   5357  15341  2.505 0.490     0.135     0.028      127     9.1  rostralmiddlefrontal
16464  11172  34451  2.755 0.525     0.125     0.026      208    16.6  superiorfrontal
 8619   5637  14588  2.334 0.461     0.128     0.024      116     8.3  superiorparietal
 9716   6439  23031  3.204 0.629     0.117     0.023      113     8.5  superiortemporal
 6854   4628  12609  2.532 0.461     0.121     0.025       92     6.4  supramarginal
  833    487   1476  2.631 0.450     0.103     0.019        7     0.6  transversetemporal
 3537   2365   7756  3.125 0.573     0.113     0.026       40     3.2  insula
PIDs (18563 18566) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 04:51:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 pctsurfcon --s 0050233 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 04:51:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts

 pctsurfcon --s 0050233 --rh-only 

Waiting for PID 18709 of (18709 18719) to complete...
Waiting for PID 18719 of (18709 18719) to complete...

 pctsurfcon --s 0050233 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts/pctsurfcon.log
Sun Oct  8 04:51:01 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-112 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-6.0.0/0050233/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18709/lh.wm.mgh --regheader 0050233 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 96635
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18709/lh.wm.mgh
Dim: 180195 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18709/lh.gm.mgh --projfrac 0.3 --regheader 0050233 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 120082
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18709/lh.gm.mgh
Dim: 180195 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18709/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18709/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.w-g.pct.mgh --annot 0050233 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/lh.w-g.pct.mgh --annot 0050233 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/lh.w-g.pct.mgh
Vertex Area is 0.660989 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 0050233 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/scripts/pctsurfcon.log
Sun Oct  8 04:51:01 CEST 2017
setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-112 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-6.0.0/0050233/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18719/rh.wm.mgh --regheader 0050233 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 97740
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18719/rh.wm.mgh
Dim: 182078 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18719/rh.gm.mgh --projfrac 0.3 --regheader 0050233 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 121446
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18719/rh.gm.mgh
Dim: 182078 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18719/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/tmp.pctsurfcon.18719/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.w-g.pct.mgh --annot 0050233 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.w-g.pct.mgh --annot 0050233 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.w-g.pct.mgh
Vertex Area is 0.659677 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 (18709 18719) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 04:51:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2310 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1547 voxels changed to hypointensity...
3680 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 04:51:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233

 mri_aparc2aseg --s 0050233 --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 04:51:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233

 mri_aparc2aseg --s 0050233 --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 04:51:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233

 mri_aparc2aseg --s 0050233 --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 18926 of (18926 18929 18932) to complete...
Waiting for PID 18929 of (18926 18929 18932) to complete...
Waiting for PID 18932 of (18926 18929 18932) to complete...

 mri_aparc2aseg --s 0050233 --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 0050233
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/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-6.0.0/0050233/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 8.14
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 65
rescaling Left_Lateral_Ventricle from 13 --> 26
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 70
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 94
rescaling Left_Caudate from 75 --> 86
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 96
rescaling Third_Ventricle from 25 --> 41
rescaling Fourth_Ventricle from 22 --> 28
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 67
rescaling Left_Amygdala from 56 --> 71
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 69
rescaling Left_VentralDC from 87 --> 95
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 67
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 68
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 81
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 68
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 79
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
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 = 660317
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 387 changed.
pass 2: 46 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050233 --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 0050233
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/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-6.0.0/0050233/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 8.14
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 65
rescaling Left_Lateral_Ventricle from 13 --> 26
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 70
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 94
rescaling Left_Caudate from 75 --> 86
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 96
rescaling Third_Ventricle from 25 --> 41
rescaling Fourth_Ventricle from 22 --> 28
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 67
rescaling Left_Amygdala from 56 --> 71
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 69
rescaling Left_VentralDC from 87 --> 95
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 67
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 68
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 81
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 68
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 79
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
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 = 660340
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 387 changed.
pass 2: 46 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050233 --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 0050233
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/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-6.0.0/0050233/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 8.14
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 65
rescaling Left_Lateral_Ventricle from 13 --> 26
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 70
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 94
rescaling Left_Caudate from 75 --> 86
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 96
rescaling Third_Ventricle from 25 --> 41
rescaling Fourth_Ventricle from 22 --> 28
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 67
rescaling Left_Amygdala from 56 --> 71
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 69
rescaling Left_VentralDC from 87 --> 95
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 67
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 68
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 81
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 68
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 79
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
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 = 660340
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 387 changed.
pass 2: 46 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (18926 18929 18932) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 04:59:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri

