ABIDE_fs-6.0.0/0050044/scripts/recon-all.log

Sat Oct  7 18:24:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050044 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050044/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050044
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-931 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    10485760 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked 64 kbytes
maxproc      1024 

             total       used       free     shared    buffers     cached
Mem:      66074808   53035224   13039584    1739748          0   49143920
-/+ buffers/cache:    3891304   62183504
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:24:02-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-931  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-6.0.0/0050044

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050044/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050044/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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/Pitt/0050044/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-6.0.0/0050044/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 18:24:06 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/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-6.0.0/0050044/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 18:24:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/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-931 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:24:17 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.25580
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25580/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25580/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.25580/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:24:20 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.25580/nu0.mnc ./tmp.mri_nu_correct.mni.25580/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25580/0/ -iterations 1000 -distance 50
[ntraut@tars-931:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/] [2017-10-07 18:24:20] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.25580/0/ ./tmp.mri_nu_correct.mni.25580/nu0.mnc ./tmp.mri_nu_correct.mni.25580/nu1.imp

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Number of iterations: 74 
CV of field change: 0.000975825
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.25580/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.25580/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.25580/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 18:25:54 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 18:25:54 CEST 2017
Ended   at Sat Oct  7 18:26:32 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 18:26:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5685, pval=0.2115 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/transforms/talairach_avi.log 

TalAviQA: 0.97574
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 18:26:34 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-6.0.0/0050044/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-931 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:26:34 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.26755
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26755/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.26755/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.26755/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:26:37 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.26755/nu0.mnc ./tmp.mri_nu_correct.mni.26755/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.26755/0/
[ntraut@tars-931:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/] [2017-10-07 18:26:37] 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.26755/0/ ./tmp.mri_nu_correct.mni.26755/nu0.mnc ./tmp.mri_nu_correct.mni.26755/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00152462
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 18:27:30 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.26755/nu1.mnc ./tmp.mri_nu_correct.mni.26755/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.26755/1/
[ntraut@tars-931:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/] [2017-10-07 18:27:30] 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.26755/1/ ./tmp.mri_nu_correct.mni.26755/nu1.mnc ./tmp.mri_nu_correct.mni.26755/nu2.imp

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Number of iterations: 50 
CV of field change: 0.00116699
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.26755/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.26755/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-6.0.0/0050044/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.26755/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.26755/ones.mgz 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.26755/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.26755/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.26755/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.26755/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26755/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.26755/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.26755/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26755/input.mean.dat 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.26755/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.26755/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.26755/ones.mgz --i ./tmp.mri_nu_correct.mni.26755/nu2.mnc --sum ./tmp.mri_nu_correct.mni.26755/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26755/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.26755/ones.mgz --i ./tmp.mri_nu_correct.mni.26755/nu2.mnc --sum ./tmp.mri_nu_correct.mni.26755/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26755/output.mean.dat 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.26755/ones.mgz
Loading ./tmp.mri_nu_correct.mni.26755/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.26755/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.26755/nu2.mnc ./tmp.mri_nu_correct.mni.26755/nu2.mnc mul .73545872954698589230
Saving result to './tmp.mri_nu_correct.mni.26755/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.26755/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.26755/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.26755/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 10 seconds.
mapping ( 9, 161) to ( 3, 110)
 
 
Sat Oct  7 18:29:06 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 18:29:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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
 1.01408   0.06212   0.02312  -1.91293;
-0.13057   0.94202   0.36724   0.63419;
-0.04002  -0.30890   1.02380   13.73550;
 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 71 (71), valley at 49 (49)
csf peak at 28, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 71 (71), valley at 37 (37)
csf peak at 36, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 58 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 18:31:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=6.0
skull bounding box = (45, 41, 19) --> (209, 243, 217)
using (100, 108, 118) as brain centroid...
mean wm in atlas = 108, using box (80,83,94) --> (120, 132,142) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.3
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.285
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.242481 @ (-9.091, -9.091, -9.091)
max log p =    -4.131187 @ (4.545, 4.545, 4.545)
max log p =    -4.067034 @ (2.273, -2.273, -6.818)
max log p =    -4.067034 @ (0.000, 0.000, 0.000)
max log p =    -4.064470 @ (-0.568, -0.568, 0.568)
max log p =    -4.064470 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, -7.4, -10.8): log p = -4.064
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.887, old_max_log_p =-4.064 (thresh=-4.1)
 1.07500   0.00000   0.00000  -12.41963;
 0.00000   1.02750   0.27532  -38.63625;
 0.00000  -0.27532   1.02750   27.03368;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.887, old_max_log_p =-3.887 (thresh=-3.9)
 1.07500   0.00000   0.00000  -12.41963;
 0.00000   1.02750   0.27532  -38.63625;
 0.00000  -0.27532   1.02750   27.03368;
 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=-3.782, old_max_log_p =-3.887 (thresh=-3.9)
 1.05218   0.05274  -0.05303  -9.03229;
-0.03990   1.05383   0.32502  -41.30393;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.781, old_max_log_p =-3.782 (thresh=-3.8)
 1.07190   0.05373  -0.05402  -11.54305;
-0.03990   1.05383   0.32502  -41.30393;
 0.06525  -0.29416   0.97866   25.52550;
 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=-3.777, old_max_log_p =-3.781 (thresh=-3.8)
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.777, old_max_log_p =-3.777 (thresh=-3.8)
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 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
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.777 (old=-4.285)
transform before final EM align:
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 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
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.2  tol 0.000000
final transform:
 1.07065   0.05366  -0.05396  -11.38318;
-0.03999   1.05630   0.32579  -41.73396;
 0.06525  -0.29416   0.97866   25.52550;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1269.966935
mri_em_register stimesec    1.585758
mri_em_register ru_maxrss   609824
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157571
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    88
mri_em_register ru_nivcsw   3005
registration took 11 minutes and 6 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=128 y=117 z=116 r=77
      first estimation of the main basin volume: 1939087 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=147, y=106, z=80, Imax=255
      CSF=12, 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=9902743069 voxels, voxel volume =1.000 
                     = 9902743069 mmm3 = 9902743.552 cm3
done.
PostAnalyze...Basin Prior
 31 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=126,y=123, z=109, r=10354 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 43211
  RIGHT_CER    CSF_MIN=0, CSF_intensity=6, CSF_MAX=33 , nb = -1028077496
  LEFT_CER     CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = -1048602907
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=34 , nb = 1076895159
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 1082161224
    OTHER      CSF_MIN=1, CSF_intensity=14, CSF_MAX=31 , nb = 1076343992
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    36,      39,        43,   66
  after  analyzing :    36,      41,        43,   47
   RIGHT_CER   
  before analyzing :    33,      36,        41,   71
  after  analyzing :    33,      39,        41,   47
   LEFT_CER    
  before analyzing :    36,      40,        45,   72
  after  analyzing :    36,      43,        45,   50
  RIGHT_BRAIN  
  before analyzing :    34,      36,        40,   66
  after  analyzing :    34,      38,        40,   45
  LEFT_BRAIN   
  before analyzing :    37,      41,        45,   66
  after  analyzing :    37,      43,        45,   48
     OTHER     
  before analyzing :    31,      26,        0,   89
  after  analyzing :    22,      26,        26,   41
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...63 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.010
curvature mean = 72.000, std = 7.095

