ABIDE_fs-6.0.0/0050310/scripts/recon-all.log

Sat Oct  7 23:29:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050310 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050310/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050310
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-948 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:      66074836   51673808   14401028    1738300          0   47770360
-/+ buffers/cache:    3903448   62171388
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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:49-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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: 2017/10/07-21:29:50-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-948  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-6.0.0/0050310

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050310/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050310/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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/UM_1/0050310/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-6.0.0/0050310/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 23:29:51 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/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-6.0.0/0050310/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 23:30:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/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-948 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 23:30:00 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.448
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.448/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.448/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.448/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 23:30:03 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.448/nu0.mnc ./tmp.mri_nu_correct.mni.448/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.448/0/ -iterations 1000 -distance 50
[ntraut@tars-948:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/] [2017-10-07 23:30:03] 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.448/0/ ./tmp.mri_nu_correct.mni.448/nu0.mnc ./tmp.mri_nu_correct.mni.448/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 49 
CV of field change: 0.000973102
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.448/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.448/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.448/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 23:31:18 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 23:31:18 CEST 2017
Ended   at Sat Oct  7 23:31:57 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 23:31:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7124, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/transforms/talairach_avi.log 

TalAviQA: 0.97463
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 23:31:59 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-6.0.0/0050310/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-948 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 23:31:59 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.1352
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1352/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1352/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.1352/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 23:32:02 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.1352/nu0.mnc ./tmp.mri_nu_correct.mni.1352/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1352/0/
[ntraut@tars-948:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/] [2017-10-07 23:32:02] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1352/0/ ./tmp.mri_nu_correct.mni.1352/nu0.mnc ./tmp.mri_nu_correct.mni.1352/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 45 
CV of field change: 0.000939709
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 23:32:51 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.1352/nu1.mnc ./tmp.mri_nu_correct.mni.1352/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1352/1/
[ntraut@tars-948:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/] [2017-10-07 23:32:51] 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.1352/1/ ./tmp.mri_nu_correct.mni.1352/nu1.mnc ./tmp.mri_nu_correct.mni.1352/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 11 
CV of field change: 0.000961361
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.1352/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1352/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-6.0.0/0050310/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1352/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1352/ones.mgz 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.1352/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.1352/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.1352/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1352/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.1352/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1352/input.mean.dat 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.1352/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.1352/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1352/ones.mgz --i ./tmp.mri_nu_correct.mni.1352/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1352/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.1352/ones.mgz --i ./tmp.mri_nu_correct.mni.1352/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1352/output.mean.dat 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.1352/ones.mgz
Loading ./tmp.mri_nu_correct.mni.1352/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.1352/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.1352/nu2.mnc ./tmp.mri_nu_correct.mni.1352/nu2.mnc mul .95947836888321853358
Saving result to './tmp.mri_nu_correct.mni.1352/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.1352/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.1352/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.1352/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (21, 106) to ( 3, 110)
 
 
Sat Oct  7 23:33:57 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 23:33:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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
 1.06881   0.00023  -0.02338  -137.36336;
 0.02768   1.05277   0.06856  -157.05052;
 0.03776   0.01603   1.09516  -79.01012;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 14
Starting OpenSpline(): npoints = 14
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 70 (70), valley at 15 (15)
csf peak at 36, setting threshold to 58
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 68 (68), valley at 14 (14)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 50 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 23:35:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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=18.0
skull bounding box = (51, 59, 30) --> (202, 195, 218)
using (101, 104, 124) as brain centroid...
mean wm in atlas = 108, using box (82,87,101) --> (119, 120,147) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 103 +- 6.0
after smoothing, mri peak at 104, scaling input intensities by 1.038
scaling channel 0 by 1.03846
initial log_p = -4.458
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.463181 @ (-9.091, -9.091, -9.091)
max log p =    -4.385185 @ (4.545, -4.545, -4.545)
max log p =    -4.285007 @ (2.273, 2.273, 2.273)
max log p =    -4.283198 @ (1.136, 1.136, 1.136)
max log p =    -4.267854 @ (-0.568, 0.568, 1.705)
max log p =    -4.267854 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -9.7, -8.5): log p = -4.268
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.116, old_max_log_p =-4.268 (thresh=-4.3)
 1.15000   0.00000   0.00000  -20.69151;
 0.00000   1.23625   0.00000  -38.02971;
 0.00000   0.00000   1.06375  -16.13740;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.116, old_max_log_p =-4.116 (thresh=-4.1)
 1.15000   0.00000   0.00000  -20.69151;
 0.00000   1.23625   0.00000  -38.02971;
 0.00000   0.00000   1.06375  -16.13740;
 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=-4.085, old_max_log_p =-4.116 (thresh=-4.1)
 1.12763   0.00000   0.00000  -15.98478;
 0.00000   1.21307   0.00000  -34.65088;
 0.00000   0.00000   1.08295  -20.23514;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.085, old_max_log_p =-4.085 (thresh=-4.1)
 1.12763   0.00000   0.00000  -15.98478;
 0.00000   1.21307   0.00000  -34.65088;
 0.00000   0.00000   1.08295  -20.23514;
 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=-4.064, old_max_log_p =-4.085 (thresh=-4.1)
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00904   0.01010   1.08414  -20.26096;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.062, old_max_log_p =-4.064 (thresh=-4.1)
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 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
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.062 (old=-4.458)
transform before final EM align:
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 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
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.5  tol 0.000000
final transform:
 1.12491  -0.00977   0.00881  -15.29533;
 0.00928   1.21441  -0.00894  -35.85798;
-0.00903   0.01008   1.08287  -20.10723;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1030.662315
mri_em_register stimesec    1.094833
mri_em_register ru_maxrss   609828
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157595
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  148912
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    85
mri_em_register ru_nivcsw   5804
registration took 9 minutes and 1 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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=125 y=124 z=122 r=63
      first estimation of the main basin volume: 1067972 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        17 found in the rest of the brain 
      global maximum in x=107, y=101, z=93, Imax=255
      CSF=19, 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=9373255791 voxels, voxel volume =1.000 
                     = 9373255791 mmm3 = 9373255.680 cm3
done.
PostAnalyze...Basin Prior
 86 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=127, z=116, r=9050 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45386
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1099623214
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1122647265
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1124236355
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1072360184
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1075132944
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    4,      7,        42,   62
  after  analyzing :    4,      30,        42,   38
   RIGHT_CER   
  before analyzing :    3,      4,        41,   65
  after  analyzing :    3,      28,        41,   37
   LEFT_CER    
  before analyzing :    3,      3,        39,   79
  after  analyzing :    3,      27,        39,   40
  RIGHT_BRAIN  
  before analyzing :    4,      7,        42,   62
  after  analyzing :    4,      30,        42,   38
  LEFT_BRAIN   
  before analyzing :    4,      7,        41,   62
  after  analyzing :    4,      29,        41,   37
     OTHER     
  before analyzing :    3,      5,        66,   91
  after  analyzing :    3,      45,        66,   56
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...64 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 71.777, std = 6.539