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

Sun Oct  8 04:59:39 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-6.0.0/0050233/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-112 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-6.0.0/0050233/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-112
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 04:59:39 CEST 2017 
Ended   at Sun Oct  8 04:59:45 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 04:59:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233

 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 0050233 


$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 0050233 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1606609 mm^3    (det: 1.212557 )
Computing euler number
orig.nofix lheno =  -86, rheno = -58
orig.nofix lhholes =   44, rhholes = 30
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
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 05:01:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233

 mri_aparc2aseg --s 0050233 --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 0050233
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-6.0.0/0050233/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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-6.0.0/0050233/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7535 vertices from left hemi
Ripped 8734 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-6.0.0/0050233/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 = 1214247
Used brute-force search on 331 voxels
Fixing Parahip LH WM
  Found 8 clusters
     0 k 2.000000
     1 k 2.000000
     2 k 1.000000
     3 k 1452.000000
     4 k 10.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 4.000000
     3 k 1.000000
     4 k 1806.000000
     5 k 18.000000
     6 k 3.000000
     7 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050233 --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 0050233 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-112
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1606609 mm^3    (det: 1.212557 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
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-6.0.0/0050233/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 05:11:33 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 20345 of (20345 20351 20357 20363 20369) to complete...
Waiting for PID 20351 of (20345 20351 20357 20363 20369) to complete...
Waiting for PID 20357 of (20345 20351 20357 20363 20369) to complete...
Waiting for PID 20363 of (20345 20351 20357 20363 20369) to complete...
Waiting for PID 20369 of (20345 20351 20357 20363 20369) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 760
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4889
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 1361
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9270
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 249
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4326
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 642
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6625
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 950
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6734
mri_label2label: Done

PIDs (20345 20351 20357 20363 20369) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 20421 of (20421 20427 20433 20439) to complete...
Waiting for PID 20427 of (20421 20427 20433 20439) to complete...
Waiting for PID 20433 of (20421 20427 20433 20439) to complete...
Waiting for PID 20439 of (20421 20427 20433 20439) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 502
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4572
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 3117
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16706
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 906
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 5087
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 1480
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4902
mri_label2label: Done

PIDs (20421 20427 20433 20439) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 20580 of (20580 20586 20592 20597 20604) to complete...
Waiting for PID 20586 of (20580 20586 20592 20597 20604) to complete...
Waiting for PID 20592 of (20580 20586 20592 20597 20604) to complete...
Waiting for PID 20597 of (20580 20586 20592 20597 20604) to complete...
Waiting for PID 20604 of (20580 20586 20592 20597 20604) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 2707
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 7348
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 5680
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 13794
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 868
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2886
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 222
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1512
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 271
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1470
mri_label2label: Done

PIDs (20580 20586 20592 20597 20604) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 20664 of (20664 20670 20676 20682 20688) to complete...
Waiting for PID 20670 of (20664 20670 20676 20682 20688) to complete...
Waiting for PID 20676 of (20664 20670 20676 20682 20688) to complete...
Waiting for PID 20682 of (20664 20670 20676 20682 20688) to complete...
Waiting for PID 20688 of (20664 20670 20676 20682 20688) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 181
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1195
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 336
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2428
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 79
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1583
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 205
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2201
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 409
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2728
mri_label2label: Done

PIDs (20664 20670 20676 20682 20688) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 20826 of (20826 20832 20838 20844) to complete...
Waiting for PID 20832 of (20826 20832 20838 20844) to complete...
Waiting for PID 20838 of (20826 20832 20838 20844) to complete...
Waiting for PID 20844 of (20826 20832 20838 20844) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 168
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1717
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 1288
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8323
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 460
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2372
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 652
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1803
mri_label2label: Done