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.14, sigma = 5.93
      after  rotation: sse = 3.14, sigma = 5.93
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.03, its var is 10.80   
      before Erosion-Dilatation  1.93% of inacurate vertices
      after  Erosion-Dilatation  3.71% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...41 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1851683 voxels, voxel volume = 1.000 mm3
           = 1851683 mmm3 = 1851.683 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    28.791623
mri_watershed stimesec    0.484926
mri_watershed ru_maxrss   844684
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   218508
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  11160
mri_watershed ru_oublock  2904
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    3876
mri_watershed ru_nivcsw   189
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:42:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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=23.0
skull bounding box = (55, 57, 33) --> (197, 208, 203)
using (102, 107, 118) as brain centroid...
mean wm in atlas = 107, using box (85,88,97) --> (119, 125,138) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 4.5
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -3.866
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.865752 @ (0.000, 0.000, 0.000)
max log p =    -3.831028 @ (-4.545, -4.545, -4.545)
max log p =    -3.716582 @ (2.273, 2.273, -2.273)
max log p =    -3.690062 @ (1.136, 1.136, -1.136)
max log p =    -3.690062 @ (0.000, 0.000, 0.000)
max log p =    -3.673856 @ (-0.852, -0.284, -0.284)
Found translation: (-2.0, -1.4, -8.2): log p = -3.674
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.462, old_max_log_p =-3.674 (thresh=-3.7)
 0.99144   0.03378  -0.12608   9.36770;
 0.00000   1.03837   0.27823  -37.68222;
 0.13053  -0.25660   0.95766   18.24726;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.462, old_max_log_p =-3.462 (thresh=-3.5)
 0.99144   0.03378  -0.12608   9.36770;
 0.00000   1.03837   0.27823  -37.68222;
 0.13053  -0.25660   0.95766   18.24726;
 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=-3.307, old_max_log_p =-3.462 (thresh=-3.5)
 1.01369   0.08633  -0.04565  -8.48455;
-0.06435   1.04560   0.31782  -34.68873;
 0.06627  -0.28761   0.93521   30.70530;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.304, old_max_log_p =-3.307 (thresh=-3.3)
 1.01573   0.01776  -0.06634   1.87567;
 0.00204   1.02934   0.30826  -40.15623;
 0.06751  -0.29300   0.95274   29.30395;
 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=-3.287, old_max_log_p =-3.304 (thresh=-3.3)
 1.01642   0.05149  -0.05656  -2.92495;
-0.03230   1.03044   0.29395  -33.87933;
 0.06711  -0.27548   0.95543   27.39232;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.278, old_max_log_p =-3.287 (thresh=-3.3)
 1.01675   0.06352  -0.03592  -6.18966;
-0.04797   1.02851   0.31123  -33.51152;
 0.05105  -0.29349   0.95240   31.49160;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.256, old_max_log_p =-3.278 (thresh=-3.3)
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.256, old_max_log_p =-3.256 (thresh=-3.3)
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.256 (old=-3.866)
transform before final EM align:
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 315557 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    3.8  tol 0.000000
final transform:
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1429.944615
mri_em_register stimesec    2.163671
mri_em_register ru_maxrss   600972
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   159474
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    166
mri_em_register ru_nivcsw   3421
registration took 12 minutes and 14 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:54:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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=23.0
skull bounding box = (55, 57, 32) --> (197, 208, 203)
using (102, 107, 118) as brain centroid...
mean wm in atlas = 107, using box (85,88,97) --> (119, 125,139) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 4.6
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 1.01178   0.07636  -0.04888  -5.71810;
-0.05667   1.03028   0.30386  -31.82297;
 0.06713  -0.28330   0.95197   28.25753;
 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 (120, 61, 33) --> (192, 173, 197)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 4556 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 59, 33) --> (131, 162, 198)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
2 of 5154 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (123, 147, 63) --> (171, 189, 117)
Left_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0
0 of 16 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (78, 147, 62) --> (123, 184, 119)
Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 25 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 132, 98) --> (143, 198, 129)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 106 (0.0%) samples deleted
using 9857 total control points for intensity normalization...
bias field = 0.974 +- 0.043
91 of 9855 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (120, 61, 33) --> (192, 173, 197)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
1 of 5176 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 59, 33) --> (131, 162, 198)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 5808 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (123, 147, 63) --> (171, 189, 117)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
13 of 78 (16.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (78, 147, 62) --> (123, 184, 119)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
17 of 98 (17.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 132, 98) --> (143, 198, 129)
Brain_Stem: limiting intensities to 88.0 --> 132.0
10 of 167 (6.0%) samples deleted
using 11327 total control points for intensity normalization...
bias field = 1.044 +- 0.045
66 of 11163 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (120, 61, 33) --> (192, 173, 197)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 5212 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 59, 33) --> (131, 162, 198)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 5859 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (123, 147, 63) --> (171, 189, 117)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
51 of 112 (45.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (78, 147, 62) --> (123, 184, 119)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
52 of 140 (37.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (108, 132, 98) --> (143, 198, 129)
Brain_Stem: limiting intensities to 88.0 --> 132.0
85 of 262 (32.4%) samples deleted
using 11585 total control points for intensity normalization...
bias field = 1.037 +- 0.040
32 of 11226 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 41 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:56:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-regularize_mean 0.500
	-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.09 (predicted orig area = 7.4)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.767, neg=0, invalid=762
0001: dt=221.952000, rms=0.713 (6.972%), neg=0, invalid=762
0002: dt=171.690037, rms=0.698 (2.109%), neg=0, invalid=762
0003: dt=185.663366, rms=0.691 (1.041%), neg=0, invalid=762
0004: dt=221.952000, rms=0.685 (0.781%), neg=0, invalid=762
0005: dt=146.526316, rms=0.682 (0.527%), neg=0, invalid=762
0006: dt=369.920000, rms=0.678 (0.578%), neg=0, invalid=762
0007: dt=129.472000, rms=0.675 (0.448%), neg=0, invalid=762
0008: dt=369.920000, rms=0.673 (0.313%), neg=0, invalid=762
0009: dt=110.976000, rms=0.671 (0.285%), neg=0, invalid=762
0010: dt=1183.744000, rms=0.667 (0.544%), neg=0, invalid=762
0011: dt=110.976000, rms=0.665 (0.348%), neg=0, invalid=762
0012: dt=443.904000, rms=0.664 (0.112%), neg=0, invalid=762
0013: dt=443.904000, rms=0.664 (-0.516%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.665, neg=0, invalid=762
0014: dt=129.472000, rms=0.663 (0.309%), neg=0, invalid=762
0015: dt=517.888000, rms=0.661 (0.233%), neg=0, invalid=762
0016: dt=517.888000, rms=0.661 (-0.056%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.664, neg=0, invalid=762
0017: dt=131.047619, rms=0.654 (1.525%), neg=0, invalid=762
0018: dt=157.866667, rms=0.642 (1.753%), neg=0, invalid=762
0019: dt=68.363636, rms=0.638 (0.645%), neg=0, invalid=762
0020: dt=331.776000, rms=0.631 (1.142%), neg=0, invalid=762
0021: dt=58.616822, rms=0.626 (0.774%), neg=0, invalid=762
0022: dt=145.152000, rms=0.623 (0.459%), neg=0, invalid=762
0023: dt=71.960199, rms=0.622 (0.163%), neg=0, invalid=762
0024: dt=71.960199, rms=0.621 (0.212%), neg=0, invalid=762
0025: dt=71.960199, rms=0.619 (0.287%), neg=0, invalid=762
0026: dt=71.960199, rms=0.617 (0.391%), neg=0, invalid=762
0027: dt=71.960199, rms=0.614 (0.403%), neg=0, invalid=762
0028: dt=71.960199, rms=0.611 (0.501%), neg=0, invalid=762
0029: dt=71.960199, rms=0.608 (0.472%), neg=0, invalid=762
0030: dt=71.960199, rms=0.605 (0.433%), neg=0, invalid=762
0031: dt=71.960199, rms=0.603 (0.358%), neg=0, invalid=762
0032: dt=71.960199, rms=0.601 (0.338%), neg=0, invalid=762
0033: dt=71.960199, rms=0.599 (0.326%), neg=0, invalid=762
0034: dt=71.960199, rms=0.598 (0.261%), neg=0, invalid=762
0035: dt=71.960199, rms=0.596 (0.235%), neg=0, invalid=762
0036: dt=71.960199, rms=0.595 (0.166%), neg=0, invalid=762
0037: dt=71.960199, rms=0.594 (0.168%), neg=0, invalid=762
0038: dt=71.960199, rms=0.593 (0.155%), neg=0, invalid=762
0039: dt=71.960199, rms=0.593 (0.141%), neg=0, invalid=762
0040: dt=71.960199, rms=0.592 (0.106%), neg=0, invalid=762
0041: dt=71.960199, rms=0.591 (0.108%), neg=0, invalid=762
0042: dt=71.960199, rms=0.591 (0.111%), neg=0, invalid=762
0043: dt=71.960199, rms=0.590 (0.103%), neg=0, invalid=762
0044: dt=36.288000, rms=0.590 (0.006%), neg=0, invalid=762
0045: dt=36.288000, rms=0.590 (0.005%), neg=0, invalid=762
0046: dt=36.288000, rms=0.590 (0.008%), neg=0, invalid=762
0047: dt=36.288000, rms=0.590 (0.014%), neg=0, invalid=762
0048: dt=36.288000, rms=0.590 (0.011%), neg=0, invalid=762
0049: dt=36.288000, rms=0.590 (0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.590, neg=0, invalid=762
0050: dt=124.416000, rms=0.588 (0.440%), neg=0, invalid=762
0051: dt=36.288000, rms=0.587 (0.058%), neg=0, invalid=762
0052: dt=36.288000, rms=0.587 (0.024%), neg=0, invalid=762
0053: dt=36.288000, rms=0.587 (0.038%), neg=0, invalid=762
0054: dt=36.288000, rms=0.587 (0.033%), neg=0, invalid=762
0055: dt=36.288000, rms=0.587 (0.033%), neg=0, invalid=762
0056: dt=36.288000, rms=0.587 (0.025%), neg=0, invalid=762
0057: dt=145.152000, rms=0.587 (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=0.610, neg=0, invalid=762
0058: dt=6.400000, rms=0.609 (0.152%), neg=0, invalid=762
0059: dt=0.700000, rms=0.609 (0.002%), neg=0, invalid=762
0060: dt=0.700000, rms=0.609 (0.001%), neg=0, invalid=762
0061: dt=0.700000, rms=0.609 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.610, neg=0, invalid=762
0062: dt=0.700000, rms=0.609 (0.109%), neg=0, invalid=762
0063: dt=0.175000, rms=0.609 (0.000%), neg=0, invalid=762
0064: dt=0.175000, rms=0.609 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.672, neg=0, invalid=762
0065: dt=5.916129, rms=0.651 (3.161%), neg=0, invalid=762
0066: dt=3.181818, rms=0.650 (0.125%), neg=0, invalid=762
0067: dt=3.181818, rms=0.650 (-0.028%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.650, neg=0, invalid=762
0068: dt=0.000000, rms=0.650 (0.088%), neg=0, invalid=762
0069: dt=0.000000, rms=0.650 (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=0.703, neg=0, invalid=762
0070: dt=1.024000, rms=0.700 (0.433%), neg=0, invalid=762
0071: dt=2.097345, rms=0.695 (0.687%), neg=0, invalid=762
0072: dt=1.024000, rms=0.694 (0.098%), neg=0, invalid=762
0073: dt=1.024000, rms=0.693 (0.193%), neg=0, invalid=762
0074: dt=1.024000, rms=0.692 (0.130%), neg=0, invalid=762
0075: dt=1.024000, rms=0.692 (-0.104%), neg=0, invalid=762
0076: dt=0.000000, rms=0.692 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.693, neg=0, invalid=762
0077: dt=1.024000, rms=0.692 (0.152%), neg=0, invalid=762
0078: dt=1.536000, rms=0.691 (0.054%), neg=0, invalid=762
0079: dt=1.536000, rms=0.691 (-0.005%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.659, neg=0, invalid=762
0080: dt=0.724138, rms=0.645 (2.247%), neg=0, invalid=762
0081: dt=0.064000, rms=0.644 (0.076%), neg=0, invalid=762
0082: dt=0.064000, rms=0.644 (-0.065%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.645, neg=0, invalid=762
0083: dt=0.024000, rms=0.644 (0.092%), neg=0, invalid=762
0084: dt=0.000375, rms=0.644 (0.000%), neg=0, invalid=762
0085: dt=0.000375, rms=0.644 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.14807 (23)
Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (669 voxels, overlap=0.760)
Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (669 voxels, peak = 22), gca=21.9
gca peak = 0.15565 (16)
mri peak = 0.17483 (23)
Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (1242 voxels, overlap=0.487)
Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (1242 voxels, peak = 22), gca=22.3
gca peak = 0.26829 (96)
mri peak = 0.08190 (93)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1071 voxels, overlap=0.988)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1071 voxels, peak = 92), gca=91.7
gca peak = 0.20183 (93)
mri peak = 0.07763 (91)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (979 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (979 voxels, peak = 90), gca=89.7
gca peak = 0.21683 (55)
mri peak = 0.10967 (63)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1093 voxels, overlap=0.506)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1093 voxels, peak = 60), gca=60.2
gca peak = 0.30730 (58)
mri peak = 0.07692 (62)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (952 voxels, overlap=0.591)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (952 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.10977 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (73539 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (73539 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.11420 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (74744 voxels, overlap=0.719)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (74744 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.03533 (63)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34718 voxels, overlap=0.566)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34718 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.03873 (65)
Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (31636 voxels, overlap=0.536)
Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (31636 voxels, peak = 66), gca=66.4
gca peak = 0.14161 (67)
mri peak = 0.11242 (76)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1103 voxels, overlap=0.420)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1103 voxels, peak = 75), gca=74.7
gca peak = 0.15243 (71)
mri peak = 0.12522 (77)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1138 voxels, overlap=0.902)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1138 voxels, peak = 73), gca=73.5
gca peak = 0.13336 (57)
mri peak = 0.04369 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (31584 voxels, overlap=0.936)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (31584 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.04492 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35419 voxels, overlap=0.923)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35419 voxels, peak = 60), gca=59.6
gca peak = 0.18181 (84)
mri peak = 0.06078 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (10592 voxels, overlap=0.784)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (10592 voxels, peak = 90), gca=90.3
gca peak = 0.20573 (83)
mri peak = 0.07188 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9355 voxels, overlap=0.924)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9355 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.07186 (61)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (499 voxels, overlap=0.450)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (499 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.10617 (63)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (626 voxels, overlap=0.296)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (626 voxels, peak = 62), gca=62.4
gca peak = 0.14181 (85)
mri peak = 0.05403 (88)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6200 voxels, overlap=0.949)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6200 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.06149 (83)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (5194 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (5194 voxels, peak = 85), gca=85.1
gca peak = 0.13399 (79)
mri peak = 0.06539 (82)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2829 voxels, overlap=0.866)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2829 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.08066 (83)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2836 voxels, overlap=0.845)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2836 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.08982 (88)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (13444 voxels, overlap=0.303)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (13444 voxels, peak = 89), gca=89.2
gca peak = 0.13281 (86)
mri peak = 0.07201 (93)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1913 voxels, overlap=0.667)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1913 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.07127 (92)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1982 voxels, overlap=0.751)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1982 voxels, peak = 95), gca=94.8
gca peak = 0.20494 (23)
mri peak = 0.12921 (19)
gca peak = 0.15061 (21)
mri peak = 0.09449 (22)
Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (442 voxels, overlap=0.858)
Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (442 voxels, peak = 23), gca=22.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.12 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.19 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=0.638, neg=0, invalid=762
0086: dt=129.796491, rms=0.628 (1.556%), neg=0, invalid=762
0087: dt=369.920000, rms=0.624 (0.660%), neg=0, invalid=762
0088: dt=129.472000, rms=0.623 (0.263%), neg=0, invalid=762
0089: dt=129.472000, rms=0.622 (0.168%), neg=0, invalid=762
0090: dt=443.904000, rms=0.620 (0.209%), neg=0, invalid=762
0091: dt=110.976000, rms=0.619 (0.177%), neg=0, invalid=762
0092: dt=129.472000, rms=0.619 (0.058%), neg=0, invalid=762
0093: dt=517.888000, rms=0.618 (0.145%), neg=0, invalid=762
0094: dt=92.480000, rms=0.617 (0.092%), neg=0, invalid=762
0095: dt=1479.680000, rms=0.616 (0.236%), neg=0, invalid=762
0096: dt=92.480000, rms=0.615 (0.154%), neg=0, invalid=762
0097: dt=517.888000, rms=0.614 (0.094%), neg=0, invalid=762
0098: dt=110.976000, rms=0.614 (0.038%), neg=0, invalid=762
0099: dt=110.976000, rms=0.614 (0.023%), neg=0, invalid=762
0100: dt=110.976000, rms=0.614 (0.037%), neg=0, invalid=762
0101: dt=110.976000, rms=0.614 (0.050%), neg=0, invalid=762
0102: dt=110.976000, rms=0.613 (0.059%), neg=0, invalid=762
0103: dt=110.976000, rms=0.613 (0.065%), neg=0, invalid=762
0104: dt=110.976000, rms=0.612 (0.069%), neg=0, invalid=762
0105: dt=110.976000, rms=0.612 (0.069%), neg=0, invalid=762
0106: dt=110.976000, rms=0.611 (0.071%), neg=0, invalid=762
0107: dt=110.976000, rms=0.611 (0.069%), neg=0, invalid=762
0108: dt=110.976000, rms=0.611 (0.067%), neg=0, invalid=762
0109: dt=110.976000, rms=0.610 (0.067%), neg=0, invalid=762
0110: dt=110.976000, rms=0.610 (0.065%), neg=0, invalid=762
0111: dt=110.976000, rms=0.609 (0.058%), neg=0, invalid=762
0112: dt=110.976000, rms=0.609 (0.055%), neg=0, invalid=762
0113: dt=110.976000, rms=0.609 (0.052%), neg=0, invalid=762
0114: dt=110.976000, rms=0.609 (0.052%), neg=0, invalid=762
0115: dt=110.976000, rms=0.608 (0.053%), neg=0, invalid=762
0116: dt=110.976000, rms=0.608 (0.050%), neg=0, invalid=762
0117: dt=110.976000, rms=0.608 (0.046%), neg=0, invalid=762
0118: dt=110.976000, rms=0.607 (0.042%), neg=0, invalid=762
0119: dt=110.976000, rms=0.607 (0.044%), neg=0, invalid=762
0120: dt=110.976000, rms=0.607 (0.045%), neg=0, invalid=762
0121: dt=110.976000, rms=0.607 (0.043%), neg=0, invalid=762
0122: dt=110.976000, rms=0.606 (0.041%), neg=0, invalid=762
0123: dt=110.976000, rms=0.606 (0.041%), neg=0, invalid=762
0124: dt=110.976000, rms=0.606 (0.040%), neg=0, invalid=762
0125: dt=110.976000, rms=0.606 (0.038%), neg=0, invalid=762
0126: dt=110.976000, rms=0.605 (0.034%), neg=0, invalid=762
0127: dt=110.976000, rms=0.605 (0.035%), neg=0, invalid=762
0128: dt=110.976000, rms=0.605 (0.036%), neg=0, invalid=762
0129: dt=110.976000, rms=0.605 (0.037%), neg=0, invalid=762
0130: dt=110.976000, rms=0.605 (0.036%), neg=0, invalid=762
0131: dt=110.976000, rms=0.604 (0.038%), neg=0, invalid=762
0132: dt=110.976000, rms=0.604 (0.037%), neg=0, invalid=762
0133: dt=110.976000, rms=0.604 (0.034%), neg=0, invalid=762
0134: dt=110.976000, rms=0.604 (0.035%), neg=0, invalid=762
0135: dt=110.976000, rms=0.603 (0.033%), neg=0, invalid=762
0136: dt=110.976000, rms=0.603 (0.033%), neg=0, invalid=762
0137: dt=110.976000, rms=0.603 (0.031%), neg=0, invalid=762
0138: dt=110.976000, rms=0.603 (0.030%), neg=0, invalid=762
0139: dt=110.976000, rms=0.603 (0.029%), neg=0, invalid=762
0140: dt=110.976000, rms=0.603 (0.028%), neg=0, invalid=762
0141: dt=110.976000, rms=0.602 (0.026%), neg=0, invalid=762
0142: dt=110.976000, rms=0.602 (0.025%), neg=0, invalid=762
0143: dt=110.976000, rms=0.602 (0.026%), neg=0, invalid=762
0144: dt=110.976000, rms=0.602 (0.030%), neg=0, invalid=762
0145: dt=110.976000, rms=0.602 (0.030%), neg=0, invalid=762
0146: dt=110.976000, rms=0.602 (0.026%), neg=0, invalid=762
0147: dt=110.976000, rms=0.601 (0.026%), neg=0, invalid=762
0148: dt=110.976000, rms=0.601 (0.024%), neg=0, invalid=762
0149: dt=110.976000, rms=0.601 (0.022%), neg=0, invalid=762
0150: dt=1479.680000, rms=0.601 (0.018%), neg=0, invalid=762
0151: dt=1479.680000, rms=0.601 (-1.804%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.602, neg=0, invalid=762
0152: dt=129.472000, rms=0.600 (0.178%), neg=0, invalid=762
0153: dt=517.888000, rms=0.600 (0.131%), neg=0, invalid=762
0154: dt=129.472000, rms=0.599 (0.033%), neg=0, invalid=762
0155: dt=129.472000, rms=0.599 (0.021%), neg=0, invalid=762
0156: dt=129.472000, rms=0.599 (0.022%), neg=0, invalid=762
0157: dt=129.472000, rms=0.599 (0.024%), neg=0, invalid=762
0158: dt=129.472000, rms=0.599 (0.027%), neg=0, invalid=762
0159: dt=129.472000, rms=0.599 (0.033%), neg=0, invalid=762
0160: dt=129.472000, rms=0.598 (0.039%), neg=0, invalid=762
0161: dt=129.472000, rms=0.598 (0.041%), neg=0, invalid=762
0162: dt=129.472000, rms=0.598 (0.039%), neg=0, invalid=762
0163: dt=129.472000, rms=0.598 (0.032%), neg=0, invalid=762
0164: dt=129.472000, rms=0.598 (0.026%), neg=0, invalid=762
0165: dt=129.472000, rms=0.597 (0.026%), neg=0, invalid=762
0166: dt=129.472000, rms=0.597 (0.024%), neg=0, invalid=762
0167: dt=129.472000, rms=0.597 (0.028%), neg=0, invalid=762
0168: dt=129.472000, rms=0.597 (0.032%), neg=0, invalid=762
0169: dt=129.472000, rms=0.597 (0.026%), neg=0, invalid=762
0170: dt=129.472000, rms=0.597 (0.025%), neg=0, invalid=762
0171: dt=129.472000, rms=0.597 (0.022%), neg=0, invalid=762
0172: dt=129.472000, rms=0.596 (0.020%), neg=0, invalid=762
0173: dt=369.920000, rms=0.596 (0.002%), neg=0, invalid=762
0174: dt=369.920000, rms=0.596 (0.004%), neg=0, invalid=762
0175: dt=369.920000, rms=0.596 (0.019%), neg=0, invalid=762
0176: dt=369.920000, rms=0.596 (0.012%), neg=0, invalid=762
0177: dt=369.920000, rms=0.596 (-0.006%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.598, neg=0, invalid=762
0178: dt=135.865922, rms=0.594 (0.640%), neg=0, invalid=762
0179: dt=179.512195, rms=0.589 (0.808%), neg=0, invalid=762
0180: dt=80.432432, rms=0.586 (0.466%), neg=0, invalid=762
0181: dt=89.841509, rms=0.584 (0.378%), neg=0, invalid=762
0182: dt=99.784946, rms=0.582 (0.333%), neg=0, invalid=762
0183: dt=82.944000, rms=0.581 (0.288%), neg=0, invalid=762
0184: dt=117.085271, rms=0.579 (0.298%), neg=0, invalid=762
0185: dt=67.187739, rms=0.577 (0.244%), neg=0, invalid=762
0186: dt=145.152000, rms=0.576 (0.311%), neg=0, invalid=762
0187: dt=69.708920, rms=0.574 (0.204%), neg=0, invalid=762
0188: dt=145.152000, rms=0.573 (0.224%), neg=0, invalid=762
0189: dt=62.992126, rms=0.572 (0.205%), neg=0, invalid=762
0190: dt=145.152000, rms=0.571 (0.238%), neg=0, invalid=762
0191: dt=73.007407, rms=0.570 (0.148%), neg=0, invalid=762
0192: dt=145.152000, rms=0.569 (0.167%), neg=0, invalid=762
0193: dt=64.306220, rms=0.568 (0.168%), neg=0, invalid=762
0194: dt=145.152000, rms=0.567 (0.166%), neg=0, invalid=762
0195: dt=73.411765, rms=0.566 (0.143%), neg=0, invalid=762
0196: dt=124.416000, rms=0.565 (0.131%), neg=0, invalid=762
0197: dt=82.944000, rms=0.565 (0.129%), neg=0, invalid=762
0198: dt=82.944000, rms=0.564 (0.096%), neg=0, invalid=762
0199: dt=103.680000, rms=0.563 (0.128%), neg=0, invalid=762
0200: dt=82.944000, rms=0.563 (0.081%), neg=0, invalid=762
0201: dt=103.680000, rms=0.562 (0.120%), neg=0, invalid=762
0202: dt=82.944000, rms=0.562 (0.079%), neg=0, invalid=762
0203: dt=103.680000, rms=0.561 (0.113%), neg=0, invalid=762
0204: dt=82.944000, rms=0.561 (0.064%), neg=0, invalid=762
0205: dt=103.680000, rms=0.560 (0.112%), neg=0, invalid=762
0206: dt=82.944000, rms=0.560 (0.061%), neg=0, invalid=762
0207: dt=103.680000, rms=0.559 (0.102%), neg=0, invalid=762
0208: dt=82.944000, rms=0.559 (0.059%), neg=0, invalid=762
0209: dt=103.680000, rms=0.558 (0.095%), neg=0, invalid=762
0210: dt=62.208000, rms=0.558 (0.053%), neg=0, invalid=762
0211: dt=331.776000, rms=0.557 (0.171%), neg=0, invalid=762
0212: dt=36.288000, rms=0.557 (0.107%), neg=0, invalid=762
0213: dt=82.944000, rms=0.556 (0.054%), neg=0, invalid=762
0214: dt=124.416000, rms=0.556 (0.101%), neg=0, invalid=762
0215: dt=36.288000, rms=0.555 (0.032%), neg=0, invalid=762
0216: dt=36.288000, rms=0.555 (0.030%), neg=0, invalid=762
0217: dt=36.288000, rms=0.555 (0.039%), neg=0, invalid=762
0218: dt=36.288000, rms=0.555 (0.062%), neg=0, invalid=762
0219: dt=36.288000, rms=0.554 (0.083%), neg=0, invalid=762
0220: dt=36.288000, rms=0.554 (0.096%), neg=0, invalid=762
0221: dt=36.288000, rms=0.553 (0.105%), neg=0, invalid=762
0222: dt=36.288000, rms=0.553 (0.114%), neg=0, invalid=762
0223: dt=36.288000, rms=0.552 (0.117%), neg=0, invalid=762
0224: dt=36.288000, rms=0.551 (0.125%), neg=0, invalid=762
0225: dt=36.288000, rms=0.551 (0.125%), neg=0, invalid=762
0226: dt=36.288000, rms=0.550 (0.129%), neg=0, invalid=762
0227: dt=36.288000, rms=0.549 (0.123%), neg=0, invalid=762
0228: dt=36.288000, rms=0.548 (0.120%), neg=0, invalid=762
0229: dt=36.288000, rms=0.548 (0.120%), neg=0, invalid=762
0230: dt=36.288000, rms=0.547 (0.112%), neg=0, invalid=762
0231: dt=36.288000, rms=0.547 (0.113%), neg=0, invalid=762
0232: dt=36.288000, rms=0.546 (0.110%), neg=0, invalid=762
0233: dt=36.288000, rms=0.545 (0.102%), neg=0, invalid=762
0234: dt=36.288000, rms=0.545 (0.009%), neg=0, invalid=762
0235: dt=36.288000, rms=0.545 (0.016%), neg=0, invalid=762
0236: dt=36.288000, rms=0.545 (0.024%), neg=0, invalid=762
0237: dt=36.288000, rms=0.545 (0.034%), neg=0, invalid=762
0238: dt=36.288000, rms=0.545 (0.039%), neg=0, invalid=762
0239: dt=36.288000, rms=0.545 (0.044%), neg=0, invalid=762
0240: dt=36.288000, rms=0.544 (0.047%), neg=0, invalid=762
0241: dt=1.134000, rms=0.544 (0.001%), neg=0, invalid=762
0242: dt=0.567000, rms=0.544 (0.000%), neg=0, invalid=762
0243: dt=0.405000, rms=0.544 (0.000%), neg=0, invalid=762
0244: dt=0.006328, rms=0.544 (0.000%), neg=0, invalid=762
0245: dt=0.003164, rms=0.544 (0.000%), neg=0, invalid=762
0246: dt=0.000396, rms=0.544 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.545, neg=0, invalid=762
0247: dt=145.152000, rms=0.542 (0.579%), neg=0, invalid=762
0248: dt=124.416000, rms=0.541 (0.141%), neg=0, invalid=762
0249: dt=82.944000, rms=0.540 (0.093%), neg=0, invalid=762
0250: dt=103.680000, rms=0.540 (0.078%), neg=0, invalid=762
0251: dt=82.944000, rms=0.540 (0.056%), neg=0, invalid=762
0252: dt=103.680000, rms=0.539 (0.062%), neg=0, invalid=762
0253: dt=82.944000, rms=0.539 (0.041%), neg=0, invalid=762
0254: dt=82.944000, rms=0.539 (0.055%), neg=0, invalid=762
0255: dt=82.944000, rms=0.538 (0.076%), neg=0, invalid=762
0256: dt=82.944000, rms=0.538 (0.100%), neg=0, invalid=762
0257: dt=82.944000, rms=0.537 (0.121%), neg=0, invalid=762
0258: dt=82.944000, rms=0.537 (0.119%), neg=0, invalid=762
0259: dt=82.944000, rms=0.536 (0.109%), neg=0, invalid=762
0260: dt=82.944000, rms=0.535 (0.121%), neg=0, invalid=762
0261: dt=82.944000, rms=0.535 (0.116%), neg=0, invalid=762
0262: dt=82.944000, rms=0.534 (0.121%), neg=0, invalid=762
0263: dt=82.944000, rms=0.534 (0.115%), neg=0, invalid=762
0264: dt=82.944000, rms=0.533 (0.120%), neg=0, invalid=762
0265: dt=82.944000, rms=0.532 (0.122%), neg=0, invalid=762
0266: dt=82.944000, rms=0.532 (0.120%), neg=0, invalid=762
0267: dt=82.944000, rms=0.532 (0.020%), neg=0, invalid=762
0268: dt=82.944000, rms=0.531 (0.031%), neg=0, invalid=762
0269: dt=82.944000, rms=0.531 (0.042%), neg=0, invalid=762
0270: dt=82.944000, rms=0.531 (0.040%), neg=0, invalid=762
0271: dt=82.944000, rms=0.531 (0.048%), neg=0, invalid=762
0272: dt=82.944000, rms=0.530 (0.063%), neg=0, invalid=762
0273: dt=82.944000, rms=0.530 (0.067%), neg=0, invalid=762
0274: dt=82.944000, rms=0.530 (0.061%), neg=0, invalid=762
0275: dt=82.944000, rms=0.529 (0.058%), neg=0, invalid=762
0276: dt=82.944000, rms=0.529 (0.067%), neg=0, invalid=762
0277: dt=82.944000, rms=0.529 (0.069%), neg=0, invalid=762
0278: dt=82.944000, rms=0.528 (0.065%), neg=0, invalid=762
0279: dt=82.944000, rms=0.528 (0.066%), neg=0, invalid=762
0280: dt=82.944000, rms=0.528 (0.072%), neg=0, invalid=762
0281: dt=82.944000, rms=0.527 (0.076%), neg=0, invalid=762
0282: dt=82.944000, rms=0.527 (0.058%), neg=0, invalid=762
0283: dt=82.944000, rms=0.526 (0.068%), neg=0, invalid=762
0284: dt=82.944000, rms=0.526 (0.072%), neg=0, invalid=762
0285: dt=82.944000, rms=0.526 (0.063%), neg=0, invalid=762
0286: dt=82.944000, rms=0.525 (0.060%), neg=0, invalid=762
0287: dt=82.944000, rms=0.525 (0.064%), neg=0, invalid=762
0288: dt=82.944000, rms=0.525 (0.061%), neg=0, invalid=762
0289: dt=82.944000, rms=0.525 (0.054%), neg=0, invalid=762
0290: dt=82.944000, rms=0.524 (0.058%), neg=0, invalid=762
0291: dt=82.944000, rms=0.524 (0.052%), neg=0, invalid=762
0292: dt=82.944000, rms=0.524 (0.055%), neg=0, invalid=762
0293: dt=82.944000, rms=0.523 (0.053%), neg=0, invalid=762
0294: dt=82.944000, rms=0.523 (0.049%), neg=0, invalid=762
0295: dt=82.944000, rms=0.523 (0.047%), neg=0, invalid=762
0296: dt=82.944000, rms=0.523 (0.050%), neg=0, invalid=762
0297: dt=82.944000, rms=0.522 (0.051%), neg=0, invalid=762
0298: dt=82.944000, rms=0.522 (0.043%), neg=0, invalid=762
0299: dt=82.944000, rms=0.522 (0.043%), neg=0, invalid=762
0300: dt=82.944000, rms=0.522 (0.048%), neg=0, invalid=762
0301: dt=82.944000, rms=0.521 (0.042%), neg=0, invalid=762
0302: dt=82.944000, rms=0.521 (0.045%), neg=0, invalid=762
0303: dt=82.944000, rms=0.521 (0.040%), neg=0, invalid=762
0304: dt=82.944000, rms=0.521 (0.037%), neg=0, invalid=762
0305: dt=82.944000, rms=0.521 (0.037%), neg=0, invalid=762
0306: dt=82.944000, rms=0.520 (0.037%), neg=0, invalid=762
0307: dt=82.944000, rms=0.520 (0.039%), neg=0, invalid=762
0308: dt=82.944000, rms=0.520 (0.038%), neg=0, invalid=762
0309: dt=82.944000, rms=0.520 (0.037%), neg=0, invalid=762
0310: dt=82.944000, rms=0.520 (0.035%), neg=0, invalid=762
0311: dt=82.944000, rms=0.519 (0.028%), neg=0, invalid=762
0312: dt=82.944000, rms=0.519 (0.035%), neg=0, invalid=762
0313: dt=82.944000, rms=0.519 (0.032%), neg=0, invalid=762
0314: dt=82.944000, rms=0.519 (0.026%), neg=0, invalid=762
0315: dt=82.944000, rms=0.519 (0.031%), neg=0, invalid=762
0316: dt=82.944000, rms=0.519 (0.003%), neg=0, invalid=762
0317: dt=82.944000, rms=0.519 (0.007%), neg=0, invalid=762
0318: dt=82.944000, rms=0.519 (0.008%), neg=0, invalid=762
0319: dt=82.944000, rms=0.519 (0.004%), neg=0, invalid=762
0320: dt=103.680000, rms=0.519 (0.000%), neg=0, invalid=762
0321: dt=12.960000, rms=0.519 (0.002%), neg=0, invalid=762
0322: dt=6.480000, rms=0.519 (0.000%), neg=0, invalid=762
0323: dt=3.240000, rms=0.519 (-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=0.529, neg=0, invalid=762
0324: dt=25.600000, rms=0.527 (0.304%), neg=0, invalid=762
0325: dt=44.800000, rms=0.526 (0.219%), neg=0, invalid=762
0326: dt=44.800000, rms=0.524 (0.341%), neg=0, invalid=762
0327: dt=44.800000, rms=0.522 (0.310%), neg=0, invalid=762
0328: dt=44.800000, rms=0.521 (0.330%), neg=0, invalid=762
0329: dt=32.000000, rms=0.520 (0.145%), neg=0, invalid=762
0330: dt=2.800000, rms=0.520 (0.041%), neg=0, invalid=762
0331: dt=0.350000, rms=0.520 (0.003%), neg=0, invalid=762
0332: dt=0.005469, rms=0.520 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0333: dt=0.002734, rms=0.520 (0.143%), neg=0, invalid=762
0334: dt=0.002734, rms=0.520 (0.000%), neg=0, invalid=762
0335: dt=0.000684, rms=0.520 (0.000%), neg=0, invalid=762
0336: dt=0.000043, rms=0.520 (0.000%), neg=0, invalid=762
0337: dt=0.000005, rms=0.520 (0.000%), neg=0, invalid=762
0338: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.543, neg=0, invalid=762
0339: dt=15.068607, rms=0.536 (1.321%), neg=0, invalid=762
0340: dt=4.032000, rms=0.535 (0.232%), neg=0, invalid=762
0341: dt=4.032000, rms=0.534 (0.204%), neg=0, invalid=762
0342: dt=4.032000, rms=0.533 (0.161%), neg=0, invalid=762
0343: dt=4.032000, rms=0.532 (0.133%), neg=0, invalid=762
0344: dt=4.032000, rms=0.531 (0.115%), neg=0, invalid=762
0345: dt=0.252000, rms=0.531 (0.006%), neg=0, invalid=762
0346: dt=0.252000, rms=0.531 (0.006%), neg=0, invalid=762
0347: dt=0.126000, rms=0.531 (0.003%), neg=0, invalid=762
0348: dt=0.031500, rms=0.531 (0.001%), neg=0, invalid=762
0349: dt=0.013500, rms=0.531 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.532, neg=0, invalid=762
0350: dt=14.684932, rms=0.529 (0.433%), neg=0, invalid=762
0351: dt=26.057143, rms=0.528 (0.222%), neg=0, invalid=762
0352: dt=13.824000, rms=0.528 (0.141%), neg=0, invalid=762
0353: dt=15.609756, rms=0.527 (0.102%), neg=0, invalid=762
0354: dt=12.000000, rms=0.527 (0.073%), neg=0, invalid=762
0355: dt=17.142857, rms=0.526 (0.086%), neg=0, invalid=762
0356: dt=11.520000, rms=0.526 (0.051%), neg=0, invalid=762
0357: dt=18.000000, rms=0.526 (0.078%), neg=0, invalid=762
0358: dt=11.600000, rms=0.525 (0.051%), neg=0, invalid=762
0359: dt=16.128000, rms=0.525 (0.059%), neg=0, invalid=762
0360: dt=11.428571, rms=0.525 (0.037%), neg=0, invalid=762
0361: dt=11.428571, rms=0.524 (0.057%), neg=0, invalid=762
0362: dt=11.428571, rms=0.524 (0.073%), neg=0, invalid=762
0363: dt=11.428571, rms=0.524 (0.025%), neg=0, invalid=762
0364: dt=11.428571, rms=0.524 (0.055%), neg=0, invalid=762
0365: dt=11.428571, rms=0.523 (0.085%), neg=0, invalid=762
0366: dt=11.428571, rms=0.523 (0.094%), neg=0, invalid=762
0367: dt=11.428571, rms=0.522 (0.109%), neg=0, invalid=762
0368: dt=11.428571, rms=0.522 (0.112%), neg=0, invalid=762
0369: dt=11.428571, rms=0.521 (0.128%), neg=0, invalid=762
0370: dt=11.428571, rms=0.520 (0.106%), neg=0, invalid=762
0371: dt=11.428571, rms=0.520 (0.092%), neg=0, invalid=762
0372: dt=11.428571, rms=0.519 (0.080%), neg=0, invalid=762
0373: dt=11.428571, rms=0.519 (0.086%), neg=0, invalid=762
0374: dt=11.428571, rms=0.519 (0.068%), neg=0, invalid=762
0375: dt=11.428571, rms=0.518 (0.062%), neg=0, invalid=762
0376: dt=11.428571, rms=0.518 (0.071%), neg=0, invalid=762
0377: dt=11.428571, rms=0.518 (0.081%), neg=0, invalid=762
0378: dt=11.428571, rms=0.517 (0.056%), neg=0, invalid=762
0379: dt=11.428571, rms=0.517 (0.032%), neg=0, invalid=762
0380: dt=11.428571, rms=0.517 (0.035%), neg=0, invalid=762
0381: dt=11.428571, rms=0.517 (0.052%), neg=0, invalid=762
0382: dt=11.428571, rms=0.516 (0.036%), neg=0, invalid=762
0383: dt=11.428571, rms=0.516 (0.025%), neg=0, invalid=762
0384: dt=11.428571, rms=0.516 (0.038%), neg=0, invalid=762
0385: dt=11.428571, rms=0.516 (0.028%), neg=0, invalid=762
0386: dt=11.428571, rms=0.516 (0.013%), neg=0, invalid=762
0387: dt=11.428571, rms=0.516 (0.016%), neg=0, invalid=762
0388: dt=11.428571, rms=0.516 (0.035%), neg=0, invalid=762
0389: dt=11.428571, rms=0.516 (0.024%), neg=0, invalid=762
0390: dt=11.428571, rms=0.516 (0.001%), neg=0, invalid=762
0391: dt=11.520000, rms=0.515 (0.023%), neg=0, invalid=762
0392: dt=0.576000, rms=0.515 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.531, neg=0, invalid=762
0393: dt=0.000000, rms=0.530 (0.095%), neg=0, invalid=762
0394: dt=0.000000, rms=0.530 (0.000%), neg=0, invalid=762
0395: dt=0.100000, rms=0.530 (-0.126%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.531, neg=0, invalid=762
0396: dt=0.000000, rms=0.530 (0.095%), neg=0, invalid=762
0397: dt=0.000000, rms=0.530 (0.000%), neg=0, invalid=762
0398: dt=0.100000, rms=0.530 (-0.116%), 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=0.506, neg=0, invalid=762
0399: dt=0.448000, rms=0.494 (2.361%), neg=0, invalid=762
0400: dt=0.448000, rms=0.491 (0.536%), neg=0, invalid=762
0401: dt=0.448000, rms=0.490 (0.319%), neg=0, invalid=762
0402: dt=0.448000, rms=0.489 (0.204%), neg=0, invalid=762
0403: dt=0.448000, rms=0.488 (0.157%), neg=0, invalid=762
0404: dt=0.448000, rms=0.487 (0.116%), neg=0, invalid=762
0405: dt=0.448000, rms=0.487 (0.091%), neg=0, invalid=762
0406: dt=0.448000, rms=0.487 (0.074%), neg=0, invalid=762
0407: dt=0.448000, rms=0.486 (0.063%), neg=0, invalid=762
0408: dt=0.448000, rms=0.486 (0.052%), neg=0, invalid=762
0409: dt=0.448000, rms=0.486 (0.045%), neg=0, invalid=762
0410: dt=0.448000, rms=0.486 (0.038%), neg=0, invalid=762
0411: dt=0.448000, rms=0.485 (0.067%), neg=0, invalid=762
0412: dt=0.448000, rms=0.485 (0.083%), neg=0, invalid=762
0413: dt=0.448000, rms=0.485 (0.083%), neg=0, invalid=762
0414: dt=0.448000, rms=0.485 (0.004%), neg=0, invalid=762
0415: dt=0.448000, rms=0.484 (0.012%), neg=0, invalid=762
0416: dt=0.448000, rms=0.484 (0.016%), neg=0, invalid=762
0417: dt=0.448000, rms=0.484 (0.019%), neg=0, invalid=762
0418: dt=0.448000, rms=0.484 (0.006%), neg=0, invalid=762
0419: dt=0.448000, rms=0.484 (0.005%), neg=0, invalid=762
0420: dt=0.448000, rms=0.484 (0.003%), neg=0, invalid=762
0421: dt=0.448000, rms=0.484 (0.006%), neg=0, invalid=762
0422: dt=0.448000, rms=0.484 (0.011%), neg=0, invalid=762
0423: dt=0.448000, rms=0.484 (0.012%), neg=0, invalid=762
0424: dt=0.448000, rms=0.484 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.485, neg=0, invalid=762
0425: dt=0.448000, rms=0.480 (0.990%), neg=0, invalid=762
0426: dt=0.448000, rms=0.479 (0.108%), neg=0, invalid=762
0427: dt=0.448000, rms=0.479 (0.025%), neg=0, invalid=762
0428: dt=0.448000, rms=0.479 (0.002%), neg=0, invalid=762
0429: dt=0.448000, rms=0.479 (-0.004%), 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=0.477, neg=0, invalid=762
0430: dt=0.000000, rms=0.477 (0.130%), neg=0, invalid=762
0431: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0432: dt=129.472000, rms=0.477 (0.175%), neg=0, invalid=762
0433: dt=369.920000, rms=0.476 (0.047%), neg=0, invalid=762
0434: dt=369.920000, rms=0.476 (-0.222%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0435: dt=36.288000, rms=0.476 (0.204%), neg=0, invalid=762
0436: dt=20.736000, rms=0.476 (0.013%), neg=0, invalid=762
0437: dt=20.736000, rms=0.476 (0.002%), neg=0, invalid=762
0438: dt=20.736000, rms=0.476 (-0.025%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0439: dt=110.840580, rms=0.474 (0.484%), neg=0, invalid=762
0440: dt=64.805031, rms=0.474 (0.153%), neg=0, invalid=762
0441: dt=64.805031, rms=0.473 (0.055%), neg=0, invalid=762
0442: dt=64.805031, rms=0.473 (0.139%), neg=0, invalid=762
0443: dt=64.805031, rms=0.472 (0.178%), neg=0, invalid=762
0444: dt=64.805031, rms=0.471 (0.124%), neg=0, invalid=762
0445: dt=64.805031, rms=0.471 (0.137%), neg=0, invalid=762
0446: dt=64.805031, rms=0.470 (0.092%), neg=0, invalid=762
0447: dt=64.805031, rms=0.470 (0.101%), neg=0, invalid=762
0448: dt=64.805031, rms=0.469 (0.092%), neg=0, invalid=762
0449: dt=36.288000, rms=0.469 (0.015%), neg=0, invalid=762
0450: dt=36.288000, rms=0.469 (0.015%), neg=0, invalid=762
0451: dt=36.288000, rms=0.469 (0.024%), neg=0, invalid=762
0452: dt=36.288000, rms=0.469 (0.032%), neg=0, invalid=762
0453: dt=36.288000, rms=0.469 (0.037%), neg=0, invalid=762
0454: dt=36.288000, rms=0.469 (0.038%), neg=0, invalid=762
0455: dt=36.288000, rms=0.468 (0.037%), neg=0, invalid=762
0456: dt=36.288000, rms=0.468 (0.036%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0457: dt=25.600000, rms=0.468 (0.373%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 0 iterations, nbhd size=0, neg = 0
0458: dt=44.800000, rms=0.467 (0.221%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 10 iterations, nbhd size=1, neg = 0
0459: dt=44.800000, rms=0.466 (0.058%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 2 iterations, nbhd size=0, neg = 0
0460: dt=44.800000, rms=0.465 (0.380%), neg=0, invalid=762
iter 0, gcam->neg = 20
after 10 iterations, nbhd size=1, neg = 0
0461: dt=44.800000, rms=0.464 (0.144%), neg=0, invalid=762
iter 0, gcam->neg = 58
after 11 iterations, nbhd size=1, neg = 0
0462: dt=44.800000, rms=0.464 (0.070%), neg=0, invalid=762
iter 0, gcam->neg = 64
after 14 iterations, nbhd size=1, neg = 0
0463: dt=44.800000, rms=0.463 (0.112%), neg=0, invalid=762
iter 0, gcam->neg = 56
after 12 iterations, nbhd size=1, neg = 0
0464: dt=44.800000, rms=0.462 (0.248%), neg=0, invalid=762
iter 0, gcam->neg = 59
after 14 iterations, nbhd size=1, neg = 0
0465: dt=44.800000, rms=0.461 (0.133%), neg=0, invalid=762
iter 0, gcam->neg = 43
after 13 iterations, nbhd size=1, neg = 0
0466: dt=44.800000, rms=0.460 (0.206%), neg=0, invalid=762
iter 0, gcam->neg = 30
after 12 iterations, nbhd size=1, neg = 0
0467: dt=44.800000, rms=0.460 (-0.011%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0468: dt=25.600000, rms=0.459 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0469: dt=32.000000, rms=0.459 (0.100%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0470: dt=57.502538, rms=0.455 (1.137%), neg=0, invalid=762
0471: dt=29.000000, rms=0.453 (0.411%), neg=0, invalid=762
0472: dt=38.400000, rms=0.451 (0.301%), neg=0, invalid=762
0473: dt=23.518072, rms=0.451 (0.122%), neg=0, invalid=762
0474: dt=23.518072, rms=0.450 (0.163%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0475: dt=23.518072, rms=0.449 (0.153%), neg=0, invalid=762
0476: dt=23.518072, rms=0.449 (0.132%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0477: dt=23.518072, rms=0.448 (0.139%), neg=0, invalid=762
0478: dt=23.518072, rms=0.448 (0.041%), neg=0, invalid=762
0479: dt=23.518072, rms=0.448 (-0.021%), neg=0, invalid=762
0480: dt=11.200000, rms=0.448 (0.025%), neg=0, invalid=762
0481: dt=44.800000, rms=0.448 (0.067%), neg=0, invalid=762
0482: dt=11.200000, rms=0.448 (0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.456, neg=0, invalid=762
0483: dt=2.260870, rms=0.455 (0.159%), neg=0, invalid=762
0484: dt=0.576000, rms=0.455 (0.004%), neg=0, invalid=762
0485: dt=0.576000, rms=0.455 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.456, neg=0, invalid=762
0486: dt=6.133333, rms=0.455 (0.237%), neg=0, invalid=762
0487: dt=4.032000, rms=0.454 (0.028%), neg=0, invalid=762
0488: dt=4.032000, rms=0.454 (0.010%), neg=0, invalid=762
0489: dt=4.032000, rms=0.454 (-0.027%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
0490: dt=0.000000, rms=0.463 (0.130%), neg=0, invalid=762
0491: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
0492: dt=1.280000, rms=0.463 (0.269%), neg=0, invalid=762
0493: dt=1.024000, rms=0.462 (0.032%), neg=0, invalid=762
0494: dt=1.024000, rms=0.462 (0.004%), neg=0, invalid=762
0495: dt=1.024000, rms=0.462 (-0.087%), 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=0.454, neg=0, invalid=762
iter 0, gcam->neg = 395
after 11 iterations, nbhd size=1, neg = 0
0496: dt=2.097020, rms=0.431 (5.053%), neg=0, invalid=762
0497: dt=0.080000, rms=0.431 (0.036%), neg=0, invalid=762
0498: dt=0.080000, rms=0.431 (-0.050%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.432, neg=0, invalid=762
0499: dt=0.080000, rms=0.431 (0.223%), neg=0, invalid=762
0500: dt=0.007000, rms=0.431 (0.002%), neg=0, invalid=762
0501: dt=0.007000, rms=0.431 (0.001%), neg=0, invalid=762
0502: dt=0.007000, rms=0.431 (-0.002%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0503: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0504: dt=73.984000, rms=0.419 (0.009%), neg=0, invalid=762
0505: dt=221.952000, rms=0.419 (0.012%), neg=0, invalid=762
0506: dt=27.744000, rms=0.419 (0.000%), neg=0, invalid=762
0507: dt=27.744000, rms=0.419 (0.000%), neg=0, invalid=762
0508: dt=27.744000, rms=0.419 (0.001%), neg=0, invalid=762
0509: dt=27.744000, rms=0.419 (0.001%), neg=0, invalid=762
0510: dt=27.744000, rms=0.419 (0.002%), neg=0, invalid=762
0511: dt=27.744000, rms=0.419 (0.002%), neg=0, invalid=762
0512: dt=27.744000, rms=0.419 (0.002%), neg=0, invalid=762
0513: dt=27.744000, rms=0.419 (0.002%), neg=0, invalid=762
0514: dt=27.744000, rms=0.419 (0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0515: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0516: dt=145.152000, rms=0.419 (0.085%), neg=0, invalid=762
0517: dt=145.152000, rms=0.419 (0.071%), neg=0, invalid=762
0518: dt=145.152000, rms=0.419 (-0.122%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0519: dt=11.200000, rms=0.419 (0.106%), neg=0, invalid=762
0520: dt=9.600000, rms=0.419 (0.027%), neg=0, invalid=762
0521: dt=9.600000, rms=0.419 (0.002%), neg=0, invalid=762
0522: dt=9.600000, rms=0.419 (-0.062%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0523: dt=61.600000, rms=0.416 (0.712%), neg=0, invalid=762
0524: dt=30.204082, rms=0.414 (0.301%), neg=0, invalid=762
0525: dt=44.800000, rms=0.414 (0.162%), neg=0, invalid=762
0526: dt=44.800000, rms=0.413 (0.124%), neg=0, invalid=762
0527: dt=44.800000, rms=0.412 (0.318%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0528: dt=44.800000, rms=0.411 (0.195%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0529: dt=44.800000, rms=0.410 (0.334%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0530: dt=44.800000, rms=0.409 (0.206%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0531: dt=44.800000, rms=0.408 (0.201%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0532: dt=44.800000, rms=0.407 (0.163%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 1 iterations, nbhd size=0, neg = 0
0533: dt=44.800000, rms=0.407 (0.137%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0534: dt=44.800000, rms=0.406 (0.109%), neg=0, invalid=762
0535: dt=44.800000, rms=0.406 (0.054%), neg=0, invalid=762
0536: dt=25.600000, rms=0.406 (0.045%), neg=0, invalid=762
0537: dt=25.600000, rms=0.406 (0.001%), neg=0, invalid=762
0538: dt=25.600000, rms=0.406 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.411, neg=0, invalid=762
0539: dt=0.045000, rms=0.411 (0.000%), neg=0, invalid=762
0540: dt=0.000450, rms=0.411 (0.000%), neg=0, invalid=762
0541: dt=0.000450, rms=0.411 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.411, neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0542: dt=2.880000, rms=0.411 (0.021%), neg=0, invalid=762
0543: dt=1.500000, rms=0.411 (0.003%), neg=0, invalid=762
0544: dt=1.500000, rms=0.411 (-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=0.420, neg=0, invalid=762
0545: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0546: dt=0.384000, rms=0.420 (0.019%), neg=0, invalid=762
0547: dt=0.112000, rms=0.420 (0.002%), neg=0, invalid=762
0548: dt=0.112000, rms=0.420 (-0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
iter 0, gcam->neg = 358
after 14 iterations, nbhd size=1, neg = 0
0549: dt=1.387483, rms=0.397 (2.198%), neg=0, invalid=762
0550: dt=0.000023, rms=0.397 (0.000%), neg=0, invalid=762
0551: dt=0.000023, rms=0.397 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.397, neg=0, invalid=762
0552: dt=0.112000, rms=0.397 (0.052%), neg=0, invalid=762
0553: dt=0.028000, rms=0.397 (0.006%), neg=0, invalid=762
0554: dt=0.028000, rms=0.397 (0.003%), neg=0, invalid=762
0555: dt=0.028000, rms=0.397 (-0.003%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 40 minutes and 50 seconds.
mri_ca_register utimesec    10685.045626
mri_ca_register stimesec    8.370727
mri_ca_register ru_maxrss   1351280
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   3890096
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63392
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    5669
mri_ca_register ru_nivcsw   35897
FSRUNTIME@ mri_ca_register  2.6806 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 21:37:26 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-931
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-6.0.0/0050044/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.35
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 = 0.15502 (23)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (736 voxels, overlap=0.862)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (736 voxels, peak = 20), gca=20.5
gca peak = 0.17677 (13)
mri peak = 0.18288 (23)
Right_Lateral_Ventricle (43): linear fit = 1.60 x + 0.0 (1284 voxels, overlap=0.340)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1284 voxels, peak = 21), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.08701 (93)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (839 voxels, overlap=1.019)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (839 voxels, peak = 91), gca=90.7
gca peak = 0.16930 (96)
mri peak = 0.09751 (95)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (877 voxels, overlap=1.011)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (877 voxels, peak = 94), gca=93.6
gca peak = 0.24553 (55)
mri peak = 0.12755 (63)
Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (998 voxels, overlap=0.476)
Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (998 voxels, peak = 61), gca=60.8
gca peak = 0.30264 (59)
mri peak = 0.09150 (63)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1067 voxels, overlap=0.715)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1067 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.11092 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57099 voxels, overlap=0.641)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57099 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.12250 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60296 voxels, overlap=0.658)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60296 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.04190 (65)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39913 voxels, overlap=0.722)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39913 voxels, peak = 66), gca=65.8
gca peak = 0.11620 (58)
mri peak = 0.04323 (67)
Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (38759 voxels, overlap=0.806)
Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (38759 voxels, peak = 65), gca=64.7
gca peak = 0.30970 (66)
mri peak = 0.13030 (78)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (1251 voxels, overlap=0.028)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (1251 voxels, peak = 76), gca=75.6
gca peak = 0.15280 (69)
mri peak = 0.15267 (76)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1229 voxels, overlap=0.673)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1229 voxels, peak = 71), gca=70.7
gca peak = 0.13902 (56)
mri peak = 0.04674 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (32858 voxels, overlap=0.957)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (32858 voxels, peak = 60), gca=59.6
gca peak = 0.14777 (55)
mri peak = 0.04871 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35206 voxels, overlap=0.940)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35206 voxels, peak = 59), gca=58.6
gca peak = 0.16765 (84)
mri peak = 0.07900 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6718 voxels, overlap=0.810)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6718 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.09376 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6854 voxels, overlap=0.802)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6854 voxels, peak = 88), gca=87.8
gca peak = 0.29869 (57)
mri peak = 0.09199 (63)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (584 voxels, overlap=0.799)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (584 voxels, peak = 62), gca=62.4
gca peak = 0.33601 (57)
mri peak = 0.09884 (63)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (677 voxels, overlap=0.296)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (677 voxels, peak = 65), gca=64.7
gca peak = 0.11131 (90)
mri peak = 0.06837 (88)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5055 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5055 voxels, peak = 90), gca=89.6
gca peak = 0.11793 (83)
mri peak = 0.06543 (83)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4817 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4817 voxels, peak = 84), gca=84.2
gca peak = 0.08324 (81)
mri peak = 0.08824 (82)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (2210 voxels, overlap=0.757)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (2210 voxels, peak = 86), gca=86.3
gca peak = 0.10360 (77)
mri peak = 0.08626 (83)
Right_Putamen (51): linear fit = 1.03 x + 0.0 (2445 voxels, overlap=0.809)
Right_Putamen (51): linear fit = 1.03 x + 0.0 (2445 voxels, peak = 80), gca=79.7
gca peak = 0.08424 (78)
mri peak = 0.08710 (88)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (12937 voxels, overlap=0.414)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (12937 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.07313 (94)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1943 voxels, overlap=0.793)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1943 voxels, peak = 94), gca=93.9
gca peak = 0.14500 (87)
mri peak = 0.07223 (92)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1973 voxels, overlap=0.878)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1973 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.16719 (20)
gca peak = 0.19357 (14)
mri peak = 0.08095 (18)
Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (377 voxels, overlap=0.873)
Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (377 voxels, peak = 17), gca=16.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.11 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 1.24 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15138 (21)
mri peak = 0.15502 (23)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (736 voxels, overlap=0.855)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (736 voxels, peak = 22), gca=22.2
gca peak = 0.13442 (19)
mri peak = 0.18288 (23)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1284 voxels, overlap=0.587)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1284 voxels, peak = 19), gca=19.5
gca peak = 0.27344 (90)
mri peak = 0.08701 (93)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (839 voxels, overlap=1.015)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (839 voxels, peak = 90), gca=89.6
gca peak = 0.20154 (94)
mri peak = 0.09751 (95)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (877 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (877 voxels, peak = 94), gca=93.5
gca peak = 0.25633 (61)
mri peak = 0.12755 (63)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (998 voxels, overlap=1.002)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (998 voxels, peak = 61), gca=61.0
gca peak = 0.28035 (59)
mri peak = 0.09150 (63)
Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (1067 voxels, overlap=1.006)
Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (1067 voxels, peak = 62), gca=62.2
gca peak = 0.07767 (104)
mri peak = 0.11092 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57099 voxels, overlap=0.690)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57099 voxels, peak = 103), gca=103.5
gca peak = 0.07714 (104)
mri peak = 0.12250 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60296 voxels, overlap=0.658)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60296 voxels, peak = 104), gca=104.0
gca peak = 0.08613 (66)
mri peak = 0.04190 (65)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (39913 voxels, overlap=0.980)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (39913 voxels, peak = 65), gca=65.0
gca peak = 0.10561 (65)
mri peak = 0.04323 (67)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (38759 voxels, overlap=0.971)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (38759 voxels, peak = 65), gca=65.0
gca peak = 0.24443 (76)
mri peak = 0.13030 (78)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1251 voxels, overlap=1.000)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1251 voxels, peak = 76), gca=76.0
gca peak = 0.15166 (70)
mri peak = 0.15267 (76)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1229 voxels, overlap=0.838)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1229 voxels, peak = 70), gca=70.0
gca peak = 0.13229 (60)
mri peak = 0.04674 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (32858 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (32858 voxels, peak = 62), gca=61.5
gca peak = 0.13819 (58)
mri peak = 0.04871 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (35206 voxels, overlap=0.995)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (35206 voxels, peak = 59), gca=59.4
gca peak = 0.15888 (90)
mri peak = 0.07900 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6718 voxels, overlap=0.975)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6718 voxels, peak = 91), gca=91.3
gca peak = 0.16977 (88)
mri peak = 0.09376 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6854 voxels, overlap=0.955)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6854 voxels, peak = 89), gca=89.3
gca peak = 0.28673 (64)
mri peak = 0.09199 (63)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (584 voxels, overlap=1.024)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (584 voxels, peak = 64), gca=64.0
gca peak = 0.30305 (65)
mri peak = 0.09884 (63)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (677 voxels, overlap=1.012)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (677 voxels, peak = 65), gca=65.0
gca peak = 0.10891 (89)
mri peak = 0.06837 (88)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5055 voxels, overlap=0.999)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5055 voxels, peak = 90), gca=90.3
gca peak = 0.11092 (82)
mri peak = 0.06543 (83)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4817 voxels, overlap=0.993)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4817 voxels, peak = 82), gca=82.0
gca peak = 0.08934 (88)
mri peak = 0.08824 (82)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2210 voxels, overlap=0.863)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2210 voxels, peak = 87), gca=86.7
gca peak = 0.10883 (78)
mri peak = 0.08626 (83)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2445 voxels, overlap=0.908)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2445 voxels, peak = 78), gca=78.0
gca peak = 0.07272 (86)
mri peak = 0.08710 (88)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12937 voxels, overlap=0.799)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12937 voxels, peak = 86), gca=85.6
gca peak = 0.14720 (94)
mri peak = 0.07313 (94)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1943 voxels, overlap=0.863)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1943 voxels, peak = 93), gca=92.6
gca peak = 0.16336 (91)
mri peak = 0.07223 (92)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1973 voxels, overlap=0.939)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1973 voxels, peak = 89), gca=88.7
gca peak = 0.16784 (32)
mri peak = 0.16719 (20)
gca peak = 0.17387 (17)
mri peak = 0.08095 (18)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (377 voxels, overlap=0.846)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (377 voxels, peak = 17), gca=17.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16503 (28)
gca peak Left_Thalamus = 0.64095 (101)
gca peak Third_Ventricle = 0.16784 (32)
gca peak CSF = 0.23889 (45)
gca peak Left_Accumbens_area = 0.88914 (64)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11916 (35)
gca peak Right_Inf_Lat_Vent = 0.19786 (25)
gca peak Right_Accumbens_area = 0.29775 (74)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14509 (37)
gca peak Fifth_Ventricle = 0.63045 (39)
gca peak WM_hypointensities = 0.07697 (76)
gca peak non_WM_hypointensities = 0.09957 (77)
gca peak Optic_Chiasm = 0.70897 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.03 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
68131 voxels changed in iteration 0 of unlikely voxel relabeling
375 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
51511 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
545 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 70976 changed. image ll: -2.129, PF=0.500
pass 2: 19798 changed. image ll: -2.128, PF=0.500
pass 3: 6465 changed.
pass 4: 2358 changed.
48901 voxels changed in iteration 0 of unlikely voxel relabeling
249 voxels changed in iteration 1 of unlikely voxel relabeling
8 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8417 voxels changed in iteration 0 of unlikely voxel relabeling
149 voxels changed in iteration 1 of unlikely voxel relabeling
13 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7378 voxels changed in iteration 0 of unlikely voxel relabeling
81 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
6397 voxels changed in iteration 0 of unlikely voxel relabeling
27 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3930.879415
mri_ca_label stimesec    1.715739
mri_ca_label ru_maxrss   2146344
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   695527
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  488
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    243
mri_ca_label ru_nivcsw   11046
auto-labeling took 64 minutes and 53 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/transforms/cc_up.lta 0050044 