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.68, sigma = 6.48
      after  rotation: sse = 4.68, sigma = 6.48
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.85, its var is  5.22   
      before Erosion-Dilatation  0.43% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...27 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1684815 voxels, voxel volume = 1.000 mm3
           = 1684815 mmm3 = 1684.815 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    19.838984
mri_watershed stimesec    0.381941
mri_watershed ru_maxrss   817680
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   210871
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  7552
mri_watershed ru_oublock  2616
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1235
mri_watershed ru_nivcsw   172
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 23:45:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = (57, 67, 39) --> (196, 184, 206)
using (103, 106, 123) as brain centroid...
mean wm in atlas = 107, using box (86,92,102) --> (120, 120,143) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 103 +- 5.2
after smoothing, mri peak at 103, scaling input intensities by 1.039
scaling channel 0 by 1.03883
initial log_p = -4.120
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.004320 @ (-9.091, -9.091, -9.091)
max log p =    -3.965561 @ (13.636, 4.545, -4.545)
max log p =    -3.775454 @ (-6.818, -2.273, 6.818)
max log p =    -3.775454 @ (0.000, 0.000, 0.000)
max log p =    -3.757424 @ (1.705, -1.705, -0.568)
max log p =    -3.757424 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, -8.5, -7.4): log p = -3.757
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.757, old_max_log_p =-3.757 (thresh=-3.8)
 1.00000   0.00000   0.00000  -0.56818;
 0.00000   1.00000   0.00000  -8.52273;
 0.00000   0.00000   1.00000  -7.38637;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 1 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.757 (thresh=-3.8)
 1.01750  -0.03331   0.00000   1.46113;
 0.03458   1.05639   0.00000  -20.13227;
 0.00000   0.00000   1.03750  -15.36752;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.627, old_max_log_p =-3.633 (thresh=-3.6)
 1.03718   0.00130   0.00000  -5.46676;
 0.00125   1.03709   0.00000  -13.42279;
 0.00000   0.00000   1.03750  -15.36752;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.627, old_max_log_p =-3.627 (thresh=-3.6)
 1.03718   0.00130   0.00000  -5.46676;
 0.00125   1.03709   0.00000  -13.42279;
 0.00000   0.00000   1.03750  -15.36752;
 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=-3.612, old_max_log_p =-3.627 (thresh=-3.6)
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00850  -0.00848   1.04108  -15.78288;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.610, old_max_log_p =-3.612 (thresh=-3.6)
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 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
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.610 (old=-4.120)
transform before final EM align:
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 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
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.0  tol 0.000000
final transform:
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    890.650600
mri_em_register stimesec    1.009846
mri_em_register ru_maxrss   599056
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158957
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    100
mri_em_register ru_nivcsw   5048
registration took 7 minutes and 44 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 23:52:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = (57, 67, 39) --> (196, 183, 206)
using (103, 106, 123) as brain centroid...
mean wm in atlas = 107, using box (86,92,102) --> (120, 120,143) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 103 +- 5.2
after smoothing, mri peak at 103, scaling input intensities by 1.039
scaling channel 0 by 1.03883
using 246344 sample points...
INFO: compute sample coordinates transform
 1.03953  -0.00712  -0.00858  -3.22344;
 0.00974   1.03582   0.00843  -15.79143;
 0.00852  -0.00850   1.04352  -16.06701;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 63, 40) --> (190, 179, 201)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
1 of 2782 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 63, 40) --> (128, 179, 201)
Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 2974 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 147, 62) --> (174, 187, 113)
Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 177 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 147, 60) --> (126, 187, 116)
Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0
0 of 96 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 139, 94) --> (144, 206, 125)
Brain_Stem: limiting intensities to 88.0 --> 132.0
1 of 107 (0.9%) samples deleted
using 6136 total control points for intensity normalization...
bias field = 0.944 +- 0.062
0 of 6134 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 63, 40) --> (190, 179, 201)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 3522 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 63, 40) --> (128, 179, 201)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 3705 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 147, 62) --> (174, 187, 113)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
31 of 294 (10.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 147, 60) --> (126, 187, 116)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
25 of 146 (17.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 139, 94) --> (144, 206, 125)
Brain_Stem: limiting intensities to 88.0 --> 132.0
102 of 250 (40.8%) samples deleted
using 7917 total control points for intensity normalization...
bias field = 1.046 +- 0.060
4 of 7714 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 63, 40) --> (190, 179, 201)
Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
1 of 3536 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 63, 40) --> (128, 179, 201)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 3814 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 147, 62) --> (174, 187, 113)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
100 of 335 (29.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 147, 60) --> (126, 187, 116)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
101 of 194 (52.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 139, 94) --> (144, 206, 125)
Brain_Stem: limiting intensities to 88.0 --> 132.0
153 of 305 (50.2%) samples deleted
using 8184 total control points for intensity normalization...
bias field = 1.040 +- 0.054
14 of 7703 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 39 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 23:54:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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) = 1.12 (predicted orig area = 7.1)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.833, neg=0, invalid=762
0001: dt=313.360158, rms=0.755 (9.323%), neg=0, invalid=762
0002: dt=178.474227, rms=0.743 (1.654%), neg=0, invalid=762
0003: dt=369.920000, rms=0.733 (1.264%), neg=0, invalid=762
0004: dt=129.472000, rms=0.728 (0.717%), neg=0, invalid=762
0005: dt=517.888000, rms=0.722 (0.758%), neg=0, invalid=762
0006: dt=129.472000, rms=0.720 (0.323%), neg=0, invalid=762
0007: dt=517.888000, rms=0.718 (0.352%), neg=0, invalid=762
0008: dt=129.472000, rms=0.716 (0.239%), neg=0, invalid=762
0009: dt=129.472000, rms=0.715 (0.110%), neg=0, invalid=762
0010: dt=129.472000, rms=0.714 (0.155%), neg=0, invalid=762
0011: dt=129.472000, rms=0.712 (0.219%), neg=0, invalid=762
0012: dt=129.472000, rms=0.711 (0.228%), neg=0, invalid=762
0013: dt=129.472000, rms=0.709 (0.242%), neg=0, invalid=762
0014: dt=129.472000, rms=0.707 (0.258%), neg=0, invalid=762
0015: dt=129.472000, rms=0.705 (0.241%), neg=0, invalid=762
0016: dt=129.472000, rms=0.704 (0.223%), neg=0, invalid=762
0017: dt=129.472000, rms=0.703 (0.182%), neg=0, invalid=762
0018: dt=129.472000, rms=0.701 (0.166%), neg=0, invalid=762
0019: dt=129.472000, rms=0.700 (0.170%), neg=0, invalid=762
0020: dt=129.472000, rms=0.699 (0.151%), neg=0, invalid=762
0021: dt=129.472000, rms=0.698 (0.165%), neg=0, invalid=762
0022: dt=129.472000, rms=0.697 (0.157%), neg=0, invalid=762
0023: dt=129.472000, rms=0.696 (0.139%), neg=0, invalid=762
0024: dt=129.472000, rms=0.695 (0.119%), neg=0, invalid=762
0025: dt=129.472000, rms=0.694 (0.105%), neg=0, invalid=762
0026: dt=369.920000, rms=0.694 (0.045%), neg=0, invalid=762
0027: dt=369.920000, rms=0.694 (-0.086%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.695, neg=0, invalid=762
0028: dt=129.472000, rms=0.693 (0.199%), neg=0, invalid=762
0029: dt=517.888000, rms=0.693 (0.095%), neg=0, invalid=762
0030: dt=517.888000, rms=0.692 (0.093%), neg=0, invalid=762
0031: dt=517.888000, rms=0.692 (-0.299%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.698, neg=0, invalid=762
0032: dt=135.284553, rms=0.691 (0.968%), neg=0, invalid=762
0033: dt=116.404973, rms=0.684 (1.006%), neg=0, invalid=762
0034: dt=63.634286, rms=0.681 (0.449%), neg=0, invalid=762
0035: dt=331.776000, rms=0.674 (1.064%), neg=0, invalid=762
0036: dt=70.981818, rms=0.670 (0.501%), neg=0, invalid=762
0037: dt=103.680000, rms=0.668 (0.321%), neg=0, invalid=762
0038: dt=64.627451, rms=0.667 (0.172%), neg=0, invalid=762
0039: dt=64.627451, rms=0.666 (0.166%), neg=0, invalid=762
0040: dt=64.627451, rms=0.664 (0.250%), neg=0, invalid=762
0041: dt=64.627451, rms=0.662 (0.329%), neg=0, invalid=762
0042: dt=64.627451, rms=0.660 (0.364%), neg=0, invalid=762
0043: dt=64.627451, rms=0.657 (0.419%), neg=0, invalid=762
0044: dt=64.627451, rms=0.654 (0.433%), neg=0, invalid=762
0045: dt=64.627451, rms=0.651 (0.392%), neg=0, invalid=762
0046: dt=64.627451, rms=0.649 (0.348%), neg=0, invalid=762
0047: dt=64.627451, rms=0.647 (0.314%), neg=0, invalid=762
0048: dt=64.627451, rms=0.645 (0.310%), neg=0, invalid=762
0049: dt=64.627451, rms=0.643 (0.305%), neg=0, invalid=762
0050: dt=64.627451, rms=0.641 (0.267%), neg=0, invalid=762
0051: dt=64.627451, rms=0.640 (0.227%), neg=0, invalid=762
0052: dt=64.627451, rms=0.639 (0.199%), neg=0, invalid=762
0053: dt=64.627451, rms=0.638 (0.187%), neg=0, invalid=762
0054: dt=64.627451, rms=0.636 (0.170%), neg=0, invalid=762
0055: dt=64.627451, rms=0.636 (0.145%), neg=0, invalid=762
0056: dt=64.627451, rms=0.635 (0.116%), neg=0, invalid=762
0057: dt=64.627451, rms=0.634 (0.098%), neg=0, invalid=762
0058: dt=414.720000, rms=0.634 (0.104%), neg=0, invalid=762
0059: dt=20.736000, rms=0.633 (0.012%), neg=0, invalid=762
0060: dt=20.736000, rms=0.633 (0.000%), neg=0, invalid=762
0061: dt=20.736000, rms=0.633 (-0.017%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.634, neg=0, invalid=762
0062: dt=68.800000, rms=0.632 (0.288%), neg=0, invalid=762
0063: dt=103.680000, rms=0.632 (0.057%), neg=0, invalid=762
0064: dt=103.680000, rms=0.632 (0.006%), neg=0, invalid=762
0065: dt=103.680000, rms=0.632 (0.032%), neg=0, invalid=762
0066: dt=103.680000, rms=0.632 (-0.047%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.658, neg=0, invalid=762
0067: dt=8.000000, rms=0.657 (0.185%), neg=0, invalid=762
0068: dt=2.800000, rms=0.657 (0.008%), neg=0, invalid=762
0069: dt=2.800000, rms=0.657 (0.001%), neg=0, invalid=762
0070: dt=2.800000, rms=0.657 (-0.028%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.658, neg=0, invalid=762
0071: dt=0.000000, rms=0.657 (0.088%), neg=0, invalid=762
0072: dt=0.000000, rms=0.657 (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=0.724, neg=0, invalid=762
0073: dt=6.092527, rms=0.703 (2.848%), neg=0, invalid=762
0074: dt=4.372093, rms=0.702 (0.221%), neg=0, invalid=762
0075: dt=4.372093, rms=0.702 (-0.028%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.702, neg=0, invalid=762
0076: dt=0.000000, rms=0.702 (0.077%), neg=0, invalid=762
0077: dt=0.000000, rms=0.702 (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=0.758, neg=0, invalid=762
0078: dt=0.448000, rms=0.756 (0.203%), neg=0, invalid=762
0079: dt=1.024000, rms=0.755 (0.198%), neg=0, invalid=762
0080: dt=1.024000, rms=0.752 (0.342%), neg=0, invalid=762
0081: dt=1.024000, rms=0.750 (0.258%), neg=0, invalid=762
0082: dt=1.024000, rms=0.750 (-0.132%), neg=0, invalid=762
0083: dt=1.792000, rms=0.749 (0.120%), neg=0, invalid=762
0084: dt=4.096000, rms=0.747 (0.358%), neg=0, invalid=762
0085: dt=0.000000, rms=0.747 (-0.000%), neg=0, invalid=762
0086: dt=0.100000, rms=0.747 (-0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.747, neg=0, invalid=762
0087: dt=0.112000, rms=0.747 (0.074%), neg=0, invalid=762
0088: dt=0.048000, rms=0.747 (0.001%), neg=0, invalid=762
0089: dt=0.048000, rms=0.747 (-0.001%), 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=0.709, neg=0, invalid=762
0090: dt=0.851549, rms=0.689 (2.711%), neg=0, invalid=762
0091: dt=0.080000, rms=0.688 (0.137%), neg=0, invalid=762
0092: dt=0.080000, rms=0.688 (-0.069%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.689, neg=0, invalid=762
0093: dt=0.028000, rms=0.688 (0.099%), neg=0, invalid=762
0094: dt=0.007000, rms=0.688 (0.002%), neg=0, invalid=762
0095: dt=0.007000, rms=0.688 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.07085 (18)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1125 voxels, overlap=0.732)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1125 voxels, peak = 20), gca=20.5
gca peak = 0.15565 (16)
mri peak = 0.05913 (16)
Right_Lateral_Ventricle (43): linear fit = 2.24 x + 0.0 (1290 voxels, overlap=0.458)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1290 voxels, peak = 36), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.06801 (90)
Right_Pallidum (52): linear fit = 0.93 x + 0.0 (1092 voxels, overlap=0.504)
Right_Pallidum (52): linear fit = 0.93 x + 0.0 (1092 voxels, peak = 89), gca=88.8
gca peak = 0.20183 (93)
mri peak = 0.06293 (79)
Left_Pallidum (13): linear fit = 0.83 x + 0.0 (979 voxels, overlap=0.614)
Left_Pallidum (13): linear fit = 0.83 x + 0.0 (979 voxels, peak = 78), gca=77.7
gca peak = 0.21683 (55)
mri peak = 0.08016 (60)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1272 voxels, overlap=0.999)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1272 voxels, peak = 57), gca=57.5
gca peak = 0.30730 (58)
mri peak = 0.07095 (63)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1261 voxels, overlap=0.995)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1261 voxels, peak = 61), gca=60.6
gca peak = 0.11430 (101)
mri peak = 0.08432 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (72345 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (72345 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.08911 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (72941 voxels, overlap=0.779)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (72941 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.04191 (63)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (40466 voxels, overlap=0.775)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (40466 voxels, peak = 65), gca=64.6
gca peak = 0.15082 (58)
mri peak = 0.04226 (62)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (38227 voxels, overlap=0.862)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (38227 voxels, peak = 64), gca=63.5
gca peak = 0.14161 (67)
mri peak = 0.08961 (71)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1238 voxels, overlap=0.894)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1238 voxels, peak = 68), gca=68.0
gca peak = 0.15243 (71)
mri peak = 0.08847 (71)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1243 voxels, overlap=0.981)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1243 voxels, peak = 70), gca=69.9
gca peak = 0.13336 (57)
mri peak = 0.04771 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (24109 voxels, overlap=0.549)
Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (24109 voxels, peak = 68), gca=67.5
gca peak = 0.13252 (56)
mri peak = 0.04699 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (29637 voxels, overlap=0.670)
Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (29637 voxels, peak = 66), gca=65.8
gca peak = 0.18181 (84)
mri peak = 0.06592 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (11436 voxels, overlap=0.784)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (11436 voxels, peak = 88), gca=87.8
gca peak = 0.20573 (83)
mri peak = 0.06803 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9866 voxels, overlap=0.806)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9866 voxels, peak = 86), gca=85.9
gca peak = 0.21969 (57)
mri peak = 0.10375 (65)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (524 voxels, overlap=0.779)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (524 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.08914 (65)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (611 voxels, overlap=0.204)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (611 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.05504 (82)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6230 voxels, overlap=0.980)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6230 voxels, peak = 85), gca=84.6
gca peak = 0.11978 (83)
mri peak = 0.06327 (83)
Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5427 voxels, overlap=0.885)
Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5427 voxels, peak = 86), gca=85.9
gca peak = 0.13399 (79)
mri peak = 0.07623 (81)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2768 voxels, overlap=0.920)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2768 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.07865 (78)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (3076 voxels, overlap=0.938)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (3076 voxels, peak = 81), gca=81.0
gca peak = 0.10025 (80)
mri peak = 0.08300 (84)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13216 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13216 voxels, peak = 88), gca=88.4
gca peak = 0.13281 (86)
mri peak = 0.09208 (88)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1380 voxels, overlap=0.724)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1380 voxels, peak = 88), gca=88.2
gca peak = 0.12801 (89)
mri peak = 0.08491 (88)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1381 voxels, overlap=0.848)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1381 voxels, peak = 90), gca=90.3
gca peak = 0.20494 (23)
mri peak = 0.04562 (31)
gca peak = 0.15061 (21)
mri peak = 0.12832 (14)
Fourth_Ventricle (15): linear fit = 0.61 x + 0.0 (290 voxels, overlap=0.110)
Fourth_Ventricle (15): linear fit = 0.61 x + 0.0 (290 voxels, peak = 13), gca=12.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.09 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.26 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=0.681, neg=0, invalid=762
0096: dt=136.619529, rms=0.669 (1.708%), neg=0, invalid=762
0097: dt=295.936000, rms=0.665 (0.712%), neg=0, invalid=762
0098: dt=110.976000, rms=0.663 (0.231%), neg=0, invalid=762
0099: dt=443.904000, rms=0.660 (0.409%), neg=0, invalid=762
0100: dt=73.984000, rms=0.659 (0.175%), neg=0, invalid=762
0101: dt=443.904000, rms=0.658 (0.123%), neg=0, invalid=762
0102: dt=129.472000, rms=0.658 (0.137%), neg=0, invalid=762
0103: dt=129.472000, rms=0.657 (0.060%), neg=0, invalid=762
0104: dt=443.904000, rms=0.656 (0.120%), neg=0, invalid=762
0105: dt=92.480000, rms=0.656 (0.085%), neg=0, invalid=762
0106: dt=1183.744000, rms=0.655 (0.187%), neg=0, invalid=762
0107: dt=92.480000, rms=0.654 (0.109%), neg=0, invalid=762
0108: dt=1183.744000, rms=0.653 (0.141%), neg=0, invalid=762
0109: dt=92.480000, rms=0.652 (0.129%), neg=0, invalid=762
0110: dt=129.472000, rms=0.652 (0.007%), neg=0, invalid=762
0111: dt=129.472000, rms=0.652 (0.023%), neg=0, invalid=762
0112: dt=129.472000, rms=0.652 (0.034%), neg=0, invalid=762
0113: dt=129.472000, rms=0.651 (0.053%), neg=0, invalid=762
0114: dt=129.472000, rms=0.651 (0.065%), neg=0, invalid=762
0115: dt=129.472000, rms=0.650 (0.074%), neg=0, invalid=762
0116: dt=129.472000, rms=0.650 (0.072%), neg=0, invalid=762
0117: dt=129.472000, rms=0.650 (0.072%), neg=0, invalid=762
0118: dt=129.472000, rms=0.649 (0.071%), neg=0, invalid=762
0119: dt=129.472000, rms=0.649 (0.076%), neg=0, invalid=762
0120: dt=129.472000, rms=0.648 (0.084%), neg=0, invalid=762
0121: dt=129.472000, rms=0.648 (0.078%), neg=0, invalid=762
0122: dt=129.472000, rms=0.647 (0.081%), neg=0, invalid=762
0123: dt=129.472000, rms=0.647 (0.076%), neg=0, invalid=762
0124: dt=129.472000, rms=0.646 (0.074%), neg=0, invalid=762
0125: dt=129.472000, rms=0.646 (0.064%), neg=0, invalid=762
0126: dt=129.472000, rms=0.645 (0.058%), neg=0, invalid=762
0127: dt=129.472000, rms=0.645 (0.051%), neg=0, invalid=762
0128: dt=129.472000, rms=0.645 (0.059%), neg=0, invalid=762
0129: dt=129.472000, rms=0.644 (0.064%), neg=0, invalid=762
0130: dt=129.472000, rms=0.644 (0.061%), neg=0, invalid=762
0131: dt=129.472000, rms=0.643 (0.056%), neg=0, invalid=762
0132: dt=129.472000, rms=0.643 (0.051%), neg=0, invalid=762
0133: dt=129.472000, rms=0.643 (0.053%), neg=0, invalid=762
0134: dt=129.472000, rms=0.642 (0.053%), neg=0, invalid=762
0135: dt=129.472000, rms=0.642 (0.055%), neg=0, invalid=762
0136: dt=129.472000, rms=0.642 (0.048%), neg=0, invalid=762
0137: dt=129.472000, rms=0.641 (0.047%), neg=0, invalid=762
0138: dt=129.472000, rms=0.641 (0.052%), neg=0, invalid=762
0139: dt=129.472000, rms=0.641 (0.049%), neg=0, invalid=762
0140: dt=129.472000, rms=0.640 (0.041%), neg=0, invalid=762
0141: dt=129.472000, rms=0.640 (0.036%), neg=0, invalid=762
0142: dt=129.472000, rms=0.640 (0.040%), neg=0, invalid=762
0143: dt=129.472000, rms=0.640 (0.040%), neg=0, invalid=762
0144: dt=129.472000, rms=0.639 (0.038%), neg=0, invalid=762
0145: dt=129.472000, rms=0.639 (0.032%), neg=0, invalid=762
0146: dt=129.472000, rms=0.639 (0.030%), neg=0, invalid=762
0147: dt=129.472000, rms=0.639 (0.030%), neg=0, invalid=762
0148: dt=129.472000, rms=0.639 (0.028%), neg=0, invalid=762
0149: dt=129.472000, rms=0.639 (0.029%), neg=0, invalid=762
0150: dt=129.472000, rms=0.638 (0.026%), neg=0, invalid=762
0151: dt=129.472000, rms=0.638 (0.026%), neg=0, invalid=762
0152: dt=129.472000, rms=0.638 (0.027%), neg=0, invalid=762
0153: dt=129.472000, rms=0.638 (0.027%), neg=0, invalid=762
0154: dt=129.472000, rms=0.638 (0.024%), neg=0, invalid=762
0155: dt=129.472000, rms=0.638 (0.026%), neg=0, invalid=762
0156: dt=129.472000, rms=0.637 (0.026%), neg=0, invalid=762
0157: dt=129.472000, rms=0.637 (0.023%), neg=0, invalid=762
0158: dt=129.472000, rms=0.637 (0.022%), neg=0, invalid=762
0159: dt=4734.976000, rms=0.637 (0.047%), neg=0, invalid=762
0160: dt=73.984000, rms=0.637 (0.014%), neg=0, invalid=762
0161: dt=73.984000, rms=0.637 (0.007%), neg=0, invalid=762
0162: dt=73.984000, rms=0.637 (0.004%), neg=0, invalid=762
0163: dt=73.984000, rms=0.637 (0.007%), neg=0, invalid=762
0164: dt=73.984000, rms=0.637 (0.010%), neg=0, invalid=762
0165: dt=73.984000, rms=0.636 (0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.637, neg=0, invalid=762
0166: dt=129.472000, rms=0.636 (0.154%), neg=0, invalid=762
0167: dt=517.888000, rms=0.636 (0.074%), neg=0, invalid=762
0168: dt=443.904000, rms=0.635 (0.118%), neg=0, invalid=762
0169: dt=32.368000, rms=0.635 (0.004%), neg=0, invalid=762
0170: dt=32.368000, rms=0.635 (0.004%), neg=0, invalid=762
0171: dt=32.368000, rms=0.635 (-0.005%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.636, neg=0, invalid=762
0172: dt=157.090909, rms=0.633 (0.572%), neg=0, invalid=762
0173: dt=141.037037, rms=0.627 (0.932%), neg=0, invalid=762
0174: dt=36.288000, rms=0.625 (0.276%), neg=0, invalid=762
0175: dt=145.152000, rms=0.623 (0.273%), neg=0, invalid=762
0176: dt=135.435685, rms=0.620 (0.639%), neg=0, invalid=762
0177: dt=36.288000, rms=0.618 (0.192%), neg=0, invalid=762
0178: dt=124.416000, rms=0.617 (0.170%), neg=0, invalid=762
0179: dt=145.152000, rms=0.614 (0.493%), neg=0, invalid=762
0180: dt=36.288000, rms=0.614 (0.106%), neg=0, invalid=762
0181: dt=145.152000, rms=0.613 (0.121%), neg=0, invalid=762
0182: dt=144.000000, rms=0.610 (0.410%), neg=0, invalid=762
0183: dt=36.288000, rms=0.610 (0.103%), neg=0, invalid=762
0184: dt=103.680000, rms=0.609 (0.076%), neg=0, invalid=762
0185: dt=145.152000, rms=0.607 (0.339%), neg=0, invalid=762
0186: dt=36.288000, rms=0.607 (0.030%), neg=0, invalid=762
0187: dt=36.288000, rms=0.607 (0.042%), neg=0, invalid=762
0188: dt=36.288000, rms=0.606 (0.068%), neg=0, invalid=762
0189: dt=36.288000, rms=0.606 (0.121%), neg=0, invalid=762
0190: dt=36.288000, rms=0.605 (0.173%), neg=0, invalid=762
0191: dt=36.288000, rms=0.603 (0.207%), neg=0, invalid=762
0192: dt=36.288000, rms=0.602 (0.210%), neg=0, invalid=762
0193: dt=36.288000, rms=0.601 (0.206%), neg=0, invalid=762
0194: dt=36.288000, rms=0.600 (0.201%), neg=0, invalid=762
0195: dt=36.288000, rms=0.598 (0.198%), neg=0, invalid=762
0196: dt=36.288000, rms=0.597 (0.200%), neg=0, invalid=762
0197: dt=36.288000, rms=0.596 (0.206%), neg=0, invalid=762
0198: dt=36.288000, rms=0.595 (0.196%), neg=0, invalid=762
0199: dt=36.288000, rms=0.594 (0.180%), neg=0, invalid=762
0200: dt=36.288000, rms=0.593 (0.170%), neg=0, invalid=762
0201: dt=36.288000, rms=0.592 (0.156%), neg=0, invalid=762
0202: dt=36.288000, rms=0.591 (0.149%), neg=0, invalid=762
0203: dt=36.288000, rms=0.590 (0.155%), neg=0, invalid=762
0204: dt=36.288000, rms=0.589 (0.168%), neg=0, invalid=762
0205: dt=36.288000, rms=0.588 (0.156%), neg=0, invalid=762
0206: dt=36.288000, rms=0.587 (0.152%), neg=0, invalid=762
0207: dt=36.288000, rms=0.586 (0.143%), neg=0, invalid=762
0208: dt=36.288000, rms=0.586 (0.132%), neg=0, invalid=762
0209: dt=36.288000, rms=0.585 (0.127%), neg=0, invalid=762
0210: dt=36.288000, rms=0.584 (0.127%), neg=0, invalid=762
0211: dt=36.288000, rms=0.583 (0.127%), neg=0, invalid=762
0212: dt=36.288000, rms=0.583 (0.121%), neg=0, invalid=762
0213: dt=36.288000, rms=0.582 (0.113%), neg=0, invalid=762
0214: dt=36.288000, rms=0.581 (0.108%), neg=0, invalid=762
0215: dt=36.288000, rms=0.581 (0.009%), neg=0, invalid=762
0216: dt=36.288000, rms=0.581 (0.020%), neg=0, invalid=762
0217: dt=36.288000, rms=0.581 (0.031%), neg=0, invalid=762
0218: dt=36.288000, rms=0.581 (0.039%), neg=0, invalid=762
0219: dt=36.288000, rms=0.581 (0.045%), neg=0, invalid=762
0220: dt=36.288000, rms=0.580 (0.047%), neg=0, invalid=762
0221: dt=36.288000, rms=0.580 (0.008%), neg=0, invalid=762
0222: dt=36.288000, rms=0.580 (0.015%), neg=0, invalid=762
0223: dt=2.268000, rms=0.580 (0.001%), neg=0, invalid=762
0224: dt=0.567000, rms=0.580 (0.000%), neg=0, invalid=762
0225: dt=0.283500, rms=0.580 (0.000%), neg=0, invalid=762
0226: dt=0.141750, rms=0.580 (0.000%), neg=0, invalid=762
0227: dt=0.070875, rms=0.580 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.581, neg=0, invalid=762
0228: dt=102.819672, rms=0.578 (0.447%), neg=0, invalid=762
0229: dt=82.944000, rms=0.578 (0.113%), neg=0, invalid=762
0230: dt=82.944000, rms=0.577 (0.103%), neg=0, invalid=762
0231: dt=82.944000, rms=0.577 (0.061%), neg=0, invalid=762
0232: dt=82.944000, rms=0.576 (0.064%), neg=0, invalid=762
0233: dt=82.944000, rms=0.576 (0.045%), neg=0, invalid=762
0234: dt=82.944000, rms=0.576 (0.052%), neg=0, invalid=762
0235: dt=82.944000, rms=0.575 (0.076%), neg=0, invalid=762
0236: dt=82.944000, rms=0.575 (0.096%), neg=0, invalid=762
0237: dt=82.944000, rms=0.574 (0.101%), neg=0, invalid=762
0238: dt=82.944000, rms=0.574 (0.085%), neg=0, invalid=762
0239: dt=82.944000, rms=0.573 (0.082%), neg=0, invalid=762
0240: dt=82.944000, rms=0.573 (0.078%), neg=0, invalid=762
0241: dt=82.944000, rms=0.572 (0.058%), neg=0, invalid=762
0242: dt=82.944000, rms=0.572 (0.050%), neg=0, invalid=762
0243: dt=82.944000, rms=0.572 (0.075%), neg=0, invalid=762
0244: dt=82.944000, rms=0.571 (0.079%), neg=0, invalid=762
0245: dt=82.944000, rms=0.571 (0.084%), neg=0, invalid=762
0246: dt=82.944000, rms=0.570 (0.067%), neg=0, invalid=762
0247: dt=82.944000, rms=0.570 (0.098%), neg=0, invalid=762
0248: dt=82.944000, rms=0.569 (0.090%), neg=0, invalid=762
0249: dt=82.944000, rms=0.569 (0.084%), neg=0, invalid=762
0250: dt=82.944000, rms=0.568 (0.087%), neg=0, invalid=762
0251: dt=82.944000, rms=0.568 (0.091%), neg=0, invalid=762
0252: dt=82.944000, rms=0.567 (0.099%), neg=0, invalid=762
0253: dt=82.944000, rms=0.567 (0.101%), neg=0, invalid=762
0254: dt=82.944000, rms=0.566 (0.088%), neg=0, invalid=762
0255: dt=82.944000, rms=0.566 (0.079%), neg=0, invalid=762
0256: dt=82.944000, rms=0.565 (0.086%), neg=0, invalid=762
0257: dt=82.944000, rms=0.565 (0.073%), neg=0, invalid=762
0258: dt=82.944000, rms=0.564 (0.074%), neg=0, invalid=762
0259: dt=82.944000, rms=0.564 (0.067%), neg=0, invalid=762
0260: dt=82.944000, rms=0.564 (0.074%), neg=0, invalid=762
0261: dt=82.944000, rms=0.563 (0.076%), neg=0, invalid=762
0262: dt=82.944000, rms=0.563 (0.060%), neg=0, invalid=762
0263: dt=82.944000, rms=0.563 (0.055%), neg=0, invalid=762
0264: dt=82.944000, rms=0.562 (0.060%), neg=0, invalid=762
0265: dt=82.944000, rms=0.562 (0.059%), neg=0, invalid=762
0266: dt=82.944000, rms=0.562 (0.045%), neg=0, invalid=762
0267: dt=82.944000, rms=0.562 (0.016%), neg=0, invalid=762
0268: dt=82.944000, rms=0.561 (0.004%), neg=0, invalid=762
0269: dt=25.920000, rms=0.561 (0.003%), neg=0, invalid=762
0270: dt=0.810000, rms=0.561 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.571, neg=0, invalid=762
0271: dt=32.000000, rms=0.568 (0.554%), neg=0, invalid=762
0272: dt=86.554374, rms=0.562 (0.988%), neg=0, invalid=762
0273: dt=25.600000, rms=0.560 (0.352%), neg=0, invalid=762
0274: dt=102.400000, rms=0.555 (0.854%), neg=0, invalid=762
0275: dt=11.200000, rms=0.553 (0.321%), neg=0, invalid=762
0276: dt=19.200000, rms=0.553 (0.119%), neg=0, invalid=762
0277: dt=44.800000, rms=0.551 (0.274%), neg=0, invalid=762
0278: dt=44.800000, rms=0.550 (0.237%), neg=0, invalid=762
0279: dt=11.200000, rms=0.550 (0.067%), neg=0, invalid=762
0280: dt=2.800000, rms=0.550 (0.013%), neg=0, invalid=762
0281: dt=1.400000, rms=0.549 (0.006%), neg=0, invalid=762
0282: dt=0.350000, rms=0.549 (0.002%), neg=0, invalid=762
0283: dt=0.043750, rms=0.549 (0.000%), neg=0, invalid=762
0284: dt=0.007812, rms=0.549 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.550, neg=0, invalid=762
0285: dt=38.400000, rms=0.547 (0.592%), neg=0, invalid=762
0286: dt=38.400000, rms=0.546 (0.223%), neg=0, invalid=762
0287: dt=25.600000, rms=0.545 (0.146%), neg=0, invalid=762
0288: dt=44.800000, rms=0.544 (0.128%), neg=0, invalid=762
0289: dt=25.600000, rms=0.543 (0.136%), neg=0, invalid=762
0290: dt=38.400000, rms=0.543 (0.108%), neg=0, invalid=762
0291: dt=25.600000, rms=0.542 (0.118%), neg=0, invalid=762
0292: dt=38.400000, rms=0.542 (0.098%), neg=0, invalid=762
0293: dt=25.600000, rms=0.541 (0.101%), neg=0, invalid=762
0294: dt=38.400000, rms=0.541 (0.092%), neg=0, invalid=762
0295: dt=25.600000, rms=0.540 (0.087%), neg=0, invalid=762
0296: dt=32.000000, rms=0.540 (0.078%), neg=0, invalid=762
0297: dt=25.600000, rms=0.539 (0.077%), neg=0, invalid=762
0298: dt=38.400000, rms=0.539 (0.076%), neg=0, invalid=762
0299: dt=25.600000, rms=0.539 (0.070%), neg=0, invalid=762
0300: dt=32.000000, rms=0.538 (0.070%), neg=0, invalid=762
0301: dt=25.600000, rms=0.538 (0.056%), neg=0, invalid=762
0302: dt=38.400000, rms=0.538 (0.071%), neg=0, invalid=762
0303: dt=25.600000, rms=0.537 (0.063%), neg=0, invalid=762
0304: dt=38.400000, rms=0.537 (0.069%), neg=0, invalid=762
0305: dt=25.600000, rms=0.536 (0.060%), neg=0, invalid=762
0306: dt=32.000000, rms=0.536 (0.065%), neg=0, invalid=762
0307: dt=2.800000, rms=0.536 (0.012%), neg=0, invalid=762
0308: dt=2.800000, rms=0.536 (0.007%), neg=0, invalid=762
0309: dt=0.087500, rms=0.536 (0.001%), neg=0, invalid=762
0310: dt=0.043750, rms=0.536 (0.000%), neg=0, invalid=762
0311: dt=0.009375, rms=0.536 (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=0.555, neg=0, invalid=762
0312: dt=0.000000, rms=0.554 (0.130%), neg=0, invalid=762
0313: dt=0.000000, rms=0.554 (0.000%), neg=0, invalid=762
0314: dt=0.150000, rms=0.554 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.555, neg=0, invalid=762
0315: dt=0.000000, rms=0.554 (0.130%), neg=0, invalid=762
0316: dt=0.000000, rms=0.554 (0.000%), neg=0, invalid=762
0317: dt=0.150000, rms=0.554 (-0.005%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.592, neg=0, invalid=762
0318: dt=1.792000, rms=0.588 (0.752%), neg=0, invalid=762
0319: dt=0.448000, rms=0.588 (0.028%), neg=0, invalid=762
0320: dt=0.448000, rms=0.588 (0.001%), neg=0, invalid=762
0321: dt=0.448000, rms=0.588 (-0.068%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.589, neg=0, invalid=762
0322: dt=1.280000, rms=0.587 (0.231%), neg=0, invalid=762
0323: dt=0.448000, rms=0.587 (0.014%), neg=0, invalid=762
0324: dt=0.448000, rms=0.587 (-0.002%), 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=0.549, neg=0, invalid=762
0325: dt=0.448000, rms=0.534 (2.827%), neg=0, invalid=762
0326: dt=0.448000, rms=0.530 (0.813%), neg=0, invalid=762
0327: dt=0.448000, rms=0.527 (0.474%), neg=0, invalid=762
0328: dt=0.448000, rms=0.525 (0.286%), neg=0, invalid=762
0329: dt=0.448000, rms=0.524 (0.201%), neg=0, invalid=762
0330: dt=0.448000, rms=0.524 (0.145%), neg=0, invalid=762
0331: dt=0.448000, rms=0.523 (0.117%), neg=0, invalid=762
0332: dt=0.448000, rms=0.523 (0.091%), neg=0, invalid=762
0333: dt=0.448000, rms=0.522 (0.080%), neg=0, invalid=762
0334: dt=0.448000, rms=0.522 (0.059%), neg=0, invalid=762
0335: dt=0.448000, rms=0.522 (0.057%), neg=0, invalid=762
0336: dt=0.448000, rms=0.521 (0.043%), neg=0, invalid=762
0337: dt=0.448000, rms=0.521 (0.043%), neg=0, invalid=762
0338: dt=0.448000, rms=0.521 (0.069%), neg=0, invalid=762
0339: dt=0.448000, rms=0.520 (0.084%), neg=0, invalid=762
0340: dt=0.448000, rms=0.520 (0.090%), neg=0, invalid=762
0341: dt=0.448000, rms=0.519 (0.086%), neg=0, invalid=762
0342: dt=0.448000, rms=0.519 (-0.007%), neg=0, invalid=762
0343: dt=0.064000, rms=0.519 (0.000%), neg=0, invalid=762
0344: dt=0.064000, rms=0.519 (0.000%), neg=0, invalid=762
0345: dt=0.112000, rms=0.519 (0.002%), neg=0, invalid=762
0346: dt=0.320000, rms=0.519 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0347: dt=0.384000, rms=0.515 (0.984%), neg=0, invalid=762
0348: dt=0.448000, rms=0.514 (0.260%), neg=0, invalid=762
0349: dt=0.448000, rms=0.513 (0.060%), neg=0, invalid=762
0350: dt=0.448000, rms=0.513 (0.012%), neg=0, invalid=762
0351: dt=0.448000, rms=0.513 (0.006%), neg=0, invalid=762
0352: dt=0.448000, rms=0.513 (-0.003%), 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=0.511, neg=0, invalid=762
0353: dt=27.744000, rms=0.511 (0.148%), neg=0, invalid=762
0354: dt=0.013547, rms=0.511 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.511, neg=0, invalid=762
0355: dt=73.984000, rms=0.510 (0.161%), neg=0, invalid=762
0356: dt=221.952000, rms=0.510 (0.022%), neg=0, invalid=762
0357: dt=221.952000, rms=0.510 (0.041%), neg=0, invalid=762
0358: dt=221.952000, rms=0.510 (-0.010%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.511, neg=0, invalid=762
0359: dt=31.104000, rms=0.510 (0.228%), neg=0, invalid=762
0360: dt=36.288000, rms=0.510 (0.043%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0361: dt=36.288000, rms=0.509 (0.023%), neg=0, invalid=762
0362: dt=36.288000, rms=0.509 (-0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.510, neg=0, invalid=762
0363: dt=68.135385, rms=0.508 (0.456%), neg=0, invalid=762
0364: dt=103.680000, rms=0.507 (0.202%), neg=0, invalid=762
0365: dt=103.680000, rms=0.507 (-0.093%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.508, neg=0, invalid=762
iter 0, gcam->neg = 6
after 1 iterations, nbhd size=0, neg = 0
0366: dt=44.800000, rms=0.501 (1.265%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 5 iterations, nbhd size=0, neg = 0
0367: dt=44.800000, rms=0.498 (0.707%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 10 iterations, nbhd size=1, neg = 0
0368: dt=21.879733, rms=0.496 (0.329%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 9 iterations, nbhd size=1, neg = 0
0369: dt=38.400000, rms=0.495 (0.245%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 9 iterations, nbhd size=1, neg = 0
0370: dt=38.400000, rms=0.494 (0.104%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 11 iterations, nbhd size=1, neg = 0
0371: dt=38.400000, rms=0.492 (0.462%), neg=0, invalid=762
iter 0, gcam->neg = 16
after 9 iterations, nbhd size=1, neg = 0
0372: dt=38.400000, rms=0.491 (0.211%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 10 iterations, nbhd size=1, neg = 0
0373: dt=38.400000, rms=0.489 (0.344%), neg=0, invalid=762
iter 0, gcam->neg = 26
after 4 iterations, nbhd size=0, neg = 0
0374: dt=38.400000, rms=0.489 (0.089%), neg=0, invalid=762
iter 0, gcam->neg = 23
after 12 iterations, nbhd size=1, neg = 0
0375: dt=38.400000, rms=0.488 (0.267%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 3 iterations, nbhd size=0, neg = 0
0376: dt=38.400000, rms=0.487 (0.154%), neg=0, invalid=762
iter 0, gcam->neg = 19
after 9 iterations, nbhd size=0, neg = 0
0377: dt=38.400000, rms=0.486 (0.161%), neg=0, invalid=762
iter 0, gcam->neg = 28
after 8 iterations, nbhd size=0, neg = 0
0378: dt=38.400000, rms=0.486 (-0.030%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0379: dt=19.200000, rms=0.485 (0.112%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 3 iterations, nbhd size=0, neg = 0
0380: dt=76.800000, rms=0.484 (0.200%), neg=0, invalid=762
0381: dt=11.200000, rms=0.484 (0.031%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.485, neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0382: dt=44.800000, rms=0.481 (0.922%), neg=0, invalid=762
0383: dt=32.000000, rms=0.479 (0.318%), neg=0, invalid=762
0384: dt=25.600000, rms=0.478 (0.150%), neg=0, invalid=762
0385: dt=25.600000, rms=0.478 (0.124%), neg=0, invalid=762
0386: dt=25.600000, rms=0.477 (0.200%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 8 iterations, nbhd size=1, neg = 0
0387: dt=25.600000, rms=0.476 (0.185%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0388: dt=25.600000, rms=0.475 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0389: dt=25.600000, rms=0.475 (0.097%), neg=0, invalid=762
0390: dt=44.800000, rms=0.474 (0.121%), neg=0, invalid=762
0391: dt=11.200000, rms=0.474 (0.037%), neg=0, invalid=762
0392: dt=11.200000, rms=0.474 (0.029%), neg=0, invalid=762
0393: dt=11.200000, rms=0.474 (0.025%), neg=0, invalid=762
0394: dt=11.200000, rms=0.474 (0.033%), neg=0, invalid=762
0395: dt=11.200000, rms=0.474 (0.043%), neg=0, invalid=762
0396: dt=11.200000, rms=0.473 (0.038%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.481, neg=0, invalid=762
0397: dt=1.666667, rms=0.480 (0.171%), neg=0, invalid=762
0398: dt=0.252000, rms=0.480 (0.001%), neg=0, invalid=762
0399: dt=0.252000, rms=0.480 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.481, neg=0, invalid=762
0400: dt=2.304000, rms=0.480 (0.177%), neg=0, invalid=762
0401: dt=1.008000, rms=0.480 (0.006%), neg=0, invalid=762
0402: dt=1.008000, rms=0.480 (0.003%), neg=0, invalid=762
0403: dt=1.008000, rms=0.480 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.493, neg=0, invalid=762
0404: dt=0.768000, rms=0.492 (0.250%), neg=0, invalid=762
0405: dt=0.384000, rms=0.492 (0.013%), neg=0, invalid=762
0406: dt=0.384000, rms=0.492 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0407: dt=1.536000, rms=0.491 (0.361%), neg=0, invalid=762
0408: dt=1.024000, rms=0.490 (0.033%), neg=0, invalid=762
0409: dt=1.024000, rms=0.490 (-0.002%), 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=0.481, neg=0, invalid=762
iter 0, gcam->neg = 750
after 13 iterations, nbhd size=1, neg = 0
0410: dt=2.110359, rms=0.451 (6.285%), neg=0, invalid=762
0411: dt=0.064000, rms=0.450 (0.036%), neg=0, invalid=762
0412: dt=0.064000, rms=0.450 (-0.032%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.451, neg=0, invalid=762
0413: dt=0.080000, rms=0.450 (0.247%), neg=0, invalid=762
0414: dt=0.007000, rms=0.450 (0.003%), neg=0, invalid=762
0415: dt=0.007000, rms=0.450 (0.000%), neg=0, invalid=762
0416: dt=0.007000, rms=0.450 (-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=0.437, neg=0, invalid=762
0417: dt=0.022578, rms=0.437 (0.000%), neg=0, invalid=762
0418: dt=0.000226, rms=0.437 (0.000%), neg=0, invalid=762
0419: dt=0.000000, rms=0.437 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0420: dt=32.368000, rms=0.437 (0.005%), neg=0, invalid=762
0421: dt=32.368000, rms=0.437 (0.001%), neg=0, invalid=762
0422: dt=32.368000, rms=0.437 (0.000%), neg=0, invalid=762
0423: dt=32.368000, rms=0.437 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0424: dt=1.620000, rms=0.437 (0.000%), neg=0, invalid=762
0425: dt=0.000000, rms=0.437 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0426: dt=82.944000, rms=0.437 (0.073%), neg=0, invalid=762
0427: dt=124.416000, rms=0.437 (0.060%), neg=0, invalid=762
0428: dt=124.416000, rms=0.437 (-0.052%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0429: dt=11.200000, rms=0.437 (0.132%), neg=0, invalid=762
0430: dt=11.200000, rms=0.436 (0.035%), neg=0, invalid=762
0431: dt=11.200000, rms=0.436 (0.009%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0432: dt=11.200000, rms=0.436 (-0.069%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.436, neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0433: dt=38.400000, rms=0.433 (0.668%), neg=0, invalid=762
0434: dt=32.000000, rms=0.432 (0.258%), neg=0, invalid=762
0435: dt=32.000000, rms=0.432 (0.169%), neg=0, invalid=762
0436: dt=32.000000, rms=0.431 (0.152%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0437: dt=32.000000, rms=0.430 (0.211%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 7 iterations, nbhd size=1, neg = 0
0438: dt=32.000000, rms=0.429 (0.232%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0439: dt=32.000000, rms=0.428 (0.247%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=1, neg = 0
0440: dt=32.000000, rms=0.427 (0.210%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 7 iterations, nbhd size=1, neg = 0
0441: dt=32.000000, rms=0.426 (0.155%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0442: dt=32.000000, rms=0.426 (0.142%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 0 iterations, nbhd size=0, neg = 0
0443: dt=32.000000, rms=0.425 (0.153%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 4 iterations, nbhd size=0, neg = 0
0444: dt=32.000000, rms=0.425 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 14 iterations, nbhd size=1, neg = 0
0445: dt=32.000000, rms=0.424 (0.077%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0446: dt=32.000000, rms=0.424 (0.033%), neg=0, invalid=762
0447: dt=32.000000, rms=0.424 (0.006%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0448: dt=32.000000, rms=0.424 (0.019%), neg=0, invalid=762
0449: dt=32.000000, rms=0.424 (0.026%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0450: dt=32.000000, rms=0.424 (0.003%), neg=0, invalid=762
0451: dt=32.000000, rms=0.424 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.429, neg=0, invalid=762
0452: dt=0.750000, rms=0.429 (0.003%), neg=0, invalid=762
0453: dt=0.108000, rms=0.429 (0.000%), neg=0, invalid=762
0454: dt=0.108000, rms=0.429 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.429, neg=0, invalid=762
0455: dt=2.304000, rms=0.429 (0.008%), neg=0, invalid=762
0456: dt=1.008000, rms=0.429 (0.002%), neg=0, invalid=762
0457: dt=1.008000, rms=0.429 (0.001%), neg=0, invalid=762
0458: dt=1.008000, rms=0.429 (-0.004%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0459: dt=0.000000, rms=0.437 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0460: dt=0.000000, rms=0.437 (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=0.423, neg=0, invalid=762
iter 0, gcam->neg = 441
after 15 iterations, nbhd size=1, neg = 0
0461: dt=1.063213, rms=0.415 (1.870%), neg=0, invalid=762
0462: dt=0.007000, rms=0.415 (0.000%), neg=0, invalid=762
0463: dt=0.007000, rms=0.415 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0464: dt=0.256000, rms=0.414 (0.224%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0465: dt=0.448000, rms=0.413 (0.288%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 1 iterations, nbhd size=0, neg = 0
0466: dt=0.448000, rms=0.412 (0.189%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 2 iterations, nbhd size=0, neg = 0
0467: dt=0.448000, rms=0.412 (0.037%), neg=0, invalid=762
iter 0, gcam->neg = 24
after 3 iterations, nbhd size=0, neg = 0
0468: dt=0.448000, rms=0.411 (0.065%), neg=0, invalid=762
iter 0, gcam->neg = 45
after 10 iterations, nbhd size=1, neg = 0
0469: dt=0.448000, rms=0.411 (-0.010%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 35 minutes and 54 seconds.
mri_ca_register utimesec    10212.315492
mri_ca_register stimesec    8.157759
mri_ca_register ru_maxrss   1334116
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4513060
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  69304
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3961
mri_ca_register ru_nivcsw   37900
FSRUNTIME@ mri_ca_register  2.5983 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 02:30:26 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-948
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-6.0.0/0050310/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 7.12
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 = 0.08092 (21)
Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (385 voxels, overlap=0.850)
Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (385 voxels, peak = 19), gca=18.7
gca peak = 0.17677 (13)
mri peak = 0.07722 (16)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (304 voxels, overlap=0.477)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (304 voxels, peak = 15), gca=15.4
gca peak = 0.28129 (95)
mri peak = 0.13142 (93)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (589 voxels, overlap=0.840)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (589 voxels, peak = 92), gca=91.7
gca peak = 0.16930 (96)
mri peak = 0.07588 (93)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (975 voxels, overlap=0.556)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (975 voxels, peak = 92), gca=91.7
gca peak = 0.24553 (55)
mri peak = 0.08438 (60)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1162 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1162 voxels, peak = 57), gca=57.5
gca peak = 0.30264 (59)
mri peak = 0.10163 (61)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1105 voxels, overlap=1.006)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1105 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.08799 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36139 voxels, overlap=0.784)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36139 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.09203 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38414 voxels, overlap=0.750)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38414 voxels, peak = 105), gca=104.5
gca peak = 0.09712 (58)
mri peak = 0.04723 (63)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (49077 voxels, overlap=0.795)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (49077 voxels, peak = 64), gca=63.5
gca peak = 0.11620 (58)
mri peak = 0.04642 (63)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (47243 voxels, overlap=0.869)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (47243 voxels, peak = 62), gca=62.4
gca peak = 0.30970 (66)
mri peak = 0.10894 (71)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (973 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (973 voxels, peak = 70), gca=70.3
gca peak = 0.15280 (69)
mri peak = 0.12719 (71)
Left_Caudate (11): linear fit = 0.96 x + 0.0 (936 voxels, overlap=0.805)
Left_Caudate (11): linear fit = 0.96 x + 0.0 (936 voxels, peak = 67), gca=66.6
gca peak = 0.13902 (56)
mri peak = 0.05439 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (29764 voxels, overlap=0.608)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (29764 voxels, peak = 65), gca=64.7
gca peak = 0.14777 (55)
mri peak = 0.05207 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (30993 voxels, overlap=0.721)
Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (30993 voxels, peak = 65), gca=64.6
gca peak = 0.16765 (84)
mri peak = 0.12631 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5081 voxels, overlap=0.729)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5081 voxels, peak = 88), gca=87.8
gca peak = 0.18739 (84)
mri peak = 0.10255 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5322 voxels, overlap=0.801)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5322 voxels, peak = 87), gca=86.9
gca peak = 0.29869 (57)
mri peak = 0.12155 (62)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (449 voxels, overlap=0.521)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (449 voxels, peak = 62), gca=62.4
gca peak = 0.33601 (57)
mri peak = 0.10868 (66)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (560 voxels, overlap=0.897)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (560 voxels, peak = 64), gca=63.6
gca peak = 0.11131 (90)
mri peak = 0.07895 (82)
Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (4446 voxels, overlap=0.912)
Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (4446 voxels, peak = 87), gca=86.8
gca peak = 0.11793 (83)
mri peak = 0.07830 (80)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4492 voxels, overlap=0.950)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4492 voxels, peak = 84), gca=84.2
gca peak = 0.08324 (81)
mri peak = 0.10647 (76)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1437 voxels, overlap=0.812)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1437 voxels, peak = 80), gca=79.8
gca peak = 0.10360 (77)
mri peak = 0.10586 (78)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2560 voxels, overlap=0.950)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2560 voxels, peak = 77), gca=77.0
gca peak = 0.08424 (78)
mri peak = 0.08293 (84)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11503 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (11503 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.10267 (90)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1634 voxels, overlap=0.823)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1634 voxels, peak = 90), gca=90.3
gca peak = 0.14500 (87)
mri peak = 0.09706 (90)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1699 voxels, overlap=0.915)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1699 voxels, peak = 89), gca=89.2
gca peak = 0.14975 (24)
mri peak = 1.00000 (52)
gca peak = 0.19357 (14)
mri peak = 0.17137 (14)
Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (253 voxels, overlap=0.254)
Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (253 voxels, peak = 10), gca=10.3
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 1.08 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.95 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.20127 (19)
mri peak = 0.08092 (21)
Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (385 voxels, overlap=0.903)
Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (385 voxels, peak = 20), gca=20.2
gca peak = 0.19068 (15)
mri peak = 0.07722 (16)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (304 voxels, overlap=0.517)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (304 voxels, peak = 15), gca=15.4
gca peak = 0.24778 (91)
mri peak = 0.13142 (93)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (589 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (589 voxels, peak = 91), gca=90.5
gca peak = 0.18419 (92)
mri peak = 0.07588 (93)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (975 voxels, overlap=1.019)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (975 voxels, peak = 92), gca=91.5
gca peak = 0.28983 (58)
mri peak = 0.08438 (60)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1162 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1162 voxels, peak = 59), gca=59.4
gca peak = 0.29346 (59)
mri peak = 0.10163 (61)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1105 voxels, overlap=1.005)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1105 voxels, peak = 59), gca=59.0
gca peak = 0.07585 (103)
mri peak = 0.08799 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36139 voxels, overlap=0.784)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36139 voxels, peak = 103), gca=103.0
gca peak = 0.07908 (105)
mri peak = 0.09203 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38414 voxels, overlap=0.772)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38414 voxels, peak = 105), gca=105.0
gca peak = 0.08755 (63)
mri peak = 0.04723 (63)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (49077 voxels, overlap=0.968)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (49077 voxels, peak = 62), gca=62.1
gca peak = 0.11098 (62)
mri peak = 0.04642 (63)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (47243 voxels, overlap=0.966)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (47243 voxels, peak = 62), gca=62.0
gca peak = 0.26033 (71)
mri peak = 0.10894 (71)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (973 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (973 voxels, peak = 71), gca=71.0
gca peak = 0.14320 (75)
mri peak = 0.12719 (71)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (936 voxels, overlap=1.000)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (936 voxels, peak = 73), gca=73.1
gca peak = 0.12456 (65)
mri peak = 0.05439 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29764 voxels, overlap=0.996)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29764 voxels, peak = 65), gca=65.0
gca peak = 0.13028 (64)
mri peak = 0.05207 (64)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30993 voxels, overlap=0.989)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30993 voxels, peak = 63), gca=63.0
gca peak = 0.15120 (88)
mri peak = 0.12631 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5081 voxels, overlap=0.925)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5081 voxels, peak = 88), gca=87.6
gca peak = 0.18140 (87)
mri peak = 0.10255 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5322 voxels, overlap=0.932)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5322 voxels, peak = 87), gca=87.0
gca peak = 0.28917 (64)
mri peak = 0.12155 (62)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (449 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (449 voxels, peak = 64), gca=64.0
gca peak = 0.29992 (64)
mri peak = 0.10868 (66)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (560 voxels, overlap=1.014)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (560 voxels, peak = 65), gca=65.0
gca peak = 0.10781 (85)
mri peak = 0.07895 (82)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4446 voxels, overlap=0.953)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4446 voxels, peak = 85), gca=85.0
gca peak = 0.11237 (82)
mri peak = 0.07830 (80)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4492 voxels, overlap=0.972)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4492 voxels, peak = 82), gca=82.0
gca peak = 0.09216 (74)
mri peak = 0.10647 (76)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (1437 voxels, overlap=0.810)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (1437 voxels, peak = 75), gca=75.1
gca peak = 0.10360 (77)
mri peak = 0.10586 (78)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2560 voxels, overlap=0.951)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2560 voxels, peak = 77), gca=77.0
gca peak = 0.07340 (89)
mri peak = 0.08293 (84)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11503 voxels, overlap=0.776)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11503 voxels, peak = 89), gca=88.6
gca peak = 0.12977 (91)
mri peak = 0.10267 (90)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1634 voxels, overlap=0.835)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1634 voxels, peak = 91), gca=90.5
gca peak = 0.14075 (88)
mri peak = 0.09706 (90)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1699 voxels, overlap=0.909)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1699 voxels, peak = 87), gca=86.7
gca peak = 0.16685 (23)
mri peak = 1.00000 (52)
gca peak = 0.22767 (12)
mri peak = 0.17137 (14)
Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (253 voxels, overlap=0.781)
Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (253 voxels, peak = 13), gca=12.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16503 (28)
gca peak Left_Thalamus = 0.36646 (100)
gca peak Third_Ventricle = 0.16685 (23)
gca peak CSF = 0.20338 (34)
gca peak Left_Accumbens_area = 0.69375 (60)
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 = 0.21972 (24)
gca peak Right_Accumbens_area = 0.29895 (69)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.51881 (31)
gca peak WM_hypointensities = 0.07623 (77)
gca peak non_WM_hypointensities = 0.07427 (44)
gca peak Optic_Chiasm = 0.70933 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.05 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
71562 voxels changed in iteration 0 of unlikely voxel relabeling
259 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
58604 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels)
423 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 74313 changed. image ll: -2.127, PF=0.500
pass 2: 20886 changed. image ll: -2.126, PF=0.500
pass 3: 6790 changed.
pass 4: 2569 changed.
50908 voxels changed in iteration 0 of unlikely voxel relabeling
302 voxels changed in iteration 1 of unlikely voxel relabeling
5 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6954 voxels changed in iteration 0 of unlikely voxel relabeling
179 voxels changed in iteration 1 of unlikely voxel relabeling
7 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6603 voxels changed in iteration 0 of unlikely voxel relabeling
105 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5996 voxels changed in iteration 0 of unlikely voxel relabeling
66 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3641.726373
mri_ca_label stimesec    1.690742
mri_ca_label ru_maxrss   2090736
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   847146
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  69296
mri_ca_label ru_oublock  480
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    261
mri_ca_label ru_nivcsw   5027
auto-labeling took 60 minutes and 0 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/transforms/cc_up.lta 0050310 