PIDs (20826 20832 20838 20844) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 20901 of (20901 20907 20913 20919 20923) to complete...
Waiting for PID 20907 of (20901 20907 20913 20919 20923) to complete...
Waiting for PID 20913 of (20901 20907 20913 20919 20923) to complete...
Waiting for PID 20919 of (20901 20907 20913 20919 20923) to complete...
Waiting for PID 20923 of (20901 20907 20913 20919 20923) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 1998
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 5403
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 2572
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5906
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 180
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 693
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 79
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 549
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 180195
Number of reverse mapping hits = 119
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 569
mri_label2label: Done

PIDs (20901 20907 20913 20919 20923) completed and logs appended.

 mris_label2annot --s 0050233 --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-6.0.0/0050233/label
cmdline mris_label2annot --s 0050233 --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-112
machine  x86_64
user     ntraut

subject 0050233
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-6.0.0/0050233/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 125134 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050233 --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-6.0.0/0050233/label
cmdline mris_label2annot --s 0050233 --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-112
machine  x86_64
user     ntraut

subject 0050233
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-6.0.0/0050233/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 148150 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 335316
Total vertex volume 331805 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1514    877   2632  2.284 0.469     0.131     0.034       25     1.9  BA1_exvivo
 5302   3540   8630  2.365 0.464     0.121     0.022       53     4.8  BA2_exvivo
 1205    796   1167  1.834 0.387     0.122     0.025       10     1.1  BA3a_exvivo
 2941   1859   4106  1.955 0.625     0.109     0.023       33     2.9  BA3b_exvivo
 2247   1333   4366  2.801 0.483     0.100     0.019       17     1.7  BA4a_exvivo
 1592    946   2353  2.499 0.447     0.090     0.040       18     3.5  BA4p_exvivo
12809   8456  28245  2.847 0.510     0.115     0.021      131    10.3  BA6_exvivo
 3130   2090   6508  2.787 0.418     0.118     0.022       36     2.7  BA44_exvivo
 4063   2725   7918  2.532 0.494     0.124     0.022       53     3.5  BA45_exvivo
 4744   3079   5191  1.745 0.531     0.139     0.036       59     6.8  V1_exvivo
11299   7174  17138  2.200 0.574     0.148     0.038      171    17.4  V2_exvivo
 2547   1710   5214  2.617 0.491     0.127     0.026       34     2.6  MT_exvivo
  718    473   1978  3.195 0.834     0.111     0.026        8     0.8  perirhinal_exvivo
  950    642   2422  3.099 0.617     0.129     0.036       14     1.2  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050233 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 335316
Total vertex volume 331805 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
  917    485   1553  2.324 0.469     0.134     0.035       15     1.1  BA1_exvivo
 1966   1269   2999  2.263 0.414     0.110     0.022       17     1.6  BA2_exvivo
 1026    687    945  1.781 0.362     0.128     0.027        8     1.0  BA3a_exvivo
 1729   1139   1962  1.617 0.395     0.084     0.013        9     1.0  BA3b_exvivo
 2117   1268   4030  2.789 0.457     0.092     0.021       13     1.8  BA4a_exvivo
 1241    767   1788  2.402 0.407     0.093     0.039       16     2.8  BA4p_exvivo
 6980   4552  15324  2.843 0.490     0.117     0.022       76     5.8  BA6_exvivo
 2096   1395   4438  2.810 0.435     0.123     0.024       28     1.9  BA44_exvivo
 1751   1143   4108  2.745 0.431     0.134     0.026       30     1.7  BA45_exvivo
 5084   3295   5566  1.749 0.520     0.138     0.036       62     7.3  V1_exvivo
 5664   3543   7963  2.106 0.568     0.154     0.039       89     9.0  V2_exvivo
  603    415   1375  2.821 0.463     0.117     0.026        8     0.5  MT_exvivo
  352    246    938  3.146 0.677     0.091     0.014        2     0.2  perirhinal_exvivo
  519    368   1253  3.051 0.580     0.146     0.040        9     0.7  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 05:15:11 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 21251 of (21251 21257 21263 21268 21274) to complete...
Waiting for PID 21257 of (21251 21257 21263 21268 21274) to complete...
Waiting for PID 21263 of (21251 21257 21263 21268 21274) to complete...
Waiting for PID 21268 of (21251 21257 21263 21268 21274) to complete...
Waiting for PID 21274 of (21251 21257 21263 21268 21274) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 628
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4590
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 663
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7350
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 358
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4338
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 568
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5090
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 1168
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6915
mri_label2label: Done