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-6.0.0/0050044/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/norm.mgz
51142 voxels in left wm, 60752 in right wm, xrange [122, 133]
searching rotation angles z=[-8  6], y=[-10  4]

searching scale 1 Z rot -8.4  
searching scale 1 Z rot -8.1  
searching scale 1 Z rot -7.9  
searching scale 1 Z rot -7.6  
searching scale 1 Z rot -7.4  
searching scale 1 Z rot -7.1  
searching scale 1 Z rot -6.9  
searching scale 1 Z rot -6.6  
searching scale 1 Z rot -6.4  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.4  global minimum found at slice 127.1, rotations (-3.25, -1.38)
final transformation (x=127.1, yr=-3.245, zr=-1.381):
 0.99811   0.02410  -0.05659   4.55491;
-0.02406   0.99971   0.00136   23.94485;
 0.05661   0.00000   0.99840   14.97434;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 107 106
eigenvectors:
 0.00044  -0.01218   0.99993;
-0.13083  -0.99133  -0.01202;
 0.99140  -0.13082  -0.00203;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.1 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 22:43:23 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 22:43:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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...
808 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 72 (72), valley at 34 (34)
csf peak at 18, setting threshold to 54
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 71 (71), valley at 34 (34)
csf peak at 20, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 8 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 22:46:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1826256 voxels in mask (pct= 10.89)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 22:46:34 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 (102.0): 102.4 +- 6.9 [79.0 --> 125.0]
GM (73.0) : 71.2 +- 9.5 [30.0 --> 95.0]
setting bottom of white matter range to 80.7
setting top of gray matter range to 90.1
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...
5061 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5411 filled
1747 bright non-wm voxels segmented.
2120 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 0.56 minutes
reading wm segmentation from wm.seg.mgz...
303 voxels added to wm to prevent paths from MTL structures to cortex
2856 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 38369 voxels turned on, 44300 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  26 found -  26 modified     |    TOTAL:  26
pass   2 (xy+):   0 found -  26 modified     |    TOTAL:  26
pass   1 (xy-):  27 found -  27 modified     |    TOTAL:  53
pass   2 (xy-):   0 found -  27 modified     |    TOTAL:  53
pass   1 (yz+):  33 found -  33 modified     |    TOTAL:  86
pass   2 (yz+):   0 found -  33 modified     |    TOTAL:  86
pass   1 (yz-):  23 found -  23 modified     |    TOTAL: 109
pass   2 (yz-):   0 found -  23 modified     |    TOTAL: 109
pass   1 (xz+):  17 found -  17 modified     |    TOTAL: 126
pass   2 (xz+):   0 found -  17 modified     |    TOTAL: 126
pass   1 (xz-):  22 found -  22 modified     |    TOTAL: 148
pass   2 (xz-):   0 found -  22 modified     |    TOTAL: 148
Iteration Number : 1
pass   1 (+++):  23 found -  23 modified     |    TOTAL:  23
pass   2 (+++):   0 found -  23 modified     |    TOTAL:  23
pass   1 (+++):  24 found -  24 modified     |    TOTAL:  47
pass   2 (+++):   0 found -  24 modified     |    TOTAL:  47
pass   1 (+++):  13 found -  13 modified     |    TOTAL:  60
pass   2 (+++):   0 found -  13 modified     |    TOTAL:  60
pass   1 (+++):  38 found -  38 modified     |    TOTAL:  98
pass   2 (+++):   0 found -  38 modified     |    TOTAL:  98
Iteration Number : 1
pass   1 (++):  49 found -  49 modified     |    TOTAL:  49
pass   2 (++):   0 found -  49 modified     |    TOTAL:  49
pass   1 (+-):  53 found -  53 modified     |    TOTAL: 102
pass   2 (+-):   0 found -  53 modified     |    TOTAL: 102
pass   1 (--):  79 found -  79 modified     |    TOTAL: 181
pass   2 (--):   0 found -  79 modified     |    TOTAL: 181
pass   1 (-+):  65 found -  65 modified     |    TOTAL: 246
pass   2 (-+):   0 found -  65 modified     |    TOTAL: 246
Iteration Number : 2
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz+):   5 found -   5 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   5 modified     |    TOTAL:   9
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  12
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  12
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  16
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  16
pass   1 (xz-):   5 found -   5 modified     |    TOTAL:  21
pass   2 (xz-):   0 found -   5 modified     |    TOTAL:  21
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   5
pass   1 (--):   2 found -   2 modified     |    TOTAL:   7
pass   2 (--):   0 found -   2 modified     |    TOTAL:   7
pass   1 (-+):   5 found -   5 modified     |    TOTAL:  12
pass   2 (-+):   0 found -   5 modified     |    TOTAL:  12
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 = 536 (out of 643383: 0.083310)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 22:48:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

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

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.01178   0.07636  -0.04888  -5.71814;
-0.05667   1.03028   0.30386  -31.82300;
 0.06713  -0.28330   0.95197   28.25749;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.01178   0.07636  -0.04888  -5.71814;
-0.05667   1.03028   0.30386  -31.82300;
 0.06713  -0.28330   0.95197   28.25749;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2575 (min = 350, max = 1400), aspect = 1.17 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 124, 149), TAL = (2.0, 21.0, 4.0)
talairach voxel to voxel transform
 0.98084  -0.05410   0.06763   1.97607;
 0.06835   0.88853  -0.28010   36.58131;
-0.04882   0.26824   0.96233  -18.93629;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  124,  149) --> (2.0, 21.0, 4.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (2.00, 21.00, 4.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 21.00, 4.00) SRC: (111.28, 112.41, 152.44)
search lh wm seed point around talairach space (-16.00, 21.00, 4.00), SRC: (146.59, 114.87, 150.68)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 22:49:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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


Iteration Number : 1
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   8
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:  10
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:  10
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:  10
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:  10
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:  10
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 = 11 (out of 311081: 0.003536)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 3139 vertices, 3323 faces
slice 50: 11572 vertices, 11936 faces
slice 60: 23293 vertices, 23765 faces
slice 70: 36627 vertices, 37089 faces
slice 80: 49729 vertices, 50191 faces
slice 90: 62505 vertices, 62934 faces
slice 100: 75297 vertices, 75738 faces
slice 110: 87667 vertices, 88125 faces
slice 120: 99253 vertices, 99661 faces
slice 130: 110509 vertices, 110976 faces
slice 140: 121560 vertices, 122025 faces
slice 150: 131426 vertices, 131873 faces
slice 160: 140475 vertices, 140838 faces
slice 170: 147313 vertices, 147602 faces
slice 180: 152684 vertices, 152937 faces
slice 190: 156231 vertices, 156416 faces
slice 200: 157586 vertices, 157678 faces
slice 210: 157586 vertices, 157678 faces
slice 220: 157586 vertices, 157678 faces
slice 230: 157586 vertices, 157678 faces
slice 240: 157586 vertices, 157678 faces
slice 250: 157586 vertices, 157678 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...
   157586 voxel in cpt #1: X=-92 [v=157586,e=473034,f=315356] located at (-27.068064, -23.411211, 9.771737)
For the whole surface: X=-92 [v=157586,e=473034,f=315356]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 22:49:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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


Iteration Number : 1
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   9
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   9
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:  10
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:  10
pass   1 (yz-):   5 found -   5 modified     |    TOTAL:  15
pass   2 (yz-):   0 found -   5 modified     |    TOTAL:  15
pass   1 (xz+):   5 found -   5 modified     |    TOTAL:  20
pass   2 (xz+):   0 found -   5 modified     |    TOTAL:  20
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  22
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  22
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (--):   2 found -   2 modified     |    TOTAL:   4
pass   2 (--):   0 found -   2 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 28 (out of 311240: 0.008996)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 586 vertices, 677 faces
slice 50: 6302 vertices, 6573 faces
slice 60: 15671 vertices, 16062 faces
slice 70: 28450 vertices, 28893 faces
slice 80: 40328 vertices, 40735 faces
slice 90: 52957 vertices, 53408 faces
slice 100: 64555 vertices, 64993 faces
slice 110: 77283 vertices, 77717 faces
slice 120: 89279 vertices, 89693 faces
slice 130: 101029 vertices, 101535 faces
slice 140: 112884 vertices, 113304 faces
slice 150: 124351 vertices, 124803 faces
slice 160: 134724 vertices, 135125 faces
slice 170: 143290 vertices, 143622 faces
slice 180: 149835 vertices, 150114 faces
slice 190: 154913 vertices, 155143 faces
slice 200: 157753 vertices, 157855 faces
slice 210: 157768 vertices, 157862 faces
slice 220: 157768 vertices, 157862 faces
slice 230: 157768 vertices, 157862 faces
slice 240: 157768 vertices, 157862 faces
slice 250: 157768 vertices, 157862 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...
   157768 voxel in cpt #1: X=-94 [v=157768,e=473586,f=315724] located at (29.508772, -16.209244, 13.841882)
For the whole surface: X=-94 [v=157768,e=473586,f=315724]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 22:49:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 22:49:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

Waiting for PID 6152 of (6152 6155) to complete...
Waiting for PID 6155 of (6152 6155) 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 (6152 6155) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 22:49:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 22:49:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

Waiting for PID 6201 of (6201 6204) to complete...
Waiting for PID 6204 of (6201 6204) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 48.8 mm, total surface area = 83172 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.156 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.061 (target=0.015)   
step 030: RMS=0.055 (target=0.015)   
step 035: RMS=0.051 (target=0.015)   
step 040: RMS=0.049 (target=0.015)   
step 045: RMS=0.047 (target=0.015)   
step 050: RMS=0.046 (target=0.015)   
step 055: RMS=0.045 (target=0.015)   
step 060: RMS=0.045 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    48.617609
mris_inflate stimesec    0.121981
mris_inflate ru_maxrss   229868
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33386
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11104
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2067
mris_inflate ru_nivcsw   3502

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.2 mm, total surface area = 83167 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.060 (target=0.015)   
step 030: RMS=0.055 (target=0.015)   
step 035: RMS=0.051 (target=0.015)   
step 040: RMS=0.048 (target=0.015)   
step 045: RMS=0.047 (target=0.015)   
step 050: RMS=0.045 (target=0.015)   
step 055: RMS=0.044 (target=0.015)   
step 060: RMS=0.044 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    48.456633
mris_inflate stimesec    0.106983
mris_inflate ru_maxrss   230136
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32941
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11120
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2302
mris_inflate ru_nivcsw   3475
PIDs (6201 6204) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 22:50:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 22:50:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

Waiting for PID 6290 of (6290 6294) to complete...
Waiting for PID 6294 of (6290 6294) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.93 +- 0.56 (0.00-->6.22) (max @ vno 63300 --> 64490)
face area 0.02 +- 0.03 (-0.19-->0.67)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.301...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.167, avgs=0
005/300: dt: 0.9000, rms radial error=175.906, avgs=0
010/300: dt: 0.9000, rms radial error=175.347, avgs=0
015/300: dt: 0.9000, rms radial error=174.612, avgs=0
020/300: dt: 0.9000, rms radial error=173.781, avgs=0
025/300: dt: 0.9000, rms radial error=172.892, avgs=0
030/300: dt: 0.9000, rms radial error=171.971, avgs=0
035/300: dt: 0.9000, rms radial error=171.033, avgs=0
040/300: dt: 0.9000, rms radial error=170.088, avgs=0
045/300: dt: 0.9000, rms radial error=169.140, avgs=0
050/300: dt: 0.9000, rms radial error=168.192, avgs=0
055/300: dt: 0.9000, rms radial error=167.247, avgs=0
060/300: dt: 0.9000, rms radial error=166.305, avgs=0
065/300: dt: 0.9000, rms radial error=165.368, avgs=0
070/300: dt: 0.9000, rms radial error=164.435, avgs=0
075/300: dt: 0.9000, rms radial error=163.508, avgs=0
080/300: dt: 0.9000, rms radial error=162.585, avgs=0
085/300: dt: 0.9000, rms radial error=161.667, avgs=0
090/300: dt: 0.9000, rms radial error=160.754, avgs=0
095/300: dt: 0.9000, rms radial error=159.846, avgs=0
100/300: dt: 0.9000, rms radial error=158.943, avgs=0
105/300: dt: 0.9000, rms radial error=158.049, avgs=0
110/300: dt: 0.9000, rms radial error=157.160, avgs=0
115/300: dt: 0.9000, rms radial error=156.276, avgs=0
120/300: dt: 0.9000, rms radial error=155.397, avgs=0
125/300: dt: 0.9000, rms radial error=154.522, avgs=0
130/300: dt: 0.9000, rms radial error=153.652, avgs=0
135/300: dt: 0.9000, rms radial error=152.788, avgs=0
140/300: dt: 0.9000, rms radial error=151.928, avgs=0
145/300: dt: 0.9000, rms radial error=151.073, avgs=0
150/300: dt: 0.9000, rms radial error=150.222, avgs=0
155/300: dt: 0.9000, rms radial error=149.376, avgs=0
160/300: dt: 0.9000, rms radial error=148.535, avgs=0
165/300: dt: 0.9000, rms radial error=147.698, avgs=0
170/300: dt: 0.9000, rms radial error=146.866, avgs=0
175/300: dt: 0.9000, rms radial error=146.039, avgs=0
180/300: dt: 0.9000, rms radial error=145.216, avgs=0
185/300: dt: 0.9000, rms radial error=144.398, avgs=0
190/300: dt: 0.9000, rms radial error=143.585, avgs=0
195/300: dt: 0.9000, rms radial error=142.776, avgs=0
200/300: dt: 0.9000, rms radial error=141.971, avgs=0
205/300: dt: 0.9000, rms radial error=141.171, avgs=0
210/300: dt: 0.9000, rms radial error=140.376, avgs=0
215/300: dt: 0.9000, rms radial error=139.585, avgs=0
220/300: dt: 0.9000, rms radial error=138.798, avgs=0
225/300: dt: 0.9000, rms radial error=138.016, avgs=0
230/300: dt: 0.9000, rms radial error=137.238, avgs=0
235/300: dt: 0.9000, rms radial error=136.464, avgs=0
240/300: dt: 0.9000, rms radial error=135.695, avgs=0
245/300: dt: 0.9000, rms radial error=134.931, avgs=0
250/300: dt: 0.9000, rms radial error=134.170, avgs=0
255/300: dt: 0.9000, rms radial error=133.414, avgs=0
260/300: dt: 0.9000, rms radial error=132.662, avgs=0
265/300: dt: 0.9000, rms radial error=131.914, avgs=0
270/300: dt: 0.9000, rms radial error=131.171, avgs=0
275/300: dt: 0.9000, rms radial error=130.431, avgs=0
280/300: dt: 0.9000, rms radial error=129.696, avgs=0
285/300: dt: 0.9000, rms radial error=128.965, avgs=0
290/300: dt: 0.9000, rms radial error=128.238, avgs=0
295/300: dt: 0.9000, rms radial error=127.515, avgs=0
300/300: dt: 0.9000, rms radial error=126.796, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18662.44
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 3227.39
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 3 (K=160.0), pass 1, starting sse = 350.46
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00341
epoch 4 (K=640.0), pass 1, starting sse = 29.00
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/12 = 0.00600
final distance error %27.50
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    341.387101
mris_sphere stimesec    0.206968
mris_sphere ru_maxrss   230088
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33440
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11088
mris_sphere ru_oublock  11128
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8479
mris_sphere ru_nivcsw   25274
FSRUNTIME@ mris_sphere  0.0949 hours 1 threads