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-6.0.0/0050310/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/norm.mgz
41396 voxels in left wm, 51394 in right wm, xrange [122, 131]
searching rotation angles z=[-5  9], y=[-6  8]

searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.8  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.3  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.8  global minimum found at slice 126.4, rotations (0.74, 2.06)
final transformation (x=126.4, yr=0.737, zr=2.061):
 0.99927  -0.03596   0.01285   4.12010;
 0.03595   0.99935   0.00046   14.47229;
-0.01286  -0.00000   0.99992   13.63544;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 127
cc center is found at 127 109 116
eigenvectors:
 0.00076  -0.00631   0.99998;
 0.14130  -0.98995  -0.00635;
 0.98997   0.14130   0.00013;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.9 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 03:31:18 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 03:31:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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...
1306 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 69 (69), valley at 23 (23)
csf peak at 35, setting threshold to 57
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 68 (68), valley at 23 (23)
csf peak at 35, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 1 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 03:34:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1607965 voxels in mask (pct=  9.58)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 03:34:21 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 (103.0): 103.0 +- 6.4 [79.0 --> 125.0]
GM (72.0) : 70.0 +- 9.7 [30.0 --> 95.0]
setting bottom of white matter range to 79.7
setting top of gray matter range to 89.5
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
7855 sparsely connected voxels removed...
thickening thin strands....
20 segments, 2820 filled
5559 bright non-wm voxels segmented.
3309 diagonally connected voxels added...
white matter segmentation took 1.8 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.61 minutes
reading wm segmentation from wm.seg.mgz...
724 voxels added to wm to prevent paths from MTL structures to cortex
3168 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 34998 voxels turned on, 54080 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 99   new 99
115,126,128 old 99   new 99
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  19 found -  19 modified     |    TOTAL:  19
pass   2 (xy+):   0 found -  19 modified     |    TOTAL:  19
pass   1 (xy-):  28 found -  28 modified     |    TOTAL:  47
pass   2 (xy-):   0 found -  28 modified     |    TOTAL:  47
pass   1 (yz+):  25 found -  25 modified     |    TOTAL:  72
pass   2 (yz+):   0 found -  25 modified     |    TOTAL:  72
pass   1 (yz-):  28 found -  28 modified     |    TOTAL: 100
pass   2 (yz-):   0 found -  28 modified     |    TOTAL: 100
pass   1 (xz+):  21 found -  21 modified     |    TOTAL: 121
pass   2 (xz+):   0 found -  21 modified     |    TOTAL: 121
pass   1 (xz-):  17 found -  17 modified     |    TOTAL: 138
pass   2 (xz-):   0 found -  17 modified     |    TOTAL: 138
Iteration Number : 1
pass   1 (+++):  30 found -  30 modified     |    TOTAL:  30
pass   2 (+++):   0 found -  30 modified     |    TOTAL:  30
pass   1 (+++):  33 found -  33 modified     |    TOTAL:  63
pass   2 (+++):   0 found -  33 modified     |    TOTAL:  63
pass   1 (+++):  29 found -  29 modified     |    TOTAL:  92
pass   2 (+++):   0 found -  29 modified     |    TOTAL:  92
pass   1 (+++):  37 found -  37 modified     |    TOTAL: 129
pass   2 (+++):   0 found -  37 modified     |    TOTAL: 129
Iteration Number : 1
pass   1 (++): 133 found - 133 modified     |    TOTAL: 133
pass   2 (++):   0 found - 133 modified     |    TOTAL: 133
pass   1 (+-): 113 found - 113 modified     |    TOTAL: 246
pass   2 (+-):   0 found - 113 modified     |    TOTAL: 246
pass   1 (--):  69 found -  69 modified     |    TOTAL: 315
pass   2 (--):   0 found -  69 modified     |    TOTAL: 315
pass   1 (-+): 114 found - 114 modified     |    TOTAL: 429
pass   2 (-+):   0 found - 114 modified     |    TOTAL: 429
Iteration Number : 2
pass   1 (xy+):   9 found -   9 modified     |    TOTAL:   9
pass   2 (xy+):   0 found -   9 modified     |    TOTAL:   9
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  14
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  14
pass   1 (yz+):  17 found -  17 modified     |    TOTAL:  31
pass   2 (yz+):   0 found -  17 modified     |    TOTAL:  31
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  35
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  35
pass   1 (xz+):   7 found -   7 modified     |    TOTAL:  42
pass   2 (xz+):   0 found -   7 modified     |    TOTAL:  42
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  49
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  49
Iteration Number : 2
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
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   4 found -   4 modified     |    TOTAL:   6
pass   2 (+-):   0 found -   4 modified     |    TOTAL:   6
pass   1 (--):   3 found -   3 modified     |    TOTAL:   9
pass   2 (--):   0 found -   3 modified     |    TOTAL:   9
pass   1 (-+):   5 found -   5 modified     |    TOTAL:  14
pass   2 (-+):   0 found -   5 modified     |    TOTAL:  14
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
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 = 765 (out of 554015: 0.138083)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 03:36:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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
 1.03953  -0.00712  -0.00858  -3.22345;
 0.00974   1.03582   0.00843  -15.79141;
 0.00852  -0.00850   1.04352  -16.06702;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.03953  -0.00712  -0.00858  -3.22345;
 0.00974   1.03582   0.00843  -15.79141;
 0.00852  -0.00850   1.04352  -16.06702;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1976 (min = 350, max = 1400), aspect = 1.14 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 114, 94), TAL = (1.0, -34.0, 14.0)
talairach voxel to voxel transform
 0.96185   0.00667   0.00785   3.33200;
-0.00898   0.96529  -0.00787   15.08792;
-0.00793   0.00781   0.95817   15.49265;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  114,  94) --> (1.0, -34.0, 14.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (1.00, -34.00, 14.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, -34.00, 14.00) SRC: (109.67, 123.41, 105.59)
search lh wm seed point around talairach space (-17.00, -34.00, 14.00), SRC: (144.30, 123.09, 105.30)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 03:37:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   6
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   7
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
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 = 9 (out of 264314: 0.003405)
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 50: 3111 vertices, 3301 faces
slice 60: 10523 vertices, 10788 faces
slice 70: 20194 vertices, 20570 faces
slice 80: 31910 vertices, 32299 faces
slice 90: 44518 vertices, 44988 faces
slice 100: 57563 vertices, 58047 faces
slice 110: 72779 vertices, 73377 faces
slice 120: 87843 vertices, 88434 faces
slice 130: 101888 vertices, 102447 faces
slice 140: 115721 vertices, 116290 faces
slice 150: 127615 vertices, 128141 faces
slice 160: 136820 vertices, 137286 faces
slice 170: 145846 vertices, 146239 faces
slice 180: 153151 vertices, 153544 faces
slice 190: 159256 vertices, 159612 faces
slice 200: 162400 vertices, 162615 faces
slice 210: 162536 vertices, 162706 faces
slice 220: 162536 vertices, 162706 faces
slice 230: 162536 vertices, 162706 faces
slice 240: 162536 vertices, 162706 faces
slice 250: 162536 vertices, 162706 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...
   162536 voxel in cpt #1: X=-170 [v=162536,e=488118,f=325412] located at (-26.498955, -12.002424, 7.362326)
For the whole surface: X=-170 [v=162536,e=488118,f=325412]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 03:37:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz+):   5 found -   5 modified     |    TOTAL:  10
pass   2 (xz+):   0 found -   5 modified     |    TOTAL:  10
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  11
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 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   4 modified     |    TOTAL:   4
pass   1 (--):   2 found -   2 modified     |    TOTAL:   6
pass   2 (--):   0 found -   2 modified     |    TOTAL:   6
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   6
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+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 23 (out of 268491: 0.008566)
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: 17 vertices, 23 faces
slice 50: 4026 vertices, 4261 faces
slice 60: 13725 vertices, 14075 faces
slice 70: 24915 vertices, 25359 faces
slice 80: 36914 vertices, 37353 faces
slice 90: 49391 vertices, 49793 faces
slice 100: 62026 vertices, 62577 faces
slice 110: 76573 vertices, 77114 faces
slice 120: 91112 vertices, 91653 faces
slice 130: 105597 vertices, 106140 faces
slice 140: 119830 vertices, 120427 faces
slice 150: 132059 vertices, 132589 faces
slice 160: 141626 vertices, 142065 faces
slice 170: 150429 vertices, 150871 faces
slice 180: 157222 vertices, 157650 faces
slice 190: 162866 vertices, 163234 faces
slice 200: 166276 vertices, 166512 faces
slice 210: 166458 vertices, 166656 faces
slice 220: 166458 vertices, 166656 faces
slice 230: 166458 vertices, 166656 faces
slice 240: 166458 vertices, 166656 faces
slice 250: 166458 vertices, 166656 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...
   166458 voxel in cpt #1: X=-198 [v=166458,e=499968,f=333312] located at (29.376635, -13.759675, 5.745359)
For the whole surface: X=-198 [v=166458,e=499968,f=333312]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 03:37:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 03:37:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

Waiting for PID 12289 of (12289 12292) to complete...
Waiting for PID 12292 of (12289 12292) 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 (12289 12292) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 03:37:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 03:37:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

Waiting for PID 12338 of (12338 12341) to complete...
Waiting for PID 12341 of (12338 12341) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 46.9 mm, total surface area = 84875 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.168 (target=0.015)   
step 005: RMS=0.131 (target=0.015)   
step 010: RMS=0.105 (target=0.015)   
step 015: RMS=0.093 (target=0.015)   
step 020: RMS=0.085 (target=0.015)   
step 025: RMS=0.079 (target=0.015)   
step 030: RMS=0.074 (target=0.015)   
step 035: RMS=0.071 (target=0.015)   
step 040: RMS=0.068 (target=0.015)   
step 045: RMS=0.066 (target=0.015)   
step 050: RMS=0.065 (target=0.015)   
step 055: RMS=0.065 (target=0.015)   
step 060: RMS=0.065 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.991400
mris_inflate stimesec    0.150977
mris_inflate ru_maxrss   237444
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34258
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11456
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2062
mris_inflate ru_nivcsw   3625

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 47.5 mm, total surface area = 86865 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.169 (target=0.015)   
step 005: RMS=0.132 (target=0.015)   
step 010: RMS=0.105 (target=0.015)   
step 015: RMS=0.095 (target=0.015)   
step 020: RMS=0.086 (target=0.015)   
step 025: RMS=0.081 (target=0.015)   
step 030: RMS=0.076 (target=0.015)   
step 035: RMS=0.074 (target=0.015)   
step 040: RMS=0.073 (target=0.015)   
step 045: RMS=0.071 (target=0.015)   
step 050: RMS=0.070 (target=0.015)   
step 055: RMS=0.069 (target=0.015)   
step 060: RMS=0.069 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    51.011245
mris_inflate stimesec    0.114982
mris_inflate ru_maxrss   243060
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35150
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11720
mris_inflate ru_oublock  11736
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2317
mris_inflate ru_nivcsw   3641
PIDs (12338 12341) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 03:38:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 03:38:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