PIDs (21251 21257 21263 21268 21274) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 21333 of (21333 21339 21345 21350) to complete...
Waiting for PID 21339 of (21333 21339 21345 21350) to complete...
Waiting for PID 21345 of (21333 21339 21345 21350) to complete...
Waiting for PID 21350 of (21333 21339 21345 21350) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 786
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5259
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 1872
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14128
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 1874
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8786
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 2043
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7398
mri_label2label: Done

PIDs (21333 21339 21345 21350) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 21404 of (21404 21410 21416 21422 21428) to complete...
Waiting for PID 21410 of (21404 21410 21416 21422 21428) to complete...
Waiting for PID 21416 of (21404 21410 21416 21422 21428) to complete...
Waiting for PID 21422 of (21404 21410 21416 21422 21428) to complete...
Waiting for PID 21428 of (21404 21410 21416 21422 21428) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 3710
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 8437
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 5793
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 13809
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 1302
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 3234
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 313
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1351
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 986
mri_label2label: Done

PIDs (21404 21410 21416 21422 21428) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 21518 of (21518 21524 21530 21534 21542) to complete...
Waiting for PID 21524 of (21518 21524 21530 21534 21542) to complete...
Waiting for PID 21530 of (21518 21524 21530 21534 21542) to complete...
Waiting for PID 21534 of (21518 21524 21530 21534 21542) to complete...
Waiting for PID 21542 of (21518 21524 21530 21534 21542) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 177
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1053
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 239
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2927
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 79
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1777
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 192
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2375
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 422
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1810
mri_label2label: Done

PIDs (21518 21524 21530 21534 21542) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 21594 of (21594 21600 21608 21614) to complete...
Waiting for PID 21600 of (21594 21600 21608 21614) to complete...
Waiting for PID 21608 of (21594 21600 21608 21614) to complete...
Waiting for PID 21614 of (21594 21600 21608 21614) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 274
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1763
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 900
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7859
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 385
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1397
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 576
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1754
mri_label2label: Done

PIDs (21594 21600 21608 21614) 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 0050233 --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 0050233 --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 0050233 --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 0050233 --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 0050233 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 21657 of (21657 21663 21669 21675 21680) to complete...
Waiting for PID 21663 of (21657 21663 21669 21675 21680) to complete...
Waiting for PID 21669 of (21657 21663 21669 21675 21680) to complete...
Waiting for PID 21675 of (21657 21663 21669 21675 21680) to complete...
Waiting for PID 21680 of (21657 21663 21669 21675 21680) 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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 2642
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 5874
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 2674
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 6111
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 209
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 477
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 224
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 918
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 0050233 --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 = 0050233
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-6.0.0/0050233/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 182078
Number of reverse mapping hits = 160
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 451
mri_label2label: Done

PIDs (21657 21663 21669 21675 21680) completed and logs appended.

 mris_label2annot --s 0050233 --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-6.0.0/0050233/label
cmdline mris_label2annot --s 0050233 --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-112
machine  x86_64
user     ntraut

subject 0050233
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-6.0.0/0050233/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 127768 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050233 --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-6.0.0/0050233/label
cmdline mris_label2annot --s 0050233 --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-112
machine  x86_64
user     ntraut