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.93 +- 0.54 (0.00-->6.92) (max @ vno 116895 --> 118171)
face area 0.02 +- 0.03 (-0.22-->0.61)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.305...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.987, avgs=0
005/300: dt: 0.9000, rms radial error=175.728, avgs=0
010/300: dt: 0.9000, rms radial error=175.173, avgs=0
015/300: dt: 0.9000, rms radial error=174.446, avgs=0
020/300: dt: 0.9000, rms radial error=173.617, avgs=0
025/300: dt: 0.9000, rms radial error=172.730, avgs=0
030/300: dt: 0.9000, rms radial error=171.811, avgs=0
035/300: dt: 0.9000, rms radial error=170.874, avgs=0
040/300: dt: 0.9000, rms radial error=169.929, avgs=0
045/300: dt: 0.9000, rms radial error=168.980, avgs=0
050/300: dt: 0.9000, rms radial error=168.031, avgs=0
055/300: dt: 0.9000, rms radial error=167.089, avgs=0
060/300: dt: 0.9000, rms radial error=166.154, avgs=0
065/300: dt: 0.9000, rms radial error=165.222, avgs=0
070/300: dt: 0.9000, rms radial error=164.295, avgs=0
075/300: dt: 0.9000, rms radial error=163.373, avgs=0
080/300: dt: 0.9000, rms radial error=162.456, avgs=0
085/300: dt: 0.9000, rms radial error=161.544, avgs=0
090/300: dt: 0.9000, rms radial error=160.636, avgs=0
095/300: dt: 0.9000, rms radial error=159.734, avgs=0
100/300: dt: 0.9000, rms radial error=158.836, avgs=0
105/300: dt: 0.9000, rms radial error=157.943, avgs=0
110/300: dt: 0.9000, rms radial error=157.055, avgs=0
115/300: dt: 0.9000, rms radial error=156.172, avgs=0
120/300: dt: 0.9000, rms radial error=155.293, avgs=0
125/300: dt: 0.9000, rms radial error=154.419, avgs=0
130/300: dt: 0.9000, rms radial error=153.550, avgs=0
135/300: dt: 0.9000, rms radial error=152.686, avgs=0
140/300: dt: 0.9000, rms radial error=151.827, avgs=0
145/300: dt: 0.9000, rms radial error=150.972, avgs=0
150/300: dt: 0.9000, rms radial error=150.122, avgs=0
155/300: dt: 0.9000, rms radial error=149.277, avgs=0
160/300: dt: 0.9000, rms radial error=148.437, avgs=0
165/300: dt: 0.9000, rms radial error=147.601, avgs=0
170/300: dt: 0.9000, rms radial error=146.770, avgs=0
175/300: dt: 0.9000, rms radial error=145.943, avgs=0
180/300: dt: 0.9000, rms radial error=145.121, avgs=0
185/300: dt: 0.9000, rms radial error=144.304, avgs=0
190/300: dt: 0.9000, rms radial error=143.491, avgs=0
195/300: dt: 0.9000, rms radial error=142.682, avgs=0
200/300: dt: 0.9000, rms radial error=141.878, avgs=0
205/300: dt: 0.9000, rms radial error=141.079, avgs=0
210/300: dt: 0.9000, rms radial error=140.283, avgs=0
215/300: dt: 0.9000, rms radial error=139.492, avgs=0
220/300: dt: 0.9000, rms radial error=138.705, avgs=0
225/300: dt: 0.9000, rms radial error=137.923, avgs=0
230/300: dt: 0.9000, rms radial error=137.145, avgs=0
235/300: dt: 0.9000, rms radial error=136.372, avgs=0
240/300: dt: 0.9000, rms radial error=135.602, avgs=0
245/300: dt: 0.9000, rms radial error=134.837, avgs=0
250/300: dt: 0.9000, rms radial error=134.076, avgs=0
255/300: dt: 0.9000, rms radial error=133.320, avgs=0
260/300: dt: 0.9000, rms radial error=132.567, avgs=0
265/300: dt: 0.9000, rms radial error=131.819, avgs=0
270/300: dt: 0.9000, rms radial error=131.075, avgs=0
275/300: dt: 0.9000, rms radial error=130.335, avgs=0
280/300: dt: 0.9000, rms radial error=129.599, avgs=0
285/300: dt: 0.9000, rms radial error=128.868, avgs=0
290/300: dt: 0.9000, rms radial error=128.140, avgs=0
295/300: dt: 0.9000, rms radial error=127.417, avgs=0
300/300: dt: 0.9000, rms radial error=126.698, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18576.75
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 2 (K=40.0), pass 1, starting sse = 3144.64
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 = 338.23
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00448
epoch 4 (K=640.0), pass 1, starting sse = 29.86
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/13 = 0.00788
final distance error %26.85
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    346.572313
mris_sphere stimesec    0.204968
mris_sphere ru_maxrss   230336
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33501
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11144
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8614
mris_sphere ru_nivcsw   24882
FSRUNTIME@ mris_sphere  0.0963 hours 1 threads
PIDs (6290 6294) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 22:56:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 22:56:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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


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

#@# Fix Topology lh Sat Oct  7 22:56:32 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050044 lh 

#@# Fix Topology rh Sat Oct  7 22:56:32 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050044 rh 

Waiting for PID 6633 of (6633 6636) to complete...
Waiting for PID 6636 of (6633 6636) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050044 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=-92 (nv=157586, nf=315356, ne=473034, g=47)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
11221 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-6.0.0/0050044/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1358  (-4.5679)
      -vertex     loglikelihood: -5.8966  (-2.9483)
      -normal dot loglikelihood: -3.6064  (-3.6064)
      -quad curv  loglikelihood: -6.1445  (-3.0723)
      Total Loglikelihood : -24.7833

CORRECTING DEFECT 0 (vertices=59, convex hull=87, v0=6486)
After retessellation of defect 0 (v0=6486), euler #=-27 (151054,451164,300083) : difference with theory (-31) = -4 

CORRECTING DEFECT 1 (vertices=19, convex hull=31, v0=16026)
After retessellation of defect 1 (v0=16026), euler #=-26 (151056,451182,300100) : difference with theory (-30) = -4 

CORRECTING DEFECT 2 (vertices=38, convex hull=83, v0=18957)
After retessellation of defect 2 (v0=18957), euler #=-25 (151077,451274,300172) : difference with theory (-29) = -4 

CORRECTING DEFECT 3 (vertices=43, convex hull=39, v0=29620)
After retessellation of defect 3 (v0=29620), euler #=-24 (151086,451317,300207) : difference with theory (-28) = -4 

CORRECTING DEFECT 4 (vertices=94, convex hull=59, v0=41663)
After retessellation of defect 4 (v0=41663), euler #=-23 (151103,451393,300267) : difference with theory (-27) = -4 

CORRECTING DEFECT 5 (vertices=12, convex hull=37, v0=49414)
After retessellation of defect 5 (v0=49414), euler #=-22 (151105,451412,300285) : difference with theory (-26) = -4 

CORRECTING DEFECT 6 (vertices=83, convex hull=89, v0=54795)
After retessellation of defect 6 (v0=54795), euler #=-21 (151141,451560,300398) : difference with theory (-25) = -4 

CORRECTING DEFECT 7 (vertices=58, convex hull=113, v0=59675)
After retessellation of defect 7 (v0=59675), euler #=-20 (151174,451710,300516) : difference with theory (-24) = -4 

CORRECTING DEFECT 8 (vertices=123, convex hull=177, v0=62088)
After retessellation of defect 8 (v0=62088), euler #=-19 (151190,451840,300631) : difference with theory (-23) = -4 

CORRECTING DEFECT 9 (vertices=26, convex hull=47, v0=68498)
After retessellation of defect 9 (v0=68498), euler #=-18 (151205,451901,300678) : difference with theory (-22) = -4 

CORRECTING DEFECT 10 (vertices=1156, convex hull=859, v0=69524)
XL defect detected...
After retessellation of defect 10 (v0=69524), euler #=-19 (151528,453329,301782) : difference with theory (-21) = -2 

CORRECTING DEFECT 11 (vertices=26, convex hull=38, v0=70811)
After retessellation of defect 11 (v0=70811), euler #=-18 (151532,453352,301802) : difference with theory (-20) = -2 

CORRECTING DEFECT 12 (vertices=29, convex hull=70, v0=82560)
After retessellation of defect 12 (v0=82560), euler #=-17 (151550,453436,301869) : difference with theory (-19) = -2 

CORRECTING DEFECT 13 (vertices=6, convex hull=27, v0=86013)
After retessellation of defect 13 (v0=86013), euler #=-16 (151553,453454,301885) : difference with theory (-18) = -2 

CORRECTING DEFECT 14 (vertices=116, convex hull=51, v0=87455)
After retessellation of defect 14 (v0=87455), euler #=-15 (151562,453502,301925) : difference with theory (-17) = -2 

CORRECTING DEFECT 15 (vertices=755, convex hull=467, v0=91367)
L defect detected...
After retessellation of defect 15 (v0=91367), euler #=-15 (151797,454459,302647) : difference with theory (-16) = -1 

CORRECTING DEFECT 16 (vertices=46, convex hull=26, v0=94059)
After retessellation of defect 16 (v0=94059), euler #=-14 (151802,454483,302667) : difference with theory (-15) = -1 

CORRECTING DEFECT 17 (vertices=60, convex hull=48, v0=96724)
After retessellation of defect 17 (v0=96724), euler #=-13 (151811,454531,302707) : difference with theory (-14) = -1 

CORRECTING DEFECT 18 (vertices=547, convex hull=304, v0=103761)
After retessellation of defect 18 (v0=103761), euler #=-13 (151939,455073,303121) : difference with theory (-13) = 0 

CORRECTING DEFECT 19 (vertices=21, convex hull=29, v0=105521)
After retessellation of defect 19 (v0=105521), euler #=-12 (151944,455099,303143) : difference with theory (-12) = 0 

CORRECTING DEFECT 20 (vertices=44, convex hull=74, v0=106284)
After retessellation of defect 20 (v0=106284), euler #=-11 (151966,455194,303217) : difference with theory (-11) = 0 

CORRECTING DEFECT 21 (vertices=2241, convex hull=665, v0=109050)
XL defect detected...
After retessellation of defect 21 (v0=109050), euler #=-10 (152537,457278,304731) : difference with theory (-10) = 0 

CORRECTING DEFECT 22 (vertices=178, convex hull=183, v0=109396)
After retessellation of defect 22 (v0=109396), euler #=-9 (152600,457547,304938) : difference with theory (-9) = 0 

CORRECTING DEFECT 23 (vertices=144, convex hull=121, v0=111280)
After retessellation of defect 23 (v0=111280), euler #=-8 (152684,457853,305161) : difference with theory (-8) = 0 

CORRECTING DEFECT 24 (vertices=7, convex hull=31, v0=111351)
After retessellation of defect 24 (v0=111351), euler #=-7 (152688,457872,305177) : difference with theory (-7) = 0 

CORRECTING DEFECT 25 (vertices=94, convex hull=35, v0=111804)
After retessellation of defect 25 (v0=111804), euler #=-6 (152700,457920,305214) : difference with theory (-6) = 0 

CORRECTING DEFECT 26 (vertices=24, convex hull=35, v0=115631)
After retessellation of defect 26 (v0=115631), euler #=-5 (152709,457958,305244) : difference with theory (-5) = 0 

CORRECTING DEFECT 27 (vertices=133, convex hull=50, v0=116010)
After retessellation of defect 27 (v0=116010), euler #=-4 (152720,458008,305284) : difference with theory (-4) = 0 

CORRECTING DEFECT 28 (vertices=111, convex hull=110, v0=116362)
After retessellation of defect 28 (v0=116362), euler #=-3 (152740,458116,305373) : difference with theory (-3) = 0 

CORRECTING DEFECT 29 (vertices=35, convex hull=21, v0=124773)
After retessellation of defect 29 (v0=124773), euler #=-2 (152741,458124,305381) : difference with theory (-2) = 0 

CORRECTING DEFECT 30 (vertices=114, convex hull=44, v0=136486)
After retessellation of defect 30 (v0=136486), euler #=-1 (152765,458214,305448) : difference with theory (-1) = 0 

CORRECTING DEFECT 31 (vertices=48, convex hull=68, v0=148889)
After retessellation of defect 31 (v0=148889), euler #=0 (152779,458283,305504) : difference with theory (0) = 0 

CORRECTING DEFECT 32 (vertices=38, convex hull=58, v0=155898)
After retessellation of defect 32 (v0=155898), euler #=1 (152788,458331,305544) : difference with theory (1) = 0 

CORRECTING DEFECT 33 (vertices=29, convex hull=66, v0=157126)
After retessellation of defect 33 (v0=157126), euler #=2 (152803,458403,305602) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.24 (0.07-->13.30) (max @ vno 111821 --> 118611)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.24 (0.07-->13.30) (max @ vno 111821 --> 118611)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
135 mutations (37.5%), 225 crossovers (62.5%), 484 vertices were eliminated
building final representation...
4783 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=152803, nf=305602, ne=458403, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 44.8 minutes
0 defective edges
removing intersecting faces
000: 547 intersecting
001: 46 intersecting
002: 13 intersecting
mris_fix_topology utimesec    2688.722252
mris_fix_topology stimesec    0.520920
mris_fix_topology ru_maxrss   523816
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   63328
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  14712
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    366
mris_fix_topology ru_nivcsw   8361
FSRUNTIME@ mris_fix_topology lh  0.7471 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050044 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=-94 (nv=157768, nf=315724, ne=473586, g=48)
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...
11894 ambiguous faces found in tessellation
segmenting defects...
40 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 24 into 22
      -merging segment 31 into 22
38 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.0773  (-4.5386)
      -vertex     loglikelihood: -5.9318  (-2.9659)
      -normal dot loglikelihood: -3.6420  (-3.6420)
      -quad curv  loglikelihood: -6.1239  (-3.0619)
      Total Loglikelihood : -24.7749

CORRECTING DEFECT 0 (vertices=54, convex hull=95, v0=87)
After retessellation of defect 0 (v0=87), euler #=-26 (150764,450011,299221) : difference with theory (-35) = -9 

CORRECTING DEFECT 1 (vertices=296, convex hull=250, v0=283)
After retessellation of defect 1 (v0=283), euler #=-25 (150805,450253,299423) : difference with theory (-34) = -9 

CORRECTING DEFECT 2 (vertices=69, convex hull=123, v0=842)
After retessellation of defect 2 (v0=842), euler #=-24 (150849,450439,299566) : difference with theory (-33) = -9 

CORRECTING DEFECT 3 (vertices=161, convex hull=214, v0=1547)
After retessellation of defect 3 (v0=1547), euler #=-23 (150923,450767,299821) : difference with theory (-32) = -9 

CORRECTING DEFECT 4 (vertices=17, convex hull=54, v0=6073)
After retessellation of defect 4 (v0=6073), euler #=-22 (150932,450816,299862) : difference with theory (-31) = -9 

CORRECTING DEFECT 5 (vertices=50, convex hull=91, v0=29653)
After retessellation of defect 5 (v0=29653), euler #=-21 (150966,450954,299967) : difference with theory (-30) = -9 

CORRECTING DEFECT 6 (vertices=177, convex hull=145, v0=30655)
After retessellation of defect 6 (v0=30655), euler #=-21 (151019,451190,300150) : difference with theory (-29) = -8 

CORRECTING DEFECT 7 (vertices=53, convex hull=46, v0=38956)
After retessellation of defect 7 (v0=38956), euler #=-20 (151023,451223,300180) : difference with theory (-28) = -8 

CORRECTING DEFECT 8 (vertices=26, convex hull=43, v0=53953)
After retessellation of defect 8 (v0=53953), euler #=-19 (151035,451274,300220) : difference with theory (-27) = -8 

CORRECTING DEFECT 9 (vertices=18, convex hull=28, v0=59909)
After retessellation of defect 9 (v0=59909), euler #=-18 (151038,451291,300235) : difference with theory (-26) = -8 

CORRECTING DEFECT 10 (vertices=29, convex hull=67, v0=65320)
After retessellation of defect 10 (v0=65320), euler #=-17 (151046,451340,300277) : difference with theory (-25) = -8 

CORRECTING DEFECT 11 (vertices=48, convex hull=26, v0=65688)
After retessellation of defect 11 (v0=65688), euler #=-16 (151052,451365,300297) : difference with theory (-24) = -8 

CORRECTING DEFECT 12 (vertices=1103, convex hull=364, v0=68309)
L defect detected...
After retessellation of defect 12 (v0=68309), euler #=-22 (151398,452634,301214) : difference with theory (-23) = -1 

CORRECTING DEFECT 13 (vertices=1687, convex hull=757, v0=69401)
XL defect detected...
After retessellation of defect 13 (v0=69401), euler #=-23 (151778,454188,302387) : difference with theory (-22) = 1 

CORRECTING DEFECT 14 (vertices=425, convex hull=412, v0=93683)
After retessellation of defect 14 (v0=93683), euler #=-22 (151954,454927,302951) : difference with theory (-21) = 1 

CORRECTING DEFECT 15 (vertices=23, convex hull=39, v0=97118)
After retessellation of defect 15 (v0=97118), euler #=-21 (151959,454954,302974) : difference with theory (-20) = 1 

CORRECTING DEFECT 16 (vertices=88, convex hull=97, v0=100965)
After retessellation of defect 16 (v0=100965), euler #=-20 (151984,455071,303067) : difference with theory (-19) = 1 

CORRECTING DEFECT 17 (vertices=38, convex hull=39, v0=101019)
After retessellation of defect 17 (v0=101019), euler #=-19 (151989,455102,303094) : difference with theory (-18) = 1 

CORRECTING DEFECT 18 (vertices=21, convex hull=31, v0=101992)
After retessellation of defect 18 (v0=101992), euler #=-18 (151995,455129,303116) : difference with theory (-17) = 1 

CORRECTING DEFECT 19 (vertices=6, convex hull=22, v0=105692)
After retessellation of defect 19 (v0=105692), euler #=-17 (151996,455139,303126) : difference with theory (-16) = 1 

CORRECTING DEFECT 20 (vertices=37, convex hull=56, v0=108012)
After retessellation of defect 20 (v0=108012), euler #=-16 (152011,455207,303180) : difference with theory (-15) = 1 

CORRECTING DEFECT 21 (vertices=13, convex hull=34, v0=108320)
After retessellation of defect 21 (v0=108320), euler #=-15 (152013,455225,303197) : difference with theory (-14) = 1 

CORRECTING DEFECT 22 (vertices=1037, convex hull=452, v0=110192)
L defect detected...
After retessellation of defect 22 (v0=110192), euler #=-13 (152259,456224,303952) : difference with theory (-13) = 0 

CORRECTING DEFECT 23 (vertices=28, convex hull=57, v0=110355)
After retessellation of defect 23 (v0=110355), euler #=-12 (152268,456272,303992) : difference with theory (-12) = 0 

CORRECTING DEFECT 24 (vertices=52, convex hull=48, v0=111594)
After retessellation of defect 24 (v0=111594), euler #=-11 (152278,456319,304030) : difference with theory (-11) = 0 

CORRECTING DEFECT 25 (vertices=41, convex hull=84, v0=111816)
After retessellation of defect 25 (v0=111816), euler #=-10 (152301,456421,304110) : difference with theory (-10) = 0 

CORRECTING DEFECT 26 (vertices=403, convex hull=90, v0=114621)
After retessellation of defect 26 (v0=114621), euler #=-9 (152329,456550,304212) : difference with theory (-9) = 0 

CORRECTING DEFECT 27 (vertices=61, convex hull=92, v0=125055)
After retessellation of defect 27 (v0=125055), euler #=-8 (152347,456642,304287) : difference with theory (-8) = 0 

CORRECTING DEFECT 28 (vertices=16, convex hull=30, v0=125557)
After retessellation of defect 28 (v0=125557), euler #=-7 (152349,456659,304303) : difference with theory (-7) = 0 

CORRECTING DEFECT 29 (vertices=78, convex hull=40, v0=129168)
After retessellation of defect 29 (v0=129168), euler #=-6 (152357,456696,304333) : difference with theory (-6) = 0 

CORRECTING DEFECT 30 (vertices=296, convex hull=108, v0=137365)
After retessellation of defect 30 (v0=137365), euler #=-5 (152400,456873,304468) : difference with theory (-5) = 0 

CORRECTING DEFECT 31 (vertices=36, convex hull=62, v0=138616)
After retessellation of defect 31 (v0=138616), euler #=-4 (152415,456938,304519) : difference with theory (-4) = 0 

CORRECTING DEFECT 32 (vertices=158, convex hull=167, v0=141706)
After retessellation of defect 32 (v0=141706), euler #=-3 (152478,457205,304724) : difference with theory (-3) = 0 

CORRECTING DEFECT 33 (vertices=39, convex hull=75, v0=146089)
After retessellation of defect 33 (v0=146089), euler #=-2 (152497,457296,304797) : difference with theory (-2) = 0 

CORRECTING DEFECT 34 (vertices=211, convex hull=162, v0=153100)
After retessellation of defect 34 (v0=153100), euler #=-1 (152579,457627,305047) : difference with theory (-1) = 0 

CORRECTING DEFECT 35 (vertices=27, convex hull=60, v0=153503)
After retessellation of defect 35 (v0=153503), euler #=0 (152592,457690,305098) : difference with theory (0) = 0 

CORRECTING DEFECT 36 (vertices=65, convex hull=102, v0=155884)
After retessellation of defect 36 (v0=155884), euler #=1 (152623,457829,305207) : difference with theory (1) = 0 

CORRECTING DEFECT 37 (vertices=41, convex hull=83, v0=156652)
After retessellation of defect 37 (v0=156652), euler #=2 (152636,457902,305268) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.24 (0.05-->11.90) (max @ vno 243 --> 6304)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.24 (0.05-->11.90) (max @ vno 243 --> 6304)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
108 mutations (33.1%), 218 crossovers (66.9%), 341 vertices were eliminated
building final representation...
5132 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=152636, nf=305268, ne=457902, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 48.2 minutes
0 defective edges
removing intersecting faces
000: 439 intersecting
001: 17 intersecting
mris_fix_topology utimesec    2891.617407
mris_fix_topology stimesec    0.234964
mris_fix_topology ru_maxrss   518640
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   59374
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22208
mris_fix_topology ru_oublock  14728
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    366
mris_fix_topology ru_nivcsw   4338
FSRUNTIME@ mris_fix_topology rh  0.8033 hours 1 threads
PIDs (6633 6636) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 152803 - 458403 + 305602 = 2 --> 0 holes
      F =2V-4:          305602 = 305606-4 (0)
      2E=3F:            916806 = 916806 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 152636 - 457902 + 305268 = 2 --> 0 holes
      F =2V-4:          305268 = 305272-4 (0)
      2E=3F:            915804 = 915804 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 181 intersecting
001: 41 intersecting
002: 16 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 107 intersecting
001: 2 intersecting
expanding nbhd size to 2
002: 5 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 23:44:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050044 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 23:44:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050044 rh 

Waiting for PID 10835 of (10835 10838) to complete...
Waiting for PID 10838 of (10835 10838) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050044 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-6.0.0/0050044/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
18193 bright wm thresholded.
2104 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.orig...
computing class statistics...
border white:    289265 voxels (1.72%)
border gray      325149 voxels (1.94%)
WM (98.0): 98.1 +- 7.7 [70.0 --> 110.0]
GM (75.0) : 74.1 +- 9.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.4 (was 70)
setting MAX_BORDER_WHITE to 110.7 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.8 (was 40)
setting MAX_GRAY to 95.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.01-->5.65) (max @ vno 93929 --> 151611)
face area 0.28 +- 0.12 (0.00-->4.68)
mean absolute distance = 0.67 +- 0.84
3727 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-6.1,    GM=72+-6.1
mean inside = 94.0, mean outside = 77.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=82.7, 62 (62) missing vertices, mean dist 0.2 [0.6 (%39.6)->0.7 (%60.4))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.24 (0.05-->4.82) (max @ vno 97873 --> 97994)
face area 0.28 +- 0.13 (0.00-->4.79)
mean absolute distance = 0.34 +- 0.57
3768 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3009469.5, rms=8.871
001: dt: 0.5000, sse=1728756.4, rms=6.148 (30.700%)
002: dt: 0.5000, sse=1188901.4, rms=4.454 (27.549%)
003: dt: 0.5000, sse=963700.3, rms=3.510 (21.198%)
004: dt: 0.5000, sse=869796.5, rms=3.024 (13.849%)
005: dt: 0.5000, sse=839450.6, rms=2.843 (5.989%)
006: dt: 0.5000, sse=827445.1, rms=2.750 (3.274%)
rms = 2.73, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=822433.5, rms=2.733 (0.611%)
008: dt: 0.2500, sse=704411.4, rms=1.716 (37.192%)
009: dt: 0.2500, sse=688032.3, rms=1.533 (10.692%)
rms = 1.49, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=685041.8, rms=1.490 (2.808%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=682797.2, rms=1.467 (1.519%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=85.4, 80 (17) missing vertices, mean dist -0.2 [0.4 (%72.5)->0.2 (%27.5))]
%77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.07-->4.87) (max @ vno 151361 --> 151402)
face area 0.35 +- 0.16 (0.00-->6.25)
mean absolute distance = 0.26 +- 0.39
3985 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1282307.4, rms=4.195
012: dt: 0.5000, sse=972206.1, rms=2.589 (38.278%)
013: dt: 0.5000, sse=919791.6, rms=2.300 (11.179%)
014: dt: 0.5000, sse=903210.6, rms=2.200 (4.329%)
rms = 2.36, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=843437.6, rms=1.621 (26.310%)
016: dt: 0.2500, sse=824589.7, rms=1.329 (18.008%)
017: dt: 0.2500, sse=814322.2, rms=1.250 (5.976%)
rms = 1.22, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=811874.1, rms=1.220 (2.387%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=810156.9, rms=1.196 (1.966%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=87.4, 70 (9) missing vertices, mean dist -0.1 [0.3 (%69.2)->0.2 (%30.8))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.08-->4.85) (max @ vno 151361 --> 151402)
face area 0.34 +- 0.16 (0.00-->6.15)
mean absolute distance = 0.22 +- 0.32
3048 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=977482.4, rms=2.824
020: dt: 0.5000, sse=861199.7, rms=1.951 (30.900%)
rms = 1.98, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=810931.7, rms=1.468 (24.786%)
022: dt: 0.2500, sse=791257.9, rms=1.171 (20.199%)
023: dt: 0.2500, sse=785011.2, rms=1.099 (6.201%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=783407.0, rms=1.091 (0.713%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=781244.1, rms=1.072 (1.759%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=88.1, 74 (7) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))]
%88 local maxima, % 7 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-6.0.0/0050044/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=799787.0, rms=1.492
026: dt: 0.5000, sse=780576.0, rms=1.260 (15.531%)
rms = 1.59, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=760557.6, rms=0.968 (23.220%)
028: dt: 0.2500, sse=756678.8, rms=0.888 (8.237%)
rms = 0.86, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=753670.7, rms=0.860 (3.129%)
rms = 0.86, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=754563.7, rms=0.856 (0.527%)
positioning took 0.7 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 8118 vertices
erasing segment 0 (vno[0] = 33401)
erasing segment 2 (vno[0] = 70395)
erasing segment 3 (vno[0] = 77438)
erasing segment 4 (vno[0] = 81407)
erasing segment 5 (vno[0] = 94537)
erasing segment 6 (vno[0] = 113812)
erasing segment 7 (vno[0] = 115838)
erasing segment 8 (vno[0] = 115896)
erasing segment 9 (vno[0] = 119536)
erasing segment 10 (vno[0] = 124363)
erasing segment 11 (vno[0] = 126140)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.01-->5.65) (max @ vno 93929 --> 151611)
face area 0.33 +- 0.16 (0.00-->5.86)
refinement took 5.9 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050044 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-6.0.0/0050044/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
18193 bright wm thresholded.
2104 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.orig...
computing class statistics...
border white:    289265 voxels (1.72%)
border gray      325149 voxels (1.94%)
WM (98.0): 98.1 +- 7.7 [70.0 --> 110.0]
GM (75.0) : 74.1 +- 9.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70)
setting MAX_BORDER_WHITE to 109.7 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 51.8 (was 40)
setting MAX_GRAY to 94.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->6.99) (max @ vno 103104 --> 151630)
face area 0.28 +- 0.13 (0.00-->4.38)
mean absolute distance = 0.68 +- 0.82
4443 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-5.2,    GM=71+-7.0
mean inside = 94.1, mean outside = 78.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=82.4, 93 (93) missing vertices, mean dist 0.3 [0.6 (%38.8)->0.8 (%61.2))]
%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 0.92 +- 0.25 (0.11-->7.54) (max @ vno 103104 --> 151630)
face area 0.28 +- 0.13 (0.00-->3.89)
mean absolute distance = 0.37 +- 0.59
4331 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3073434.0, rms=9.101
001: dt: 0.5000, sse=1791477.2, rms=6.338 (30.356%)
002: dt: 0.5000, sse=1227687.0, rms=4.605 (27.339%)
003: dt: 0.5000, sse=985069.6, rms=3.602 (21.779%)
004: dt: 0.5000, sse=876224.3, rms=3.046 (15.436%)
005: dt: 0.5000, sse=837976.4, rms=2.818 (7.485%)
006: dt: 0.5000, sse=818942.5, rms=2.702 (4.141%)
rms = 2.68, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=820530.1, rms=2.682 (0.738%)
008: dt: 0.2500, sse=699634.0, rms=1.637 (38.965%)
009: dt: 0.2500, sse=681437.1, rms=1.434 (12.358%)
rms = 1.39, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=680043.6, rms=1.395 (2.785%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=678281.5, rms=1.365 (2.087%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=85.2, 90 (20) missing vertices, mean dist -0.2 [0.4 (%72.3)->0.2 (%27.7))]
%80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.03-->7.56) (max @ vno 103104 --> 151630)
face area 0.35 +- 0.16 (0.00-->5.92)
mean absolute distance = 0.27 +- 0.39
4567 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1361341.4, rms=4.460
012: dt: 0.5000, sse=1002413.1, rms=2.774 (37.799%)
013: dt: 0.5000, sse=943914.9, rms=2.410 (13.127%)
014: dt: 0.5000, sse=926823.1, rms=2.301 (4.537%)
rms = 2.44, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=861072.8, rms=1.712 (25.582%)
016: dt: 0.2500, sse=834906.6, rms=1.405 (17.952%)
017: dt: 0.2500, sse=827520.2, rms=1.306 (7.055%)
018: dt: 0.2500, sse=824334.8, rms=1.255 (3.883%)
rms = 1.22, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=825086.2, rms=1.217 (3.026%)
rms = 1.19, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=820340.1, rms=1.188 (2.386%)
positioning took 1.1 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
removing 4 vertex label from ripped group
mean border=87.3, 81 (11) missing vertices, mean dist -0.1 [0.3 (%70.0)->0.2 (%30.0))]
%87 local maxima, % 9 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 (0.06-->7.46) (max @ vno 103104 --> 151630)
face area 0.34 +- 0.16 (0.00-->6.24)
mean absolute distance = 0.22 +- 0.32
3453 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1014136.8, rms=2.984
021: dt: 0.5000, sse=876846.9, rms=2.022 (32.235%)
rms = 2.00, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=872133.1, rms=2.004 (0.909%)
023: dt: 0.2500, sse=797123.4, rms=1.195 (40.366%)
024: dt: 0.2500, sse=788358.7, rms=1.088 (8.920%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=788422.9, rms=1.083 (0.499%)
rms = 1.06, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=786393.1, rms=1.055 (2.553%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.0, 106 (8) missing vertices, mean dist -0.0 [0.2 (%57.1)->0.2 (%42.9))]
%90 local maxima, % 6 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-6.0.0/0050044/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=801996.9, rms=1.465
027: dt: 0.5000, sse=784604.1, rms=1.246 (15.006%)
rms = 1.59, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=764945.4, rms=0.946 (24.080%)
029: dt: 0.2500, sse=761342.4, rms=0.880 (6.929%)
rms = 0.84, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=758373.5, rms=0.842 (4.356%)
rms = 0.83, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=757332.4, rms=0.831 (1.223%)
positioning took 0.7 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7329 vertices
erasing segment 0 (vno[0] = 47895)
erasing segment 2 (vno[0] = 86354)
erasing segment 3 (vno[0] = 87402)
erasing segment 4 (vno[0] = 106099)
erasing segment 5 (vno[0] = 106446)
erasing segment 6 (vno[0] = 107470)
erasing segment 7 (vno[0] = 110285)
erasing segment 8 (vno[0] = 110414)
erasing segment 9 (vno[0] = 111235)
erasing segment 10 (vno[0] = 111257)
erasing segment 11 (vno[0] = 112143)
erasing segment 12 (vno[0] = 114513)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.04-->7.33) (max @ vno 103104 --> 151630)
face area 0.33 +- 0.16 (0.00-->6.42)
refinement took 5.8 minutes
PIDs (10835 10838) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 23:50:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 23:50:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