Waiting for PID 12431 of (12431 12435) to complete...
Waiting for PID 12435 of (12431 12435) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.91 +- 0.56 (0.00-->8.34) (max @ vno 61356 --> 61357)
face area 0.02 +- 0.03 (-0.21-->0.67)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.300...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.408, avgs=0
005/300: dt: 0.9000, rms radial error=176.150, avgs=0
010/300: dt: 0.9000, rms radial error=175.595, avgs=0
015/300: dt: 0.9000, rms radial error=174.866, avgs=0
020/300: dt: 0.9000, rms radial error=174.036, avgs=0
025/300: dt: 0.9000, rms radial error=173.148, avgs=0
030/300: dt: 0.9000, rms radial error=172.228, avgs=0
035/300: dt: 0.9000, rms radial error=171.291, avgs=0
040/300: dt: 0.9000, rms radial error=170.346, avgs=0
045/300: dt: 0.9000, rms radial error=169.398, avgs=0
050/300: dt: 0.9000, rms radial error=168.450, avgs=0
055/300: dt: 0.9000, rms radial error=167.505, avgs=0
060/300: dt: 0.9000, rms radial error=166.564, avgs=0
065/300: dt: 0.9000, rms radial error=165.629, avgs=0
070/300: dt: 0.9000, rms radial error=164.702, avgs=0
075/300: dt: 0.9000, rms radial error=163.779, avgs=0
080/300: dt: 0.9000, rms radial error=162.861, avgs=0
085/300: dt: 0.9000, rms radial error=161.949, avgs=0
090/300: dt: 0.9000, rms radial error=161.041, avgs=0
095/300: dt: 0.9000, rms radial error=160.138, avgs=0
100/300: dt: 0.9000, rms radial error=159.239, avgs=0
105/300: dt: 0.9000, rms radial error=158.346, avgs=0
110/300: dt: 0.9000, rms radial error=157.457, avgs=0
115/300: dt: 0.9000, rms radial error=156.573, avgs=0
120/300: dt: 0.9000, rms radial error=155.694, avgs=0
125/300: dt: 0.9000, rms radial error=154.819, avgs=0
130/300: dt: 0.9000, rms radial error=153.949, avgs=0
135/300: dt: 0.9000, rms radial error=153.083, avgs=0
140/300: dt: 0.9000, rms radial error=152.223, avgs=0
145/300: dt: 0.9000, rms radial error=151.367, avgs=0
150/300: dt: 0.9000, rms radial error=150.517, avgs=0
155/300: dt: 0.9000, rms radial error=149.671, avgs=0
160/300: dt: 0.9000, rms radial error=148.829, avgs=0
165/300: dt: 0.9000, rms radial error=147.993, avgs=0
170/300: dt: 0.9000, rms radial error=147.160, avgs=0
175/300: dt: 0.9000, rms radial error=146.333, avgs=0
180/300: dt: 0.9000, rms radial error=145.510, avgs=0
185/300: dt: 0.9000, rms radial error=144.691, avgs=0
190/300: dt: 0.9000, rms radial error=143.877, avgs=0
195/300: dt: 0.9000, rms radial error=143.067, avgs=0
200/300: dt: 0.9000, rms radial error=142.262, avgs=0
205/300: dt: 0.9000, rms radial error=141.461, avgs=0
210/300: dt: 0.9000, rms radial error=140.664, avgs=0
215/300: dt: 0.9000, rms radial error=139.872, avgs=0
220/300: dt: 0.9000, rms radial error=139.085, avgs=0
225/300: dt: 0.9000, rms radial error=138.301, avgs=0
230/300: dt: 0.9000, rms radial error=137.522, avgs=0
235/300: dt: 0.9000, rms radial error=136.748, avgs=0
240/300: dt: 0.9000, rms radial error=135.978, avgs=0
245/300: dt: 0.9000, rms radial error=135.211, avgs=0
250/300: dt: 0.9000, rms radial error=134.450, avgs=0
255/300: dt: 0.9000, rms radial error=133.692, avgs=0
260/300: dt: 0.9000, rms radial error=132.939, avgs=0
265/300: dt: 0.9000, rms radial error=132.189, avgs=0
270/300: dt: 0.9000, rms radial error=131.445, avgs=0
275/300: dt: 0.9000, rms radial error=130.704, avgs=0
280/300: dt: 0.9000, rms radial error=129.967, avgs=0
285/300: dt: 0.9000, rms radial error=129.234, avgs=0
290/300: dt: 0.9000, rms radial error=128.506, avgs=0
295/300: dt: 0.9000, rms radial error=127.781, avgs=0
300/300: dt: 0.9000, rms radial error=127.061, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19312.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 2 (K=40.0), pass 1, starting sse = 3371.76
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
epoch 3 (K=160.0), pass 1, starting sse = 391.55
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00271
epoch 4 (K=640.0), pass 1, starting sse = 43.34
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00515
final distance error %26.95
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    282.667028
mris_sphere stimesec    0.191970
mris_sphere ru_maxrss   237648
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   34309
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11480
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    7943
mris_sphere ru_nivcsw   21240
FSRUNTIME@ mris_sphere  0.0785 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 0.90 +- 0.58 (0.00-->7.01) (max @ vno 107943 --> 109345)
face area 0.02 +- 0.03 (-0.14-->0.69)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.296...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.439, avgs=0
005/300: dt: 0.9000, rms radial error=176.180, avgs=0
010/300: dt: 0.9000, rms radial error=175.623, avgs=0
015/300: dt: 0.9000, rms radial error=174.892, avgs=0
020/300: dt: 0.9000, rms radial error=174.062, avgs=0
025/300: dt: 0.9000, rms radial error=173.175, avgs=0
030/300: dt: 0.9000, rms radial error=172.257, avgs=0
035/300: dt: 0.9000, rms radial error=171.322, avgs=0
040/300: dt: 0.9000, rms radial error=170.380, avgs=0
045/300: dt: 0.9000, rms radial error=169.436, avgs=0
050/300: dt: 0.9000, rms radial error=168.493, avgs=0
055/300: dt: 0.9000, rms radial error=167.552, avgs=0
060/300: dt: 0.9000, rms radial error=166.614, avgs=0
065/300: dt: 0.9000, rms radial error=165.681, avgs=0
070/300: dt: 0.9000, rms radial error=164.752, avgs=0
075/300: dt: 0.9000, rms radial error=163.828, avgs=0
080/300: dt: 0.9000, rms radial error=162.909, avgs=0
085/300: dt: 0.9000, rms radial error=161.995, avgs=0
090/300: dt: 0.9000, rms radial error=161.085, avgs=0
095/300: dt: 0.9000, rms radial error=160.180, avgs=0
100/300: dt: 0.9000, rms radial error=159.280, avgs=0
105/300: dt: 0.9000, rms radial error=158.384, avgs=0
110/300: dt: 0.9000, rms radial error=157.494, avgs=0
115/300: dt: 0.9000, rms radial error=156.609, avgs=0
120/300: dt: 0.9000, rms radial error=155.729, avgs=0
125/300: dt: 0.9000, rms radial error=154.854, avgs=0
130/300: dt: 0.9000, rms radial error=153.983, avgs=0
135/300: dt: 0.9000, rms radial error=153.117, avgs=0
140/300: dt: 0.9000, rms radial error=152.256, avgs=0
145/300: dt: 0.9000, rms radial error=151.399, avgs=0
150/300: dt: 0.9000, rms radial error=150.547, avgs=0
155/300: dt: 0.9000, rms radial error=149.700, avgs=0
160/300: dt: 0.9000, rms radial error=148.858, avgs=0
165/300: dt: 0.9000, rms radial error=148.021, avgs=0
170/300: dt: 0.9000, rms radial error=147.189, avgs=0
175/300: dt: 0.9000, rms radial error=146.361, avgs=0
180/300: dt: 0.9000, rms radial error=145.538, avgs=0
185/300: dt: 0.9000, rms radial error=144.719, avgs=0
190/300: dt: 0.9000, rms radial error=143.904, avgs=0
195/300: dt: 0.9000, rms radial error=143.094, avgs=0
200/300: dt: 0.9000, rms radial error=142.289, avgs=0
205/300: dt: 0.9000, rms radial error=141.488, avgs=0
210/300: dt: 0.9000, rms radial error=140.691, avgs=0
215/300: dt: 0.9000, rms radial error=139.899, avgs=0
220/300: dt: 0.9000, rms radial error=139.111, avgs=0
225/300: dt: 0.9000, rms radial error=138.328, avgs=0
230/300: dt: 0.9000, rms radial error=137.548, avgs=0
235/300: dt: 0.9000, rms radial error=136.773, avgs=0
240/300: dt: 0.9000, rms radial error=136.003, avgs=0
245/300: dt: 0.9000, rms radial error=135.236, avgs=0
250/300: dt: 0.9000, rms radial error=134.474, avgs=0
255/300: dt: 0.9000, rms radial error=133.716, avgs=0
260/300: dt: 0.9000, rms radial error=132.963, avgs=0
265/300: dt: 0.9000, rms radial error=132.213, avgs=0
270/300: dt: 0.9000, rms radial error=131.468, avgs=0
275/300: dt: 0.9000, rms radial error=130.726, avgs=0
280/300: dt: 0.9000, rms radial error=129.989, avgs=0
285/300: dt: 0.9000, rms radial error=129.256, avgs=0
290/300: dt: 0.9000, rms radial error=128.528, avgs=0
295/300: dt: 0.9000, rms radial error=127.803, avgs=0
300/300: dt: 0.9000, rms radial error=127.083, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19863.71
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
epoch 2 (K=40.0), pass 1, starting sse = 3511.48
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 422.05
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00318
epoch 4 (K=640.0), pass 1, starting sse = 47.60
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00575
final distance error %28.43
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    293.740344
mris_sphere stimesec    0.262960
mris_sphere ru_maxrss   243260
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   35203
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11760
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8033
mris_sphere ru_nivcsw   21282
FSRUNTIME@ mris_sphere  0.0806 hours 1 threads
PIDs (12431 12435) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 03:43:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 03:43:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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


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

#@# Fix Topology lh Sun Oct  8 03:43:33 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050310 lh 

#@# Fix Topology rh Sun Oct  8 03:43:33 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050310 rh 

Waiting for PID 12733 of (12733 12736) to complete...
Waiting for PID 12736 of (12733 12736) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050310 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=-170 (nv=162536, nf=325412, ne=488118, g=86)
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...
20022 ambiguous faces found in tessellation
segmenting defects...
96 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 7 into 6
      -merging segment 54 into 31
      -merging segment 71 into 64
      -merging segment 84 into 82
92 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2792  (-4.6396)
      -vertex     loglikelihood: -6.0485  (-3.0243)
      -normal dot loglikelihood: -3.5772  (-3.5772)
      -quad curv  loglikelihood: -6.1480  (-3.0740)
      Total Loglikelihood : -25.0530

CORRECTING DEFECT 0 (vertices=35, convex hull=55, v0=1174)
After retessellation of defect 0 (v0=1174), euler #=-84 (150970,449637,298583) : difference with theory (-89) = -5 

CORRECTING DEFECT 1 (vertices=5, convex hull=20, v0=1496)
After retessellation of defect 1 (v0=1496), euler #=-83 (150970,449641,298588) : difference with theory (-88) = -5 

CORRECTING DEFECT 2 (vertices=777, convex hull=259, v0=1948)
After retessellation of defect 2 (v0=1948), euler #=-84 (151068,450072,298920) : difference with theory (-87) = -3 

CORRECTING DEFECT 3 (vertices=30, convex hull=61, v0=3387)
After retessellation of defect 3 (v0=3387), euler #=-83 (151079,450130,298968) : difference with theory (-86) = -3 

CORRECTING DEFECT 4 (vertices=55, convex hull=89, v0=3489)
After retessellation of defect 4 (v0=3489), euler #=-82 (151087,450193,299024) : difference with theory (-85) = -3 

CORRECTING DEFECT 5 (vertices=9, convex hull=26, v0=4611)
After retessellation of defect 5 (v0=4611), euler #=-81 (151088,450203,299034) : difference with theory (-84) = -3 

CORRECTING DEFECT 6 (vertices=67, convex hull=87, v0=5172)
After retessellation of defect 6 (v0=5172), euler #=-79 (151112,450317,299126) : difference with theory (-83) = -4 

CORRECTING DEFECT 7 (vertices=24, convex hull=28, v0=6061)
After retessellation of defect 7 (v0=6061), euler #=-78 (151114,450331,299139) : difference with theory (-82) = -4 

CORRECTING DEFECT 8 (vertices=96, convex hull=30, v0=6591)
After retessellation of defect 8 (v0=6591), euler #=-77 (151117,450349,299155) : difference with theory (-81) = -4 

CORRECTING DEFECT 9 (vertices=68, convex hull=48, v0=7277)
After retessellation of defect 9 (v0=7277), euler #=-76 (151122,450378,299180) : difference with theory (-80) = -4 

CORRECTING DEFECT 10 (vertices=35, convex hull=31, v0=7693)
After retessellation of defect 10 (v0=7693), euler #=-75 (151124,450393,299194) : difference with theory (-79) = -4 

CORRECTING DEFECT 11 (vertices=167, convex hull=51, v0=10534)
After retessellation of defect 11 (v0=10534), euler #=-74 (151137,450450,299239) : difference with theory (-78) = -4 

CORRECTING DEFECT 12 (vertices=13, convex hull=34, v0=11862)
After retessellation of defect 12 (v0=11862), euler #=-73 (151138,450464,299253) : difference with theory (-77) = -4 

CORRECTING DEFECT 13 (vertices=97, convex hull=113, v0=13095)
After retessellation of defect 13 (v0=13095), euler #=-72 (151191,450672,299409) : difference with theory (-76) = -4 

CORRECTING DEFECT 14 (vertices=29, convex hull=39, v0=13669)
After retessellation of defect 14 (v0=13669), euler #=-71 (151197,450705,299437) : difference with theory (-75) = -4 

CORRECTING DEFECT 15 (vertices=50, convex hull=36, v0=14347)
After retessellation of defect 15 (v0=14347), euler #=-70 (151200,450725,299455) : difference with theory (-74) = -4 

CORRECTING DEFECT 16 (vertices=61, convex hull=88, v0=14989)
After retessellation of defect 16 (v0=14989), euler #=-69 (151227,450839,299543) : difference with theory (-73) = -4 

CORRECTING DEFECT 17 (vertices=87, convex hull=122, v0=16552)
After retessellation of defect 17 (v0=16552), euler #=-68 (151273,451032,299691) : difference with theory (-72) = -4 

CORRECTING DEFECT 18 (vertices=88, convex hull=63, v0=16879)
After retessellation of defect 18 (v0=16879), euler #=-67 (151281,451080,299732) : difference with theory (-71) = -4 

CORRECTING DEFECT 19 (vertices=22, convex hull=52, v0=18613)
After retessellation of defect 19 (v0=18613), euler #=-66 (151289,451125,299770) : difference with theory (-70) = -4 

CORRECTING DEFECT 20 (vertices=31, convex hull=36, v0=18792)
After retessellation of defect 20 (v0=18792), euler #=-65 (151295,451154,299794) : difference with theory (-69) = -4 

CORRECTING DEFECT 21 (vertices=27, convex hull=43, v0=19153)
After retessellation of defect 21 (v0=19153), euler #=-64 (151306,451206,299836) : difference with theory (-68) = -4 

CORRECTING DEFECT 22 (vertices=35, convex hull=97, v0=20362)
After retessellation of defect 22 (v0=20362), euler #=-63 (151319,451281,299899) : difference with theory (-67) = -4 

CORRECTING DEFECT 23 (vertices=98, convex hull=81, v0=23706)
After retessellation of defect 23 (v0=23706), euler #=-62 (151362,451443,300019) : difference with theory (-66) = -4 

CORRECTING DEFECT 24 (vertices=39, convex hull=36, v0=24410)
After retessellation of defect 24 (v0=24410), euler #=-61 (151368,451476,300047) : difference with theory (-65) = -4 

CORRECTING DEFECT 25 (vertices=5, convex hull=31, v0=24495)
After retessellation of defect 25 (v0=24495), euler #=-60 (151369,451488,300059) : difference with theory (-64) = -4 

CORRECTING DEFECT 26 (vertices=82, convex hull=72, v0=26779)
After retessellation of defect 26 (v0=26779), euler #=-59 (151391,451584,300134) : difference with theory (-63) = -4 

CORRECTING DEFECT 27 (vertices=91, convex hull=119, v0=28101)
After retessellation of defect 27 (v0=28101), euler #=-58 (151446,451803,300299) : difference with theory (-62) = -4 

CORRECTING DEFECT 28 (vertices=59, convex hull=72, v0=29397)
After retessellation of defect 28 (v0=29397), euler #=-57 (151463,451881,300361) : difference with theory (-61) = -4 

CORRECTING DEFECT 29 (vertices=25, convex hull=49, v0=34526)
After retessellation of defect 29 (v0=34526), euler #=-56 (151480,451952,300416) : difference with theory (-60) = -4 

CORRECTING DEFECT 30 (vertices=1268, convex hull=333, v0=35219)
After retessellation of defect 30 (v0=35219), euler #=-54 (151545,452311,300712) : difference with theory (-59) = -5 

CORRECTING DEFECT 31 (vertices=39, convex hull=81, v0=36307)
After retessellation of defect 31 (v0=36307), euler #=-53 (151571,452422,300798) : difference with theory (-58) = -5 

CORRECTING DEFECT 32 (vertices=63, convex hull=79, v0=36433)
After retessellation of defect 32 (v0=36433), euler #=-52 (151597,452532,300883) : difference with theory (-57) = -5 

CORRECTING DEFECT 33 (vertices=55, convex hull=81, v0=37252)
After retessellation of defect 33 (v0=37252), euler #=-51 (151618,452629,300960) : difference with theory (-56) = -5 

CORRECTING DEFECT 34 (vertices=6, convex hull=26, v0=37293)
After retessellation of defect 34 (v0=37293), euler #=-50 (151620,452642,300972) : difference with theory (-55) = -5 

CORRECTING DEFECT 35 (vertices=32, convex hull=73, v0=39774)
After retessellation of defect 35 (v0=39774), euler #=-49 (151632,452707,301026) : difference with theory (-54) = -5 

CORRECTING DEFECT 36 (vertices=51, convex hull=81, v0=43295)
After retessellation of defect 36 (v0=43295), euler #=-48 (151660,452822,301114) : difference with theory (-53) = -5 

CORRECTING DEFECT 37 (vertices=30, convex hull=44, v0=43399)
After retessellation of defect 37 (v0=43399), euler #=-47 (151663,452846,301136) : difference with theory (-52) = -5 

CORRECTING DEFECT 38 (vertices=55, convex hull=41, v0=45347)
After retessellation of defect 38 (v0=45347), euler #=-46 (151665,452868,301157) : difference with theory (-51) = -5 

CORRECTING DEFECT 39 (vertices=29, convex hull=32, v0=45451)
After retessellation of defect 39 (v0=45451), euler #=-45 (151670,452892,301177) : difference with theory (-50) = -5 

CORRECTING DEFECT 40 (vertices=29, convex hull=50, v0=49722)
After retessellation of defect 40 (v0=49722), euler #=-44 (151686,452956,301226) : difference with theory (-49) = -5 

CORRECTING DEFECT 41 (vertices=82, convex hull=120, v0=50351)
After retessellation of defect 41 (v0=50351), euler #=-43 (151742,453174,301389) : difference with theory (-48) = -5 

CORRECTING DEFECT 42 (vertices=1388, convex hull=307, v0=54386)
After retessellation of defect 42 (v0=54386), euler #=-44 (151793,453478,301641) : difference with theory (-47) = -3 

CORRECTING DEFECT 43 (vertices=299, convex hull=308, v0=57522)
After retessellation of defect 43 (v0=57522), euler #=-43 (151884,453903,301976) : difference with theory (-46) = -3 

CORRECTING DEFECT 44 (vertices=116, convex hull=96, v0=58568)
After retessellation of defect 44 (v0=58568), euler #=-42 (151941,454117,302134) : difference with theory (-45) = -3 

CORRECTING DEFECT 45 (vertices=204, convex hull=70, v0=58719)
After retessellation of defect 45 (v0=58719), euler #=-42 (151976,454255,302237) : difference with theory (-44) = -2 

CORRECTING DEFECT 46 (vertices=52, convex hull=44, v0=58893)
After retessellation of defect 46 (v0=58893), euler #=-41 (151986,454300,302273) : difference with theory (-43) = -2 

CORRECTING DEFECT 47 (vertices=163, convex hull=151, v0=65809)
After retessellation of defect 47 (v0=65809), euler #=-40 (152056,454580,302484) : difference with theory (-42) = -2 

CORRECTING DEFECT 48 (vertices=82, convex hull=35, v0=67349)
After retessellation of defect 48 (v0=67349), euler #=-39 (152075,454653,302539) : difference with theory (-41) = -2 

CORRECTING DEFECT 49 (vertices=82, convex hull=38, v0=70288)
After retessellation of defect 49 (v0=70288), euler #=-39 (152080,454691,302572) : difference with theory (-40) = -1 

CORRECTING DEFECT 50 (vertices=35, convex hull=63, v0=74940)
After retessellation of defect 50 (v0=74940), euler #=-38 (152098,454768,302632) : difference with theory (-39) = -1 

CORRECTING DEFECT 51 (vertices=278, convex hull=196, v0=75182)
After retessellation of defect 51 (v0=75182), euler #=-37 (152185,455126,302904) : difference with theory (-38) = -1 

CORRECTING DEFECT 52 (vertices=72, convex hull=26, v0=75753)
After retessellation of defect 52 (v0=75753), euler #=-36 (152187,455141,302918) : difference with theory (-37) = -1 

CORRECTING DEFECT 53 (vertices=251, convex hull=43, v0=83223)
After retessellation of defect 53 (v0=83223), euler #=-35 (152202,455202,302965) : difference with theory (-36) = -1 

CORRECTING DEFECT 54 (vertices=33, convex hull=67, v0=89230)
After retessellation of defect 54 (v0=89230), euler #=-34 (152211,455256,303011) : difference with theory (-35) = -1 

CORRECTING DEFECT 55 (vertices=11, convex hull=24, v0=90789)
After retessellation of defect 55 (v0=90789), euler #=-33 (152212,455266,303021) : difference with theory (-34) = -1 

CORRECTING DEFECT 56 (vertices=30, convex hull=61, v0=94103)
After retessellation of defect 56 (v0=94103), euler #=-32 (152220,455309,303057) : difference with theory (-33) = -1 

CORRECTING DEFECT 57 (vertices=46, convex hull=87, v0=94681)
After retessellation of defect 57 (v0=94681), euler #=-31 (152245,455420,303144) : difference with theory (-32) = -1 

CORRECTING DEFECT 58 (vertices=70, convex hull=47, v0=95994)
After retessellation of defect 58 (v0=95994), euler #=-30 (152250,455459,303179) : difference with theory (-31) = -1 

CORRECTING DEFECT 59 (vertices=85, convex hull=83, v0=106104)
After retessellation of defect 59 (v0=106104), euler #=-29 (152275,455566,303262) : difference with theory (-30) = -1 

CORRECTING DEFECT 60 (vertices=37, convex hull=55, v0=106874)
After retessellation of defect 60 (v0=106874), euler #=-28 (152291,455636,303317) : difference with theory (-29) = -1 

CORRECTING DEFECT 61 (vertices=807, convex hull=408, v0=109824)
L defect detected...
After retessellation of defect 61 (v0=109824), euler #=-28 (152468,456388,303892) : difference with theory (-28) = 0 

CORRECTING DEFECT 62 (vertices=241, convex hull=195, v0=111390)
After retessellation of defect 62 (v0=111390), euler #=-26 (152534,456677,304117) : difference with theory (-27) = -1 

CORRECTING DEFECT 63 (vertices=42, convex hull=77, v0=111490)
After retessellation of defect 63 (v0=111490), euler #=-25 (152556,456773,304192) : difference with theory (-26) = -1 

CORRECTING DEFECT 64 (vertices=114, convex hull=53, v0=112654)
After retessellation of defect 64 (v0=112654), euler #=-24 (152564,456822,304234) : difference with theory (-25) = -1 

CORRECTING DEFECT 65 (vertices=7, convex hull=21, v0=112736)
After retessellation of defect 65 (v0=112736), euler #=-23 (152565,456829,304241) : difference with theory (-24) = -1 

CORRECTING DEFECT 66 (vertices=6, convex hull=20, v0=113881)
After retessellation of defect 66 (v0=113881), euler #=-22 (152565,456835,304248) : difference with theory (-23) = -1 

CORRECTING DEFECT 67 (vertices=9, convex hull=20, v0=114150)
After retessellation of defect 67 (v0=114150), euler #=-21 (152565,456841,304255) : difference with theory (-22) = -1 

CORRECTING DEFECT 68 (vertices=601, convex hull=247, v0=115309)
After retessellation of defect 68 (v0=115309), euler #=-20 (152642,457191,304529) : difference with theory (-21) = -1 

CORRECTING DEFECT 69 (vertices=42, convex hull=90, v0=118319)
After retessellation of defect 69 (v0=118319), euler #=-19 (152650,457252,304583) : difference with theory (-20) = -1 

CORRECTING DEFECT 70 (vertices=571, convex hull=324, v0=119269)
After retessellation of defect 70 (v0=119269), euler #=-19 (152759,457741,304963) : difference with theory (-19) = 0 

CORRECTING DEFECT 71 (vertices=85, convex hull=54, v0=119479)
After retessellation of defect 71 (v0=119479), euler #=-18 (152769,457793,305006) : difference with theory (-18) = 0 

CORRECTING DEFECT 72 (vertices=6, convex hull=27, v0=129444)
After retessellation of defect 72 (v0=129444), euler #=-17 (152770,457803,305016) : difference with theory (-17) = 0 

CORRECTING DEFECT 73 (vertices=141, convex hull=89, v0=130518)
After retessellation of defect 73 (v0=130518), euler #=-16 (152802,457939,305121) : difference with theory (-16) = 0 

CORRECTING DEFECT 74 (vertices=20, convex hull=27, v0=131878)
After retessellation of defect 74 (v0=131878), euler #=-15 (152806,457960,305139) : difference with theory (-15) = 0 

CORRECTING DEFECT 75 (vertices=108, convex hull=40, v0=132010)
After retessellation of defect 75 (v0=132010), euler #=-14 (152818,458009,305177) : difference with theory (-14) = 0 

CORRECTING DEFECT 76 (vertices=94, convex hull=51, v0=136498)
After retessellation of defect 76 (v0=136498), euler #=-13 (152826,458056,305217) : difference with theory (-13) = 0 

CORRECTING DEFECT 77 (vertices=17, convex hull=38, v0=136508)
After retessellation of defect 77 (v0=136508), euler #=-12 (152835,458097,305250) : difference with theory (-12) = 0 

CORRECTING DEFECT 78 (vertices=63, convex hull=106, v0=136559)
After retessellation of defect 78 (v0=136559), euler #=-11 (152853,458196,305332) : difference with theory (-11) = 0 

CORRECTING DEFECT 79 (vertices=165, convex hull=78, v0=136731)
After retessellation of defect 79 (v0=136731), euler #=-9 (152877,458302,305416) : difference with theory (-10) = -1 

CORRECTING DEFECT 80 (vertices=222, convex hull=139, v0=136800)
After retessellation of defect 80 (v0=136800), euler #=-8 (152928,458519,305583) : difference with theory (-9) = -1 

CORRECTING DEFECT 81 (vertices=109, convex hull=85, v0=147323)
After retessellation of defect 81 (v0=147323), euler #=-7 (152937,458584,305640) : difference with theory (-8) = -1 

CORRECTING DEFECT 82 (vertices=37, convex hull=76, v0=148220)
After retessellation of defect 82 (v0=148220), euler #=-6 (152958,458681,305717) : difference with theory (-7) = -1 

CORRECTING DEFECT 83 (vertices=156, convex hull=55, v0=148805)
After retessellation of defect 83 (v0=148805), euler #=-5 (152973,458752,305774) : difference with theory (-6) = -1 

CORRECTING DEFECT 84 (vertices=21, convex hull=45, v0=150179)
After retessellation of defect 84 (v0=150179), euler #=-4 (152979,458785,305802) : difference with theory (-5) = -1 

CORRECTING DEFECT 85 (vertices=8, convex hull=26, v0=154264)
After retessellation of defect 85 (v0=154264), euler #=-3 (152980,458797,305814) : difference with theory (-4) = -1 

CORRECTING DEFECT 86 (vertices=165, convex hull=47, v0=154268)
After retessellation of defect 86 (v0=154268), euler #=-3 (152988,458846,305855) : difference with theory (-3) = 0 

CORRECTING DEFECT 87 (vertices=43, convex hull=22, v0=156125)
After retessellation of defect 87 (v0=156125), euler #=-2 (152989,458856,305865) : difference with theory (-2) = 0 

CORRECTING DEFECT 88 (vertices=26, convex hull=86, v0=157201)
After retessellation of defect 88 (v0=157201), euler #=-1 (153003,458928,305924) : difference with theory (-1) = 0 

CORRECTING DEFECT 89 (vertices=20, convex hull=22, v0=160174)
After retessellation of defect 89 (v0=160174), euler #=0 (153004,458940,305936) : difference with theory (0) = 0 

CORRECTING DEFECT 90 (vertices=34, convex hull=83, v0=160962)
After retessellation of defect 90 (v0=160962), euler #=1 (153017,459014,305998) : difference with theory (1) = 0 

CORRECTING DEFECT 91 (vertices=202, convex hull=65, v0=161200)
After retessellation of defect 91 (v0=161200), euler #=2 (153035,459099,306066) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.29 (0.04-->17.50) (max @ vno 51537 --> 68675)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.29 (0.04-->17.50) (max @ vno 51537 --> 68675)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
293 mutations (35.9%), 523 crossovers (64.1%), 890 vertices were eliminated
building final representation...
9501 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=153035, nf=306066, ne=459099, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 72.3 minutes
0 defective edges
removing intersecting faces
000: 1043 intersecting
001: 143 intersecting
002: 99 intersecting
003: 82 intersecting
004: 61 intersecting
005: 57 intersecting
006: 52 intersecting
expanding nbhd size to 2
007: 55 intersecting
008: 51 intersecting
009: 48 intersecting
010: 45 intersecting
011: 43 intersecting
012: 34 intersecting
013: 31 intersecting
014: 30 intersecting
015: 26 intersecting
016: 22 intersecting
017: 21 intersecting
018: 18 intersecting
019: 12 intersecting
020: 9 intersecting
021: 4 intersecting
mris_fix_topology utimesec    4338.572436
mris_fix_topology stimesec    0.244962
mris_fix_topology ru_maxrss   513204
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   58995
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22880
mris_fix_topology ru_oublock  15064
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    397
mris_fix_topology ru_nivcsw   16321
FSRUNTIME@ mris_fix_topology lh  1.2053 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050310 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=-198 (nv=166458, nf=333312, ne=499968, g=100)
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...
23749 ambiguous faces found in tessellation
segmenting defects...
89 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 14 into 11
      -merging segment 35 into 31
      -merging segment 50 into 47
      -merging segment 57 into 48
      -merging segment 76 into 75
84 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3484  (-4.6742)
      -vertex     loglikelihood: -6.0651  (-3.0326)
      -normal dot loglikelihood: -3.5420  (-3.5420)
      -quad curv  loglikelihood: -5.9111  (-2.9555)
      Total Loglikelihood : -24.8666