subject 0050233
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-6.0.0/0050233/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 151145 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/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 0050233 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 336476
Total vertex volume 332585 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
 1111    648   2259  2.437 0.575     0.125     0.027       17     0.9  BA1_exvivo
 3599   2369   5115  2.146 0.444     0.106     0.020       31     2.8  BA2_exvivo
 1323    897   1290  1.816 0.437     0.125     0.023       10     1.2  BA3a_exvivo
 2409   1573   3081  1.761 0.509     0.098     0.018       20     1.8  BA3b_exvivo
 2335   1361   4111  2.666 0.429     0.087     0.019       18     1.8  BA4a_exvivo
 1748   1005   2622  2.618 0.350     0.079     0.015       12     1.0  BA4p_exvivo
 9520   6356  21691  2.901 0.496     0.120     0.022      101     8.2  BA6_exvivo
 4880   3265   9561  2.821 0.423     0.115     0.020       49     4.0  BA44_exvivo
 5634   3711  11756  2.732 0.527     0.133     0.027       88     6.1  BA45_exvivo
 6023   3678   6998  1.900 0.560     0.127     0.031       72     7.8  V1_exvivo
11238   7228  17135  2.196 0.613     0.146     0.036      173    16.0  V2_exvivo
 3194   2098   6083  2.531 0.462     0.129     0.024       48     3.1  MT_exvivo
  764    494   2225  3.208 0.954     0.126     0.048       10     1.1  perirhinal_exvivo
  532    332   1180  2.758 0.970     0.115     0.067       10     1.5  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 0050233 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050233/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 336476
Total vertex volume 332585 (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) = 1606609 mm^3    (det: 1.212557 )
lhCtxGM: 330726.091 329974.000  diff=  752.1  pctdiff= 0.227
rhCtxGM: 331249.620 330555.000  diff=  694.6  pctdiff= 0.210
lhCtxWM: 279088.312 279716.000  diff= -627.7  pctdiff=-0.225
rhCtxWM: 277572.305 278301.000  diff= -728.7  pctdiff=-0.263
SubCortGMVol  67666.000
SupraTentVol  1309045.329 (1305907.000) diff=3138.329 pctdiff=0.240
SupraTentVolNotVent  1289411.329 (1286273.000) diff=3138.329 pctdiff=0.243
BrainSegVol  1486121.000 (1484029.000) diff=2092.000 pctdiff=0.141
BrainSegVolNotVent  1463419.000 (1463411.329) diff= 7.671 pctdiff=0.001
BrainSegVolNotVent  1463419.000
CerebellumVol 177048.000
VentChorVol   19634.000
3rd4th5thCSF   3068.000
CSFVol   976.000, OptChiasmVol    98.000
MaskVol 2050661.000
  857    489   1511  2.236 0.573     0.120     0.022       12     0.6  BA1_exvivo
 2070   1364   3127  2.123 0.444     0.089     0.015       15     1.3  BA2_exvivo
 1142    774    999  1.791 0.403     0.126     0.022        8     1.0  BA3a_exvivo
 1842   1247   2005  1.585 0.343     0.086     0.013       10     1.1  BA3b_exvivo
 1528    882   2719  2.637 0.462     0.096     0.019       13     1.2  BA4a_exvivo
 1389    813   2058  2.655 0.316     0.068     0.014        7     0.8  BA4p_exvivo
 5968   3964  13580  2.921 0.488     0.116     0.021       59     4.8  BA6_exvivo
 1304    883   2969  2.837 0.443     0.112     0.019       17     1.0  BA44_exvivo
 1688   1124   3932  2.847 0.540     0.136     0.032       31     2.1  BA45_exvivo
 5788   3518   6660  1.909 0.566     0.124     0.030       67     7.3  V1_exvivo
 5995   3842   8277  2.042 0.618     0.153     0.040       99     9.7  V2_exvivo
  473    288    979  2.596 0.508     0.121     0.020        7     0.3  MT_exvivo
  473    303   1276  3.072 0.878     0.126     0.060        7     0.9  perirhinal_exvivo
  416    243    658  2.383 0.704     0.147     0.088       11     1.5  entorhinal_exvivo

Started at Sat Oct 7 19:27:16 CEST 2017 
Ended   at Sun Oct 8 05:18:52 CEST 2017
#@#%# recon-all-run-time-hours 9.860
recon-all -s 0050233 finished without error at Sun Oct  8 05:18:52 CEST 2017