Waiting for PID 11058 of (11058 11061) to complete...
Waiting for PID 11061 of (11058 11061) 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 (11058 11061) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 23:50:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 23:50:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 11108 of (11108 11111) to complete...
Waiting for PID 11111 of (11108 11111) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.3 mm, total surface area = 92237 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.174 (target=0.015)   
step 005: RMS=0.122 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.051 (target=0.015)   
step 030: RMS=0.043 (target=0.015)   
step 035: RMS=0.036 (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=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 1.1 minutes
mris_inflate utimesec    62.995423
mris_inflate stimesec    0.123981
mris_inflate ru_maxrss   223252
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32371
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11968
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2016
mris_inflate ru_nivcsw   5005

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.6 mm, total surface area = 92315 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.175 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.051 (target=0.015)   
step 030: RMS=0.044 (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=0.024 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
inflation took 1.1 minutes
mris_inflate utimesec    67.806691
mris_inflate stimesec    0.136979
mris_inflate ru_maxrss   223080
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32327
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10736
mris_inflate ru_oublock  11960
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1940
mris_inflate ru_nivcsw   5963
PIDs (11108 11111) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 23:52:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sat Oct  7 23:52:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 11216 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11219 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11222 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11225 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11228 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11231 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11234 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11237 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11240 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11243 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11246 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...
Waiting for PID 11249 of (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = -0.682*4pi (-8.570) --> 2 handles
ICI = 177.0, FI = 1847.3, variation=29150.916
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
212 vertices thresholded to be in k1 ~ [-0.22 0.36], k2 ~ [-0.12 0.05]
total integrated curvature = 0.556*4pi (6.991) --> 0 handles
ICI = 1.6, FI = 9.9, variation=170.049
153 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
156 vertices thresholded to be in [-0.15 0.17]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 4.836*4pi (60.772) --> -4 handles
ICI = 186.1, FI = 1915.1, variation=30245.234
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
241 vertices thresholded to be in k1 ~ [-0.19 0.42], k2 ~ [-0.11 0.04]
total integrated curvature = 0.545*4pi (6.847) --> 0 handles
ICI = 1.5, FI = 10.1, variation=170.360
127 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
168 vertices thresholded to be in [-0.11 0.21]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022
done.
PIDs (11216 11219 11222 11225 11228 11231 11234 11237 11240 11243 11246 11249) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 23:53:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050044 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      [ 0050044/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                      [ 251 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.463186
WARN:    S explicit min:                          0.000000	vertex = 1481

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 23:53:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050044 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      [ 0050044/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                      [ 290 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.504992
WARN:    S explicit min:                          0.000000	vertex = 40
#--------------------------------------------
#@# Sphere lh Sat Oct  7 23:53:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 23:53:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 11440 of (11440 11444) to complete...
Waiting for PID 11444 of (11440 11444) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0.283...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.25
pass 1: epoch 2 of 3 starting distance error %20.22
unfolding complete - removing small folds...
starting distance error %20.15
removing remaining folds...
final distance error %20.16
MRISunfold() return, current seed 1234
-01: dt=0.0000, 176 negative triangles
156: dt=0.9900, 176 negative triangles
157: dt=0.9900, 104 negative triangles
158: dt=0.9900, 85 negative triangles
159: dt=0.9900, 68 negative triangles
160: dt=0.9900, 65 negative triangles
161: dt=0.9900, 69 negative triangles
162: dt=0.9900, 72 negative triangles
163: dt=0.9900, 67 negative triangles
164: dt=0.9900, 62 negative triangles
165: dt=0.9900, 72 negative triangles
166: dt=0.9900, 58 negative triangles
167: dt=0.9900, 61 negative triangles
168: dt=0.9900, 56 negative triangles
169: dt=0.9900, 55 negative triangles
170: dt=0.9900, 48 negative triangles
171: dt=0.9900, 44 negative triangles
172: dt=0.9900, 43 negative triangles
173: dt=0.9900, 39 negative triangles
174: dt=0.9900, 39 negative triangles
175: dt=0.9900, 33 negative triangles
176: dt=0.9900, 35 negative triangles
177: dt=0.9900, 32 negative triangles
178: dt=0.9900, 32 negative triangles
179: dt=0.9900, 35 negative triangles
180: dt=0.9900, 32 negative triangles
181: dt=0.9900, 34 negative triangles
182: dt=0.9900, 31 negative triangles
183: dt=0.9900, 28 negative triangles
184: dt=0.9900, 30 negative triangles
185: dt=0.9900, 30 negative triangles
186: dt=0.9900, 24 negative triangles
187: dt=0.9900, 30 negative triangles
188: dt=0.9900, 25 negative triangles
189: dt=0.9900, 28 negative triangles
190: dt=0.9900, 28 negative triangles
191: dt=0.9900, 29 negative triangles
192: dt=0.9900, 27 negative triangles
193: dt=0.9900, 27 negative triangles
194: dt=0.9900, 24 negative triangles
195: dt=0.9900, 27 negative triangles
196: dt=0.9405, 27 negative triangles
197: dt=0.9405, 25 negative triangles
198: dt=0.9405, 25 negative triangles
199: dt=0.9405, 28 negative triangles
200: dt=0.9405, 24 negative triangles
201: dt=0.9405, 25 negative triangles
202: dt=0.9405, 25 negative triangles
203: dt=0.9405, 26 negative triangles
204: dt=0.9405, 25 negative triangles
205: dt=0.9405, 28 negative triangles
206: dt=0.9405, 23 negative triangles
207: dt=0.9405, 23 negative triangles
208: dt=0.9405, 24 negative triangles
209: dt=0.9405, 24 negative triangles
210: dt=0.9405, 23 negative triangles
211: dt=0.9405, 24 negative triangles
212: dt=0.9405, 26 negative triangles
213: dt=0.9405, 25 negative triangles
214: dt=0.9405, 23 negative triangles
215: dt=0.9405, 28 negative triangles
216: dt=0.8935, 26 negative triangles
217: dt=0.8935, 25 negative triangles
218: dt=0.8935, 27 negative triangles
219: dt=0.8935, 24 negative triangles
220: dt=0.8935, 24 negative triangles
221: dt=0.8935, 23 negative triangles
222: dt=0.8935, 20 negative triangles
223: dt=0.8935, 29 negative triangles
224: dt=0.8935, 23 negative triangles
225: dt=0.8935, 25 negative triangles
226: dt=0.8935, 24 negative triangles
227: dt=0.8935, 26 negative triangles
228: dt=0.8935, 23 negative triangles
229: dt=0.8935, 26 negative triangles
230: dt=0.8935, 25 negative triangles
231: dt=0.8935, 25 negative triangles
232: dt=0.8488, 27 negative triangles
233: dt=0.8488, 25 negative triangles
234: dt=0.8488, 23 negative triangles
235: dt=0.8488, 26 negative triangles
236: dt=0.8488, 23 negative triangles
237: dt=0.8488, 24 negative triangles
238: dt=0.8488, 23 negative triangles
239: dt=0.8488, 26 negative triangles
240: dt=0.8488, 23 negative triangles
241: dt=0.8488, 26 negative triangles
242: dt=0.8064, 25 negative triangles
243: dt=0.8064, 26 negative triangles
244: dt=0.8064, 25 negative triangles
245: dt=0.8064, 26 negative triangles
246: dt=0.8064, 27 negative triangles
247: dt=0.8064, 26 negative triangles
248: dt=0.8064, 23 negative triangles
249: dt=0.8064, 26 negative triangles
250: dt=0.8064, 23 negative triangles
251: dt=0.8064, 25 negative triangles
252: dt=0.7660, 23 negative triangles
253: dt=0.7660, 26 negative triangles
254: dt=0.7660, 24 negative triangles
255: dt=0.7660, 24 negative triangles
256: dt=0.7660, 25 negative triangles
257: dt=0.7660, 26 negative triangles
258: dt=0.7660, 26 negative triangles
259: dt=0.7660, 26 negative triangles
260: dt=0.7660, 26 negative triangles
261: dt=0.7660, 26 negative triangles
262: dt=0.7277, 23 negative triangles
263: dt=0.7277, 27 negative triangles
264: dt=0.7277, 23 negative triangles
265: dt=0.7277, 25 negative triangles
266: dt=0.7277, 23 negative triangles
267: dt=0.7277, 24 negative triangles
268: dt=0.7277, 23 negative triangles
269: dt=0.7277, 28 negative triangles
270: dt=0.7277, 23 negative triangles
271: dt=0.7277, 27 negative triangles
272: dt=0.6914, 24 negative triangles
expanding nbhd size to 1
273: dt=0.9900, 25 negative triangles
274: dt=0.9900, 29 negative triangles
275: dt=0.9900, 23 negative triangles
276: dt=0.9900, 25 negative triangles
277: dt=0.9900, 24 negative triangles
278: dt=0.9900, 27 negative triangles
279: dt=0.9900, 23 negative triangles
280: dt=0.9900, 20 negative triangles
281: dt=0.9900, 18 negative triangles
282: dt=0.9900, 14 negative triangles
283: dt=0.9900, 16 negative triangles
284: dt=0.9900, 14 negative triangles
285: dt=0.9900, 16 negative triangles
286: dt=0.9900, 13 negative triangles
287: dt=0.9900, 13 negative triangles
288: dt=0.9900, 13 negative triangles
289: dt=0.9900, 14 negative triangles
290: dt=0.9900, 12 negative triangles
291: dt=0.9900, 10 negative triangles
292: dt=0.9900, 12 negative triangles
293: dt=0.9900, 10 negative triangles
294: dt=0.9900, 14 negative triangles
295: dt=0.9900, 14 negative triangles
296: dt=0.9900, 19 negative triangles
297: dt=0.9900, 19 negative triangles
298: dt=0.9900, 24 negative triangles
299: dt=0.9900, 22 negative triangles
300: dt=0.9900, 22 negative triangles
301: dt=0.9405, 23 negative triangles
302: dt=0.9405, 19 negative triangles
303: dt=0.9405, 23 negative triangles
304: dt=0.9405, 20 negative triangles
305: dt=0.9405, 20 negative triangles
306: dt=0.9405, 21 negative triangles
307: dt=0.9405, 20 negative triangles
308: dt=0.9405, 20 negative triangles
309: dt=0.9405, 20 negative triangles
310: dt=0.9405, 23 negative triangles
311: dt=0.8935, 20 negative triangles
312: dt=0.8935, 20 negative triangles
313: dt=0.8935, 20 negative triangles
314: dt=0.8935, 21 negative triangles
315: dt=0.8935, 19 negative triangles
316: dt=0.8935, 19 negative triangles
317: dt=0.8935, 18 negative triangles
318: dt=0.8935, 21 negative triangles
319: dt=0.8935, 18 negative triangles
320: dt=0.8935, 19 negative triangles
321: dt=0.8488, 17 negative triangles
322: dt=0.8488, 18 negative triangles
323: dt=0.8488, 17 negative triangles
324: dt=0.8488, 20 negative triangles
325: dt=0.8488, 17 negative triangles
326: dt=0.8488, 17 negative triangles
327: dt=0.8488, 18 negative triangles
328: dt=0.8488, 17 negative triangles
329: dt=0.8488, 18 negative triangles
330: dt=0.8488, 17 negative triangles
331: dt=0.8064, 18 negative triangles
332: dt=0.8064, 18 negative triangles
333: dt=0.8064, 17 negative triangles
334: dt=0.8064, 16 negative triangles
335: dt=0.8064, 16 negative triangles
336: dt=0.8064, 17 negative triangles
337: dt=0.8064, 15 negative triangles
338: dt=0.8064, 16 negative triangles
339: dt=0.8064, 15 negative triangles
340: dt=0.8064, 15 negative triangles
341: dt=0.7660, 15 negative triangles
342: dt=0.7660, 15 negative triangles
343: dt=0.7660, 15 negative triangles
344: dt=0.7660, 14 negative triangles
345: dt=0.7660, 13 negative triangles
346: dt=0.7660, 14 negative triangles
347: dt=0.7660, 12 negative triangles
348: dt=0.7660, 12 negative triangles
349: dt=0.7660, 11 negative triangles
350: dt=0.7660, 11 negative triangles
351: dt=0.7277, 11 negative triangles
352: dt=0.7277, 11 negative triangles
353: dt=0.7277, 11 negative triangles
354: dt=0.7277, 11 negative triangles
355: dt=0.7277, 11 negative triangles
356: dt=0.7277, 11 negative triangles
357: dt=0.7277, 11 negative triangles
358: dt=0.7277, 10 negative triangles
359: dt=0.7277, 9 negative triangles
360: dt=0.7277, 9 negative triangles
361: dt=0.7277, 9 negative triangles
362: dt=0.7277, 8 negative triangles
363: dt=0.7277, 8 negative triangles
364: dt=0.7277, 7 negative triangles
365: dt=0.7277, 7 negative triangles
366: dt=0.7277, 7 negative triangles
367: dt=0.7277, 7 negative triangles
368: dt=0.7277, 7 negative triangles
369: dt=0.7277, 6 negative triangles
370: dt=0.7277, 6 negative triangles
371: dt=0.7277, 6 negative triangles
372: dt=0.7277, 6 negative triangles
373: dt=0.7277, 6 negative triangles
374: dt=0.7277, 5 negative triangles
375: dt=0.7277, 3 negative triangles
376: dt=0.7277, 3 negative triangles
377: dt=0.7277, 3 negative triangles
378: dt=0.7277, 3 negative triangles
379: dt=0.7277, 2 negative triangles
380: dt=0.7277, 2 negative triangles
381: dt=0.7277, 2 negative triangles
382: dt=0.7277, 2 negative triangles
383: dt=0.7277, 2 negative triangles
384: dt=0.7277, 2 negative triangles
385: dt=0.7277, 2 negative triangles
386: dt=0.7277, 2 negative triangles
387: dt=0.7277, 2 negative triangles
388: dt=0.7277, 2 negative triangles
389: dt=0.6914, 2 negative triangles
390: dt=0.6914, 2 negative triangles
391: dt=0.6914, 2 negative triangles
392: dt=0.6914, 1 negative triangles
393: dt=0.6914, 1 negative triangles
394: dt=0.6914, 1 negative triangles
395: dt=0.6914, 1 negative triangles
396: dt=0.6914, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.17 hours
mris_sphere utimesec    4715.554126
mris_sphere stimesec    2.420632
mris_sphere ru_maxrss   316280
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55234
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10904
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    125017
mris_sphere ru_nivcsw   307541
FSRUNTIME@ mris_sphere  1.1690 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0.285...
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

singular matrix in quadratic form
--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.54
pass 1: epoch 2 of 3 starting distance error %19.51
unfolding complete - removing small folds...
starting distance error %19.46
removing remaining folds...
final distance error %19.48
MRISunfold() return, current seed 1234
-01: dt=0.0000, 86 negative triangles
175: dt=0.9900, 86 negative triangles
176: dt=0.9900, 34 negative triangles
177: dt=0.9900, 20 negative triangles
178: dt=0.9900, 11 negative triangles
179: dt=0.9900, 10 negative triangles
180: dt=0.9900, 6 negative triangles
181: dt=0.9900, 1 negative triangles
182: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.01 hours
mris_sphere utimesec    3620.512598
mris_sphere stimesec    1.906710
mris_sphere ru_maxrss   312600
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   54839
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10776
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    123202
mris_sphere ru_nivcsw   286477
FSRUNTIME@ mris_sphere  1.0062 hours 1 threads
PIDs (11440 11444) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 01:04:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 01:04:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 14120 of (14120 14123) to complete...
Waiting for PID 14123 of (14120 14123) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 5.639
curvature mean = 0.033, std = 0.822
curvature mean = 0.022, std = 0.852
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 293683.1, tmin=1.1628
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 273436.0, tmin=2.3428
  d=16.00 min @ (-4.00, -4.00, 0.00) sse = 235592.0, tmin=3.5217
  d=8.00 min @ (2.00, 0.00, -2.00) sse = 220634.1, tmin=4.7240
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 219990.9, tmin=5.9547
  d=2.00 min @ (0.50, 0.50, 0.00) sse = 219619.8, tmin=7.1827
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 219444.3, tmin=8.3912
  d=0.50 min @ (0.12, 0.12, -0.12) sse = 219369.2, tmin=9.6029
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.60 min
curvature mean = 0.011, std = 0.830
curvature mean = 0.007, std = 0.942
curvature mean = 0.007, std = 0.839
curvature mean = 0.003, std = 0.975
curvature mean = 0.006, std = 0.840
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.029, std = 0.276
curvature mean = 0.042, std = 0.249
curvature mean = 0.063, std = 0.357
curvature mean = 0.039, std = 0.305
curvature mean = 0.035, std = 0.561
curvature mean = 0.038, std = 0.331
curvature mean = 0.018, std = 0.708
curvature mean = 0.038, std = 0.342
curvature mean = 0.006, std = 0.815
MRISregister() return, current seed 0
-01: dt=0.0000, 58 negative triangles
116: dt=0.9900, 58 negative triangles
expanding nbhd size to 1
117: dt=0.9900, 86 negative triangles
118: dt=0.9900, 60 negative triangles
119: dt=0.9900, 63 negative triangles
120: dt=0.9405, 59 negative triangles
121: dt=0.9405, 54 negative triangles
122: dt=0.9405, 45 negative triangles
123: dt=0.9405, 47 negative triangles
124: dt=0.9405, 44 negative triangles
125: dt=0.9405, 40 negative triangles
126: dt=0.9405, 39 negative triangles
127: dt=0.9405, 39 negative triangles
128: dt=0.9405, 37 negative triangles
129: dt=0.9405, 38 negative triangles
130: dt=0.9405, 34 negative triangles
131: dt=0.9405, 35 negative triangles
132: dt=0.9405, 34 negative triangles
133: dt=0.9405, 34 negative triangles
134: dt=0.9405, 32 negative triangles
135: dt=0.9405, 33 negative triangles
136: dt=0.9405, 35 negative triangles
137: dt=0.9405, 33 negative triangles
138: dt=0.9405, 31 negative triangles
139: dt=0.9405, 32 negative triangles
140: dt=0.9405, 33 negative triangles
141: dt=0.9405, 31 negative triangles
142: dt=0.9405, 32 negative triangles
143: dt=0.9405, 32 negative triangles
144: dt=0.9405, 30 negative triangles
145: dt=0.9405, 33 negative triangles
146: dt=0.9405, 30 negative triangles
147: dt=0.9405, 30 negative triangles
148: dt=0.9405, 28 negative triangles
149: dt=0.9405, 28 negative triangles
150: dt=0.9405, 27 negative triangles
151: dt=0.9405, 26 negative triangles
152: dt=0.9405, 28 negative triangles
153: dt=0.9405, 26 negative triangles
154: dt=0.9405, 26 negative triangles
155: dt=0.9405, 24 negative triangles
156: dt=0.9405, 26 negative triangles
157: dt=0.9405, 24 negative triangles
158: dt=0.9405, 26 negative triangles
159: dt=0.9405, 24 negative triangles
160: dt=0.9405, 24 negative triangles
161: dt=0.9405, 22 negative triangles
162: dt=0.9405, 22 negative triangles
163: dt=0.9405, 23 negative triangles
164: dt=0.9405, 20 negative triangles
165: dt=0.9405, 21 negative triangles
166: dt=0.9405, 22 negative triangles
167: dt=0.9405, 18 negative triangles
168: dt=0.9405, 19 negative triangles
169: dt=0.9405, 21 negative triangles
170: dt=0.9405, 18 negative triangles
171: dt=0.9405, 19 negative triangles
172: dt=0.9405, 19 negative triangles
173: dt=0.9405, 20 negative triangles
174: dt=0.9405, 18 negative triangles
175: dt=0.9405, 18 negative triangles
176: dt=0.9405, 18 negative triangles
177: dt=0.8935, 18 negative triangles
178: dt=0.8935, 17 negative triangles
179: dt=0.8935, 17 negative triangles
180: dt=0.8935, 16 negative triangles
181: dt=0.8935, 16 negative triangles
182: dt=0.8935, 16 negative triangles
183: dt=0.8935, 15 negative triangles
184: dt=0.8935, 15 negative triangles
185: dt=0.8935, 15 negative triangles
186: dt=0.8935, 16 negative triangles
187: dt=0.8935, 16 negative triangles
188: dt=0.8935, 16 negative triangles
189: dt=0.8935, 15 negative triangles
190: dt=0.8935, 15 negative triangles
191: dt=0.8935, 15 negative triangles
192: dt=0.8935, 15 negative triangles
193: dt=0.8488, 15 negative triangles
194: dt=0.8488, 15 negative triangles
195: dt=0.8488, 15 negative triangles
196: dt=0.8488, 15 negative triangles
197: dt=0.8488, 15 negative triangles
198: dt=0.8488, 15 negative triangles
199: dt=0.8488, 15 negative triangles
200: dt=0.8488, 15 negative triangles
201: dt=0.8488, 15 negative triangles
202: dt=0.8488, 15 negative triangles
203: dt=0.8064, 15 negative triangles
204: dt=0.8064, 14 negative triangles
205: dt=0.8064, 15 negative triangles
206: dt=0.8064, 15 negative triangles
207: dt=0.8064, 14 negative triangles
208: dt=0.8064, 15 negative triangles
209: dt=0.8064, 14 negative triangles
210: dt=0.8064, 15 negative triangles
211: dt=0.8064, 14 negative triangles
212: dt=0.8064, 15 negative triangles
213: dt=0.8064, 14 negative triangles
214: dt=0.7660, 15 negative triangles
215: dt=0.7660, 14 negative triangles
216: dt=0.7660, 14 negative triangles
217: dt=0.7660, 12 negative triangles
218: dt=0.7660, 13 negative triangles
219: dt=0.7660, 12 negative triangles
220: dt=0.7660, 13 negative triangles
221: dt=0.7660, 12 negative triangles
222: dt=0.7660, 13 negative triangles
223: dt=0.7660, 12 negative triangles
224: dt=0.7660, 12 negative triangles
225: dt=0.7660, 11 negative triangles
226: dt=0.7660, 11 negative triangles
227: dt=0.7660, 11 negative triangles
228: dt=0.7660, 11 negative triangles
229: dt=0.7660, 10 negative triangles
230: dt=0.7660, 10 negative triangles
231: dt=0.7660, 10 negative triangles
232: dt=0.7660, 10 negative triangles
233: dt=0.7660, 9 negative triangles
234: dt=0.7660, 9 negative triangles
235: dt=0.7660, 9 negative triangles
236: dt=0.7660, 8 negative triangles
237: dt=0.7660, 7 negative triangles
238: dt=0.7660, 7 negative triangles
239: dt=0.7660, 7 negative triangles
240: dt=0.7660, 6 negative triangles
241: dt=0.7660, 6 negative triangles
242: dt=0.7660, 6 negative triangles
243: dt=0.7660, 5 negative triangles
244: dt=0.7660, 5 negative triangles
245: dt=0.7660, 5 negative triangles
246: dt=0.7660, 5 negative triangles
247: dt=0.7660, 5 negative triangles
248: dt=0.7660, 3 negative triangles
249: dt=0.7660, 2 negative triangles
250: dt=0.7660, 3 negative triangles
251: dt=0.7660, 2 negative triangles
252: dt=0.7660, 2 negative triangles
253: dt=0.7660, 2 negative triangles
254: dt=0.7660, 2 negative triangles
255: dt=0.7660, 2 negative triangles
256: dt=0.7660, 2 negative triangles
257: dt=0.7660, 2 negative triangles
258: dt=0.7660, 2 negative triangles
259: dt=0.7277, 2 negative triangles
260: dt=0.7277, 2 negative triangles
261: dt=0.7277, 2 negative triangles
262: dt=0.7277, 1 negative triangles
263: dt=0.7277, 3 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.26 hours
mris_register utimesec    4516.102448
mris_register stimesec    5.152216
mris_register ru_maxrss   278924
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   40073
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10880
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    352493
mris_register ru_nivcsw   224536
FSRUNTIME@ mris_register  1.2557 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 5.708
curvature mean = 0.032, std = 0.815
curvature mean = 0.020, std = 0.859
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 378277.4, tmin=1.3510
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 315022.8, tmin=2.7111
  d=16.00 min @ (0.00, -4.00, -4.00) sse = 281055.2, tmin=4.0728
  d=8.00 min @ (2.00, 0.00, 2.00) sse = 275906.4, tmin=5.4935
  d=4.00 min @ (0.00, 1.00, -1.00) sse = 273774.4, tmin=6.8365
  d=2.00 min @ (-0.50, -0.50, 0.00) sse = 273468.0, tmin=8.2496
  d=1.00 min @ (0.25, 0.25, 0.25) sse = 273320.3, tmin=9.6536
  d=0.50 min @ (-0.12, -0.12, 0.00) sse = 273301.0, tmin=11.0330
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  11.03 min
curvature mean = -0.003, std = 0.825
curvature mean = 0.008, std = 0.947
curvature mean = -0.008, std = 0.833
curvature mean = 0.003, std = 0.979
curvature mean = -0.012, std = 0.833
curvature mean = 0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.028, std = 0.278
curvature mean = 0.034, std = 0.245
curvature mean = 0.064, std = 0.355
curvature mean = 0.030, std = 0.302
curvature mean = 0.033, std = 0.551
curvature mean = 0.029, std = 0.328
curvature mean = 0.017, std = 0.700
curvature mean = 0.029, std = 0.340
curvature mean = 0.006, std = 0.808
MRISregister() return, current seed 0
-01: dt=0.0000, 48 negative triangles
127: dt=0.9900, 48 negative triangles
expanding nbhd size to 1
128: dt=0.9900, 65 negative triangles
129: dt=0.9900, 53 negative triangles
130: dt=0.9405, 52 negative triangles
131: dt=0.9405, 53 negative triangles
132: dt=0.9405, 53 negative triangles
133: dt=0.9405, 55 negative triangles
134: dt=0.9405, 51 negative triangles
135: dt=0.9405, 58 negative triangles
136: dt=0.9405, 58 negative triangles
137: dt=0.9405, 51 negative triangles
138: dt=0.9405, 56 negative triangles
139: dt=0.9405, 49 negative triangles
140: dt=0.8935, 48 negative triangles
141: dt=0.8935, 46 negative triangles
142: dt=0.8935, 44 negative triangles
143: dt=0.8935, 39 negative triangles
144: dt=0.8935, 38 negative triangles
145: dt=0.8935, 31 negative triangles
146: dt=0.8935, 28 negative triangles
147: dt=0.8935, 27 negative triangles
148: dt=0.8935, 27 negative triangles
149: dt=0.8935, 23 negative triangles
150: dt=0.8935, 22 negative triangles
151: dt=0.8935, 21 negative triangles
152: dt=0.8935, 23 negative triangles
153: dt=0.8935, 16 negative triangles
154: dt=0.8935, 15 negative triangles
155: dt=0.8935, 12 negative triangles
156: dt=0.8935, 14 negative triangles
157: dt=0.8935, 17 negative triangles
158: dt=0.8935, 13 negative triangles
159: dt=0.8935, 12 negative triangles
160: dt=0.8935, 13 negative triangles
161: dt=0.8935, 12 negative triangles
162: dt=0.8935, 13 negative triangles
163: dt=0.8935, 9 negative triangles
164: dt=0.8935, 7 negative triangles
165: dt=0.8935, 9 negative triangles
166: dt=0.8935, 7 negative triangles
167: dt=0.8935, 7 negative triangles
168: dt=0.8935, 6 negative triangles
169: dt=0.8935, 5 negative triangles
170: dt=0.8935, 4 negative triangles
171: dt=0.8935, 3 negative triangles
172: dt=0.8935, 2 negative triangles
173: dt=0.8935, 4 negative triangles
174: dt=0.8935, 1 negative triangles
175: dt=0.8935, 1 negative triangles
176: dt=0.8935, 1 negative triangles
177: dt=0.8935, 1 negative triangles
178: dt=0.8935, 1 negative triangles
179: dt=0.8935, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.60 hours
mris_register utimesec    6562.961278
mris_register stimesec    5.425175
mris_register ru_maxrss   276016
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39137
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  10744
mris_register ru_oublock  10840
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    340218
mris_register ru_nivcsw   211450
FSRUNTIME@ mris_register  1.5990 hours 1 threads
PIDs (14120 14123) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 02:39:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 02:39:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

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

Waiting for PID 21202 of (21202 21205) to complete...
Waiting for PID 21205 of (21202 21205) 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 (21202 21205) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 02:40:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv 