CORRECTING DEFECT 0 (vertices=8, convex hull=22, v0=295)
After retessellation of defect 0 (v0=295), euler #=-82 (152863,454949,302004) : difference with theory (-81) = 1 

CORRECTING DEFECT 1 (vertices=45, convex hull=81, v0=501)
After retessellation of defect 1 (v0=501), euler #=-81 (152888,455056,302087) : difference with theory (-80) = 1 

CORRECTING DEFECT 2 (vertices=1003, convex hull=307, v0=1130)
After retessellation of defect 2 (v0=1130), euler #=-80 (152964,455441,302397) : difference with theory (-79) = 1 

CORRECTING DEFECT 3 (vertices=510, convex hull=321, v0=2125)
After retessellation of defect 3 (v0=2125), euler #=-79 (153047,455842,302716) : difference with theory (-78) = 1 

CORRECTING DEFECT 4 (vertices=21, convex hull=62, v0=5892)
After retessellation of defect 4 (v0=5892), euler #=-78 (153057,455896,302761) : difference with theory (-77) = 1 

CORRECTING DEFECT 5 (vertices=155, convex hull=63, v0=6462)
After retessellation of defect 5 (v0=6462), euler #=-77 (153075,455974,302822) : difference with theory (-76) = 1 

CORRECTING DEFECT 6 (vertices=283, convex hull=93, v0=6585)
After retessellation of defect 6 (v0=6585), euler #=-76 (153095,456077,302906) : difference with theory (-75) = 1 

CORRECTING DEFECT 7 (vertices=270, convex hull=121, v0=8334)
After retessellation of defect 7 (v0=8334), euler #=-75 (153137,456253,303041) : difference with theory (-74) = 1 

CORRECTING DEFECT 8 (vertices=92, convex hull=38, v0=10570)
After retessellation of defect 8 (v0=10570), euler #=-74 (153144,456289,303071) : difference with theory (-73) = 1 

CORRECTING DEFECT 9 (vertices=48, convex hull=77, v0=11729)
After retessellation of defect 9 (v0=11729), euler #=-73 (153167,456390,303150) : difference with theory (-72) = 1 

CORRECTING DEFECT 10 (vertices=5, convex hull=26, v0=12722)
After retessellation of defect 10 (v0=12722), euler #=-72 (153168,456399,303159) : difference with theory (-71) = 1 

CORRECTING DEFECT 11 (vertices=160, convex hull=123, v0=15956)
After retessellation of defect 11 (v0=15956), euler #=-70 (153207,456576,303299) : difference with theory (-70) = 0 

CORRECTING DEFECT 12 (vertices=92, convex hull=60, v0=16868)
After retessellation of defect 12 (v0=16868), euler #=-69 (153215,456624,303340) : difference with theory (-69) = 0 

CORRECTING DEFECT 13 (vertices=38, convex hull=64, v0=21424)
After retessellation of defect 13 (v0=21424), euler #=-68 (153232,456703,303403) : difference with theory (-68) = 0 

CORRECTING DEFECT 14 (vertices=28, convex hull=62, v0=23886)
After retessellation of defect 14 (v0=23886), euler #=-67 (153244,456762,303451) : difference with theory (-67) = 0 

CORRECTING DEFECT 15 (vertices=36, convex hull=73, v0=24603)
After retessellation of defect 15 (v0=24603), euler #=-66 (153253,456819,303500) : difference with theory (-66) = 0 

CORRECTING DEFECT 16 (vertices=285, convex hull=94, v0=26862)
After retessellation of defect 16 (v0=26862), euler #=-65 (153282,456951,303604) : difference with theory (-65) = 0 

CORRECTING DEFECT 17 (vertices=18, convex hull=36, v0=29507)
After retessellation of defect 17 (v0=29507), euler #=-64 (153283,456963,303616) : difference with theory (-64) = 0 

CORRECTING DEFECT 18 (vertices=443, convex hull=318, v0=31619)
After retessellation of defect 18 (v0=31619), euler #=-64 (153410,457516,304042) : difference with theory (-63) = 1 

CORRECTING DEFECT 19 (vertices=27, convex hull=67, v0=39301)
After retessellation of defect 19 (v0=39301), euler #=-63 (153425,457585,304097) : difference with theory (-62) = 1 

CORRECTING DEFECT 20 (vertices=791, convex hull=289, v0=40330)
After retessellation of defect 20 (v0=40330), euler #=-62 (153498,457943,304383) : difference with theory (-61) = 1 

CORRECTING DEFECT 21 (vertices=27, convex hull=57, v0=45234)
After retessellation of defect 21 (v0=45234), euler #=-61 (153508,457994,304425) : difference with theory (-60) = 1 

CORRECTING DEFECT 22 (vertices=14, convex hull=25, v0=48003)
After retessellation of defect 22 (v0=48003), euler #=-60 (153510,458009,304439) : difference with theory (-59) = 1 

CORRECTING DEFECT 23 (vertices=68, convex hull=98, v0=52442)
After retessellation of defect 23 (v0=52442), euler #=-59 (153537,458132,304536) : difference with theory (-58) = 1 

CORRECTING DEFECT 24 (vertices=21, convex hull=56, v0=54511)
After retessellation of defect 24 (v0=54511), euler #=-58 (153548,458188,304582) : difference with theory (-57) = 1 

CORRECTING DEFECT 25 (vertices=72, convex hull=80, v0=54886)
After retessellation of defect 25 (v0=54886), euler #=-57 (153563,458267,304647) : difference with theory (-56) = 1 

CORRECTING DEFECT 26 (vertices=67, convex hull=92, v0=55966)
After retessellation of defect 26 (v0=55966), euler #=-56 (153584,458363,304723) : difference with theory (-55) = 1 

CORRECTING DEFECT 27 (vertices=839, convex hull=251, v0=57694)
After retessellation of defect 27 (v0=57694), euler #=-55 (153683,458784,305046) : difference with theory (-54) = 1 

CORRECTING DEFECT 28 (vertices=170, convex hull=67, v0=60574)
After retessellation of defect 28 (v0=60574), euler #=-54 (153692,458842,305096) : difference with theory (-53) = 1 

CORRECTING DEFECT 29 (vertices=94, convex hull=37, v0=63540)
After retessellation of defect 29 (v0=63540), euler #=-53 (153701,458882,305128) : difference with theory (-52) = 1 

CORRECTING DEFECT 30 (vertices=205, convex hull=289, v0=69284)
After retessellation of defect 30 (v0=69284), euler #=-51 (153830,459404,305523) : difference with theory (-51) = 0 

CORRECTING DEFECT 31 (vertices=5, convex hull=16, v0=72307)
After retessellation of defect 31 (v0=72307), euler #=-50 (153830,459408,305528) : difference with theory (-50) = 0 

CORRECTING DEFECT 32 (vertices=104, convex hull=42, v0=74746)
After retessellation of defect 32 (v0=74746), euler #=-49 (153836,459449,305564) : difference with theory (-49) = 0 

CORRECTING DEFECT 33 (vertices=21, convex hull=24, v0=79384)
After retessellation of defect 33 (v0=79384), euler #=-48 (153838,459464,305578) : difference with theory (-48) = 0 

CORRECTING DEFECT 34 (vertices=70, convex hull=84, v0=85179)
After retessellation of defect 34 (v0=85179), euler #=-47 (153862,459575,305666) : difference with theory (-47) = 0 

CORRECTING DEFECT 35 (vertices=24, convex hull=49, v0=87763)
After retessellation of defect 35 (v0=87763), euler #=-46 (153871,459618,305701) : difference with theory (-46) = 0 

CORRECTING DEFECT 36 (vertices=41, convex hull=90, v0=87938)
After retessellation of defect 36 (v0=87938), euler #=-45 (153890,459716,305781) : difference with theory (-45) = 0 

CORRECTING DEFECT 37 (vertices=619, convex hull=211, v0=88069)
After retessellation of defect 37 (v0=88069), euler #=-44 (153924,459918,305950) : difference with theory (-44) = 0 

CORRECTING DEFECT 38 (vertices=44, convex hull=51, v0=89090)
After retessellation of defect 38 (v0=89090), euler #=-43 (153930,459955,305982) : difference with theory (-43) = 0 

CORRECTING DEFECT 39 (vertices=46, convex hull=35, v0=89640)
After retessellation of defect 39 (v0=89640), euler #=-42 (153934,459980,306004) : difference with theory (-42) = 0 

CORRECTING DEFECT 40 (vertices=109, convex hull=106, v0=94844)
After retessellation of defect 40 (v0=94844), euler #=-41 (153963,460118,306114) : difference with theory (-41) = 0 

CORRECTING DEFECT 41 (vertices=1333, convex hull=387, v0=95034)
L defect detected...
After retessellation of defect 41 (v0=95034), euler #=-40 (154153,460884,306691) : difference with theory (-40) = 0 

CORRECTING DEFECT 42 (vertices=44, convex hull=69, v0=96775)
After retessellation of defect 42 (v0=96775), euler #=-39 (154177,460981,306765) : difference with theory (-39) = 0 

CORRECTING DEFECT 43 (vertices=73, convex hull=112, v0=96960)
After retessellation of defect 43 (v0=96960), euler #=-38 (154223,461166,306905) : difference with theory (-38) = 0 

CORRECTING DEFECT 44 (vertices=40, convex hull=76, v0=97754)
After retessellation of defect 44 (v0=97754), euler #=-37 (154243,461261,306981) : difference with theory (-37) = 0 

CORRECTING DEFECT 45 (vertices=148, convex hull=97, v0=101171)
After retessellation of defect 45 (v0=101171), euler #=-35 (154252,461334,307047) : difference with theory (-36) = -1 

CORRECTING DEFECT 46 (vertices=114, convex hull=131, v0=103046)
After retessellation of defect 46 (v0=103046), euler #=-33 (154298,461531,307200) : difference with theory (-35) = -2 

CORRECTING DEFECT 47 (vertices=922, convex hull=353, v0=107911)
After retessellation of defect 47 (v0=107911), euler #=-32 (154386,461974,307556) : difference with theory (-34) = -2 

CORRECTING DEFECT 48 (vertices=27, convex hull=60, v0=108841)
After retessellation of defect 48 (v0=108841), euler #=-31 (154402,462046,307613) : difference with theory (-33) = -2 

CORRECTING DEFECT 49 (vertices=111, convex hull=62, v0=109054)
After retessellation of defect 49 (v0=109054), euler #=-30 (154418,462122,307674) : difference with theory (-32) = -2 

CORRECTING DEFECT 50 (vertices=968, convex hull=305, v0=109568)
After retessellation of defect 50 (v0=109568), euler #=-31 (154525,462604,308048) : difference with theory (-31) = 0 

CORRECTING DEFECT 51 (vertices=164, convex hull=57, v0=109718)
After retessellation of defect 51 (v0=109718), euler #=-30 (154552,462707,308125) : difference with theory (-30) = 0 

CORRECTING DEFECT 52 (vertices=31, convex hull=59, v0=110293)
After retessellation of defect 52 (v0=110293), euler #=-29 (154572,462789,308188) : difference with theory (-29) = 0 

CORRECTING DEFECT 53 (vertices=30, convex hull=39, v0=112551)
After retessellation of defect 53 (v0=112551), euler #=-28 (154586,462844,308230) : difference with theory (-28) = 0 

CORRECTING DEFECT 54 (vertices=17, convex hull=28, v0=113768)
After retessellation of defect 54 (v0=113768), euler #=-27 (154591,462865,308247) : difference with theory (-27) = 0 

CORRECTING DEFECT 55 (vertices=104, convex hull=91, v0=116612)
After retessellation of defect 55 (v0=116612), euler #=-26 (154645,463069,308398) : difference with theory (-26) = 0 

CORRECTING DEFECT 56 (vertices=68, convex hull=36, v0=116785)
After retessellation of defect 56 (v0=116785), euler #=-25 (154648,463092,308419) : difference with theory (-25) = 0 

CORRECTING DEFECT 57 (vertices=43, convex hull=37, v0=119407)
After retessellation of defect 57 (v0=119407), euler #=-24 (154653,463121,308444) : difference with theory (-24) = 0 

CORRECTING DEFECT 58 (vertices=170, convex hull=126, v0=119435)
After retessellation of defect 58 (v0=119435), euler #=-23 (154692,463299,308584) : difference with theory (-23) = 0 

CORRECTING DEFECT 59 (vertices=92, convex hull=116, v0=121972)
After retessellation of defect 59 (v0=121972), euler #=-22 (154746,463506,308738) : difference with theory (-22) = 0 

CORRECTING DEFECT 60 (vertices=90, convex hull=97, v0=122335)
After retessellation of defect 60 (v0=122335), euler #=-21 (154771,463623,308831) : difference with theory (-21) = 0 

CORRECTING DEFECT 61 (vertices=59, convex hull=52, v0=123529)
After retessellation of defect 61 (v0=123529), euler #=-20 (154782,463674,308872) : difference with theory (-20) = 0 

CORRECTING DEFECT 62 (vertices=83, convex hull=90, v0=124965)
After retessellation of defect 62 (v0=124965), euler #=-19 (154798,463763,308946) : difference with theory (-19) = 0 

CORRECTING DEFECT 63 (vertices=696, convex hull=298, v0=125039)
After retessellation of defect 63 (v0=125039), euler #=-19 (154938,464340,309383) : difference with theory (-18) = 1 

CORRECTING DEFECT 64 (vertices=12, convex hull=22, v0=127430)
After retessellation of defect 64 (v0=127430), euler #=-18 (154940,464353,309395) : difference with theory (-17) = 1 

CORRECTING DEFECT 65 (vertices=39, convex hull=81, v0=128261)
After retessellation of defect 65 (v0=128261), euler #=-17 (154961,464445,309467) : difference with theory (-16) = 1 

CORRECTING DEFECT 66 (vertices=63, convex hull=55, v0=128904)
After retessellation of defect 66 (v0=128904), euler #=-16 (154972,464498,309510) : difference with theory (-15) = 1 

CORRECTING DEFECT 67 (vertices=102, convex hull=51, v0=130623)
After retessellation of defect 67 (v0=130623), euler #=-15 (154980,464540,309545) : difference with theory (-14) = 1 

CORRECTING DEFECT 68 (vertices=66, convex hull=33, v0=134170)
After retessellation of defect 68 (v0=134170), euler #=-14 (154982,464556,309560) : difference with theory (-13) = 1 

CORRECTING DEFECT 69 (vertices=47, convex hull=55, v0=137285)
After retessellation of defect 69 (v0=137285), euler #=-13 (154997,464625,309615) : difference with theory (-12) = 1 

CORRECTING DEFECT 70 (vertices=36, convex hull=33, v0=137459)
After retessellation of defect 70 (v0=137459), euler #=-12 (154997,464637,309628) : difference with theory (-11) = 1 

CORRECTING DEFECT 71 (vertices=67, convex hull=74, v0=144145)
After retessellation of defect 71 (v0=144145), euler #=-10 (155022,464748,309716) : difference with theory (-10) = 0 

CORRECTING DEFECT 72 (vertices=41, convex hull=57, v0=146942)
After retessellation of defect 72 (v0=146942), euler #=-9 (155027,464790,309754) : difference with theory (-9) = 0 

CORRECTING DEFECT 73 (vertices=60, convex hull=37, v0=152916)
After retessellation of defect 73 (v0=152916), euler #=-8 (155032,464819,309779) : difference with theory (-8) = 0 

CORRECTING DEFECT 74 (vertices=146, convex hull=75, v0=154988)
After retessellation of defect 74 (v0=154988), euler #=-7 (155041,464883,309835) : difference with theory (-7) = 0 

CORRECTING DEFECT 75 (vertices=117, convex hull=29, v0=155929)
After retessellation of defect 75 (v0=155929), euler #=-6 (155045,464904,309853) : difference with theory (-6) = 0 

CORRECTING DEFECT 76 (vertices=78, convex hull=105, v0=156171)
After retessellation of defect 76 (v0=156171), euler #=-5 (155070,465026,309951) : difference with theory (-5) = 0 

CORRECTING DEFECT 77 (vertices=22, convex hull=62, v0=157221)
After retessellation of defect 77 (v0=157221), euler #=-4 (155081,465083,309998) : difference with theory (-4) = 0 

CORRECTING DEFECT 78 (vertices=34, convex hull=59, v0=158362)
After retessellation of defect 78 (v0=158362), euler #=-3 (155090,465131,310038) : difference with theory (-3) = 0 

CORRECTING DEFECT 79 (vertices=48, convex hull=72, v0=161584)
After retessellation of defect 79 (v0=161584), euler #=-2 (155108,465217,310107) : difference with theory (-2) = 0 

CORRECTING DEFECT 80 (vertices=77, convex hull=41, v0=161773)
After retessellation of defect 80 (v0=161773), euler #=-1 (155115,465258,310142) : difference with theory (-1) = 0 

CORRECTING DEFECT 81 (vertices=21, convex hull=51, v0=164659)
After retessellation of defect 81 (v0=164659), euler #=0 (155122,465300,310178) : difference with theory (0) = 0 

CORRECTING DEFECT 82 (vertices=33, convex hull=74, v0=165645)
After retessellation of defect 82 (v0=165645), euler #=1 (155141,465387,310247) : difference with theory (1) = 0 

CORRECTING DEFECT 83 (vertices=28, convex hull=77, v0=165991)
After retessellation of defect 83 (v0=165991), euler #=2 (155154,465456,310304) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.27 (0.03-->14.98) (max @ vno 111305 --> 119395)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.27 (0.03-->14.98) (max @ vno 111305 --> 119395)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
287 mutations (34.7%), 541 crossovers (65.3%), 1134 vertices were eliminated
building final representation...
11304 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=155154, nf=310304, ne=465456, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 80.5 minutes
0 defective edges
removing intersecting faces
000: 960 intersecting
001: 26 intersecting
002: 2 intersecting
mris_fix_topology utimesec    4829.249842
mris_fix_topology stimesec    0.801878
mris_fix_topology ru_maxrss   526340
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   61667
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23040
mris_fix_topology ru_oublock  15288
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    594
mris_fix_topology ru_nivcsw   10302
FSRUNTIME@ mris_fix_topology rh  1.3413 hours 1 threads
PIDs (12733 12736) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 153035 - 459099 + 306066 = 2 --> 0 holes
      F =2V-4:          306066 = 306070-4 (0)
      2E=3F:            918198 = 918198 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 155154 - 465456 + 310304 = 2 --> 0 holes
      F =2V-4:          310304 = 310308-4 (0)
      2E=3F:            930912 = 930912 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

intersection removal took 0.01 hours
removing intersecting faces
000: 357 intersecting
001: 101 intersecting
002: 93 intersecting
003: 80 intersecting
004: 61 intersecting
005: 60 intersecting
006: 49 intersecting
expanding nbhd size to 2
007: 59 intersecting
008: 54 intersecting
009: 46 intersecting
010: 45 intersecting
011: 40 intersecting
012: 34 intersecting
013: 31 intersecting
014: 29 intersecting
015: 24 intersecting
016: 20 intersecting
017: 19 intersecting
018: 14 intersecting
019: 11 intersecting
020: 5 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 207 intersecting
001: 13 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 05:04:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050310 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 05:04:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050310 rh 

Waiting for PID 16242 of (16242 16249) to complete...
Waiting for PID 16249 of (16242 16249) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050310 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-6.0.0/0050310/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
14638 bright wm thresholded.
5630 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.orig...
computing class statistics...
border white:    290293 voxels (1.73%)
border gray      364215 voxels (2.17%)
WM (95.0): 96.0 +- 8.2 [70.0 --> 110.0]
GM (73.0) : 72.1 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70)
setting MAX_BORDER_WHITE to 108.2 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 49.0 (was 40)
setting MAX_GRAY to 91.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.9 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.01-->8.46) (max @ vno 123146 --> 152621)
face area 0.28 +- 0.13 (0.00-->5.82)
mean absolute distance = 0.68 +- 0.84
4487 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=69+-7.0
mean inside = 92.1, mean outside = 76.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=80.4, 210 (210) missing vertices, mean dist 0.3 [0.6 (%35.8)->0.8 (%64.2))]
%76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.10-->8.46) (max @ vno 123146 --> 152621)
face area 0.28 +- 0.14 (0.00-->5.40)
mean absolute distance = 0.37 +- 0.59
4450 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3022447.2, rms=8.730
001: dt: 0.5000, sse=1745970.6, rms=6.135 (29.733%)
002: dt: 0.5000, sse=1269184.6, rms=4.669 (23.897%)
003: dt: 0.5000, sse=1064708.5, rms=3.892 (16.637%)
004: dt: 0.5000, sse=973236.1, rms=3.477 (10.652%)
005: dt: 0.5000, sse=928769.5, rms=3.252 (6.481%)
006: dt: 0.5000, sse=904237.9, rms=3.120 (4.065%)
007: dt: 0.5000, sse=900493.6, rms=3.031 (2.830%)
rms = 2.99, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=883308.5, rms=2.990 (1.383%)
009: dt: 0.2500, sse=763421.0, rms=2.016 (32.576%)
010: dt: 0.2500, sse=728831.2, rms=1.817 (9.842%)
011: dt: 0.2500, sse=722383.2, rms=1.744 (4.034%)
rms = 1.71, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=718451.0, rms=1.708 (2.084%)
rms = 1.68, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=714085.2, rms=1.678 (1.736%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=83.1, 199 (62) missing vertices, mean dist -0.2 [0.4 (%72.9)->0.3 (%27.1))]
%83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.07-->8.28) (max @ vno 123146 --> 152621)
face area 0.35 +- 0.17 (0.00-->8.37)
mean absolute distance = 0.27 +- 0.43
4430 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1287111.2, rms=4.126
014: dt: 0.5000, sse=989215.6, rms=2.565 (37.838%)
015: dt: 0.5000, sse=959155.7, rms=2.411 (5.997%)
rms = 2.38, time step reduction 1 of 3 to 0.250...
016: dt: 0.5000, sse=950605.2, rms=2.383 (1.136%)
017: dt: 0.2500, sse=863952.8, rms=1.569 (34.182%)
018: dt: 0.2500, sse=848597.9, rms=1.412 (9.990%)
rms = 1.39, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=843720.4, rms=1.391 (1.521%)
rms = 1.35, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=839397.2, rms=1.355 (2.591%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=84.6, 193 (37) missing vertices, mean dist -0.1 [0.3 (%64.3)->0.3 (%35.7))]
%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 0.90 +- 0.26 (0.06-->8.24) (max @ vno 123146 --> 152621)
face area 0.34 +- 0.17 (0.00-->8.88)
mean absolute distance = 0.25 +- 0.38
3989 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=950952.6, rms=2.482
021: dt: 0.5000, sse=900250.0, rms=2.011 (18.951%)
rms = 2.13, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=841788.9, rms=1.535 (23.680%)
023: dt: 0.2500, sse=822299.9, rms=1.315 (14.331%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=818671.5, rms=1.265 (3.784%)
rms = 1.23, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=822289.1, rms=1.233 (2.558%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=85.1, 229 (24) missing vertices, mean dist -0.0 [0.3 (%53.9)->0.2 (%46.1))]
%89 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-6.0.0/0050310/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=835451.9, rms=1.487
026: dt: 0.5000, sse=823994.9, rms=1.351 (9.100%)
rms = 1.71, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=796689.9, rms=1.079 (20.117%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=793511.7, rms=1.056 (2.166%)
029: dt: 0.1250, sse=788391.0, rms=0.997 (5.578%)
rms = 0.98, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=790453.9, rms=0.983 (1.460%)
positioning took 0.6 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 6413 vertices
erasing segment 0 (vno[0] = 30436)
erasing segment 1 (vno[0] = 38939)
erasing segment 2 (vno[0] = 44172)
erasing segment 4 (vno[0] = 55344)
erasing segment 5 (vno[0] = 101196)
erasing segment 6 (vno[0] = 106341)
erasing segment 7 (vno[0] = 107649)
erasing segment 8 (vno[0] = 108639)
erasing segment 9 (vno[0] = 108711)
erasing segment 10 (vno[0] = 109923)
erasing segment 11 (vno[0] = 109925)
erasing segment 12 (vno[0] = 109993)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.area
vertex spacing 0.90 +- 0.26 (0.04-->7.94) (max @ vno 70000 --> 151789)
face area 0.34 +- 0.17 (0.00-->8.85)
refinement took 5.4 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050310 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-6.0.0/0050310/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
14638 bright wm thresholded.
5630 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.orig...
computing class statistics...
border white:    290293 voxels (1.73%)
border gray      364215 voxels (2.17%)
WM (95.0): 96.0 +- 8.2 [70.0 --> 110.0]
GM (73.0) : 72.1 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70)
setting MAX_BORDER_WHITE to 109.2 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 49.0 (was 40)
setting MAX_GRAY to 92.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.9 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.03-->6.83) (max @ vno 154377 --> 154379)
face area 0.28 +- 0.13 (0.00-->9.68)
mean absolute distance = 0.67 +- 0.82
4885 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.8,    GM=69+-7.0
mean inside = 92.0, mean outside = 76.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=80.8, 273 (273) missing vertices, mean dist 0.3 [0.6 (%37.2)->0.7 (%62.8))]
%77 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.26 (0.05-->6.75) (max @ vno 154377 --> 154379)
face area 0.28 +- 0.14 (0.00-->7.56)
mean absolute distance = 0.38 +- 0.62
5440 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2955437.2, rms=8.697
001: dt: 0.5000, sse=1726806.2, rms=6.037 (30.586%)
002: dt: 0.5000, sse=1227540.0, rms=4.468 (25.990%)
003: dt: 0.5000, sse=1025784.9, rms=3.650 (18.300%)
004: dt: 0.5000, sse=939285.8, rms=3.229 (11.540%)
005: dt: 0.5000, sse=916791.1, rms=3.063 (5.157%)
006: dt: 0.5000, sse=893234.4, rms=2.931 (4.279%)
007: dt: 0.5000, sse=887472.3, rms=2.879 (1.796%)
rms = 2.84, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=873224.6, rms=2.841 (1.326%)
009: dt: 0.2500, sse=744356.8, rms=1.837 (35.336%)
010: dt: 0.2500, sse=725668.9, rms=1.639 (10.788%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=719134.4, rms=1.600 (2.350%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=715481.4, rms=1.565 (2.181%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=83.4, 178 (61) missing vertices, mean dist -0.2 [0.4 (%72.2)->0.3 (%27.8))]
%84 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.07-->6.68) (max @ vno 154377 --> 154379)
face area 0.35 +- 0.17 (0.00-->9.49)
mean absolute distance = 0.28 +- 0.44
4468 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1287346.2, rms=4.070
013: dt: 0.5000, sse=991324.8, rms=2.521 (38.074%)
014: dt: 0.5000, sse=964344.6, rms=2.369 (6.001%)
rms = 2.35, time step reduction 1 of 3 to 0.250...
015: dt: 0.5000, sse=956343.2, rms=2.353 (0.684%)
016: dt: 0.2500, sse=868624.8, rms=1.591 (32.389%)
017: dt: 0.2500, sse=855183.1, rms=1.455 (8.517%)
rms = 1.42, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=851240.9, rms=1.419 (2.530%)
rms = 1.38, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=847067.8, rms=1.379 (2.773%)
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 2 vertex label from ripped group
removing 1 vertex label from ripped group
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=84.8, 198 (35) missing vertices, mean dist -0.1 [0.3 (%63.7)->0.3 (%36.3))]
%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 0.90 +- 0.25 (0.05-->6.62) (max @ vno 154377 --> 154379)
face area 0.34 +- 0.17 (0.00-->9.33)
mean absolute distance = 0.26 +- 0.38
4304 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=966584.5, rms=2.531
020: dt: 0.5000, sse=918147.9, rms=1.978 (21.868%)
rms = 2.07, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=850207.9, rms=1.544 (21.943%)
022: dt: 0.2500, sse=841724.3, rms=1.332 (13.734%)
023: dt: 0.2500, sse=827184.8, rms=1.273 (4.385%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=826963.4, rms=1.273 (0.022%)
rms = 1.23, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=823214.4, rms=1.230 (3.389%)
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 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=85.3, 241 (26) missing vertices, mean dist -0.0 [0.3 (%53.9)->0.3 (%46.1))]
%89 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-6.0.0/0050310/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=838298.5, rms=1.494
026: dt: 0.5000, sse=835301.1, rms=1.353 (9.465%)
rms = 1.70, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=804569.9, rms=1.084 (19.865%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=801605.9, rms=1.056 (2.558%)
029: dt: 0.1250, sse=817972.5, rms=0.995 (5.850%)
rms = 0.97, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=795803.6, rms=0.974 (2.102%)
positioning took 0.6 minutes
generating cortex label...
15 non-cortical segments detected
only using segment with 6728 vertices
erasing segment 0 (vno[0] = 47508)
erasing segment 1 (vno[0] = 51387)
erasing segment 3 (vno[0] = 65292)
erasing segment 4 (vno[0] = 105488)
erasing segment 5 (vno[0] = 106805)
erasing segment 6 (vno[0] = 109091)
erasing segment 7 (vno[0] = 110179)
erasing segment 8 (vno[0] = 110226)
erasing segment 9 (vno[0] = 111347)
erasing segment 10 (vno[0] = 112455)
erasing segment 11 (vno[0] = 112465)
erasing segment 12 (vno[0] = 114601)
erasing segment 13 (vno[0] = 154467)
erasing segment 14 (vno[0] = 154516)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.area
vertex spacing 0.90 +- 0.26 (0.03-->6.64) (max @ vno 154377 --> 154379)
face area 0.34 +- 0.17 (0.00-->9.13)
refinement took 5.5 minutes
PIDs (16242 16249) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 05:10:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 05:10:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