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 02:40:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 21248 of (21248 21251) to complete...
Waiting for PID 21251 of (21248 21251) 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 (21248 21251) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 02:40:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 02:40:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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 21313 of (21313 21316) to complete...
Waiting for PID 21316 of (21313 21316) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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...
1081 labels changed using aseg
relabeling using gibbs priors...
000:   3451 changed, 152803 examined...
001:    868 changed, 14584 examined...
002:    228 changed, 4707 examined...
003:     90 changed, 1404 examined...
004:     39 changed, 555 examined...
005:     14 changed, 255 examined...
006:      6 changed, 73 examined...
007:      3 changed, 40 examined...
008:      0 changed, 20 examined...
303 labels changed using aseg
000: 140 total segments, 96 labels (433 vertices) changed
001: 46 total segments, 2 labels (2 vertices) changed
002: 44 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2147 vertices marked for relabeling...
2147 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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...
1162 labels changed using aseg
relabeling using gibbs priors...
000:   3072 changed, 152636 examined...
001:    719 changed, 13070 examined...
002:    167 changed, 3996 examined...
003:     59 changed, 1047 examined...
004:     16 changed, 325 examined...
005:      7 changed, 91 examined...
006:      2 changed, 39 examined...
007:      1 changed, 12 examined...
008:      1 changed, 7 examined...
009:      1 changed, 6 examined...
010:      1 changed, 7 examined...
011:      1 changed, 7 examined...
012:      0 changed, 5 examined...
173 labels changed using aseg
000: 96 total segments, 56 labels (193 vertices) changed
001: 42 total segments, 2 labels (2 vertices) changed
002: 40 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2025 vertices marked for relabeling...
2025 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 17 seconds.
PIDs (21313 21316) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 02:40:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050044 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 02:40:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050044 rh 

Waiting for PID 21481 of (21481 21484) to complete...
Waiting for PID 21484 of (21481 21484) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050044 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-6.0.0/0050044/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
18193 bright wm thresholded.
2104 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.orig...
computing class statistics...
border white:    289265 voxels (1.72%)
border gray      325149 voxels (1.94%)
WM (98.0): 98.1 +- 7.7 [70.0 --> 110.0]
GM (75.0) : 74.1 +- 9.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.4 (was 70)
setting MAX_BORDER_WHITE to 110.7 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.8 (was 40)
setting MAX_GRAY to 95.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-6.1,    GM=72+-6.1
mean inside = 94.0, mean outside = 77.9
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.01-->5.65) (max @ vno 93929 --> 151611)
face area 0.33 +- 0.15 (0.00-->5.79)
mean absolute distance = 0.60 +- 0.83
2934 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 107 points - only 0.00% unknown
deleting segment 1 with 55 points - only 0.00% unknown
deleting segment 4 with 20 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 42 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
deleting segment 8 with 73 points - only 0.00% unknown
deleting segment 9 with 21 points - only 0.00% unknown
deleting segment 10 with 23 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 10 points - only 0.00% unknown
deleting segment 13 with 22 points - only 0.00% unknown
deleting segment 14 with 18 points - only 0.00% unknown
deleting segment 15 with 6 points - only 0.00% unknown
deleting segment 16 with 24 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 17 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 18 with 1 points - only 0.00% unknown
deleting segment 19 with 10 points - only 0.00% unknown
mean border=82.5, 68 (66) missing vertices, mean dist 0.4 [0.8 (%14.4)->0.6 (%85.6))]
%67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.12-->4.72) (max @ vno 94955 --> 95922)
face area 0.33 +- 0.15 (0.00-->5.82)
mean absolute distance = 0.34 +- 0.56
3318 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2271104.2, rms=7.264
001: dt: 0.5000, sse=1292669.8, rms=4.401 (39.418%)
002: dt: 0.5000, sse=992814.8, rms=3.054 (30.596%)
003: dt: 0.5000, sse=919693.9, rms=2.636 (13.700%)
004: dt: 0.5000, sse=887732.2, rms=2.432 (7.752%)
rms = 2.48, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=824337.9, rms=1.865 (23.284%)
006: dt: 0.2500, sse=797240.8, rms=1.567 (16.010%)
007: dt: 0.2500, sse=789961.4, rms=1.475 (5.869%)
rms = 1.43, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=786990.7, rms=1.433 (2.864%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=784492.7, rms=1.404 (1.988%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 109 points - only 0.00% unknown
deleting segment 1 with 57 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 32 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 25 points - only 0.00% unknown
deleting segment 11 with 68 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
deleting segment 13 with 20 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
deleting segment 15 with 19 points - only 0.00% unknown
deleting segment 16 with 8 points - only 0.00% unknown
mean border=85.4, 57 (17) missing vertices, mean dist -0.2 [0.4 (%72.8)->0.2 (%27.2))]
%77 local maxima, %18 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 (0.10-->4.94) (max @ vno 94955 --> 95922)
face area 0.35 +- 0.17 (0.00-->6.43)
mean absolute distance = 0.26 +- 0.40
3357 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1278087.8, rms=4.135
010: dt: 0.5000, sse=965095.8, rms=2.531 (38.787%)
011: dt: 0.5000, sse=918506.5, rms=2.205 (12.864%)
012: dt: 0.5000, sse=904944.5, rms=2.124 (3.677%)
rms = 2.28, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=847641.1, rms=1.544 (27.318%)
014: dt: 0.2500, sse=826429.4, rms=1.249 (19.089%)
015: dt: 0.2500, sse=821350.9, rms=1.184 (5.199%)
rms = 1.17, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=819934.9, rms=1.171 (1.158%)
rms = 1.15, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=818722.2, rms=1.152 (1.618%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 119 points - only 0.00% unknown
deleting segment 1 with 57 points - only 0.00% unknown
deleting segment 3 with 17 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 30 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 24 points - only 0.00% unknown
deleting segment 8 with 70 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
deleting segment 10 with 20 points - only 0.00% unknown
deleting segment 11 with 14 points - only 0.00% unknown
deleting segment 12 with 9 points - only 0.00% unknown
deleting segment 13 with 22 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 with 1 points - only 0.00% unknown
deleting segment 16 with 8 points - only 0.00% unknown
mean border=87.4, 55 (11) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.2 (%30.5))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.07-->5.19) (max @ vno 94955 --> 95922)
face area 0.34 +- 0.16 (0.00-->6.26)
mean absolute distance = 0.23 +- 0.32
3151 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=982973.1, rms=2.816
018: dt: 0.5000, sse=865913.0, rms=1.940 (31.129%)
rms = 1.96, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=819381.4, rms=1.451 (25.204%)
020: dt: 0.2500, sse=793984.6, rms=1.152 (20.580%)
021: dt: 0.2500, sse=788759.8, rms=1.077 (6.485%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=797865.0, rms=1.070 (0.713%)
rms = 1.05, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=791940.1, rms=1.053 (1.597%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 123 points - only 0.00% unknown
deleting segment 1 with 53 points - only 0.00% unknown
deleting segment 2 with 33 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 40 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
deleting segment 7 with 71 points - only 0.00% unknown
deleting segment 8 with 26 points - only 0.00% unknown
deleting segment 9 with 10 points - only 0.00% unknown
deleting segment 10 with 23 points - only 0.00% unknown
deleting segment 11 with 19 points - only 0.00% unknown
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 20 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 with 1 points - only 0.00% unknown
deleting segment 16 with 5 points - only 0.00% unknown
deleting segment 17 with 11 points - only 0.00% unknown
mean border=88.1, 73 (9) missing vertices, mean dist -0.1 [0.2 (%57.0)->0.2 (%43.0))]
%88 local maxima, % 7 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-6.0.0/0050044/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=811573.3, rms=1.489
024: dt: 0.5000, sse=788857.3, rms=1.256 (15.617%)
rms = 1.59, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=768252.9, rms=0.965 (23.189%)
026: dt: 0.2500, sse=764018.7, rms=0.894 (7.315%)
rms = 0.86, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=766173.9, rms=0.857 (4.235%)
rms = 0.85, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=759884.5, rms=0.853 (0.407%)
positioning took 0.6 minutes
generating cortex label...
19 non-cortical segments detected
only using segment with 8103 vertices
erasing segment 0 (vno[0] = 33401)
erasing segment 1 (vno[0] = 34780)
erasing segment 2 (vno[0] = 38807)
erasing segment 4 (vno[0] = 78601)
erasing segment 5 (vno[0] = 79742)
erasing segment 6 (vno[0] = 79749)
erasing segment 7 (vno[0] = 81407)
erasing segment 8 (vno[0] = 93530)
erasing segment 9 (vno[0] = 99253)
erasing segment 10 (vno[0] = 105073)
erasing segment 11 (vno[0] = 113812)
erasing segment 12 (vno[0] = 115838)
erasing segment 13 (vno[0] = 115896)
erasing segment 14 (vno[0] = 119536)
erasing segment 15 (vno[0] = 124363)
erasing segment 16 (vno[0] = 126140)
erasing segment 17 (vno[0] = 128627)
erasing segment 18 (vno[0] = 133820)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.area
vertex spacing 0.89 +- 0.26 (0.01-->5.65) (max @ vno 93929 --> 151611)
face area 0.33 +- 0.16 (0.00-->5.94)
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 36 points - only 0.00% unknown
deleting segment 1 with 118 points - only 0.00% unknown
deleting segment 4 with 14 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 14 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=60.7, 76 (76) missing vertices, mean dist 1.7 [0.9 (%0.0)->2.8 (%100.0))]
%15 local maxima, %43 large gradients and %38 min vals, 437 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=23877592.0, rms=28.133
001: dt: 0.0500, sse=21264032.0, rms=26.497 (5.813%)
002: dt: 0.0500, sse=19402078.0, rms=25.268 (4.641%)
003: dt: 0.0500, sse=17972318.0, rms=24.281 (3.905%)
004: dt: 0.0500, sse=16809326.0, rms=23.448 (3.431%)
005: dt: 0.0500, sse=15824279.0, rms=22.718 (3.112%)
006: dt: 0.0500, sse=14966415.0, rms=22.063 (2.884%)
007: dt: 0.0500, sse=14203612.0, rms=21.464 (2.717%)
008: dt: 0.0500, sse=13514465.0, rms=20.907 (2.592%)
009: dt: 0.0500, sse=12884008.0, rms=20.385 (2.499%)
010: dt: 0.0500, sse=12302511.0, rms=19.891 (2.424%)
positioning took 1.0 minutes
mean border=60.5, 76 (33) missing vertices, mean dist 1.4 [0.6 (%0.1)->2.3 (%99.9))]
%16 local maxima, %42 large gradients and %37 min vals, 421 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=12985320.0, rms=20.470
011: dt: 0.0500, sse=12442113.0, rms=20.011 (2.243%)
012: dt: 0.0500, sse=11936108.0, rms=19.573 (2.186%)
013: dt: 0.0500, sse=11462539.0, rms=19.155 (2.138%)
014: dt: 0.0500, sse=11018664.0, rms=18.754 (2.092%)
015: dt: 0.0500, sse=10601863.0, rms=18.370 (2.049%)
016: dt: 0.0500, sse=10210217.0, rms=18.001 (2.007%)
017: dt: 0.0500, sse=9841705.0, rms=17.647 (1.967%)
018: dt: 0.0500, sse=9495368.0, rms=17.308 (1.924%)
019: dt: 0.0500, sse=9169491.0, rms=16.982 (1.882%)
020: dt: 0.0500, sse=8862809.0, rms=16.669 (1.840%)
positioning took 1.0 minutes
mean border=60.4, 88 (25) missing vertices, mean dist 1.2 [0.1 (%0.6)->2.0 (%99.4))]
%16 local maxima, %42 large gradients and %37 min vals, 433 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=8959179.0, rms=16.774
021: dt: 0.0500, sse=8664736.0, rms=16.470 (1.810%)
022: dt: 0.0500, sse=8387818.0, rms=16.179 (1.766%)
023: dt: 0.0500, sse=8125924.5, rms=15.899 (1.731%)
024: dt: 0.0500, sse=7879659.0, rms=15.631 (1.686%)
025: dt: 0.0500, sse=7647748.0, rms=15.374 (1.643%)
026: dt: 0.0500, sse=7428787.5, rms=15.128 (1.604%)
027: dt: 0.0500, sse=7221362.5, rms=14.890 (1.569%)
028: dt: 0.0500, sse=7023415.0, rms=14.660 (1.546%)
029: dt: 0.0500, sse=6834140.5, rms=14.436 (1.526%)
030: dt: 0.0500, sse=6653406.5, rms=14.219 (1.503%)
positioning took 1.0 minutes
mean border=60.3, 97 (18) missing vertices, mean dist 1.0 [0.1 (%7.2)->1.7 (%92.8))]
%17 local maxima, %43 large gradients and %36 min vals, 390 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=6723805.0, rms=14.304
031: dt: 0.5000, sse=5453434.0, rms=12.685 (11.317%)
032: dt: 0.5000, sse=4544415.0, rms=11.380 (10.294%)
033: dt: 0.5000, sse=3829306.5, rms=10.237 (10.040%)
034: dt: 0.5000, sse=3244368.8, rms=9.192 (10.211%)
035: dt: 0.5000, sse=2756292.5, rms=8.220 (10.570%)
036: dt: 0.5000, sse=2350253.8, rms=7.311 (11.062%)
037: dt: 0.5000, sse=2025075.8, rms=6.496 (11.150%)
038: dt: 0.5000, sse=1784654.1, rms=5.816 (10.460%)
039: dt: 0.5000, sse=1612945.1, rms=5.283 (9.175%)
040: dt: 0.5000, sse=1502294.8, rms=4.902 (7.205%)
041: dt: 0.5000, sse=1431720.5, rms=4.648 (5.177%)
042: dt: 0.5000, sse=1394275.5, rms=4.502 (3.149%)
043: dt: 0.5000, sse=1368759.4, rms=4.405 (2.144%)
rms = 4.36, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1357323.2, rms=4.356 (1.119%)
045: dt: 0.2500, sse=1266108.0, rms=3.927 (9.844%)
046: dt: 0.2500, sse=1243480.0, rms=3.824 (2.637%)
rms = 3.81, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1242045.4, rms=3.813 (0.273%)
048: dt: 0.1250, sse=1229778.2, rms=3.752 (1.611%)
rms = 3.74, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1227643.9, rms=3.742 (0.268%)
positioning took 2.6 minutes
mean border=59.3, 2318 (11) missing vertices, mean dist 0.1 [0.2 (%46.8)->0.5 (%53.2))]
%29 local maxima, %34 large gradients and %32 min vals, 262 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1504088.6, rms=4.145
050: dt: 0.5000, sse=1424281.0, rms=3.805 (8.206%)
051: dt: 0.5000, sse=1404989.4, rms=3.746 (1.549%)
rms = 3.81, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1323037.9, rms=3.302 (11.866%)
053: dt: 0.2500, sse=1298937.8, rms=3.155 (4.433%)
rms = 3.14, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1295501.5, rms=3.135 (0.631%)
055: dt: 0.1250, sse=1284165.2, rms=3.064 (2.259%)
rms = 3.06, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1283138.1, rms=3.059 (0.163%)
positioning took 1.2 minutes
mean border=58.6, 2725 (9) missing vertices, mean dist 0.1 [0.2 (%46.3)->0.4 (%53.7))]
%40 local maxima, %23 large gradients and %31 min vals, 258 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=1336709.2, rms=3.336
rms = 3.47, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1310288.1, rms=3.190 (4.380%)
058: dt: 0.2500, sse=1299215.4, rms=3.131 (1.866%)
rms = 3.11, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1294735.8, rms=3.112 (0.597%)
rms = 3.07, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1288619.2, rms=3.074 (1.226%)
positioning took 0.8 minutes
mean border=58.1, 5325 (8) missing vertices, mean dist 0.1 [0.2 (%47.0)->0.3 (%53.0))]
%45 local maxima, %18 large gradients and %30 min vals, 265 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-6.0.0/0050044/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1313232.6, rms=3.196
rms = 3.22, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1294416.5, rms=3.090 (3.330%)
062: dt: 0.2500, sse=1272857.6, rms=2.980 (3.560%)
063: dt: 0.2500, sse=1260043.5, rms=2.912 (2.267%)
064: dt: 0.2500, sse=1247911.4, rms=2.849 (2.178%)
rms = 2.82, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1241964.2, rms=2.819 (1.050%)
066: dt: 0.1250, sse=1232457.9, rms=2.756 (2.213%)
rms = 2.74, time step reduction 3 of 3 to 0.062...
067: dt: 0.1250, sse=1228699.0, rms=2.736 (0.725%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.area.pial
vertex spacing 1.01 +- 0.43 (0.02-->8.25) (max @ vno 105037 --> 105022)
face area 0.40 +- 0.31 (0.00-->5.81)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 152803 vertices processed
25000 of 152803 vertices processed
50000 of 152803 vertices processed
75000 of 152803 vertices processed
100000 of 152803 vertices processed
125000 of 152803 vertices processed
150000 of 152803 vertices processed
0 of 152803 vertices processed
25000 of 152803 vertices processed
50000 of 152803 vertices processed
75000 of 152803 vertices processed
100000 of 152803 vertices processed
125000 of 152803 vertices processed
150000 of 152803 vertices processed
thickness calculation complete, 417:922 truncations.
36982 vertices at 0 distance
109067 vertices at 1 distance
89305 vertices at 2 distance
38111 vertices at 3 distance
12798 vertices at 4 distance
4048 vertices at 5 distance
1391 vertices at 6 distance
490 vertices at 7 distance
184 vertices at 8 distance
72 vertices at 9 distance
38 vertices at 10 distance
20 vertices at 11 distance
16 vertices at 12 distance
28 vertices at 13 distance
22 vertices at 14 distance
15 vertices at 15 distance
12 vertices at 16 distance
8 vertices at 17 distance
9 vertices at 18 distance
2 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.thickness
positioning took 16.9 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050044 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-6.0.0/0050044/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
18193 bright wm thresholded.
2104 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.orig...
computing class statistics...
border white:    289265 voxels (1.72%)
border gray      325149 voxels (1.94%)
WM (98.0): 98.1 +- 7.7 [70.0 --> 110.0]
GM (75.0) : 74.1 +- 9.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70)
setting MAX_BORDER_WHITE to 109.7 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 51.8 (was 40)
setting MAX_GRAY to 94.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-5.2,    GM=71+-7.0
mean inside = 94.1, mean outside = 78.0
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.04-->7.33) (max @ vno 103104 --> 151630)
face area 0.33 +- 0.16 (0.00-->6.35)
mean absolute distance = 0.62 +- 0.83
3282 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 65 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 6 with 148 points - only 0.00% unknown
deleting segment 7 with 14 points - only 14.29% unknown
deleting segment 8 with 31 points - only 54.84% unknown
deleting segment 9 with 10 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=82.2, 155 (152) missing vertices, mean dist 0.4 [0.7 (%15.0)->0.6 (%85.0))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.10-->7.38) (max @ vno 103104 --> 151630)
face area 0.33 +- 0.16 (0.00-->6.15)
mean absolute distance = 0.36 +- 0.57
4284 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2435546.2, rms=7.632
001: dt: 0.5000, sse=1368542.4, rms=4.679 (38.695%)
002: dt: 0.5000, sse=1023107.1, rms=3.201 (31.588%)
003: dt: 0.5000, sse=933638.1, rms=2.697 (15.727%)
004: dt: 0.5000, sse=898491.8, rms=2.465 (8.630%)
rms = 2.49, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=832434.6, rms=1.897 (23.014%)
006: dt: 0.2500, sse=803838.0, rms=1.589 (16.265%)
007: dt: 0.2500, sse=795263.3, rms=1.490 (6.229%)
rms = 1.44, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=792914.9, rms=1.441 (3.306%)
rms = 1.41, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=789090.4, rms=1.406 (2.393%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 58 points - only 0.00% unknown
deleting segment 1 with 11 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 106 points - only 0.00% unknown
deleting segment 4 with 26 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
deleting segment 9 with 8 points - only 0.00% unknown
mean border=85.2, 116 (42) missing vertices, mean dist -0.2 [0.4 (%72.6)->0.2 (%27.4))]
%79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.08-->7.32) (max @ vno 103104 --> 151630)
face area 0.36 +- 0.17 (0.00-->6.90)
mean absolute distance = 0.27 +- 0.39
4616 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1338655.1, rms=4.337
010: dt: 0.5000, sse=993296.8, rms=2.645 (39.008%)
011: dt: 0.5000, sse=934304.6, rms=2.265 (14.359%)
012: dt: 0.5000, sse=920287.3, rms=2.175 (3.986%)
rms = 2.32, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=858604.3, rms=1.567 (27.956%)
014: dt: 0.2500, sse=834631.6, rms=1.244 (20.591%)
015: dt: 0.2500, sse=828693.1, rms=1.163 (6.536%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=826893.8, rms=1.143 (1.747%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=825557.6, rms=1.118 (2.182%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 64 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 122 points - only 0.00% unknown
deleting segment 5 with 17 points - only 0.00% unknown
deleting segment 6 with 13 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 6 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
mean border=87.3, 131 (31) missing vertices, mean dist -0.1 [0.3 (%70.2)->0.2 (%29.8))]
%87 local maxima, % 9 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 (0.05-->7.24) (max @ vno 103104 --> 151630)
face area 0.34 +- 0.17 (0.00-->6.77)
mean absolute distance = 0.23 +- 0.32
3499 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1017163.5, rms=2.974
018: dt: 0.5000, sse=879764.4, rms=1.999 (32.772%)
rms = 1.97, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=883322.2, rms=1.973 (1.338%)
020: dt: 0.2500, sse=799795.1, rms=1.152 (41.603%)
021: dt: 0.2500, sse=793501.6, rms=1.049 (8.901%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=792815.9, rms=1.047 (0.249%)
rms = 1.02, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=790325.2, rms=1.020 (2.563%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 61 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 125 points - only 0.00% unknown
deleting segment 5 with 26 points - only 0.00% unknown
deleting segment 6 with 13 points - only 0.00% unknown
deleting segment 7 with 31 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 6 points - only 0.00% unknown
mean border=88.0, 136 (26) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))]
%90 local maxima, % 6 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-6.0.0/0050044/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=806905.0, rms=1.462
024: dt: 0.5000, sse=790881.1, rms=1.229 (15.962%)
rms = 1.57, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=769783.4, rms=0.921 (25.060%)
026: dt: 0.2500, sse=766823.6, rms=0.860 (6.589%)
rms = 0.81, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=779159.3, rms=0.812 (5.659%)
rms = 0.80, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=761807.8, rms=0.805 (0.810%)
positioning took 0.6 minutes
generating cortex label...
16 non-cortical segments detected
only using segment with 7291 vertices
erasing segment 0 (vno[0] = 47895)
erasing segment 1 (vno[0] = 47912)
erasing segment 3 (vno[0] = 87402)
erasing segment 4 (vno[0] = 105257)
erasing segment 5 (vno[0] = 105353)
erasing segment 6 (vno[0] = 106099)
erasing segment 7 (vno[0] = 106733)
erasing segment 8 (vno[0] = 107470)
erasing segment 9 (vno[0] = 110285)
erasing segment 10 (vno[0] = 110414)
erasing segment 11 (vno[0] = 111235)
erasing segment 12 (vno[0] = 111257)
erasing segment 13 (vno[0] = 112143)
erasing segment 14 (vno[0] = 114514)
erasing segment 15 (vno[0] = 114552)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.area
vertex spacing 0.89 +- 0.26 (0.05-->7.15) (max @ vno 103104 --> 151630)
face area 0.34 +- 0.17 (0.00-->6.70)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
deleting segment 1 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 17 points - only 11.76% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=59.9, 167 (167) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.9 (%100.0))]
%15 local maxima, %41 large gradients and %40 min vals, 457 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=25158568.0, rms=28.901
001: dt: 0.0500, sse=22469404.0, rms=27.265 (5.664%)
002: dt: 0.0500, sse=20550006.0, rms=26.033 (4.516%)
003: dt: 0.0500, sse=19074950.0, rms=25.046 (3.793%)
004: dt: 0.0500, sse=17876158.0, rms=24.213 (3.323%)
005: dt: 0.0500, sse=16861728.0, rms=23.486 (3.004%)
006: dt: 0.0500, sse=15978558.0, rms=22.834 (2.777%)
007: dt: 0.0500, sse=15192632.0, rms=22.237 (2.613%)
008: dt: 0.0500, sse=14482564.0, rms=21.684 (2.488%)
009: dt: 0.0500, sse=13833620.0, rms=21.166 (2.390%)
010: dt: 0.0500, sse=13235814.0, rms=20.677 (2.310%)
positioning took 1.0 minutes
mean border=59.7, 134 (98) missing vertices, mean dist 1.4 [0.2 (%0.0)->2.4 (%100.0))]
%15 local maxima, %41 large gradients and %39 min vals, 396 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=13954601.0, rms=21.262
011: dt: 0.0500, sse=13396733.0, rms=20.808 (2.134%)
012: dt: 0.0500, sse=12876293.0, rms=20.376 (2.078%)
013: dt: 0.0500, sse=12388982.0, rms=19.963 (2.029%)
014: dt: 0.0500, sse=11931666.0, rms=19.567 (1.984%)
015: dt: 0.0500, sse=11501937.0, rms=19.187 (1.940%)
016: dt: 0.0500, sse=11097062.0, rms=18.822 (1.901%)
017: dt: 0.0500, sse=10715535.0, rms=18.472 (1.862%)
018: dt: 0.0500, sse=10355740.0, rms=18.135 (1.823%)
019: dt: 0.0500, sse=10015807.0, rms=17.811 (1.787%)
020: dt: 0.0500, sse=9694760.0, rms=17.499 (1.750%)
positioning took 1.0 minutes
mean border=59.6, 128 (65) missing vertices, mean dist 1.2 [0.1 (%0.3)->2.1 (%99.7))]
%16 local maxima, %41 large gradients and %39 min vals, 432 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=9800204.0, rms=17.607
021: dt: 0.0500, sse=9492018.0, rms=17.304 (1.719%)
022: dt: 0.0500, sse=9200518.0, rms=17.013 (1.683%)
023: dt: 0.0500, sse=8924347.0, rms=16.732 (1.650%)
024: dt: 0.0500, sse=8663402.0, rms=16.462 (1.612%)
025: dt: 0.0500, sse=8416273.0, rms=16.203 (1.577%)
026: dt: 0.0500, sse=8181940.5, rms=15.953 (1.544%)
027: dt: 0.0500, sse=7958607.5, rms=15.710 (1.519%)
028: dt: 0.0500, sse=7744524.0, rms=15.475 (1.501%)
029: dt: 0.0500, sse=7539083.0, rms=15.245 (1.485%)
030: dt: 0.0500, sse=7341772.0, rms=15.021 (1.470%)
positioning took 1.0 minutes
mean border=59.5, 171 (52) missing vertices, mean dist 1.0 [0.1 (%5.0)->1.8 (%95.0))]
%16 local maxima, %41 large gradients and %38 min vals, 409 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=7422643.0, rms=15.113
031: dt: 0.5000, sse=6024354.0, rms=13.429 (11.144%)
032: dt: 0.5000, sse=4978729.5, rms=12.010 (10.566%)
033: dt: 0.5000, sse=4137161.0, rms=10.734 (10.628%)
034: dt: 0.5000, sse=3445322.5, rms=9.553 (11.005%)
035: dt: 0.5000, sse=2886019.8, rms=8.478 (11.245%)
036: dt: 0.5000, sse=2441083.5, rms=7.512 (11.395%)
037: dt: 0.5000, sse=2099972.8, rms=6.680 (11.084%)
038: dt: 0.5000, sse=1841784.4, rms=5.972 (10.596%)
039: dt: 0.5000, sse=1661983.5, rms=5.426 (9.142%)
040: dt: 0.5000, sse=1540964.9, rms=5.024 (7.406%)
041: dt: 0.5000, sse=1471450.5, rms=4.778 (4.900%)
042: dt: 0.5000, sse=1427389.8, rms=4.612 (3.466%)
043: dt: 0.5000, sse=1404661.8, rms=4.527 (1.840%)
044: dt: 0.5000, sse=1386326.2, rms=4.453 (1.643%)
rms = 4.42, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1377492.6, rms=4.420 (0.750%)
046: dt: 0.2500, sse=1286111.0, rms=3.991 (9.706%)
047: dt: 0.2500, sse=1261397.2, rms=3.882 (2.726%)
rms = 3.88, time step reduction 2 of 3 to 0.125...
048: dt: 0.2500, sse=1262173.4, rms=3.881 (0.033%)
049: dt: 0.1250, sse=1250348.4, rms=3.822 (1.504%)
rms = 3.82, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1249062.4, rms=3.816 (0.159%)
positioning took 2.8 minutes
mean border=58.6, 2326 (23) missing vertices, mean dist 0.1 [0.2 (%46.1)->0.6 (%53.9))]
%28 local maxima, %32 large gradients and %34 min vals, 173 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=1503649.8, rms=4.116
051: dt: 0.5000, sse=1420616.6, rms=3.759 (8.661%)
rms = 3.74, time step reduction 1 of 3 to 0.250...
052: dt: 0.5000, sse=1409568.4, rms=3.739 (0.542%)
053: dt: 0.2500, sse=1319772.9, rms=3.233 (13.534%)
054: dt: 0.2500, sse=1302641.6, rms=3.140 (2.875%)
rms = 3.13, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1301848.5, rms=3.133 (0.223%)
056: dt: 0.1250, sse=1290597.4, rms=3.064 (2.208%)
rms = 3.06, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1289163.5, rms=3.057 (0.210%)
positioning took 1.2 minutes
mean border=58.0, 2619 (19) missing vertices, mean dist 0.1 [0.2 (%46.5)->0.4 (%53.5))]
%39 local maxima, %22 large gradients and %33 min vals, 225 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=1341501.4, rms=3.339
rms = 3.47, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1315101.2, rms=3.194 (4.350%)
059: dt: 0.2500, sse=1304012.4, rms=3.135 (1.837%)
rms = 3.11, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1298315.5, rms=3.111 (0.778%)
rms = 3.06, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1290791.2, rms=3.064 (1.502%)
positioning took 0.8 minutes
mean border=57.5, 5228 (16) missing vertices, mean dist 0.1 [0.2 (%47.5)->0.3 (%52.5))]
%43 local maxima, %18 large gradients and %32 min vals, 200 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-6.0.0/0050044/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1305840.9, rms=3.138
rms = 3.19, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1288483.2, rms=3.040 (3.135%)
063: dt: 0.2500, sse=1269041.9, rms=2.943 (3.203%)
064: dt: 0.2500, sse=1257892.0, rms=2.885 (1.969%)
065: dt: 0.2500, sse=1246545.9, rms=2.827 (1.994%)
rms = 2.80, time step reduction 2 of 3 to 0.125...
066: dt: 0.2500, sse=1241852.1, rms=2.805 (0.796%)
067: dt: 0.1250, sse=1232584.6, rms=2.743 (2.207%)
rms = 2.73, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1229428.5, rms=2.726 (0.617%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.area.pial
vertex spacing 1.00 +- 0.43 (0.07-->8.33) (max @ vno 81552 --> 151371)
face area 0.40 +- 0.31 (0.00-->8.45)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 152636 vertices processed
25000 of 152636 vertices processed
50000 of 152636 vertices processed
75000 of 152636 vertices processed
100000 of 152636 vertices processed
125000 of 152636 vertices processed
150000 of 152636 vertices processed
0 of 152636 vertices processed
25000 of 152636 vertices processed
50000 of 152636 vertices processed
75000 of 152636 vertices processed
100000 of 152636 vertices processed
125000 of 152636 vertices processed
150000 of 152636 vertices processed
thickness calculation complete, 322:906 truncations.
34288 vertices at 0 distance
106055 vertices at 1 distance
92547 vertices at 2 distance
39987 vertices at 3 distance
13387 vertices at 4 distance
4249 vertices at 5 distance
1316 vertices at 6 distance
425 vertices at 7 distance
173 vertices at 8 distance
84 vertices at 9 distance
51 vertices at 10 distance
38 vertices at 11 distance
32 vertices at 12 distance
30 vertices at 13 distance
24 vertices at 14 distance
21 vertices at 15 distance
21 vertices at 16 distance
8 vertices at 17 distance
12 vertices at 18 distance
7 vertices at 19 distance
15 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.thickness
positioning took 16.9 minutes
PIDs (21481 21484) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 02:57:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label
Total face volume 279810
Total vertex volume 276389 (mask=0)
#@# 0050044 lh 276389
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 02:57:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label
Total face volume 284685
Total vertex volume 281522 (mask=0)
#@# 0050044 rh 281522
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 02:57:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 

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 = 125
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/ribbon.mgz
mris_volmask took 12.23 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 03:09:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 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 0050044 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 03:09:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 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 0050044 rh pial 

Waiting for PID 23668 of (23668 23671 23674 23677) to complete...
Waiting for PID 23671 of (23668 23671 23674 23677) to complete...
Waiting for PID 23674 of (23668 23671 23674 23677) to complete...
Waiting for PID 23677 of (23668 23671 23674 23677) 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 0050044 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 279810
Total vertex volume 276389 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1601   1118   2760  2.435 0.561     0.088     0.013        8     0.9  bankssts
 1116    723   1998  2.523 0.731     0.155     0.027       23     1.2  caudalanteriorcingulate
 3606   2431   7222  2.735 0.516     0.100     0.018       28     2.3  caudalmiddlefrontal
 2434   1555   3014  1.819 0.419     0.151     0.037       37     3.7  cuneus
  844    586   2967  3.702 0.852     0.124     0.025        8     0.9  entorhinal
 5720   3877  12056  2.770 0.612     0.130     0.030       71     6.9  fusiform
 7099   4702  12355  2.388 0.583     0.121     0.026       82     7.2  inferiorparietal
 5196   3569  11240  2.708 0.691     0.128     0.028       71     6.0  inferiortemporal
 1450    963   2805  2.666 0.707     0.131     0.032       23     1.5  isthmuscingulate
 8994   5583  13247  2.227 0.606     0.137     0.035      121    13.0  lateraloccipital
 4832   3283   9721  2.738 0.719     0.134     0.034       62     6.4  lateralorbitofrontal
 5653   3955   8310  1.993 0.582     0.151     0.041       85     9.5  lingual
 3540   2328   6165  2.293 0.731     0.134     0.047       69     7.3  medialorbitofrontal
 5375   3666  12341  2.759 0.663     0.140     0.035       84     7.8  middletemporal
 1304    876   3099  2.940 0.666     0.114     0.025       12     1.2  parahippocampal
 2669   1635   4322  2.400 0.517     0.095     0.016       19     1.8  paracentral
 2587   1712   5635  2.809 0.610     0.126     0.027       30     2.9  parsopercularis
 1353    871   3475  3.102 0.650     0.146     0.037       22     2.0  parsorbitalis
 2023   1359   4090  2.639 0.655     0.128     0.030       22     2.4  parstriangularis
 2856   1895   2709  1.650 0.423     0.141     0.036       36     4.3  pericalcarine
 6746   4256  10467  2.176 0.665     0.110     0.022       62     5.9  postcentral
 1728   1159   3262  2.582 0.681     0.139     0.029       28     1.9  posteriorcingulate
 9657   5893  18230  2.831 0.632     0.108     0.023       80     9.1  precentral
 5629   3883   9755  2.310 0.534     0.125     0.025       67     5.7  precuneus
 1327    880   2790  2.773 0.570     0.143     0.034       28     1.9  rostralanteriorcingulate
 9648   6399  18679  2.527 0.602     0.135     0.032      132    12.1  rostralmiddlefrontal
12451   8341  29107  3.045 0.631     0.118     0.030      132    12.9  superiorfrontal
 8810   5793  14405  2.232 0.563     0.122     0.024       98     8.2  superiorparietal
 6263   4239  14875  3.000 0.684     0.119     0.031       91     8.5  superiortemporal
 6426   4346  12814  2.631 0.632     0.125     0.025       75     6.2  supramarginal
  386    270   1147  2.944 0.682     0.189     0.055       10     1.0  frontalpole
  677    501   2532  3.456 0.719     0.142     0.038        9     1.2  temporalpole
  697    486   1175  2.563 0.507     0.184     0.056       14     1.8  transversetemporal
 3663   2487   7604  3.208 0.735     0.116     0.034       35     5.2  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050044 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 279810
Total vertex volume 276389 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1601   1107   2760  2.435 0.561     0.113     0.025       16     1.8  bankssts
 1116    853   1998  2.523 0.731     0.159     0.048       27     2.1  caudalanteriorcingulate
 3606   2732   7222  2.735 0.516     0.111     0.020       46     2.9  caudalmiddlefrontal
 2434   1825   3014  1.819 0.419     0.138     0.031       30     3.3  cuneus
  844   1086   2967  3.702 0.852     0.199     0.043        9     1.8  entorhinal
 5720   4732  12056  2.770 0.612     0.152     0.039       99    10.0  fusiform
 7099   5610  12355  2.388 0.583     0.139     0.029       80     9.5  inferiorparietal
 5196   4622  11240  2.708 0.691     0.157     0.038       72     9.5  inferiortemporal
 1450   1183   2805  2.666 0.707     0.153     0.042       42     2.6  isthmuscingulate
 8994   6438  13247  2.227 0.606     0.127     0.031      145    12.8  lateraloccipital
 4832   3834   9721  2.738 0.719     0.151     0.037       81     8.2  lateralorbitofrontal
 5653   4630   8310  1.993 0.582     0.152     0.040       85    10.9  lingual
 3540   2940   6165  2.293 0.731     0.161     0.050       74     8.6  medialorbitofrontal
 5375   5096  12341  2.759 0.663     0.160     0.035       67     8.9  middletemporal
 1304   1280   3099  2.940 0.666     0.155     0.040       13     2.3  parahippocampal
 2669   1965   4322  2.400 0.517     0.103     0.017       19     2.0  paracentral
 2587   2225   5635  2.809 0.610     0.152     0.036       34     4.5  parsopercularis
 1353   1351   3475  3.102 0.650     0.158     0.037       15     2.4  parsorbitalis
 2023   1636   4090  2.639 0.655     0.145     0.035       25     3.3  parstriangularis
 2856   1547   2709  1.650 0.423     0.115     0.062       57    10.7  pericalcarine
 6746   5407  10467  2.176 0.665     0.127     0.023       65     6.7  postcentral
 1728   1336   3262  2.582 0.681     0.148     0.040       32     3.2  posteriorcingulate
 9657   6876  18230  2.831 0.632     0.121     0.090     1447    60.6  precentral
 5629   4467   9755  2.310 0.534     0.142     0.030       78     7.1  precuneus
 1327   1195   2790  2.773 0.570     0.182     0.051       27     2.9  rostralanteriorcingulate
 9648   8121  18679  2.527 0.602     0.154     0.034      129    14.8  rostralmiddlefrontal
12451  10367  29107  3.045 0.631     0.135     0.031      178    16.3  superiorfrontal
 8810   6840  14405  2.232 0.563     0.133     0.026       97    10.1  superiorparietal
 6263   5539  14875  3.000 0.684     0.151     0.037       93    10.8  superiortemporal
 6426   5226  12814  2.631 0.632     0.136     0.029       93     8.5  supramarginal
  386    498   1147  2.944 0.682     0.214     0.033        5     0.7  frontalpole
  677    941   2532  3.456 0.719     0.216     0.048       10     1.7  temporalpole
  697    487   1175  2.563 0.507     0.127     0.040       14     1.2  transversetemporal
 3663   2309   7604  3.208 0.735     0.157     0.052      103     8.5  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 0050044 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 284685
Total vertex volume 281522 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1121    786   2077  2.775 0.439     0.122     0.027       10     1.2  bankssts
 1093    726   1927  2.334 0.765     0.139     0.026       18     1.2  caudalanteriorcingulate
 3829   2493   7983  2.882 0.459     0.107     0.022       35     3.5  caudalmiddlefrontal
 3151   2037   4677  2.121 0.530     0.156     0.039       50     5.3  cuneus
  591    431   2028  3.689 0.938     0.132     0.044       10     1.2  entorhinal
 5902   4061  12902  2.844 0.611     0.133     0.033       80     7.6  fusiform
 6470   4330  12422  2.602 0.583     0.126     0.028       77     7.2  inferiorparietal
 5320   3558  12251  2.842 0.757     0.133     0.037       88     8.5  inferiortemporal
 1476    983   2841  2.486 0.803     0.139     0.042       31     2.4  isthmuscingulate
 9006   5789  14622  2.327 0.581     0.143     0.038      127    13.6  lateraloccipital
 5016   3374   9224  2.536 0.770     0.141     0.045       83     8.5  lateralorbitofrontal
 5149   3591   7656  2.007 0.585     0.153     0.044       72     9.5  lingual
 3459   2355   6401  2.425 0.664     0.129     0.035       55     4.9  medialorbitofrontal
 5145   3580  12742  2.972 0.671     0.127     0.025       65     5.4  middletemporal
 1340    853   2644  2.718 0.689     0.096     0.028       12     1.4  parahippocampal
 2786   1661   5053  2.753 0.586     0.094     0.017       20     1.9  paracentral
 2916   1905   5912  2.791 0.486     0.107     0.020       32     2.4  parsopercularis
 1513   1050   3449  2.761 0.690     0.156     0.044       24     2.8  parsorbitalis
 3095   2037   6315  2.686 0.672     0.118     0.023       32     2.9  parstriangularis
 3151   2217   3049  1.611 0.442     0.154     0.041       45     5.3  pericalcarine
 7078   4409  10698  2.152 0.623     0.104     0.023       65     6.3  postcentral
 1776   1186   3601  2.636 0.823     0.129     0.024       24     1.6  posteriorcingulate
 8872   5409  16722  2.814 0.604     0.103     0.022       67     7.9  precentral
 6025   4112  10521  2.464 0.569     0.123     0.025       66     5.9  precuneus
  999    648   2091  2.788 0.671     0.144     0.036       20     1.3  rostralanteriorcingulate
 9563   6546  18025  2.431 0.537     0.138     0.032      146    12.5  rostralmiddlefrontal
11230   7501  26346  3.040 0.620     0.122     0.028      111    12.4  superiorfrontal
 9033   5874  15521  2.342 0.550     0.122     0.024      100     8.7  superiorparietal
 6992   4652  15854  3.042 0.683     0.117     0.023       78     6.3  superiortemporal
 6550   4324  13213  2.716 0.556     0.122     0.026       71     6.6  supramarginal
  450    316   1296  3.175 0.659     0.177     0.076       11     1.5  frontalpole
  731    493   2777  3.923 0.721     0.121     0.034        9     1.0  temporalpole
  685    439   1237  2.447 0.454     0.130     0.035        9     1.0  transversetemporal
 3347   2320   7245  3.199 0.778     0.128     0.038       36     5.4  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050044 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 284685
Total vertex volume 281522 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1121    707   2077  2.775 0.439     0.133     0.036       19     1.8  bankssts
 1093    898   1927  2.334 0.765     0.167     0.044       28     1.7  caudalanteriorcingulate
 3829   3001   7983  2.882 0.459     0.119     0.026       36     4.4  caudalmiddlefrontal
 3151   2483   4677  2.121 0.530     0.148     0.036       55     5.3  cuneus
  591    640   2028  3.689 0.938     0.166     0.038        5     1.0  entorhinal
 5902   4877  12902  2.844 0.611     0.146     0.035       88     9.7  fusiform
 6470   5199  12422  2.602 0.583     0.141     0.037       89    11.5  inferiorparietal
 5320   4837  12251  2.842 0.757     0.158     0.040      106    10.6  inferiortemporal
 1476   1196   2841  2.486 0.803     0.136     0.034       22     1.9  isthmuscingulate
 9006   6862  14622  2.327 0.581     0.131     0.031      118    12.6  lateraloccipital
 5016   3895   9224  2.536 0.770     0.149     0.041       92     9.1  lateralorbitofrontal
 5149   4276   7656  2.007 0.585     0.147     0.039       89     8.7  lingual
 3459   2965   6401  2.425 0.664     0.154     0.037       54     5.8  medialorbitofrontal
 5145   4826  12742  2.972 0.671     0.149     0.031       60     7.3  middletemporal
 1340   1097   2644  2.718 0.689     0.136     0.036       13     2.0  parahippocampal
 2786   2060   5053  2.753 0.586     0.113     0.021       30     2.6  paracentral
 2916   2347   5912  2.791 0.486     0.136     0.031       30     4.3  parsopercularis
 1513   1352   3449  2.761 0.690     0.152     0.034       28     2.5  parsorbitalis
 3095   2579   6315  2.686 0.672     0.145     0.034       42     4.8  parstriangularis
 3151   1879   3049  1.611 0.442     0.120     0.032       60     4.9  pericalcarine
 7078   5475  10698  2.152 0.623     0.118     0.024       54     7.5  postcentral
 1776   1437   3601  2.636 0.823     0.147     0.037       51     2.6  posteriorcingulate
 8872   6336  16722  2.814 0.604     0.108     0.022       88     8.7  precentral
 6025   4332  10521  2.464 0.569     0.130     0.032       84     8.1  precuneus
  999    876   2091  2.788 0.671     0.175     0.043       40     1.9  rostralanteriorcingulate
 9563   8165  18025  2.431 0.537     0.155     0.035      128    14.9  rostralmiddlefrontal
11230   9356  26346  3.040 0.620     0.138     0.032      135    16.1  superiorfrontal
 9033   7138  15521  2.342 0.550     0.132     0.028      103    11.2  superiorparietal
 6992   5772  15854  3.042 0.683     0.141     0.035      102    10.9  superiortemporal
 6550   5125  13213  2.716 0.556     0.137     0.030       88     8.6  supramarginal
  450    518   1296  3.175 0.659     0.217     0.048        5     1.2  frontalpole
  731    956   2777  3.923 0.721     0.185     0.043        7     1.5  temporalpole
  685    584   1237  2.447 0.454     0.152     0.043        8     1.3  transversetemporal
 3347   2152   7245  3.199 0.778     0.172     0.054       80     8.7  insula
PIDs (23668 23671 23674 23677) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 03:11:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 03:11:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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 23781 of (23781 23784) to complete...
Waiting for PID 23784 of (23781 23784) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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...
71 labels changed using aseg
relabeling using gibbs priors...
000:   9702 changed, 152803 examined...
001:   2327 changed, 37779 examined...
002:    642 changed, 12034 examined...
003:    282 changed, 3634 examined...
004:    134 changed, 1581 examined...
005:     54 changed, 742 examined...
006:     20 changed, 328 examined...
007:      7 changed, 118 examined...
008:      3 changed, 43 examined...
009:      1 changed, 18 examined...
010:      0 changed, 5 examined...
11 labels changed using aseg
000: 291 total segments, 206 labels (2898 vertices) changed
001: 100 total segments, 16 labels (354 vertices) changed
002: 85 total segments, 1 labels (2 vertices) changed
003: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 52 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1200 vertices marked for relabeling...
1200 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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...
10 labels changed using aseg
relabeling using gibbs priors...
000:  10063 changed, 152636 examined...
001:   2365 changed, 39173 examined...
002:    694 changed, 12544 examined...
003:    259 changed, 3841 examined...
004:    124 changed, 1536 examined...
005:     68 changed, 727 examined...
006:     35 changed, 386 examined...
007:     19 changed, 194 examined...
008:      3 changed, 103 examined...
009:      2 changed, 18 examined...
010:      1 changed, 10 examined...
011:      1 changed, 7 examined...
012:      0 changed, 6 examined...
5 labels changed using aseg
000: 301 total segments, 214 labels (3390 vertices) changed
001: 100 total segments, 14 labels (52 vertices) changed
002: 87 total segments, 1 labels (1 vertices) changed
003: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 51 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1525 vertices marked for relabeling...
1525 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.
PIDs (23781 23784) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 03:11:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 03:11:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 rh white 

Waiting for PID 23918 of (23918 23921) to complete...
Waiting for PID 23921 of (23918 23921) 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 0050044 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 279810
Total vertex volume 276389 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1471   1035   2594  2.316 0.606     0.140     0.031       19     2.0  G&S_frontomargin
 1723   1128   3118  2.626 0.621     0.136     0.033       22     2.3  G&S_occipital_inf
 2161   1207   3468  2.389 0.598     0.104     0.023       22     2.0  G&S_paracentral
 1778   1208   4129  2.883 0.574     0.136     0.031       22     2.3  G&S_subcentral
  780    510   2002  2.837 0.705     0.175     0.052       17     1.7  G&S_transv_frontopol
 2302   1569   5045  2.806 0.539     0.126     0.030       34     2.7  G&S_cingul-Ant
 1467   1029   2881  2.815 0.560     0.128     0.020       19     1.2  G&S_cingul-Mid-Ant
 1735   1190   3267  2.675 0.541     0.115     0.023       19     1.6  G&S_cingul-Mid-Post
  534    377   1413  2.880 0.452     0.150     0.034        9     0.7  G_cingul-Post-dorsal
  294    189    652  2.898 0.615     0.116     0.036        4     0.2  G_cingul-Post-ventral
 2439   1537   3031  1.766 0.492     0.156     0.039       39     4.1  G_cuneus
 1590   1037   4188  3.019 0.552     0.138     0.033       23     2.2  G_front_inf-Opercular
  553    322   1522  3.264 0.496     0.127     0.039        9     0.8  G_front_inf-Orbital
 1192    769   2936  2.781 0.647     0.147     0.039       19     1.8  G_front_inf-Triangul
 5263   3385  13160  2.846 0.583     0.140     0.037       89     7.3  G_front_middle
 8650   5561  21742  3.150 0.663     0.127     0.036      111    10.6  G_front_sup
  728    496   1661  3.308 0.793     0.132     0.052        9     1.5  G_Ins_lg&S_cent_ins
  766    462   2050  3.440 0.762     0.115     0.037       10     1.1  G_insular_short
 2932   1718   5440  2.380 0.570     0.138     0.035       48     4.2  G_occipital_middle
 1298    783   2227  2.359 0.558     0.130     0.027       17     1.2  G_occipital_sup
 2513   1676   6320  2.907 0.542     0.150     0.038       46     3.7  G_oc-temp_lat-fusifor
 4113   2795   6113  1.906 0.543     0.163     0.049       78     8.1  G_oc-temp_med-Lingual
 1821   1204   5358  3.335 0.835     0.113     0.026       19     1.7  G_oc-temp_med-Parahip
 3109   1995   7659  2.822 0.803     0.144     0.042       54     4.9  G_orbital
 2595   1663   5848  2.718 0.602     0.139     0.035       47     3.3  G_pariet_inf-Angular
 3227   2140   7739  2.845 0.649     0.142     0.030       52     3.6  G_pariet_inf-Supramar
 3159   2027   5949  2.288 0.646     0.125     0.027       42     3.1  G_parietal_sup
 2632   1495   4144  2.245 0.578     0.105     0.024       25     2.6  G_postcentral
 3784   2019   8219  3.072 0.583     0.104     0.026       35     3.7  G_precentral
 3017   2006   6340  2.462 0.545     0.133     0.027       47     3.4  G_precuneus
 1213    783   2653  2.454 0.755     0.155     0.063       36     3.6  G_rectus
  888    534   1279  2.102 0.872     0.132     0.067       18     2.4  G_subcallosal
  506    307   1023  2.619 0.616     0.161     0.050       13     0.9  G_temp_sup-G_T_transv
 2059   1343   6728  3.438 0.629     0.144     0.038       33     3.0  G_temp_sup-Lateral
  686    486   2051  3.423 0.715     0.086     0.018        3     0.5  G_temp_sup-Plan_polar
 1310    911   2611  2.673 0.548     0.099     0.019        7     1.1  G_temp_sup-Plan_tempo
 2542   1724   6216  2.699 0.748     0.133     0.035       45     3.6  G_temporal_inf
 3350   2234   8949  2.824 0.695     0.147     0.038       60     5.2  G_temporal_middle
  309    220    471  2.237 0.465     0.087     0.011        1     0.2  Lat_Fis-ant-Horizont
  264    188    406  2.396 0.483     0.118     0.019        2     0.2  Lat_Fis-ant-Vertical
 1331    924   1972  2.770 0.574     0.133     0.049       38     3.3  Lat_Fis-post
 2293   1377   2822  1.902 0.514     0.140     0.043       35     4.2  Pole_occipital
 1442    998   4739  3.218 0.772     0.144     0.038       22     2.4  Pole_temporal
 3142   2272   3625  1.825 0.601     0.140     0.033       34     4.6  S_calcarine
 3500   2384   4174  1.990 0.562     0.112     0.020       24     2.9  S_central
 1130    759   1846  2.382 0.601     0.103     0.020        9     0.7  S_cingul-Marginalis
  660    462   1292  3.325 0.531     0.116     0.022        3     0.6  S_circular_insula_ant
 1331    930   2397  3.233 0.579     0.097     0.020        7     1.2  S_circular_insula_inf
 1972   1379   3228  2.931 0.581     0.105     0.020       12     1.8  S_circular_insula_sup
 1264    878   2084  2.661 0.540     0.101     0.016        7     0.8  S_collat_transv_ant
  517    369    531  1.852 0.397     0.139     0.026        4     0.6  S_collat_transv_post
 2483   1664   3517  2.249 0.452     0.109     0.020       21     1.9  S_front_inf
 1545   1088   2221  2.334 0.510     0.118     0.021       10     1.3  S_front_middle
 3322   2304   5853  2.682 0.415     0.092     0.015       17     1.9  S_front_sup
  456    330    670  2.344 0.365     0.104     0.015        2     0.3  S_interm_prim-Jensen
 3730   2551   5164  2.193 0.424     0.118     0.021       32     3.1  S_intrapariet&P_trans
 1359    914   1468  1.977 0.417     0.138     0.033       13     1.8  S_oc_middle&Lunatus
 1208    795   1379  1.874 0.382     0.109     0.021        8     1.0  S_oc_sup&transversal
 1213    824   1770  2.441 0.485     0.136     0.032       14     1.6  S_occipital_ant
  829    609   1432  2.493 0.712     0.109     0.017        6     0.6  S_oc-temp_lat
 2549   1780   4024  2.590 0.582     0.118     0.026       20     2.7  S_oc-temp_med&Lingual
  453    323    607  2.316 0.550     0.142     0.035        4     0.6  S_orbital_lateral
  934    669   1445  2.508 0.665     0.116     0.016        7     0.6  S_orbital_med-olfact
 1835   1272   3499  2.694 0.623     0.126     0.028       19     2.0  S_orbital-H_Shaped
 1821   1273   2450  1.984 0.454     0.118     0.023       17     1.5  S_parieto_occipital
 1226    734   1120  2.130 0.802     0.155     0.032       29     1.4  S_pericallosal
 3057   2076   4123  2.100 0.503     0.100     0.016       18     1.9  S_postcentral
 2371   1641   4173  2.713 0.516     0.109     0.017       18     1.8  S_precentral-inf-part
 1313    911   2023  2.599 0.378     0.078     0.010        4     0.6  S_precentral-sup-part
  955    658   1381  2.305 0.495     0.129     0.018       11     0.7  S_suborbital
 1232    845   1702  2.344 0.405     0.107     0.017        8     0.9  S_subparietal
 1919   1335   3289  2.600 0.580     0.124     0.023       17     1.9  S_temporal_inf
 6777   4703  11166  2.453 0.525     0.108     0.022       54     5.9  S_temporal_sup
  442    332    600  2.345 0.434     0.162     0.045        5     1.3  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 0050044 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 284685
Total vertex volume 281522 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1189    825   2717  2.838 0.671     0.165     0.046       23     2.2  G&S_frontomargin
 1744   1158   3430  2.576 0.625     0.141     0.037       25     2.4  G&S_occipital_inf
 1793    990   3496  2.734 0.569     0.102     0.024       15     1.7  G&S_paracentral
 1706   1154   3619  2.696 0.643     0.132     0.031       24     1.9  G&S_subcentral
 1197    825   2727  2.448 0.666     0.148     0.042       23     2.1  G&S_transv_frontopol
 2951   2006   6144  2.782 0.547     0.125     0.028       37     3.2  G&S_cingul-Ant
 1333    925   2750  2.762 0.548     0.121     0.022       15     1.3  G&S_cingul-Mid-Ant
 1334    940   2730  2.809 0.528     0.112     0.020       10     1.0  G&S_cingul-Mid-Post
  693    459   2138  3.269 0.472     0.151     0.034       13     0.9  G_cingul-Post-dorsal
  317    206    788  2.846 0.855     0.149     0.054        9     0.7  G_cingul-Post-ventral
 3141   2037   4449  1.992 0.528     0.161     0.041       52     5.4  G_cuneus
 1665   1064   4318  2.964 0.487     0.127     0.027       29     1.7  G_front_inf-Opercular
  575    359   1607  3.155 0.668     0.154     0.040       12     0.8  G_front_inf-Orbital
 1270    802   2858  2.682 0.595     0.132     0.031       18     1.6  G_front_inf-Triangul
 4281   2787  10324  2.766 0.555     0.141     0.036       80     6.2  G_front_middle
 7836   4971  20198  3.220 0.602     0.127     0.033       91    10.3  G_front_sup
  569    397   1420  3.280 0.945     0.146     0.042       10     1.0  G_Ins_lg&S_cent_ins
  752    497   2207  3.496 0.645     0.130     0.036        8     1.3  G_insular_short
 2508   1544   5328  2.628 0.485     0.142     0.034       43     3.5  G_occipital_middle
 1814   1151   3050  2.236 0.466     0.138     0.035       25     2.4  G_occipital_sup
 2720   1848   6674  2.856 0.622     0.145     0.036       46     3.7  G_oc-temp_lat-fusifor
 3316   2269   5306  2.006 0.619     0.167     0.052       53     7.6  G_oc-temp_med-Lingual
 2134   1408   5177  2.926 0.982     0.140     0.062       43     5.2  G_oc-temp_med-Parahip
 3390   2325   7915  2.664 0.753     0.165     0.056       74     8.0  G_orbital
 2764   1757   6732  2.909 0.594     0.151     0.040       52     4.7  G_pariet_inf-Angular
 2734   1763   6916  2.988 0.497     0.133     0.031       39     3.1  G_pariet_inf-Supramar
 3063   1910   6536  2.587 0.573     0.127     0.026       43     3.3  G_parietal_sup
 2566   1455   3879  2.138 0.500     0.111     0.027       29     2.9  G_postcentral
 3721   1994   8263  3.067 0.538     0.099     0.024       32     3.5  G_precentral
 2652   1772   5620  2.591 0.617     0.132     0.028       38     3.0  G_precuneus
 1073    739   2267  2.272 0.725     0.152     0.048       25     2.3  G_rectus
  717    424    807  1.735 0.745     0.116     0.076       15     1.4  G_subcallosal
  663    409   1388  2.667 0.566     0.147     0.040       10     1.1  G_temp_sup-G_T_transv
 2337   1535   6630  3.267 0.626     0.144     0.032       39     3.0  G_temp_sup-Lateral
  801    547   2426  3.682 0.708     0.086     0.015        4     0.5  G_temp_sup-Plan_polar
 1325    884   2649  2.707 0.548     0.098     0.019       11     0.9  G_temp_sup-Plan_tempo
 2879   1892   7818  2.885 0.845     0.150     0.052       70     6.4  G_temporal_inf
 3036   2076   9242  3.134 0.647     0.139     0.031       50     3.8  G_temporal_middle
  584    400   1208  2.819 0.709     0.087     0.012        3     0.3  Lat_Fis-ant-Horizont
  471    333    700  2.481 0.528     0.112     0.014        3     0.3  Lat_Fis-ant-Vertical
 1690   1148   2428  2.582 0.526     0.107     0.021       12     1.4  Lat_Fis-post
 4072   2666   5674  2.037 0.607     0.152     0.045       63     7.3  Pole_occipital
 1587   1085   5566  3.547 0.699     0.141     0.035       24     2.4  Pole_temporal
 3089   2130   3223  1.806 0.554     0.143     0.037       40     4.4  S_calcarine
 3347   2212   3858  1.991 0.595     0.099     0.019       19     2.7  S_central
 1381    931   2422  2.452 0.527     0.099     0.014       12     0.8  S_cingul-Marginalis
  460    316    875  3.140 0.516     0.093     0.017        2     0.3  S_circular_insula_ant
 1427    988   2676  3.364 0.708     0.084     0.016        6     0.9  S_circular_insula_inf
 1328    930   2282  3.027 0.507     0.105     0.018        6     1.1  S_circular_insula_sup
 1226    860   2192  3.083 0.519     0.097     0.015        6     0.8  S_collat_transv_ant
  720    501   1071  2.396 0.500     0.137     0.034        7     1.0  S_collat_transv_post
 3193   2178   4814  2.340 0.427     0.109     0.020       24     2.6  S_front_inf
 2278   1572   3346  2.300 0.478     0.123     0.024       22     2.3  S_front_middle
 3027   2092   5372  2.653 0.426     0.100     0.018       20     2.2  S_front_sup
  629    427    886  2.464 0.456     0.119     0.018        4     0.6  S_interm_prim-Jensen
 3381   2312   4610  2.208 0.426     0.111     0.020       26     2.5  S_intrapariet&P_trans
 1101    771   1367  2.203 0.518     0.138     0.033       10     1.4  S_oc_middle&Lunatus
 1249    856   1563  2.059 0.381     0.123     0.028       10     1.4  S_oc_sup&transversal
  838    573   1301  2.427 0.450     0.125     0.027        8     0.9  S_occipital_ant
 1152    815   2027  2.790 0.524     0.102     0.019        6     0.9  S_oc-temp_lat
 2297   1616   3533  2.464 0.558     0.116     0.026       19     2.3  S_oc-temp_med&Lingual
  484    349    626  2.087 0.361     0.139     0.019        5     0.5  S_orbital_lateral
  977    694   1465  2.462 0.749     0.122     0.023       10     0.8  S_orbital_med-olfact
 1784   1235   3347  2.762 0.593     0.133     0.029       21     2.1  S_orbital-H_Shaped
 2571   1742   3781  2.300 0.503     0.118     0.024       24     2.6  S_parieto_occipital
 1614    970   1296  1.825 0.729     0.139     0.032       32     1.8  S_pericallosal
 3215   2128   4259  2.158 0.428     0.097     0.015       20     1.9  S_postcentral
 1995   1351   3276  2.711 0.376     0.095     0.015       11     1.2  S_precentral-inf-part
 1809   1236   2884  2.692 0.440     0.084     0.011        7     0.8  S_precentral-sup-part
  526    354    750  2.604 0.547     0.113     0.016        5     0.3  S_suborbital
 1352    951   2146  2.491 0.498     0.115     0.022       11     1.1  S_subparietal
 1442    999   2082  2.537 0.595     0.113     0.019        9     1.1  S_temporal_inf
 5778   4064   9565  2.600 0.513     0.111     0.019       43     4.6  S_temporal_sup
  328    220    510  2.821 0.468     0.107     0.014        2     0.1  S_temporal_transverse
PIDs (23918 23921) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 03:12:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 03:12:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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 24129 of (24129 24132) to complete...
Waiting for PID 24132 of (24129 24132) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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...
1513 labels changed using aseg
relabeling using gibbs priors...
000:   2293 changed, 152803 examined...
001:    519 changed, 10440 examined...
002:    143 changed, 2921 examined...
003:     64 changed, 843 examined...
004:     34 changed, 367 examined...
005:     16 changed, 200 examined...
006:     11 changed, 89 examined...
007:     14 changed, 67 examined...
008:      8 changed, 68 examined...
009:      7 changed, 55 examined...
010:      6 changed, 45 examined...
011:      2 changed, 38 examined...
012:      1 changed, 14 examined...
013:      0 changed, 7 examined...
281 labels changed using aseg
000: 75 total segments, 42 labels (246 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, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
808 vertices marked for relabeling...
808 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050044 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...
1451 labels changed using aseg
relabeling using gibbs priors...
000:   2213 changed, 152636 examined...
001:    506 changed, 10264 examined...
002:    146 changed, 2912 examined...
003:     62 changed, 852 examined...
004:     37 changed, 366 examined...
005:     25 changed, 222 examined...
006:     21 changed, 128 examined...
007:     16 changed, 115 examined...
008:      8 changed, 83 examined...
009:      7 changed, 46 examined...
010:      4 changed, 44 examined...
011:      4 changed, 20 examined...
012:      5 changed, 23 examined...
013:      4 changed, 27 examined...
014:      3 changed, 21 examined...
015:      5 changed, 21 examined...
016:      4 changed, 23 examined...
017:      2 changed, 24 examined...
018:      2 changed, 8 examined...
019:      1 changed, 10 examined...
020:      3 changed, 7 examined...
021:      2 changed, 12 examined...
022:      2 changed, 10 examined...
023:      2 changed, 13 examined...
024:      2 changed, 10 examined...
025:      2 changed, 12 examined...
026:      1 changed, 14 examined...
027:      0 changed, 7 examined...
261 labels changed using aseg
000: 51 total segments, 18 labels (533 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, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1013 vertices marked for relabeling...
1013 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (24129 24132) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 03:12:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 03:12:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 rh white 