Waiting for PID 16530 of (16530 16533) to complete...
Waiting for PID 16533 of (16530 16533) 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 (16530 16533) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 05:10:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 05:10:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 16578 of (16578 16581) to complete...
Waiting for PID 16581 of (16578 16581) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 46.8 mm, total surface area = 94098 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.183 (target=0.015)   
step 005: RMS=0.131 (target=0.015)   
step 010: RMS=0.102 (target=0.015)   
step 015: RMS=0.086 (target=0.015)   
step 020: RMS=0.072 (target=0.015)   
step 025: RMS=0.062 (target=0.015)   
step 030: RMS=0.054 (target=0.015)   
step 035: RMS=0.046 (target=0.015)   
step 040: RMS=0.040 (target=0.015)   
step 045: RMS=0.036 (target=0.015)   
step 050: RMS=0.033 (target=0.015)   
step 055: RMS=0.031 (target=0.015)   
step 060: RMS=0.029 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    47.470783
mris_inflate stimesec    0.102984
mris_inflate ru_maxrss   224088
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32580
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11984
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2043
mris_inflate ru_nivcsw   4077

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 47.2 mm, total surface area = 94692 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.181 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.072 (target=0.015)   
step 025: RMS=0.062 (target=0.015)   
step 030: RMS=0.054 (target=0.015)   
step 035: RMS=0.048 (target=0.015)   
step 040: RMS=0.043 (target=0.015)   
step 045: RMS=0.040 (target=0.015)   
step 050: RMS=0.036 (target=0.015)   
step 055: RMS=0.034 (target=0.015)   
step 060: RMS=0.031 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    47.905717
mris_inflate stimesec    0.096985
mris_inflate ru_maxrss   226980
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33302
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10920
mris_inflate ru_oublock  12152
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2319
mris_inflate ru_nivcsw   3602
PIDs (16578 16581) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 05:10:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 05:10:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 16674 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16677 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16680 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16683 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16686 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16689 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16692 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16695 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16700 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16703 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16706 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...
Waiting for PID 16710 of (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 22.322*4pi (280.502) --> -21 handles
ICI = 232.1, FI = 2071.1, variation=33526.695
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
223 vertices thresholded to be in k1 ~ [-0.25 2.99], k2 ~ [-0.15 0.08]
total integrated curvature = 0.239*4pi (3.000) --> 1 handles
ICI = 1.5, FI = 10.1, variation=173.958
141 vertices thresholded to be in [-0.02 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
111 vertices thresholded to be in [-0.15 0.58]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 24.531*4pi (308.266) --> -24 handles
ICI = 237.6, FI = 2061.8, variation=33608.969
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
224 vertices thresholded to be in k1 ~ [-0.42 1.28], k2 ~ [-0.17 0.21]
total integrated curvature = 0.227*4pi (2.850) --> 1 handles
ICI = 1.5, FI = 12.0, variation=199.368
164 vertices thresholded to be in [-0.08 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
121 vertices thresholded to be in [-0.19 0.29]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.025
done.
PIDs (16674 16677 16680 16683 16686 16689 16692 16695 16700 16703 16706 16710) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 05:12:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050310 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      [ 0050310/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                      [ 295 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.565602
WARN:    S explicit min:                          0.000000	vertex = 495

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 05:12:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050310 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      [ 0050310/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                      [ 293 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.634375
WARN:    S explicit min:                          0.000000	vertex = 702
#--------------------------------------------
#@# Sphere lh Sun Oct  8 05:12:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 05:12:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 16866 of (16866 16869) to complete...
Waiting for PID 16869 of (16866 16869) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0.280...
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 %20.81
pass 1: epoch 2 of 3 starting distance error %20.74
unfolding complete - removing small folds...
starting distance error %20.62
removing remaining folds...
final distance error %20.65
MRISunfold() return, current seed 1234
-01: dt=0.0000, 301 negative triangles
213: dt=0.9900, 301 negative triangles
214: dt=0.9900, 170 negative triangles
215: dt=0.9900, 151 negative triangles
216: dt=0.9900, 131 negative triangles
217: dt=0.9900, 109 negative triangles
218: dt=0.9900, 103 negative triangles
219: dt=0.9900, 92 negative triangles
220: dt=0.9900, 88 negative triangles
221: dt=0.9900, 87 negative triangles
222: dt=0.9900, 95 negative triangles
223: dt=0.9900, 79 negative triangles
224: dt=0.9900, 72 negative triangles
225: dt=0.9900, 65 negative triangles
226: dt=0.9900, 65 negative triangles
227: dt=0.9900, 59 negative triangles
228: dt=0.9900, 56 negative triangles
229: dt=0.9900, 51 negative triangles
230: dt=0.9900, 43 negative triangles
231: dt=0.9900, 45 negative triangles
232: dt=0.9900, 38 negative triangles
233: dt=0.9900, 37 negative triangles
234: dt=0.9900, 31 negative triangles
235: dt=0.9900, 38 negative triangles
236: dt=0.9900, 30 negative triangles
237: dt=0.9900, 31 negative triangles
238: dt=0.9900, 34 negative triangles
239: dt=0.9900, 29 negative triangles
240: dt=0.9900, 24 negative triangles
241: dt=0.9900, 28 negative triangles
242: dt=0.9900, 23 negative triangles
243: dt=0.9900, 21 negative triangles
244: dt=0.9900, 23 negative triangles
245: dt=0.9900, 24 negative triangles
246: dt=0.9900, 20 negative triangles
247: dt=0.9900, 23 negative triangles
248: dt=0.9900, 17 negative triangles
249: dt=0.9900, 18 negative triangles
250: dt=0.9900, 19 negative triangles
251: dt=0.9900, 15 negative triangles
252: dt=0.9900, 18 negative triangles
253: dt=0.9900, 20 negative triangles
254: dt=0.9900, 15 negative triangles
255: dt=0.9900, 17 negative triangles
256: dt=0.9900, 18 negative triangles
257: dt=0.9900, 15 negative triangles
258: dt=0.9900, 17 negative triangles
259: dt=0.9900, 18 negative triangles
260: dt=0.9900, 15 negative triangles
261: dt=0.9405, 16 negative triangles
262: dt=0.9405, 19 negative triangles
263: dt=0.9405, 15 negative triangles
264: dt=0.9405, 15 negative triangles
265: dt=0.9405, 17 negative triangles
266: dt=0.9405, 14 negative triangles
267: dt=0.9405, 15 negative triangles
268: dt=0.9405, 17 negative triangles
269: dt=0.9405, 14 negative triangles
270: dt=0.9405, 14 negative triangles
271: dt=0.9405, 17 negative triangles
272: dt=0.9405, 12 negative triangles
273: dt=0.9405, 12 negative triangles
274: dt=0.9405, 13 negative triangles
275: dt=0.9405, 15 negative triangles
276: dt=0.9405, 10 negative triangles
277: dt=0.9405, 7 negative triangles
278: dt=0.9405, 11 negative triangles
279: dt=0.9405, 11 negative triangles
280: dt=0.9405, 8 negative triangles
281: dt=0.9405, 7 negative triangles
282: dt=0.9405, 9 negative triangles
283: dt=0.9405, 9 negative triangles
284: dt=0.9405, 6 negative triangles
285: dt=0.9405, 6 negative triangles
286: dt=0.9405, 7 negative triangles
287: dt=0.9405, 5 negative triangles
288: dt=0.9405, 5 negative triangles
289: dt=0.9405, 5 negative triangles
290: dt=0.9405, 2 negative triangles
291: dt=0.9405, 2 negative triangles
292: dt=0.9405, 2 negative triangles
293: dt=0.9405, 2 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.06 hours
mris_sphere utimesec    3831.176572
mris_sphere stimesec    1.338796
mris_sphere ru_maxrss   314448
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55306
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10856
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    135543
mris_sphere ru_nivcsw   324365
FSRUNTIME@ mris_sphere  1.0643 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0.277...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.14
pass 1: epoch 2 of 3 starting distance error %21.10
unfolding complete - removing small folds...
starting distance error %20.89
removing remaining folds...
final distance error %20.92
MRISunfold() return, current seed 1234
-01: dt=0.0000, 276 negative triangles
209: dt=0.9900, 276 negative triangles
210: dt=0.9900, 173 negative triangles
211: dt=0.9900, 147 negative triangles
212: dt=0.9900, 119 negative triangles
213: dt=0.9900, 102 negative triangles
214: dt=0.9900, 107 negative triangles
215: dt=0.9900, 93 negative triangles
216: dt=0.9900, 99 negative triangles
217: dt=0.9900, 92 negative triangles
218: dt=0.9900, 98 negative triangles
219: dt=0.9900, 90 negative triangles
220: dt=0.9900, 93 negative triangles
221: dt=0.9900, 78 negative triangles
222: dt=0.9900, 93 negative triangles
223: dt=0.9900, 82 negative triangles
224: dt=0.9900, 85 negative triangles
225: dt=0.9900, 70 negative triangles
226: dt=0.9900, 65 negative triangles
227: dt=0.9900, 56 negative triangles
228: dt=0.9900, 55 negative triangles
229: dt=0.9900, 55 negative triangles
230: dt=0.9900, 57 negative triangles
231: dt=0.9900, 43 negative triangles
232: dt=0.9900, 46 negative triangles
233: dt=0.9900, 48 negative triangles
234: dt=0.9900, 44 negative triangles
235: dt=0.9900, 37 negative triangles
236: dt=0.9900, 34 negative triangles
237: dt=0.9900, 36 negative triangles
238: dt=0.9900, 21 negative triangles
239: dt=0.9900, 26 negative triangles
240: dt=0.9900, 28 negative triangles
241: dt=0.9900, 22 negative triangles
242: dt=0.9900, 20 negative triangles
243: dt=0.9900, 16 negative triangles
244: dt=0.9900, 12 negative triangles
245: dt=0.9900, 15 negative triangles
246: dt=0.9900, 15 negative triangles
247: dt=0.9900, 16 negative triangles
248: dt=0.9900, 15 negative triangles
249: dt=0.9900, 9 negative triangles
250: dt=0.9900, 14 negative triangles
251: dt=0.9900, 10 negative triangles
252: dt=0.9900, 8 negative triangles
253: dt=0.9900, 13 negative triangles
254: dt=0.9900, 10 negative triangles
255: dt=0.9900, 8 negative triangles
256: dt=0.9900, 13 negative triangles
257: dt=0.9900, 7 negative triangles
258: dt=0.9900, 11 negative triangles
259: dt=0.9900, 10 negative triangles
260: dt=0.9900, 7 negative triangles
261: dt=0.9900, 5 negative triangles
262: dt=0.9900, 4 negative triangles
263: dt=0.9900, 2 negative triangles
264: dt=0.9900, 4 negative triangles
265: dt=0.9900, 2 negative triangles
266: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.07 hours
mris_sphere utimesec    3900.499034
mris_sphere stimesec    1.713739
mris_sphere ru_maxrss   318720
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   56373
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10976
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    141254
mris_sphere ru_nivcsw   318709
FSRUNTIME@ mris_sphere  1.0746 hours 1 threads
PIDs (16866 16869) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 06:17:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 06:17:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 19554 of (19554 19557) to complete...
Waiting for PID 19557 of (19554 19557) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 5.852
curvature mean = 0.035, std = 0.815
curvature mean = 0.016, std = 0.856
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, 0.00, 16.00) sse = 303803.1, tmin=1.1500
  d=16.00 min @ (0.00, -4.00, -4.00) sse = 285608.6, tmin=3.4909
  d=8.00 min @ (2.00, 2.00, 2.00) sse = 279221.4, tmin=4.7020
  d=4.00 min @ (0.00, -1.00, -1.00) sse = 277049.1, tmin=5.9288
  d=2.00 min @ (-0.50, 0.00, 0.50) sse = 276756.8, tmin=7.1545
  d=1.00 min @ (0.00, 0.00, -0.25) sse = 276683.6, tmin=8.3700
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   9.58 min
curvature mean = 0.013, std = 0.829
curvature mean = 0.006, std = 0.942
curvature mean = 0.010, std = 0.838
curvature mean = 0.002, std = 0.974
curvature mean = 0.009, std = 0.841
curvature mean = 0.001, std = 0.988
2 Reading smoothwm
curvature mean = -0.038, std = 0.325
curvature mean = 0.041, std = 0.246
curvature mean = 0.073, std = 0.309
curvature mean = 0.035, std = 0.303
curvature mean = 0.055, std = 0.465
curvature mean = 0.034, std = 0.330
curvature mean = 0.033, std = 0.599
curvature mean = 0.034, std = 0.341
curvature mean = 0.012, std = 0.716
MRISregister() return, current seed 0
-01: dt=0.0000, 132 negative triangles
135: dt=0.9900, 132 negative triangles
expanding nbhd size to 1
136: dt=0.9900, 157 negative triangles
137: dt=0.9900, 129 negative triangles
138: dt=0.9900, 129 negative triangles
139: dt=0.9900, 133 negative triangles
140: dt=0.9900, 129 negative triangles
141: dt=0.9900, 127 negative triangles
142: dt=0.9900, 119 negative triangles
143: dt=0.9900, 119 negative triangles
144: dt=0.9900, 113 negative triangles
145: dt=0.9900, 108 negative triangles
146: dt=0.9900, 106 negative triangles
147: dt=0.9900, 103 negative triangles
148: dt=0.9900, 95 negative triangles
149: dt=0.9900, 91 negative triangles
150: dt=0.9900, 86 negative triangles
151: dt=0.9900, 85 negative triangles
152: dt=0.9900, 81 negative triangles
153: dt=0.9900, 69 negative triangles
154: dt=0.9900, 65 negative triangles
155: dt=0.9900, 66 negative triangles
156: dt=0.9900, 68 negative triangles
157: dt=0.9900, 64 negative triangles
158: dt=0.9900, 62 negative triangles
159: dt=0.9900, 59 negative triangles
160: dt=0.9900, 61 negative triangles
161: dt=0.9900, 58 negative triangles
162: dt=0.9900, 50 negative triangles
163: dt=0.9900, 44 negative triangles
164: dt=0.9900, 43 negative triangles
165: dt=0.9900, 43 negative triangles
166: dt=0.9900, 44 negative triangles
167: dt=0.9900, 41 negative triangles
168: dt=0.9900, 44 negative triangles
169: dt=0.9900, 45 negative triangles
170: dt=0.9900, 40 negative triangles
171: dt=0.9900, 39 negative triangles
172: dt=0.9900, 37 negative triangles
173: dt=0.9900, 31 negative triangles
174: dt=0.9900, 29 negative triangles
175: dt=0.9900, 30 negative triangles
176: dt=0.9900, 30 negative triangles
177: dt=0.9900, 31 negative triangles
178: dt=0.9900, 32 negative triangles
179: dt=0.9900, 30 negative triangles
180: dt=0.9900, 24 negative triangles
181: dt=0.9900, 24 negative triangles
182: dt=0.9900, 25 negative triangles
183: dt=0.9900, 27 negative triangles
184: dt=0.9900, 24 negative triangles
185: dt=0.9900, 23 negative triangles
186: dt=0.9900, 22 negative triangles
187: dt=0.9900, 24 negative triangles
188: dt=0.9900, 22 negative triangles
189: dt=0.9900, 20 negative triangles
190: dt=0.9900, 20 negative triangles
191: dt=0.9900, 20 negative triangles
192: dt=0.9900, 18 negative triangles
193: dt=0.9900, 19 negative triangles
194: dt=0.9900, 16 negative triangles
195: dt=0.9900, 17 negative triangles
196: dt=0.9900, 14 negative triangles
197: dt=0.9900, 11 negative triangles
198: dt=0.9900, 11 negative triangles
199: dt=0.9900, 9 negative triangles
200: dt=0.9900, 9 negative triangles
201: dt=0.9900, 9 negative triangles
202: dt=0.9900, 10 negative triangles
203: dt=0.9900, 7 negative triangles
204: dt=0.9900, 7 negative triangles
205: dt=0.9900, 7 negative triangles
206: dt=0.9900, 5 negative triangles
207: dt=0.9900, 6 negative triangles
208: dt=0.9900, 6 negative triangles
209: dt=0.9900, 3 negative triangles
210: dt=0.9900, 5 negative triangles
211: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.53 hours
mris_register utimesec    5512.981899
mris_register stimesec    4.434325
mris_register ru_maxrss   276676
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   41427
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10856
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    406865
mris_register ru_nivcsw   266645
FSRUNTIME@ mris_register  1.5325 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 5.823
curvature mean = 0.030, std = 0.811
curvature mean = 0.018, std = 0.858
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 416170.5, tmin=1.1663
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 314138.7, tmin=2.3630
  d=16.00 min @ (0.00, 0.00, -4.00) sse = 310206.8, tmin=3.5702
  d=8.00 min @ (2.00, 0.00, 2.00) sse = 305562.3, tmin=4.7805
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 304284.7, tmin=6.0041
  d=2.00 min @ (0.00, -0.50, 0.00) sse = 304001.2, tmin=7.2268
  d=1.00 min @ (0.00, 0.25, -0.25) sse = 303941.9, tmin=8.4496
  d=0.50 min @ (0.00, -0.12, 0.12) sse = 303914.6, tmin=9.6769
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   9.68 min
curvature mean = 0.003, std = 0.822
curvature mean = 0.007, std = 0.943
curvature mean = -0.000, std = 0.831
curvature mean = 0.003, std = 0.976
curvature mean = -0.002, std = 0.832
curvature mean = 0.001, std = 0.990
2 Reading smoothwm
curvature mean = -0.041, std = 0.348
curvature mean = 0.035, std = 0.239
curvature mean = 0.071, std = 0.289
curvature mean = 0.029, std = 0.296
curvature mean = 0.052, std = 0.434
curvature mean = 0.028, std = 0.322
curvature mean = 0.032, std = 0.557
curvature mean = 0.028, std = 0.333
curvature mean = 0.013, std = 0.669
MRISregister() return, current seed 0
-01: dt=0.0000, 162 negative triangles
137: dt=0.9900, 162 negative triangles
expanding nbhd size to 1
138: dt=0.9900, 200 negative triangles
139: dt=0.9900, 140 negative triangles
140: dt=0.9900, 152 negative triangles
141: dt=0.9900, 147 negative triangles
142: dt=0.9900, 141 negative triangles
143: dt=0.9900, 134 negative triangles
144: dt=0.9900, 131 negative triangles
145: dt=0.9900, 117 negative triangles
146: dt=0.9900, 120 negative triangles
147: dt=0.9900, 105 negative triangles
148: dt=0.9900, 103 negative triangles
149: dt=0.9900, 92 negative triangles
150: dt=0.9900, 83 negative triangles
151: dt=0.9900, 84 negative triangles
152: dt=0.9900, 75 negative triangles
153: dt=0.9900, 71 negative triangles
154: dt=0.9900, 63 negative triangles
155: dt=0.9900, 68 negative triangles
156: dt=0.9900, 63 negative triangles
157: dt=0.9900, 59 negative triangles
158: dt=0.9900, 60 negative triangles
159: dt=0.9900, 60 negative triangles
160: dt=0.9900, 57 negative triangles
161: dt=0.9900, 59 negative triangles
162: dt=0.9900, 59 negative triangles
163: dt=0.9900, 56 negative triangles
164: dt=0.9900, 55 negative triangles
165: dt=0.9900, 54 negative triangles
166: dt=0.9900, 53 negative triangles
167: dt=0.9900, 55 negative triangles
168: dt=0.9900, 50 negative triangles
169: dt=0.9900, 51 negative triangles
170: dt=0.9900, 45 negative triangles
171: dt=0.9900, 47 negative triangles
172: dt=0.9900, 44 negative triangles
173: dt=0.9900, 46 negative triangles
174: dt=0.9900, 44 negative triangles
175: dt=0.9900, 47 negative triangles
176: dt=0.9900, 43 negative triangles
177: dt=0.9900, 44 negative triangles
178: dt=0.9900, 40 negative triangles
179: dt=0.9900, 42 negative triangles
180: dt=0.9900, 38 negative triangles
181: dt=0.9900, 39 negative triangles
182: dt=0.9900, 37 negative triangles
183: dt=0.9900, 37 negative triangles
184: dt=0.9900, 37 negative triangles
185: dt=0.9900, 39 negative triangles
186: dt=0.9900, 37 negative triangles
187: dt=0.9900, 35 negative triangles
188: dt=0.9900, 34 negative triangles
189: dt=0.9900, 34 negative triangles
190: dt=0.9900, 32 negative triangles
191: dt=0.9900, 35 negative triangles
192: dt=0.9900, 32 negative triangles
193: dt=0.9900, 30 negative triangles
194: dt=0.9900, 31 negative triangles
195: dt=0.9900, 31 negative triangles
196: dt=0.9900, 30 negative triangles
197: dt=0.9900, 30 negative triangles
198: dt=0.9900, 27 negative triangles
199: dt=0.9900, 27 negative triangles
200: dt=0.9900, 25 negative triangles
201: dt=0.9900, 23 negative triangles
202: dt=0.9900, 20 negative triangles
203: dt=0.9900, 19 negative triangles
204: dt=0.9900, 19 negative triangles
205: dt=0.9900, 18 negative triangles
206: dt=0.9900, 19 negative triangles
207: dt=0.9900, 21 negative triangles
208: dt=0.9900, 20 negative triangles
209: dt=0.9900, 17 negative triangles
210: dt=0.9900, 13 negative triangles
211: dt=0.9900, 11 negative triangles
212: dt=0.9900, 12 negative triangles
213: dt=0.9900, 11 negative triangles
214: dt=0.9900, 12 negative triangles
215: dt=0.9900, 11 negative triangles
216: dt=0.9900, 14 negative triangles
217: dt=0.9900, 13 negative triangles
218: dt=0.9900, 12 negative triangles
219: dt=0.9900, 8 negative triangles
220: dt=0.9900, 5 negative triangles
221: dt=0.9900, 5 negative triangles
222: dt=0.9900, 3 negative triangles
223: dt=0.9900, 3 negative triangles
224: dt=0.9900, 2 negative triangles
225: dt=0.9900, 3 negative triangles
226: dt=0.9900, 2 negative triangles
227: dt=0.9900, 2 negative triangles
228: dt=0.9900, 2 negative triangles
229: dt=0.9900, 2 negative triangles
230: dt=0.9900, 2 negative triangles
231: dt=0.9900, 2 negative triangles
232: dt=0.9900, 2 negative triangles
233: dt=0.9900, 2 negative triangles
234: dt=0.9900, 1 negative triangles
235: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.69 hours
mris_register utimesec    6427.395887
mris_register stimesec    4.758276
mris_register ru_maxrss   281144
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39853
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  11024
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    459856
mris_register ru_nivcsw   269573
FSRUNTIME@ mris_register  1.6945 hours 1 threads
PIDs (19554 19557) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 07:58:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 07:58:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