Waiting for PID 24254 of (24254 24257) to complete...
Waiting for PID 24257 of (24254 24257) 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 0050044 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 279810
Total vertex volume 276389 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1803   1177   3503  2.658 0.648     0.141     0.026       33     1.8  caudalanteriorcingulate
 3891   2630   7710  2.728 0.512     0.102     0.018       31     2.7  caudalmiddlefrontal
 3037   1990   3902  1.837 0.476     0.145     0.033       42     4.2  cuneus
  950    658   3199  3.590 0.895     0.116     0.026       10     0.9  entorhinal
 5148   3528  10658  2.768 0.602     0.132     0.030       62     6.3  fusiform
 7058   4640  12394  2.402 0.583     0.123     0.028       85     7.2  inferiorparietal
 5337   3623  11904  2.712 0.710     0.126     0.029       74     6.4  inferiortemporal
 1456    967   2800  2.672 0.696     0.130     0.032       22     1.5  isthmuscingulate
 8838   5458  13068  2.229 0.595     0.135     0.034      114    12.0  lateraloccipital
 5398   3649  10961  2.629 0.760     0.137     0.038       77     8.3  lateralorbitofrontal
 5813   4056   8458  1.975 0.582     0.152     0.043       93    10.2  lingual
 2864   1877   5287  2.397 0.721     0.137     0.045       56     5.8  medialorbitofrontal
 7004   4835  15248  2.700 0.654     0.132     0.031       92     8.9  middletemporal
 1348    898   3160  2.929 0.669     0.114     0.026       13     1.3  parahippocampal
 3163   1963   5223  2.459 0.512     0.097     0.016       23     2.2  paracentral
 2345   1551   5262  2.870 0.585     0.126     0.028       27     2.6  parsopercularis
 1262    818   3108  3.099 0.615     0.127     0.030       17     1.4  parsorbitalis
 2677   1789   5050  2.551 0.616     0.134     0.033       33     3.3  parstriangularis
 2774   1837   2634  1.653 0.423     0.141     0.037       35     4.3  pericalcarine
 7562   4822  11705  2.202 0.671     0.111     0.022       70     6.6  postcentral
 1876   1265   3488  2.596 0.679     0.135     0.029       29     2.0  posteriorcingulate
 9495   5803  17926  2.841 0.629     0.109     0.023       79     9.0  precentral
 5666   3882  10153  2.342 0.539     0.127     0.026       70     6.0  precuneus
 1842   1239   3514  2.639 0.607     0.131     0.030       32     2.2  rostralanteriorcingulate
 6989   4583  14043  2.630 0.631     0.133     0.031       93     8.6  rostralmiddlefrontal
13541   9095  31224  2.950 0.694     0.125     0.032      157    16.1  superiorfrontal
 7322   4808  11877  2.232 0.552     0.122     0.024       81     6.8  superiorparietal
 8206   5632  19559  2.982 0.721     0.118     0.030      109    10.7  superiortemporal
 5955   4036  11817  2.641 0.640     0.125     0.024       68     5.8  supramarginal
  748    506   1232  2.531 0.525     0.184     0.065       16     2.3  transversetemporal
 2996   2008   6324  3.215 0.706     0.110     0.032       28     4.0  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 0050044 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 284685
Total vertex volume 281522 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1264    835   2297  2.400 0.774     0.139     0.027       21     1.4  caudalanteriorcingulate
 4071   2647   8260  2.847 0.478     0.108     0.022       38     3.6  caudalmiddlefrontal
 3810   2469   5620  2.111 0.508     0.151     0.038       57     6.1  cuneus
  566    416   1928  3.612 0.926     0.139     0.048       10     1.2  entorhinal
 5472   3781  11677  2.811 0.596     0.134     0.033       75     7.0  fusiform
 6508   4324  12413  2.608 0.585     0.129     0.030       81     7.8  inferiorparietal
 5798   3860  13612  2.863 0.765     0.132     0.037       94     9.0  inferiortemporal
 1521   1012   2845  2.421 0.791     0.138     0.042       31     2.5  isthmuscingulate
 9052   5821  14641  2.320 0.585     0.143     0.038      126    13.6  lateraloccipital
 5439   3730  10697  2.623 0.738     0.151     0.047       96    10.3  lateralorbitofrontal
 5102   3559   7571  2.008 0.580     0.154     0.045       71     9.6  lingual
 2676   1793   4648  2.274 0.780     0.127     0.045       45     4.3  medialorbitofrontal
 6056   4220  14336  2.923 0.645     0.129     0.026       76     6.7  middletemporal
 1412    907   2801  2.714 0.693     0.099     0.029       13     1.6  parahippocampal
 2910   1747   5290  2.763 0.580     0.095     0.017       20     2.0  paracentral
 3276   2149   6720  2.785 0.481     0.109     0.020       36     2.7  parsopercularis
 1131    789   2539  2.793 0.680     0.141     0.039       15     1.9  parsorbitalis
 3275   2149   6672  2.649 0.667     0.123     0.025       38     3.4  parstriangularis
 3081   2170   2980  1.606 0.444     0.153     0.041       44     5.1  pericalcarine
 7848   4914  11844  2.161 0.618     0.107     0.022       74     6.9  postcentral
 1839   1234   3696  2.651 0.810     0.128     0.023       25     1.6  posteriorcingulate
 8521   5201  16103  2.808 0.594     0.104     0.022       65     7.7  precentral
 6219   4232  11170  2.481 0.582     0.121     0.024       68     5.9  precuneus
 1331    876   2568  2.678 0.657     0.130     0.032       22     1.4  rostralanteriorcingulate
 6932   4754  12876  2.439 0.538     0.139     0.032      106     8.9  rostralmiddlefrontal
14276   9530  32399  2.922 0.661     0.124     0.030      160    17.0  superiorfrontal
 7222   4715  12589  2.359 0.548     0.122     0.024       81     6.6  superiorparietal
 8568   5773  20516  3.118 0.733     0.118     0.025       97     8.7  superiortemporal
 6239   4105  12561  2.721 0.551     0.118     0.025       65     6.0  supramarginal
  711    445   1269  2.452 0.443     0.126     0.035        9     1.0  transversetemporal
 2835   1954   6382  3.324 0.668     0.122     0.029       26     3.5  insula
PIDs (24254 24257) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 03:13:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 pctsurfcon --s 0050044 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 03:13:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts

 pctsurfcon --s 0050044 --rh-only 

Waiting for PID 24432 of (24432 24443) to complete...
Waiting for PID 24443 of (24432 24443) to complete...

 pctsurfcon --s 0050044 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts/pctsurfcon.log
Sun Oct  8 03:13:08 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-6.0.0/0050044/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-931 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-6.0.0/0050044/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24432/lh.wm.mgh --regheader 0050044 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00006;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 78547
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24432/lh.wm.mgh
Dim: 152803 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24432/lh.gm.mgh --projfrac 0.3 --regheader 0050044 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00006;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 93778
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24432/lh.gm.mgh
Dim: 152803 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24432/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24432/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.w-g.pct.mgh --annot 0050044 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/lh.w-g.pct.mgh --annot 0050044 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/lh.w-g.pct.mgh
Vertex Area is 0.662577 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 0050044 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/scripts/pctsurfcon.log
Sun Oct  8 03:13:08 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-6.0.0/0050044/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-931 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-6.0.0/0050044/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24443/rh.wm.mgh --regheader 0050044 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00006;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 78352
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24443/rh.wm.mgh
Dim: 152636 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24443/rh.gm.mgh --projfrac 0.3 --regheader 0050044 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00006;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 93537
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24443/rh.gm.mgh
Dim: 152636 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24443/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/tmp.pctsurfcon.24443/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.w-g.pct.mgh --annot 0050044 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.w-g.pct.mgh --annot 0050044 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.w-g.pct.mgh
Vertex Area is 0.664618 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 (24432 24443) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 03:13:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2167 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2541 voxels changed to hypointensity...
4832 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 03:13:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044

 mri_aparc2aseg --s 0050044 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 03:13:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044

 mri_aparc2aseg --s 0050044 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 03:13:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044

 mri_aparc2aseg --s 0050044 --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 24637 of (24637 24640 24643) to complete...
Waiting for PID 24640 of (24637 24640 24643) to complete...
Waiting for PID 24643 of (24637 24640 24643) to complete...

 mri_aparc2aseg --s 0050044 --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 0050044
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/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-6.0.0/0050044/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.35
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 --> 22
rescaling Left_Inf_Lat_Vent from 34 --> 30
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 70
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 17
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 64
rescaling CSF from 32 --> 47
rescaling Left_Accumbens_area from 62 --> 64
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 19
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 59
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 90
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 77
  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 = 553563
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 158 changed.
pass 2: 10 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050044 --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 0050044
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/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-6.0.0/0050044/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.35
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 --> 22
rescaling Left_Inf_Lat_Vent from 34 --> 30
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 70
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 17
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 64
rescaling CSF from 32 --> 47
rescaling Left_Accumbens_area from 62 --> 64
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 19
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 59
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 90
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 77
  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 = 553737
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 158 changed.
pass 2: 10 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050044 --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 0050044
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/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-6.0.0/0050044/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.35
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 --> 22
rescaling Left_Inf_Lat_Vent from 34 --> 30
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 90
rescaling Left_Caudate from 75 --> 70
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 17
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 64
rescaling CSF from 32 --> 47
rescaling Left_Accumbens_area from 62 --> 64
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 19
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 59
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 90
rescaling Right_Hippocampus from 53 --> 61
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 77
  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 = 553737
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 158 changed.
pass 2: 10 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (24637 24640 24643) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 03:20:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri

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

Sun Oct  8 03:20:36 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-6.0.0/0050044/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-931 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-6.0.0/0050044/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-931
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 03:20:36 CEST 2017 
Ended   at Sun Oct  8 03:20:42 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 03:20:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044

 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 0050044 


$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 0050044 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1767377 mm^3    (det: 1.102258 )
Computing euler number
orig.nofix lheno =  -92, rheno = -94
orig.nofix lhholes =   47, rhholes = 48
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 03:22:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044

 mri_aparc2aseg --s 0050044 --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 0050044
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-6.0.0/0050044/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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-6.0.0/0050044/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8443 vertices from left hemi
Ripped 7776 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-6.0.0/0050044/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 = 1078271
Used brute-force search on 369 voxels
Fixing Parahip LH WM
  Found 12 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 2.000000
     3 k 2.000000
     4 k 1882.000000
     5 k 30.000000
     6 k 1.000000
     7 k 1.000000
     8 k 5.000000
     9 k 1.000000
     10 k 1.000000
     11 k 1.000000
Fixing Parahip RH WM
  Found 11 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 5.000000
     3 k 1.000000
     4 k 2.000000
     5 k 1.000000
     6 k 10.000000
     7 k 1.000000
     8 k 1.000000
     9 k 1.000000
     10 k 2055.000000
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 0050044 --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 0050044 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-931
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1767377 mm^3    (det: 1.102258 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
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-6.0.0/0050044/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 03:31:33 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 25985 of (25985 25991 25997 26003 26009) to complete...
Waiting for PID 25991 of (25985 25991 25997 26003 26009) to complete...
Waiting for PID 25997 of (25985 25991 25997 26003 26009) to complete...
Waiting for PID 26003 of (25985 25991 25997 26003 26009) to complete...
Waiting for PID 26009 of (25985 25991 25997 26003 26009) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 394
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4523
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 639
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8548
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 229
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4306
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 382
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6365
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 787
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6571
mri_label2label: Done

PIDs (25985 25991 25997 26003 26009) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 26061 of (26061 26067 26073 26079) to complete...
Waiting for PID 26067 of (26061 26067 26073 26079) to complete...
Waiting for PID 26073 of (26061 26067 26073 26079) to complete...
Waiting for PID 26079 of (26061 26067 26073 26079) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 514
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4584
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 2327
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15916
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 601
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4782
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 932
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4354
mri_label2label: Done

PIDs (26061 26067 26073 26079) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 26151 of (26151 26157 26163 26169 26173) to complete...
Waiting for PID 26157 of (26151 26157 26163 26169 26173) to complete...
Waiting for PID 26163 of (26151 26157 26163 26169 26173) to complete...
Waiting for PID 26169 of (26151 26157 26163 26169 26173) to complete...
Waiting for PID 26173 of (26151 26157 26163 26169 26173) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 2483
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 7124
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 3493
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11607
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 1083
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 3101
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 218
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1508
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 255
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1454
mri_label2label: Done

PIDs (26151 26157 26163 26169 26173) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 26267 of (26267 26273 26279 26284 26291) to complete...
Waiting for PID 26273 of (26267 26273 26279 26284 26291) to complete...
Waiting for PID 26279 of (26267 26273 26279 26284 26291) to complete...
Waiting for PID 26284 of (26267 26273 26279 26284 26291) to complete...
Waiting for PID 26291 of (26267 26273 26279 26284 26291) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 154
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1168
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 198
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2290
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1575
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 125
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2121
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 361
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2680
mri_label2label: Done

PIDs (26267 26273 26279 26284 26291) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 26348 of (26348 26354 26360 26365) to complete...
Waiting for PID 26354 of (26348 26354 26360 26365) to complete...
Waiting for PID 26360 of (26348 26354 26360 26365) to complete...
Waiting for PID 26365 of (26348 26354 26360 26365) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 188
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1737
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 935
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7970
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 175
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2087
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 307
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1458
mri_label2label: Done

PIDs (26348 26354 26360 26365) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 26404 of (26404 26410 26416 26422 26426) to complete...
Waiting for PID 26410 of (26404 26410 26416 26422 26426) to complete...
Waiting for PID 26416 of (26404 26410 26416 26422 26426) to complete...
Waiting for PID 26422 of (26404 26410 26416 26422 26426) to complete...
Waiting for PID 26426 of (26404 26410 26416 26422 26426) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 1960
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 5365
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 1543
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4877
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 310
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 823
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 97
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 567
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152803
Number of reverse mapping hits = 107
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 557
mri_label2label: Done

PIDs (26404 26410 26416 26422 26426) completed and logs appended.

 mris_label2annot --s 0050044 --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-6.0.0/0050044/label
cmdline mris_label2annot --s 0050044 --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-931
machine  x86_64
user     ntraut

subject 0050044
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-6.0.0/0050044/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 104188 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050044 --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-6.0.0/0050044/label
cmdline mris_label2annot --s 0050044 --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-931
machine  x86_64
user     ntraut

subject 0050044
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-6.0.0/0050044/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 124017 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 279810
Total vertex volume 276389 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1283    699   2150  2.340 0.514     0.129     0.033       18     1.6  BA1_exvivo
 4184   2729   6325  2.236 0.571     0.105     0.018       30     3.1  BA2_exvivo
 1182    818   1178  1.804 0.441     0.143     0.029       13     1.3  BA3a_exvivo
 2543   1637   3760  2.015 0.696     0.112     0.022       24     2.5  BA3b_exvivo
 2059   1082   3471  2.729 0.562     0.081     0.017       13     1.4  BA4a_exvivo
 1691   1040   2648  2.656 0.592     0.099     0.019       10     1.5  BA4p_exvivo
11448   7246  25864  3.022 0.604     0.113     0.028      111    10.8  BA6_exvivo
 2598   1735   5803  2.947 0.571     0.116     0.025       25     2.5  BA44_exvivo
 3327   2226   6321  2.461 0.648     0.129     0.030       40     4.0  BA45_exvivo
 4857   3117   5158  1.690 0.449     0.143     0.041       68     7.9  V1_exvivo
 8855   5932  12199  1.960 0.553     0.153     0.039      137    14.9  V2_exvivo
 2949   1868   4989  2.490 0.572     0.124     0.029       32     3.4  MT_exvivo
  745    517   2271  3.569 0.798     0.095     0.020        5     0.5  perirhinal_exvivo
  894    634   2817  3.053 0.873     0.133     0.031       12     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 0050044 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 279810
Total vertex volume 276389 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
  909    439   1401  2.356 0.471     0.120     0.028       11     1.2  BA1_exvivo
 1692   1068   2591  2.244 0.553     0.092     0.017       10     1.1  BA2_exvivo
  983    684    940  1.799 0.412     0.144     0.028       10     1.0  BA3a_exvivo
 1526   1031   1778  1.651 0.393     0.094     0.015        9     1.0  BA3b_exvivo
 2086   1095   3634  2.840 0.584     0.083     0.018       13     1.5  BA4a_exvivo
 1348    839   1912  2.460 0.503     0.105     0.020       10     1.3  BA4p_exvivo
 6085   3720  12770  2.952 0.586     0.105     0.029       53     5.4  BA6_exvivo
 1572   1065   3734  2.949 0.563     0.126     0.028       19     1.8  BA44_exvivo
 1256    857   2835  2.620 0.640     0.140     0.036       17     1.7  BA45_exvivo
 5126   3316   5552  1.686 0.447     0.146     0.042       75     8.8  V1_exvivo
 4512   3060   5963  1.890 0.527     0.157     0.041       75     8.0  V2_exvivo
  808    499   1467  2.570 0.593     0.121     0.026        9     0.9  MT_exvivo
  389    281   1150  3.681 0.770     0.091     0.017        2     0.2  perirhinal_exvivo
  494    344   1780  3.230 0.732     0.137     0.033        8     0.6  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 03:34:52 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 26544 of (26544 26550 26556 26562 26566) to complete...
Waiting for PID 26550 of (26544 26550 26556 26562 26566) to complete...
Waiting for PID 26556 of (26544 26550 26556 26562 26566) to complete...
Waiting for PID 26562 of (26544 26550 26556 26562 26566) to complete...
Waiting for PID 26566 of (26544 26550 26556 26562 26566) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 437
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4399
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 647
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7334
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 248
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4228
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 421
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4943
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 920
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6667
mri_label2label: Done

PIDs (26544 26550 26556 26562 26566) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 26671 of (26671 26677 26683 26687) to complete...
Waiting for PID 26677 of (26671 26677 26683 26687) to complete...
Waiting for PID 26683 of (26671 26677 26683 26687) to complete...
Waiting for PID 26687 of (26671 26677 26683 26687) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 535
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5008
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 1917
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14173
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 1694
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8606
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 2299
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7654
mri_label2label: Done

PIDs (26671 26677 26683 26687) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 26759 of (26759 26765 26771 26777 26782) to complete...
Waiting for PID 26765 of (26759 26765 26771 26777 26782) to complete...
Waiting for PID 26771 of (26759 26765 26771 26777 26782) to complete...
Waiting for PID 26777 of (26759 26765 26771 26777 26782) to complete...
Waiting for PID 26782 of (26759 26765 26771 26777 26782) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 2862
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 7589
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 4183
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12199
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 721
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2653
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 202
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1240
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 172
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 924
mri_label2label: Done

PIDs (26759 26765 26771 26777 26782) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 26862 of (26862 26868 26874 26880 26884) to complete...
Waiting for PID 26868 of (26862 26868 26874 26880 26884) to complete...
Waiting for PID 26874 of (26862 26868 26874 26880 26884) to complete...
Waiting for PID 26880 of (26862 26868 26874 26880 26884) to complete...
Waiting for PID 26884 of (26862 26868 26874 26880 26884) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 94
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 970
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 216
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2904
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 94
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1792
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2357
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 292
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1680
mri_label2label: Done

PIDs (26862 26868 26874 26880 26884) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 26936 of (26936 26942 26948 26952) to complete...
Waiting for PID 26942 of (26936 26942 26948 26952) to complete...
Waiting for PID 26948 of (26936 26942 26948 26952) to complete...
Waiting for PID 26952 of (26936 26942 26948 26952) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 115
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1604
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 1039
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7998
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 342
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1354
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 425
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1603
mri_label2label: Done

PIDs (26936 26942 26948 26952) 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 0050044 --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 0050044 --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 0050044 --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 0050044 --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 0050044 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27001 of (27001 27007 27013 27018 27023) to complete...
Waiting for PID 27007 of (27001 27007 27013 27018 27023) to complete...
Waiting for PID 27013 of (27001 27007 27013 27018 27023) to complete...
Waiting for PID 27018 of (27001 27007 27013 27018 27023) to complete...
Waiting for PID 27023 of (27001 27007 27013 27018 27023) 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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 2007
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 5239
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 2053
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5490
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 136
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 404
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 142
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 836
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 0050044 --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 = 0050044
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-6.0.0/0050044/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 152636
Number of reverse mapping hits = 76
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 367
mri_label2label: Done

PIDs (27001 27007 27013 27018 27023) completed and logs appended.

 mris_label2annot --s 0050044 --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-6.0.0/0050044/label
cmdline mris_label2annot --s 0050044 --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-931
machine  x86_64
user     ntraut

subject 0050044
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-6.0.0/0050044/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 102455 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050044 --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-6.0.0/0050044/label
cmdline mris_label2annot --s 0050044 --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-931
machine  x86_64
user     ntraut

subject 0050044
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-6.0.0/0050044/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 124236 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/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 0050044 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 284685
Total vertex volume 281522 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
 1066    563   1848  2.370 0.434     0.120     0.028       15     1.2  BA1_exvivo
 3809   2451   5492  2.175 0.431     0.095     0.016       24     2.4  BA2_exvivo
 1192    795   1107  1.789 0.475     0.129     0.028       11     1.2  BA3a_exvivo
 2203   1400   2853  1.829 0.556     0.102     0.025       18     2.1  BA3b_exvivo
 2060   1083   3749  2.952 0.474     0.083     0.020       11     1.7  BA4a_exvivo
 1457    911   2357  2.616 0.566     0.094     0.019        8     1.2  BA4p_exvivo
 9809   6120  22326  3.044 0.576     0.106     0.023       79     8.7  BA6_exvivo
 4461   2996   8735  2.752 0.483     0.111     0.020       44     3.7  BA44_exvivo
 5819   3859  11755  2.597 0.623     0.128     0.028       73     6.5  BA45_exvivo
 5163   3592   6101  1.690 0.498     0.153     0.043       75     9.0  V1_exvivo
 9578   6297  13845  2.108 0.550     0.155     0.043      145    16.8  V2_exvivo
 2388   1599   4199  2.481 0.462     0.139     0.036       31     3.5  MT_exvivo
  672    484   2311  3.593 0.874     0.134     0.042       11     1.4  perirhinal_exvivo
  504    302   1289  2.974 0.967     0.125     0.054       11     1.2  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 0050044 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050044/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 284685
Total vertex volume 281522 (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) = 1767377 mm^3    (det: 1.102258 )
lhCtxGM: 274538.315 274108.000  diff=  430.3  pctdiff= 0.157
rhCtxGM: 279970.761 279500.000  diff=  470.8  pctdiff= 0.168
lhCtxWM: 262883.806 263319.500  diff= -435.7  pctdiff=-0.166
rhCtxWM: 264022.064 264912.500  diff= -890.4  pctdiff=-0.337
SubCortGMVol  66833.000
SupraTentVol  1164321.945 (1161589.000) diff=2732.945 pctdiff=0.235
SupraTentVolNotVent  1151414.945 (1148682.000) diff=2732.945 pctdiff=0.237
BrainSegVol  1336009.000 (1332951.000) diff=3058.000 pctdiff=0.229
BrainSegVolNotVent  1319017.000 (1318484.945) diff=532.055 pctdiff=0.040
BrainSegVolNotVent  1319017.000
CerebellumVol 170228.000
VentChorVol   12907.000
3rd4th5thCSF   4085.000
CSFVol  1027.000, OptChiasmVol   107.000
MaskVol 1849633.000
  753    383   1266  2.289 0.431     0.122     0.023       10     0.7  BA1_exvivo
 2125   1348   3017  2.097 0.401     0.085     0.015       13     1.4  BA2_exvivo
 1073    718    904  1.764 0.419     0.137     0.029       10     1.2  BA3a_exvivo
 1684   1104   1839  1.657 0.399     0.091     0.019       10     1.2  BA3b_exvivo
 1308    643   2469  3.084 0.507     0.085     0.022        7     1.2  BA4a_exvivo
 1166    735   1868  2.627 0.541     0.080     0.016        4     0.7  BA4p_exvivo
 6276   3917  13730  3.013 0.578     0.105     0.022       47     5.3  BA6_exvivo
 1248    839   2898  2.857 0.457     0.114     0.019       16     1.1  BA44_exvivo
 1483    960   3130  2.623 0.590     0.125     0.027       19     1.5  BA45_exvivo
 4964   3454   5627  1.667 0.488     0.154     0.043       74     8.7  V1_exvivo
 5196   3424   7404  2.039 0.543     0.160     0.045       81    10.0  V2_exvivo
  394    247    843  2.610 0.431     0.098     0.019        3     0.3  MT_exvivo
  415    293   1269  3.343 0.906     0.131     0.047        8     1.0  perirhinal_exvivo
  315    205    837  3.344 1.122     0.126     0.053        5     0.8  entorhinal_exvivo

Started at Sat Oct 7 18:24:02 CEST 2017 
Ended   at Sun Oct 8 03:38:08 CEST 2017
#@#%# recon-all-run-time-hours 9.235
recon-all -s 0050044 finished without error at Sun Oct  8 03:38:08 CEST 2017