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

Waiting for PID 23595 of (23595 23598) to complete...
Waiting for PID 23598 of (23595 23598) 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 (23595 23598) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 07:58:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 07:58:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 23642 of (23642 23645) to complete...
Waiting for PID 23645 of (23642 23645) 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 (23642 23645) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 07:58:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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 07:58:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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 23686 of (23686 23689) to complete...
Waiting for PID 23689 of (23686 23689) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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...
1584 labels changed using aseg
relabeling using gibbs priors...
000:   3481 changed, 153035 examined...
001:    783 changed, 14450 examined...
002:    182 changed, 4458 examined...
003:     70 changed, 1118 examined...
004:     35 changed, 417 examined...
005:      9 changed, 216 examined...
006:      4 changed, 54 examined...
007:      5 changed, 25 examined...
008:      5 changed, 28 examined...
009:      1 changed, 30 examined...
010:      1 changed, 6 examined...
011:      2 changed, 9 examined...
012:      1 changed, 6 examined...
013:      0 changed, 9 examined...
259 labels changed using aseg
000: 130 total segments, 85 labels (626 vertices) changed
001: 42 total segments, 5 labels (27 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1917 vertices marked for relabeling...
1917 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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...
1285 labels changed using aseg
relabeling using gibbs priors...
000:   3174 changed, 155154 examined...
001:    709 changed, 13608 examined...
002:    145 changed, 4020 examined...
003:     54 changed, 916 examined...
004:     17 changed, 323 examined...
005:      7 changed, 99 examined...
006:      1 changed, 42 examined...
007:      0 changed, 5 examined...
129 labels changed using aseg
000: 99 total segments, 62 labels (335 vertices) changed
001: 38 total segments, 1 labels (1 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 13 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1516 vertices marked for relabeling...
1516 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 16 seconds.
PIDs (23686 23689) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 07:59:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050310 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 07:59:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050310 rh 

Waiting for PID 23743 of (23743 23746) to complete...
Waiting for PID 23746 of (23743 23746) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050310 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-6.0.0/0050310/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
14638 bright wm thresholded.
5630 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.orig...
computing class statistics...
border white:    290293 voxels (1.73%)
border gray      364215 voxels (2.17%)
WM (95.0): 96.0 +- 8.2 [70.0 --> 110.0]
GM (73.0) : 72.1 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70)
setting MAX_BORDER_WHITE to 108.2 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 49.0 (was 40)
setting MAX_GRAY to 91.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.9 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=69+-7.0
mean inside = 92.1, mean outside = 76.3
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.26 (0.04-->7.94) (max @ vno 70000 --> 151789)
face area 0.34 +- 0.17 (0.00-->8.80)
mean absolute distance = 0.57 +- 0.82
4283 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 104 points - only 0.00% unknown
deleting segment 1 with 54 points - only 0.00% unknown
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 4 with 23 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 372 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 46 points - only 0.00% unknown
deleting segment 9 with 13 points - only 7.69% unknown
deleting segment 10 with 11 points - only 0.00% unknown
deleting segment 11 with 22 points - only 0.00% unknown
deleting segment 12 with 32 points - only 0.00% unknown
deleting segment 13 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
mean border=80.1, 179 (173) missing vertices, mean dist 0.4 [0.6 (%17.2)->0.6 (%82.8))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.27 (0.08-->7.96) (max @ vno 151789 --> 70000)
face area 0.34 +- 0.17 (0.00-->8.34)
mean absolute distance = 0.37 +- 0.60
4236 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2088015.0, rms=6.705
001: dt: 0.5000, sse=1247016.9, rms=4.036 (39.809%)
002: dt: 0.5000, sse=1025854.9, rms=3.023 (25.107%)
003: dt: 0.5000, sse=986118.2, rms=2.786 (7.829%)
004: dt: 0.5000, sse=966556.9, rms=2.664 (4.392%)
rms = 2.72, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=884855.7, rms=2.074 (22.119%)
006: dt: 0.2500, sse=854830.2, rms=1.783 (14.063%)
007: dt: 0.2500, sse=847364.1, rms=1.707 (4.271%)
rms = 1.67, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=849026.2, rms=1.674 (1.937%)
rms = 1.65, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=842583.9, rms=1.647 (1.583%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 196 points - only 0.00% unknown
deleting segment 1 with 30 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 139 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 41 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 11 points - only 0.00% unknown
deleting segment 9 with 15 points - only 0.00% unknown
deleting segment 10 with 32 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 12 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=83.0, 174 (60) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))]
%83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.05-->7.99) (max @ vno 151789 --> 70000)
face area 0.36 +- 0.18 (0.00-->9.12)
mean absolute distance = 0.27 +- 0.44
3690 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1298903.0, rms=4.099
010: dt: 0.5000, sse=994654.2, rms=2.511 (38.741%)
011: dt: 0.5000, sse=967367.2, rms=2.347 (6.540%)
rms = 2.33, time step reduction 1 of 3 to 0.250...
012: dt: 0.5000, sse=964896.0, rms=2.326 (0.877%)
013: dt: 0.2500, sse=871673.0, rms=1.520 (34.646%)
014: dt: 0.2500, sse=859677.3, rms=1.381 (9.173%)
rms = 1.36, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=858182.2, rms=1.360 (1.529%)
rms = 1.33, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=854068.9, rms=1.328 (2.315%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 233 points - only 0.00% unknown
deleting segment 1 with 30 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 223 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 43 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 11 points - only 0.00% unknown
deleting segment 9 with 25 points - only 0.00% unknown
deleting segment 10 with 31 points - only 0.00% unknown
deleting segment 11 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=84.5, 210 (45) missing vertices, mean dist -0.1 [0.3 (%64.7)->0.3 (%35.3))]
%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 0.91 +- 0.26 (0.07-->8.00) (max @ vno 151789 --> 70000)
face area 0.35 +- 0.18 (0.00-->8.97)
mean absolute distance = 0.25 +- 0.38
3863 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=957245.7, rms=2.459
017: dt: 0.5000, sse=903411.7, rms=1.991 (19.054%)
rms = 2.11, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=850506.2, rms=1.512 (24.053%)
019: dt: 0.2500, sse=832215.5, rms=1.308 (13.481%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=829649.4, rms=1.260 (3.695%)
rms = 1.23, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=823537.8, rms=1.228 (2.503%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 224 points - only 0.00% unknown
deleting segment 1 with 30 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 214 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 44 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 11 points - only 0.00% unknown
deleting segment 9 with 19 points - only 0.00% unknown
deleting segment 10 with 31 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 6 points - only 0.00% unknown
mean border=85.1, 217 (38) missing vertices, mean dist -0.0 [0.3 (%53.9)->0.2 (%46.1))]
%89 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-6.0.0/0050310/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=836429.9, rms=1.485
022: dt: 0.5000, sse=838050.2, rms=1.360 (8.448%)
rms = 1.70, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=807258.2, rms=1.081 (20.469%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=826100.1, rms=1.052 (2.688%)
025: dt: 0.1250, sse=801322.9, rms=1.000 (5.012%)
rms = 0.98, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=797426.6, rms=0.978 (2.125%)
positioning took 0.6 minutes
generating cortex label...
14 non-cortical segments detected
only using segment with 6426 vertices
erasing segment 0 (vno[0] = 30426)
erasing segment 1 (vno[0] = 36277)
erasing segment 2 (vno[0] = 38899)
erasing segment 4 (vno[0] = 55343)
erasing segment 5 (vno[0] = 103812)
erasing segment 6 (vno[0] = 106341)
erasing segment 7 (vno[0] = 106391)
erasing segment 8 (vno[0] = 106426)
erasing segment 9 (vno[0] = 108639)
erasing segment 10 (vno[0] = 108711)
erasing segment 11 (vno[0] = 109923)
erasing segment 12 (vno[0] = 109925)
erasing segment 13 (vno[0] = 109993)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.area
vertex spacing 0.90 +- 0.27 (0.04-->8.01) (max @ vno 70000 --> 151789)
face area 0.34 +- 0.17 (0.00-->8.91)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 139 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 61 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=58.3, 191 (191) missing vertices, mean dist 1.4 [1.8 (%0.0)->3.2 (%100.0))]
%11 local maxima, %33 large gradients and %53 min vals, 738 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=23148330.0, rms=27.543
001: dt: 0.0500, sse=20592708.0, rms=25.923 (5.880%)
002: dt: 0.0500, sse=18761988.0, rms=24.698 (4.727%)
003: dt: 0.0500, sse=17353328.0, rms=23.712 (3.993%)
004: dt: 0.0500, sse=16207914.0, rms=22.878 (3.514%)
005: dt: 0.0500, sse=15238313.0, rms=22.148 (3.191%)
006: dt: 0.0500, sse=14394860.0, rms=21.493 (2.959%)
007: dt: 0.0500, sse=13646656.0, rms=20.895 (2.785%)
008: dt: 0.0500, sse=12972398.0, rms=20.340 (2.654%)
009: dt: 0.0500, sse=12358921.0, rms=19.822 (2.547%)
010: dt: 0.0500, sse=11794906.0, rms=19.333 (2.465%)
positioning took 1.1 minutes
mean border=58.0, 168 (106) missing vertices, mean dist 1.2 [0.6 (%0.1)->2.7 (%99.9))]
%11 local maxima, %33 large gradients and %52 min vals, 702 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=12736598.0, rms=20.141
011: dt: 0.0500, sse=12207779.0, rms=19.691 (2.235%)
012: dt: 0.0500, sse=11716565.0, rms=19.264 (2.172%)
013: dt: 0.0500, sse=11259814.0, rms=18.857 (2.110%)
014: dt: 0.0500, sse=10833392.0, rms=18.470 (2.055%)
015: dt: 0.0500, sse=10437058.0, rms=18.102 (1.991%)
016: dt: 0.0500, sse=10067547.0, rms=17.752 (1.933%)
017: dt: 0.0500, sse=9721959.0, rms=17.418 (1.880%)
018: dt: 0.0500, sse=9399314.0, rms=17.101 (1.823%)
019: dt: 0.0500, sse=9097674.0, rms=16.798 (1.768%)
020: dt: 0.0500, sse=8815904.0, rms=16.511 (1.712%)
positioning took 1.1 minutes
mean border=57.9, 197 (85) missing vertices, mean dist 1.1 [0.1 (%1.2)->2.4 (%98.8))]
%12 local maxima, %34 large gradients and %51 min vals, 670 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=8929555.0, rms=16.633
021: dt: 0.0500, sse=8660268.0, rms=16.355 (1.668%)
022: dt: 0.0500, sse=8408985.0, rms=16.092 (1.610%)
023: dt: 0.0500, sse=8172172.0, rms=15.840 (1.568%)
024: dt: 0.0500, sse=7950562.0, rms=15.600 (1.515%)
025: dt: 0.0500, sse=7742339.0, rms=15.371 (1.467%)
026: dt: 0.0500, sse=7546353.5, rms=15.152 (1.423%)
027: dt: 0.0500, sse=7361261.0, rms=14.943 (1.384%)
028: dt: 0.0500, sse=7185261.0, rms=14.740 (1.353%)
029: dt: 0.0500, sse=7017515.0, rms=14.545 (1.326%)
030: dt: 0.0500, sse=6857804.5, rms=14.356 (1.297%)
positioning took 1.1 minutes
mean border=57.9, 251 (77) missing vertices, mean dist 1.0 [0.1 (%7.6)->2.2 (%92.4))]
%12 local maxima, %34 large gradients and %51 min vals, 611 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=6955443.0, rms=14.473
031: dt: 0.5000, sse=5820222.5, rms=13.066 (9.721%)
032: dt: 0.5000, sse=5023298.5, rms=11.972 (8.373%)
033: dt: 0.5000, sse=4415673.5, rms=11.065 (7.578%)
034: dt: 0.5000, sse=3938243.8, rms=10.290 (7.002%)
035: dt: 0.5000, sse=3543898.8, rms=9.604 (6.666%)
036: dt: 0.5000, sse=3210311.5, rms=8.981 (6.490%)
037: dt: 0.5000, sse=2910396.8, rms=8.384 (6.640%)
038: dt: 0.5000, sse=2653626.8, rms=7.836 (6.536%)
039: dt: 0.5000, sse=2435428.5, rms=7.342 (6.304%)
040: dt: 0.5000, sse=2262423.2, rms=6.922 (5.720%)
041: dt: 0.5000, sse=2120842.8, rms=6.562 (5.199%)
042: dt: 0.5000, sse=2019864.9, rms=6.290 (4.156%)
043: dt: 0.5000, sse=1942284.5, rms=6.075 (3.413%)
044: dt: 0.5000, sse=1890144.4, rms=5.924 (2.483%)
045: dt: 0.5000, sse=1853282.8, rms=5.817 (1.817%)
046: dt: 0.5000, sse=1831486.5, rms=5.750 (1.151%)
047: dt: 0.5000, sse=1808934.8, rms=5.683 (1.158%)
rms = 5.64, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1795978.5, rms=5.643 (0.705%)
049: dt: 0.2500, sse=1713004.5, rms=5.353 (5.135%)
050: dt: 0.2500, sse=1682067.2, rms=5.253 (1.866%)
rms = 5.26, time step reduction 2 of 3 to 0.125...
rms = 5.21, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1669133.5, rms=5.209 (0.847%)
positioning took 3.2 minutes
mean border=57.2, 3918 (51) missing vertices, mean dist 0.2 [0.2 (%45.8)->0.8 (%54.2))]
%21 local maxima, %28 large gradients and %46 min vals, 368 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=1914729.8, rms=5.228
052: dt: 0.5000, sse=1872352.4, rms=5.098 (2.481%)
053: dt: 0.5000, sse=1778485.5, rms=4.794 (5.965%)
rms = 4.97, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1690095.6, rms=4.435 (7.483%)
055: dt: 0.2500, sse=1677451.5, rms=4.373 (1.406%)
rms = 4.41, time step reduction 2 of 3 to 0.125...
056: dt: 0.1250, sse=1663370.2, rms=4.313 (1.359%)
057: dt: 0.1250, sse=1646314.4, rms=4.240 (1.700%)
rms = 4.21, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1639459.9, rms=4.211 (0.670%)
positioning took 1.6 minutes
mean border=56.7, 4634 (48) missing vertices, mean dist 0.1 [0.2 (%43.5)->0.5 (%56.5))]
%28 local maxima, %21 large gradients and %45 min vals, 443 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=1679428.0, rms=4.345
rms = 4.66, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1654668.0, rms=4.242 (2.358%)
rms = 4.23, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1649186.8, rms=4.226 (0.379%)
061: dt: 0.1250, sse=1634699.0, rms=4.162 (1.511%)
rms = 4.12, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1624623.6, rms=4.123 (0.932%)
positioning took 1.0 minutes
mean border=56.3, 9016 (43) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.4 (%57.0))]
%31 local maxima, %17 large gradients and %43 min vals, 493 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-6.0.0/0050310/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1646749.5, rms=4.193
rms = 4.35, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1623660.8, rms=4.099 (2.233%)
064: dt: 0.2500, sse=1599822.0, rms=4.019 (1.954%)
rms = 4.02, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1596073.9, rms=4.015 (0.094%)
066: dt: 0.1250, sse=1559754.1, rms=3.854 (4.023%)
067: dt: 0.1250, sse=1546402.0, rms=3.799 (1.411%)
rms = 3.77, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1539355.1, rms=3.772 (0.731%)
positioning took 1.5 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.area.pial
vertex spacing 1.04 +- 0.50 (0.04-->8.46) (max @ vno 61828 --> 63074)
face area 0.43 +- 0.38 (0.00-->11.40)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 153035 vertices processed
25000 of 153035 vertices processed
50000 of 153035 vertices processed
75000 of 153035 vertices processed
100000 of 153035 vertices processed
125000 of 153035 vertices processed
150000 of 153035 vertices processed
0 of 153035 vertices processed
25000 of 153035 vertices processed
50000 of 153035 vertices processed
75000 of 153035 vertices processed
100000 of 153035 vertices processed
125000 of 153035 vertices processed
150000 of 153035 vertices processed
thickness calculation complete, 632:2228 truncations.
30793 vertices at 0 distance
94966 vertices at 1 distance
92797 vertices at 2 distance
47487 vertices at 3 distance
18276 vertices at 4 distance
6517 vertices at 5 distance
2498 vertices at 6 distance
976 vertices at 7 distance
420 vertices at 8 distance
207 vertices at 9 distance
137 vertices at 10 distance
103 vertices at 11 distance
59 vertices at 12 distance
50 vertices at 13 distance
56 vertices at 14 distance
46 vertices at 15 distance
34 vertices at 16 distance
34 vertices at 17 distance
26 vertices at 18 distance
16 vertices at 19 distance
24 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.thickness
positioning took 18.1 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050310 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-6.0.0/0050310/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
14638 bright wm thresholded.
5630 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.orig...
computing class statistics...
border white:    290293 voxels (1.73%)
border gray      364215 voxels (2.17%)
WM (95.0): 96.0 +- 8.2 [70.0 --> 110.0]
GM (73.0) : 72.1 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70)
setting MAX_BORDER_WHITE to 109.2 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 49.0 (was 40)
setting MAX_GRAY to 92.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 59.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 38.9 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.8,    GM=69+-7.0
mean inside = 92.0, mean outside = 76.3
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.26 (0.03-->6.64) (max @ vno 154377 --> 154379)
face area 0.34 +- 0.16 (0.00-->9.07)
mean absolute distance = 0.58 +- 0.83
4997 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 15 points - only 0.00% unknown
deleting segment 7 with 85 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 13 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 123 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
deleting segment 14 with 41 points - only 0.00% unknown
deleting segment 15 with 10 points - only 0.00% unknown
deleting segment 16 with 8 points - only 0.00% unknown
deleting segment 17 with 54 points - only 0.00% unknown
deleting segment 18 with 9 points - only 0.00% unknown
deleting segment 19 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 20 with 3 points - only 0.00% unknown
mean border=80.4, 329 (328) missing vertices, mean dist 0.4 [0.6 (%17.5)->0.6 (%82.5))]
%75 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.09-->6.72) (max @ vno 154377 --> 154379)
face area 0.34 +- 0.17 (0.00-->7.95)
mean absolute distance = 0.37 +- 0.60
4805 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2069390.2, rms=6.598
001: dt: 0.5000, sse=1246981.2, rms=4.019 (39.091%)
002: dt: 0.5000, sse=1028794.5, rms=2.974 (26.009%)
003: dt: 0.5000, sse=980380.4, rms=2.727 (8.280%)
004: dt: 0.5000, sse=994790.3, rms=2.588 (5.094%)
rms = 2.65, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=887858.4, rms=2.013 (22.232%)
006: dt: 0.2500, sse=856198.1, rms=1.730 (14.067%)
007: dt: 0.2500, sse=847040.8, rms=1.643 (5.006%)
rms = 1.61, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=843100.6, rms=1.609 (2.068%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=841769.3, rms=1.572 (2.319%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 0 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 11 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 118 points - only 0.00% unknown
deleting segment 12 with 30 points - only 43.33% unknown
deleting segment 13 with 103 points - only 0.00% unknown
deleting segment 14 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 16 with 4 points - only 0.00% unknown
mean border=83.3, 175 (67) missing vertices, mean dist -0.2 [0.4 (%73.9)->0.3 (%26.1))]
%84 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.06-->6.70) (max @ vno 154377 --> 154379)
face area 0.35 +- 0.18 (0.00-->8.69)
mean absolute distance = 0.28 +- 0.44
4275 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1281856.2, rms=3.979
010: dt: 0.5000, sse=986691.6, rms=2.423 (39.108%)
011: dt: 0.5000, sse=976386.6, rms=2.231 (7.938%)
rms = 2.22, time step reduction 1 of 3 to 0.250...
012: dt: 0.5000, sse=952448.1, rms=2.225 (0.269%)
013: dt: 0.2500, sse=873455.4, rms=1.438 (35.337%)
014: dt: 0.2500, sse=858167.8, rms=1.299 (9.663%)
rms = 1.28, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=859182.6, rms=1.283 (1.265%)
rms = 1.25, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=854419.1, rms=1.250 (2.581%)
positioning took 0.8 minutes
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 12 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 24 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 118 points - only 0.00% unknown
deleting segment 10 with 43 points - only 30.23% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 120 points - only 0.00% unknown
deleting segment 13 with 11 points - only 0.00% unknown
deleting segment 14 with 8 points - only 0.00% unknown
deleting segment 15 with 7 points - only 0.00% unknown
mean border=84.8, 186 (29) missing vertices, mean dist -0.1 [0.3 (%64.1)->0.3 (%35.9))]
%88 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 0.90 +- 0.26 (0.04-->6.77) (max @ vno 154377 --> 154379)
face area 0.34 +- 0.17 (0.00-->8.81)
mean absolute distance = 0.26 +- 0.38
4275 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=966220.7, rms=2.460
017: dt: 0.5000, sse=899963.7, rms=1.913 (22.235%)
rms = 2.00, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=850677.2, rms=1.460 (23.706%)
019: dt: 0.2500, sse=840590.9, rms=1.248 (14.492%)
rms = 1.20, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=829575.4, rms=1.200 (3.881%)
rms = 1.16, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=840992.4, rms=1.161 (3.248%)
positioning took 0.7 minutes
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 50 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 119 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 30 points - only 43.33% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
deleting segment 10 with 118 points - only 0.00% unknown
deleting segment 11 with 11 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
deleting segment 13 with 8 points - only 0.00% unknown
mean border=85.3, 218 (23) missing vertices, mean dist -0.0 [0.3 (%53.9)->0.3 (%46.1))]
%89 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-6.0.0/0050310/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=855475.8, rms=1.437
022: dt: 0.5000, sse=839700.1, rms=1.314 (8.521%)
rms = 1.64, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=807195.7, rms=1.033 (21.394%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=816130.0, rms=1.006 (2.654%)
025: dt: 0.1250, sse=801023.7, rms=0.954 (5.155%)
rms = 0.93, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=800416.3, rms=0.932 (2.305%)
positioning took 0.7 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 6808 vertices
erasing segment 0 (vno[0] = 54859)
erasing segment 2 (vno[0] = 65292)
erasing segment 3 (vno[0] = 109091)
erasing segment 4 (vno[0] = 110179)
erasing segment 5 (vno[0] = 110226)
erasing segment 6 (vno[0] = 111347)
erasing segment 7 (vno[0] = 112484)
erasing segment 8 (vno[0] = 114601)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.area
vertex spacing 0.90 +- 0.26 (0.03-->6.67) (max @ vno 154377 --> 154379)
face area 0.34 +- 0.17 (0.00-->8.77)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=58.4, 337 (337) missing vertices, mean dist 1.4 [0.8 (%0.0)->3.2 (%100.0))]
%10 local maxima, %31 large gradients and %56 min vals, 727 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=23659622.0, rms=27.678
001: dt: 0.0500, sse=21085666.0, rms=26.076 (5.787%)
002: dt: 0.0500, sse=19248700.0, rms=24.870 (4.627%)
003: dt: 0.0500, sse=17834684.0, rms=23.900 (3.901%)
004: dt: 0.0500, sse=16684374.0, rms=23.080 (3.429%)
005: dt: 0.0500, sse=15713525.0, rms=22.365 (3.098%)
006: dt: 0.0500, sse=14869335.0, rms=21.724 (2.866%)
007: dt: 0.0500, sse=14119656.0, rms=21.138 (2.696%)
008: dt: 0.0500, sse=13443621.0, rms=20.596 (2.566%)
009: dt: 0.0500, sse=12827557.0, rms=20.089 (2.462%)
010: dt: 0.0500, sse=12260767.0, rms=19.611 (2.381%)
positioning took 1.1 minutes
mean border=58.2, 268 (188) missing vertices, mean dist 1.2 [0.1 (%0.0)->2.8 (%100.0))]
%11 local maxima, %31 large gradients and %54 min vals, 677 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=13317012.0, rms=20.486
011: dt: 0.0500, sse=12783422.0, rms=20.046 (2.151%)
012: dt: 0.0500, sse=12287519.0, rms=19.627 (2.087%)
013: dt: 0.0500, sse=11825471.0, rms=19.229 (2.028%)
014: dt: 0.0500, sse=11394068.0, rms=18.850 (1.973%)
015: dt: 0.0500, sse=10991119.0, rms=18.488 (1.918%)
016: dt: 0.0500, sse=10613444.0, rms=18.143 (1.868%)
017: dt: 0.0500, sse=10259983.0, rms=17.813 (1.816%)
018: dt: 0.0500, sse=9929074.0, rms=17.499 (1.763%)
019: dt: 0.0500, sse=9618586.0, rms=17.199 (1.715%)
020: dt: 0.0500, sse=9327308.0, rms=16.913 (1.665%)
positioning took 1.1 minutes
mean border=58.0, 307 (160) missing vertices, mean dist 1.1 [0.1 (%1.0)->2.5 (%99.0))]
%11 local maxima, %32 large gradients and %54 min vals, 672 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=9453345.0, rms=17.042
021: dt: 0.0500, sse=9174019.0, rms=16.765 (1.626%)
022: dt: 0.0500, sse=8912160.0, rms=16.500 (1.576%)
023: dt: 0.0500, sse=8665480.0, rms=16.248 (1.532%)
024: dt: 0.0500, sse=8433327.0, rms=16.006 (1.488%)
025: dt: 0.0500, sse=8215203.5, rms=15.775 (1.441%)
026: dt: 0.0500, sse=8009146.0, rms=15.554 (1.401%)
027: dt: 0.0500, sse=7814055.5, rms=15.342 (1.365%)
028: dt: 0.0500, sse=7628324.0, rms=15.137 (1.336%)
029: dt: 0.0500, sse=7451088.5, rms=14.939 (1.310%)
030: dt: 0.0500, sse=7281610.0, rms=14.746 (1.287%)
positioning took 1.1 minutes
mean border=58.0, 313 (137) missing vertices, mean dist 1.0 [0.1 (%7.2)->2.3 (%92.8))]
%11 local maxima, %32 large gradients and %53 min vals, 635 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=7394460.0, rms=14.874
031: dt: 0.5000, sse=6181257.0, rms=13.431 (9.700%)
032: dt: 0.5000, sse=5308909.0, rms=12.282 (8.555%)
033: dt: 0.5000, sse=4639820.0, rms=11.322 (7.823%)
034: dt: 0.5000, sse=4129003.0, rms=10.523 (7.053%)
035: dt: 0.5000, sse=3726284.0, rms=9.848 (6.412%)
036: dt: 0.5000, sse=3391887.0, rms=9.248 (6.090%)
037: dt: 0.5000, sse=3096115.5, rms=8.687 (6.066%)
038: dt: 0.5000, sse=2840536.0, rms=8.170 (5.960%)
039: dt: 0.5000, sse=2613046.0, rms=7.684 (5.943%)
040: dt: 0.5000, sse=2425498.2, rms=7.257 (5.556%)
041: dt: 0.5000, sse=2260239.0, rms=6.863 (5.435%)
042: dt: 0.5000, sse=2141876.5, rms=6.562 (4.381%)
043: dt: 0.5000, sse=2046607.9, rms=6.313 (3.792%)
044: dt: 0.5000, sse=1989307.8, rms=6.155 (2.500%)
045: dt: 0.5000, sse=1943852.8, rms=6.030 (2.033%)
046: dt: 0.5000, sse=1915636.0, rms=5.949 (1.349%)
047: dt: 0.5000, sse=1885110.8, rms=5.862 (1.464%)
rms = 5.81, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1868676.5, rms=5.812 (0.843%)
049: dt: 0.2500, sse=1773501.8, rms=5.497 (5.422%)
050: dt: 0.2500, sse=1738913.8, rms=5.390 (1.953%)
rms = 5.40, time step reduction 2 of 3 to 0.125...
051: dt: 0.1250, sse=1721895.9, rms=5.334 (1.036%)
052: dt: 0.1250, sse=1700797.5, rms=5.264 (1.322%)
rms = 5.25, time step reduction 3 of 3 to 0.062...
053: dt: 0.1250, sse=1695474.6, rms=5.245 (0.344%)
positioning took 3.7 minutes
mean border=57.4, 4633 (43) missing vertices, mean dist 0.2 [0.2 (%46.4)->0.8 (%53.6))]
%18 local maxima, %26 large gradients and %49 min vals, 321 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=1926024.8, rms=5.217
rms = 5.28, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1831907.5, rms=4.891 (6.255%)
055: dt: 0.2500, sse=1785526.6, rms=4.718 (3.520%)
rms = 4.70, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1779890.5, rms=4.704 (0.303%)
057: dt: 0.1250, sse=1717189.9, rms=4.465 (5.079%)
058: dt: 0.1250, sse=1701906.1, rms=4.410 (1.245%)
rms = 4.39, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1696578.4, rms=4.392 (0.398%)
positioning took 1.3 minutes
mean border=57.0, 5238 (35) missing vertices, mean dist 0.1 [0.2 (%43.9)->0.6 (%56.1))]
%25 local maxima, %20 large gradients and %48 min vals, 429 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=1718168.6, rms=4.474
rms = 4.80, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1691585.9, rms=4.372 (2.276%)
rms = 4.37, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1687653.5, rms=4.367 (0.108%)
062: dt: 0.1250, sse=1670407.1, rms=4.297 (1.597%)
rms = 4.26, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1659796.4, rms=4.260 (0.877%)
positioning took 1.0 minutes
mean border=56.6, 10333 (34) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.5 (%56.3))]
%27 local maxima, %17 large gradients and %46 min vals, 451 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-6.0.0/0050310/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1681302.2, rms=4.302
rms = 4.49, time step reduction 1 of 3 to 0.250...
064: dt: 0.2500, sse=1654476.8, rms=4.198 (2.414%)
065: dt: 0.2500, sse=1627654.6, rms=4.113 (2.047%)
rms = 4.12, time step reduction 2 of 3 to 0.125...
rms = 4.07, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1616680.4, rms=4.065 (1.150%)
positioning took 0.9 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.area.pial
vertex spacing 1.04 +- 0.48 (0.05-->7.21) (max @ vno 100422 --> 99147)
face area 0.42 +- 0.37 (0.00-->8.25)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 155154 vertices processed
25000 of 155154 vertices processed
50000 of 155154 vertices processed
75000 of 155154 vertices processed
100000 of 155154 vertices processed
125000 of 155154 vertices processed
150000 of 155154 vertices processed
0 of 155154 vertices processed
25000 of 155154 vertices processed
50000 of 155154 vertices processed
75000 of 155154 vertices processed
100000 of 155154 vertices processed
125000 of 155154 vertices processed
150000 of 155154 vertices processed
thickness calculation complete, 534:2370 truncations.
31415 vertices at 0 distance
97545 vertices at 1 distance
93872 vertices at 2 distance
47352 vertices at 3 distance
18438 vertices at 4 distance
6437 vertices at 5 distance
2222 vertices at 6 distance
957 vertices at 7 distance
442 vertices at 8 distance
218 vertices at 9 distance
142 vertices at 10 distance
124 vertices at 11 distance
95 vertices at 12 distance
70 vertices at 13 distance
51 vertices at 14 distance
49 vertices at 15 distance
25 vertices at 16 distance
23 vertices at 17 distance
31 vertices at 18 distance
22 vertices at 19 distance
38 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.thickness
positioning took 17.8 minutes
PIDs (23743 23746) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 08:17:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label
Total face volume 315041
Total vertex volume 311966 (mask=0)
#@# 0050310 lh 311966
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 08:17:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label
Total face volume 315565
Total vertex volume 311618 (mask=0)
#@# 0050310 rh 311618
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 08:17:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 

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 = 465
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/ribbon.mgz
mris_volmask took 15.06 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 08:32:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 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 0050310 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 08:32:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 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 0050310 rh pial 

Waiting for PID 25100 of (25100 25103 25106 25109) to complete...
Waiting for PID 25103 of (25100 25103 25106 25109) to complete...
Waiting for PID 25106 of (25100 25103 25106 25109) to complete...
Waiting for PID 25109 of (25100 25103 25106 25109) 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 0050310 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315041
Total vertex volume 311966 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1380    966   2663  2.709 0.680     0.088     0.012        6     0.6  bankssts
 1283    837   2782  3.055 0.579     0.124     0.024       15     1.2  caudalanteriorcingulate
 3430   2312   7461  2.966 0.683     0.103     0.024       25     3.3  caudalmiddlefrontal
 2499   1722   4049  2.036 0.567     0.166     0.053       56     5.8  cuneus
  686    469   1627  2.474 0.955     0.152     0.054       12     1.6  entorhinal
 5405   3795  12573  2.843 0.719     0.139     0.039       79     8.7  fusiform
 8950   5961  17505  2.609 0.695     0.124     0.037      117    14.0  inferiorparietal
 6300   4346  15727  2.871 0.802     0.131     0.041       94    10.8  inferiortemporal
 1619   1119   3179  2.730 0.816     0.137     0.035       20     2.3  isthmuscingulate
 8655   5717  14637  2.288 0.658     0.140     0.039      137    14.0  lateraloccipital
 4234   2852   8884  2.842 0.783     0.139     0.045       61     7.4  lateralorbitofrontal
 4981   3590   8770  2.335 0.737     0.162     0.043       79     9.1  lingual
 2605   1846   6006  2.803 0.922     0.146     0.053       50     6.0  medialorbitofrontal
 5114   3711  14214  2.876 0.765     0.153     0.047       96    10.5  middletemporal
  982    654   2133  2.912 0.758     0.107     0.025       13     0.8  parahippocampal
 2634   1799   5674  2.867 0.794     0.114     0.023       21     2.4  paracentral
 3202   2285   7689  2.900 0.511     0.123     0.029       43     3.8  parsopercularis
 1118    820   3768  3.109 0.693     0.168     0.052       27     2.3  parsorbitalis
 2206   1568   5280  2.827 0.660     0.130     0.032       27     3.1  parstriangularis
 2649   1836   3137  1.785 0.535     0.147     0.038       38     4.4  pericalcarine
 7507   4848  11911  2.228 0.754     0.104     0.025       69     7.6  postcentral
 2257   1514   4528  2.900 0.718     0.122     0.025       23     2.2  posteriorcingulate
 8605   5445  16155  2.773 0.679     0.111     0.033       83    12.0  precentral
 6142   4371  13176  2.737 0.646     0.124     0.031       75     8.0  precuneus
 1221    835   2646  2.857 0.751     0.127     0.039       22     2.0  rostralanteriorcingulate
 9643   6623  23510  2.906 0.712     0.132     0.034      137    13.7  rostralmiddlefrontal
11330   7785  29170  3.154 0.796     0.134     0.039      137    18.5  superiorfrontal
10370   6924  18429  2.398 0.621     0.122     0.035      136    15.7  superiorparietal
 5856   4141  13541  2.764 0.684     0.120     0.033       74     8.3  superiortemporal
 7959   5435  17759  2.941 0.629     0.128     0.030      100     9.7  supramarginal
  406    283   1294  2.892 0.815     0.219     0.098       16     1.9  frontalpole
  666    520   3075  3.663 0.828     0.152     0.050       10     1.3  temporalpole
  706    490   1427  2.539 0.469     0.157     0.048       13     1.5  transversetemporal
 3587   2461   7546  3.157 0.846     0.134     0.038       37     5.8  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 0050310 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315041
Total vertex volume 311966 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1380    976   2663  2.709 0.680     0.140     0.031       18     2.2  bankssts
 1283    999   2782  3.055 0.579     0.131     0.034       31     1.7  caudalanteriorcingulate
 3430   2766   7461  2.966 0.683     0.120     0.026       35     3.9  caudalmiddlefrontal
 2499   2256   4049  2.036 0.567     0.160     0.041       47     4.5  cuneus
  686    804   1627  2.474 0.955     0.200     0.048        9     1.7  entorhinal
 5405   5048  12573  2.843 0.719     0.174     0.044       84    11.4  fusiform
 8950   7417  17505  2.609 0.695     0.149     0.036      130    16.4  inferiorparietal
 6300   6273  15727  2.871 0.802     0.176     0.044       91    12.9  inferiortemporal
 1619   1306   3179  2.730 0.816     0.175     0.061       60     4.9  isthmuscingulate
 8655   7100  14637  2.288 0.658     0.141     0.033      148    13.5  lateraloccipital
 4234   3484   8884  2.842 0.783     0.162     0.053      142    11.7  lateralorbitofrontal
 4981   4297   8770  2.335 0.737     0.168     0.046      249    10.6  lingual
 2605   2465   6006  2.803 0.922     0.190     0.061       54     6.9  medialorbitofrontal
 5114   5920  14214  2.876 0.765     0.207     0.052      102    13.1  middletemporal
  982    890   2133  2.912 0.758     0.174     0.044       13     2.0  parahippocampal
 2634   2166   5674  2.867 0.794     0.138     0.034       31     3.9  paracentral
 3202   3050   7689  2.900 0.511     0.157     0.034       41     5.2  parsopercularis
 1118   1499   3768  3.109 0.693     0.228     0.046       17     2.6  parsorbitalis
 2206   2098   5280  2.827 0.660     0.175     0.043       30     4.5  parstriangularis
 2649   1701   3137  1.785 0.535     0.138     0.036       68     4.2  pericalcarine
 7507   6003  11911  2.228 0.754     0.128     0.028       69    10.3  postcentral
 2257   1760   4528  2.900 0.718     0.155     0.043       48     4.3  posteriorcingulate
 8605   6063  16155  2.773 0.679     0.115     0.029      102    10.3  precentral
 6142   5212  13176  2.737 0.646     0.157     0.046      127    14.9  precuneus
 1221   1073   2646  2.857 0.751     0.175     0.050       27     2.8  rostralanteriorcingulate
 9643   9047  23510  2.906 0.712     0.170     0.040      135    18.8  rostralmiddlefrontal
11330  10208  29170  3.154 0.796     0.161     0.041      162    21.5  superiorfrontal
10370   8363  18429  2.398 0.621     0.135     0.033      155    15.3  superiorparietal
 5856   5575  13541  2.764 0.684     0.168     0.044       86    11.7  superiortemporal
 7959   6687  17759  2.941 0.629     0.149     0.035      120    12.7  supramarginal
  406    583   1294  2.892 0.815     0.277     0.061        7     1.4  frontalpole
  666   1150   3075  3.663 0.828     0.243     0.046        8     1.5  temporalpole
  706    703   1427  2.539 0.469     0.190     0.049        9     1.6  transversetemporal
 3587   2271   7546  3.157 0.846     0.146     0.047       66     7.3  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 0050310 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315565
Total vertex volume 311618 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1652   1201   3647  3.304 0.617     0.112     0.017       13     1.3  bankssts
 1129    773   2591  2.886 0.640     0.141     0.030       19     1.3  caudalanteriorcingulate
 4950   3169   9998  2.837 0.652     0.122     0.040       62     8.5  caudalmiddlefrontal
 2466   1604   3852  2.302 0.635     0.159     0.042       41     4.4  cuneus
  610    434   1880  3.135 0.735     0.131     0.045        9     1.0  entorhinal
 4785   3334  10150  2.680 0.682     0.141     0.038       69     7.8  fusiform
11196   7577  24444  2.839 0.721     0.122     0.032      128    14.3  inferiorparietal
 5424   3618  13670  3.030 0.800     0.129     0.042       74     9.1  inferiortemporal
 1353    927   2977  2.675 0.959     0.125     0.036       24     1.6  isthmuscingulate
 7569   5015  13567  2.374 0.755     0.143     0.044      137    14.2  lateraloccipital
 4454   3002   8268  2.630 0.678     0.141     0.042       67     8.2  lateralorbitofrontal
 5496   3831   9587  2.292 0.718     0.155     0.046       90    10.4  lingual
 2699   1933   6325  2.741 0.863     0.134     0.045       45     5.4  medialorbitofrontal
 6099   4259  15847  3.010 0.762     0.139     0.039      100    10.9  middletemporal
 1047    669   2296  2.901 0.790     0.094     0.020        7     0.8  parahippocampal
 2904   1895   5773  2.773 0.723     0.111     0.027       26     3.2  paracentral
 2780   1978   5675  2.648 0.607     0.128     0.029       34     3.6  parsopercularis
 1148    824   3047  2.812 0.699     0.149     0.038       25     1.7  parsorbitalis
 2702   1938   6480  2.724 0.698     0.139     0.041       46     4.8  parstriangularis
 2848   1915   3029  1.735 0.519     0.137     0.030       34     3.3  pericalcarine
 7718   4836  11928  2.213 0.702     0.107     0.029       83     9.5  postcentral
 2245   1539   4810  2.839 0.714     0.144     0.033       30     3.3  posteriorcingulate
 8958   5726  16085  2.643 0.606     0.119     0.035       95    13.2  precentral
 6675   4560  13518  2.748 0.678     0.122     0.028       73     7.7  precuneus
  726    494   1461  2.705 0.747     0.115     0.021        6     0.6  rostralanteriorcingulate
 9581   6611  22868  2.844 0.717     0.134     0.039      143    15.6  rostralmiddlefrontal
10933   7428  27301  3.037 0.794     0.131     0.039      136    18.9  superiorfrontal
 9743   6509  18091  2.428 0.635     0.121     0.037      116    15.0  superiorparietal
 5300   3822  12683  2.921 0.727     0.119     0.034       62     7.6  superiortemporal
 7911   5360  17576  2.894 0.700     0.123     0.030       91     9.7  supramarginal
  571    398   1944  3.199 0.772     0.214     0.085       20     2.2  frontalpole
  630    499   2755  3.474 0.711     0.159     0.046        9     1.3  temporalpole
  527    353    975  2.685 0.733     0.152     0.041        8     0.8  transversetemporal
 3204   2134   6452  3.053 0.759     0.132     0.037       38     4.7  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050310 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315565
Total vertex volume 311618 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1652   1035   3647  3.304 0.617     0.122     0.032       23     2.6  bankssts
 1129   1050   2591  2.886 0.640     0.169     0.043       21     2.2  caudalanteriorcingulate
 4950   3809   9998  2.837 0.652     0.134     0.040       79    10.3  caudalmiddlefrontal
 2466   1932   3852  2.302 0.635     0.147     0.038       42     4.4  cuneus
  610    726   1880  3.135 0.735     0.186     0.041        9     1.2  entorhinal
 4785   4234  10150  2.680 0.682     0.162     0.040      107     9.9  fusiform
11196   9405  24444  2.839 0.721     0.141     0.033      168    17.0  inferiorparietal
 5424   5177  13670  3.030 0.800     0.169     0.044       91    10.8  inferiortemporal
 1353   1185   2977  2.675 0.959     0.162     0.040       19     2.4  isthmuscingulate
 7569   6319  13567  2.374 0.755     0.143     0.041      234    13.8  lateraloccipital
 4454   3541   8268  2.630 0.678     0.162     0.052      232    12.0  lateralorbitofrontal
 5496   4787   9587  2.292 0.718     0.166     0.044      110    11.3  lingual
 2699   2652   6325  2.741 0.863     0.190     0.052       53     6.6  medialorbitofrontal
 6099   6241  15847  3.010 0.762     0.180     0.041       94    12.4  middletemporal
 1047    895   2296  2.901 0.790     0.163     0.041       13     2.1  parahippocampal
 2904   2284   5773  2.773 0.723     0.134     0.032       34     4.4  paracentral
 2780   2369   5675  2.648 0.607     0.156     0.038       51     5.0  parsopercularis
 1148   1296   3047  2.812 0.699     0.181     0.041       16     2.3  parsorbitalis
 2702   2791   6480  2.724 0.698     0.184     0.039       40     5.2  parstriangularis
 2848   1723   3029  1.735 0.519     0.137     0.041       91     6.1  pericalcarine
 7718   6040  11928  2.213 0.702     0.124     0.031       78    11.4  postcentral
 2245   1941   4810  2.839 0.714     0.169     0.039       44     4.1  posteriorcingulate
 8958   6443  16085  2.643 0.606     0.119     0.028      105    11.4  precentral
 6675   5321  13518  2.748 0.678     0.145     0.036       89    11.0  precuneus
  726    629   1461  2.705 0.747     0.157     0.033        9     1.2  rostralanteriorcingulate
 9581   9119  22868  2.844 0.717     0.172     0.039      145    18.8  rostralmiddlefrontal
10933  10043  27301  3.037 0.794     0.157     0.037      173    19.6  superiorfrontal
 9743   8273  18091  2.428 0.635     0.136     0.032      119    14.0  superiorparietal
 5300   5054  12683  2.921 0.727     0.170     0.043       96    10.4  superiortemporal
 7911   6635  17576  2.894 0.700     0.148     0.035      320    12.7  supramarginal
  571    789   1944  3.199 0.772     0.243     0.061        9     1.8  frontalpole
  630   1025   2755  3.474 0.711     0.275     0.061       11     2.0  temporalpole
  527    406    975  2.685 0.733     0.160     0.046        5     1.2  transversetemporal
 3204   2038   6452  3.053 0.759     0.141     0.042       58     6.0  insula
PIDs (25100 25103 25106 25109) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 08:33:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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 08:33:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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 25193 of (25193 25196) to complete...
Waiting for PID 25196 of (25193 25196) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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...
63 labels changed using aseg
relabeling using gibbs priors...
000:  10099 changed, 153035 examined...
001:   2272 changed, 39162 examined...
002:    651 changed, 11904 examined...
003:    260 changed, 3726 examined...
004:    143 changed, 1503 examined...
005:     70 changed, 800 examined...
006:     25 changed, 380 examined...
007:     13 changed, 149 examined...
008:      6 changed, 73 examined...
009:      1 changed, 42 examined...
010:      0 changed, 5 examined...
15 labels changed using aseg
000: 295 total segments, 208 labels (2552 vertices) changed
001: 107 total segments, 20 labels (115 vertices) changed
002: 87 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 38 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1388 vertices marked for relabeling...
1388 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 0050310 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...
27 labels changed using aseg
relabeling using gibbs priors...
000:  10402 changed, 155154 examined...
001:   2469 changed, 40158 examined...
002:    749 changed, 12774 examined...
003:    304 changed, 4219 examined...
004:    148 changed, 1719 examined...
005:     94 changed, 862 examined...
006:     43 changed, 538 examined...
007:     20 changed, 231 examined...
008:     11 changed, 103 examined...
009:     10 changed, 65 examined...
010:      7 changed, 58 examined...
011:      3 changed, 39 examined...
012:      3 changed, 17 examined...
013:      2 changed, 12 examined...
014:      0 changed, 10 examined...
7 labels changed using aseg
000: 275 total segments, 195 labels (3055 vertices) changed
001: 91 total segments, 12 labels (107 vertices) changed
002: 79 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 49 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
997 vertices marked for relabeling...
997 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.
PIDs (25193 25196) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 08:34:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 08:34:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 rh white 

Waiting for PID 25267 of (25267 25270) to complete...
Waiting for PID 25270 of (25267 25270) 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 0050310 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315041
Total vertex volume 311966 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1481   1045   3816  2.764 0.778     0.159     0.050       28     3.4  G&S_frontomargin
 1580   1097   3315  2.525 0.604     0.131     0.034       21     2.0  G&S_occipital_inf
 1950   1364   3685  2.314 0.800     0.119     0.043       19     4.0  G&S_paracentral
 1859   1272   4487  2.954 0.577     0.142     0.040       31     2.8  G&S_subcentral
  754    545   3047  3.346 0.876     0.222     0.094       28     3.1  G&S_transv_frontopol
 2295   1631   5325  3.164 0.717     0.127     0.039       34     3.7  G&S_cingul-Ant
 1458    998   3035  2.965 0.486     0.111     0.022       12     1.3  G&S_cingul-Mid-Ant
 1596   1098   3154  2.851 0.614     0.112     0.024       13     1.4  G&S_cingul-Mid-Post
  780    529   2481  3.432 0.715     0.158     0.038       13     1.2  G_cingul-Post-dorsal
  361    244    719  2.538 0.873     0.143     0.052        5     0.8  G_cingul-Post-ventral
 2375   1636   3509  1.879 0.561     0.180     0.064       63     6.6  G_cuneus
 1986   1407   5330  2.969 0.552     0.141     0.042       31     3.4  G_front_inf-Opercular
  423    318   1530  3.100 0.641     0.177     0.050       11     0.8  G_front_inf-Orbital
 1315    952   4081  3.013 0.679     0.158     0.049       26     2.6  G_front_inf-Triangul
 5260   3476  16037  3.218 0.734     0.136     0.037       85     8.2  G_front_middle
 7693   5168  21748  3.218 0.829     0.146     0.045      112    14.8  G_front_sup
  667    457   1673  3.283 0.966     0.151     0.050       10     1.4  G_Ins_lg&S_cent_ins
  777    532   2352  3.654 0.913     0.129     0.040        8     1.4  G_insular_short
 2815   1758   5741  2.460 0.789     0.155     0.060       55     7.2  G_occipital_middle
 1607   1085   3269  2.315 0.687     0.159     0.055       33     3.9  G_occipital_sup
 2393   1627   6289  3.032 0.674     0.150     0.046       44     4.5  G_oc-temp_lat-fusifor
 3412   2448   6336  2.273 0.750     0.176     0.050       66     7.3  G_oc-temp_med-Lingual
 1349    919   3102  2.679 0.871     0.134     0.044       24     2.2  G_oc-temp_med-Parahip
 2925   1966   7933  2.936 0.768     0.163     0.058       65     7.2  G_orbital
 3832   2505   9200  2.686 0.763     0.142     0.051       76     8.3  G_pariet_inf-Angular
 3715   2556   9743  3.052 0.675     0.153     0.043       68     6.9  G_pariet_inf-Supramar
 4130   2644   8221  2.491 0.690     0.134     0.048       74     8.7  G_parietal_sup
 2831   1678   4348  2.094 0.669     0.101     0.028       28     3.3  G_postcentral
 3125   1744   6346  2.861 0.700     0.123     0.047       43     5.8  G_precentral
 3027   2092   8055  2.869 0.663     0.135     0.036       49     4.1  G_precuneus
  847    618   2247  2.520 0.772     0.172     0.062       24     2.4  G_rectus
  800    497   1216  2.353 0.999     0.136     0.070       16     2.5  G_subcallosal
  581    394   1327  2.635 0.495     0.163     0.058       11     1.4  G_temp_sup-G_T_transv
 1949   1461   6288  2.914 0.775     0.165     0.055       47     4.4  G_temp_sup-Lateral
  762    550   2116  3.046 1.039     0.101     0.037        6     1.0  G_temp_sup-Plan_polar
 1250    876   2685  2.963 0.502     0.095     0.019        9     1.0  G_temp_sup-Plan_tempo
 3843   2607  11404  3.001 0.835     0.157     0.059       85     9.8  G_temporal_inf
 2836   2135   9970  2.963 0.837     0.178     0.062       75     7.6  G_temporal_middle
  368    242    582  2.714 0.451     0.097     0.015        2     0.2  Lat_Fis-ant-Horizont
  312    234    460  2.363 0.561     0.096     0.011        1     0.1  Lat_Fis-ant-Vertical
 1271    886   1836  2.664 0.498     0.117     0.021       10     1.2  Lat_Fis-post
 2345   1487   3070  1.898 0.644     0.142     0.041       43     4.1  Pole_occipital
 1650   1231   6523  3.368 0.808     0.154     0.051       30     3.5  Pole_temporal
 3418   2503   4524  2.021 0.636     0.152     0.038       44     6.1  S_calcarine
 3600   2403   4612  2.199 0.756     0.088     0.014       18     2.0  S_central
 1491   1015   2452  2.941 0.613     0.112     0.019       11     1.2  S_cingul-Marginalis
  477    341    898  3.237 0.631     0.101     0.022        2     0.4  S_circular_insula_ant
 1286    844   1871  2.645 0.700     0.089     0.019        6     1.1  S_circular_insula_inf
 1989   1375   3276  3.013 0.444     0.115     0.021       14     1.9  S_circular_insula_sup
 1082    779   1816  2.436 0.635     0.123     0.029       10     1.2  S_collat_transv_ant
  620    419    764  2.104 0.476     0.128     0.031        6     0.7  S_collat_transv_post
 2832   1954   5022  2.746 0.582     0.109     0.021       20     2.2  S_front_inf
 1562   1094   2476  2.547 0.509     0.104     0.022       11     1.2  S_front_middle
 3296   2302   6505  2.920 0.609     0.103     0.021       21     2.6  S_front_sup
  209    145    346  2.752 0.519     0.110     0.012        1     0.1  S_interm_prim-Jensen
 3798   2623   5860  2.382 0.531     0.095     0.016       22     2.5  S_intrapariet&P_trans
 1530   1048   2311  2.339 0.499     0.127     0.022       15     1.4  S_oc_middle&Lunatus
 1610   1077   2374  2.482 0.523     0.105     0.018       11     1.2  S_oc_sup&transversal
  923    639   1600  2.554 0.541     0.132     0.030       11     1.0  S_occipital_ant
 1087    777   1715  2.303 0.619     0.092     0.015        6     0.5  S_oc-temp_lat
 2124   1467   3645  2.800 0.694     0.118     0.024       16     2.0  S_oc-temp_med&Lingual
  346    245    669  2.865 0.715     0.117     0.020        2     0.3  S_orbital_lateral
  506    392    758  2.130 0.479     0.150     0.033        6     0.6  S_orbital_med-olfact
 1543   1064   2914  2.900 0.746     0.125     0.034       14     2.0  S_orbital-H_Shaped
 2380   1654   3985  2.444 0.554     0.101     0.023       19     2.3  S_parieto_occipital
 1532    959   1995  2.641 0.775     0.129     0.027       21     1.5  S_pericallosal
 4391   2952   7081  2.583 0.593     0.099     0.017       26     2.9  S_postcentral
 1891   1343   3443  2.605 0.540     0.090     0.013       13     1.1  S_precentral-inf-part
 1478   1047   2661  2.858 0.587     0.087     0.014        6     0.8  S_precentral-sup-part
  663    474   1564  3.451 0.708     0.108     0.022        3     0.6  S_suborbital
  899    680   1653  2.750 0.474     0.127     0.024        8     0.8  S_subparietal
 2073   1484   3222  2.642 0.511     0.109     0.018       11     1.8  S_temporal_inf
 6488   4458  11661  2.727 0.609     0.099     0.019       42     4.6  S_temporal_sup
  472    316    660  2.517 0.433     0.099     0.013        3     0.2  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 0050310 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315565
Total vertex volume 311618 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1165    806   3157  3.015 0.824     0.168     0.061       25     3.1  G&S_frontomargin
 1519   1004   3120  2.316 0.794     0.154     0.062       39     4.4  G&S_occipital_inf
 1572   1020   3171  2.591 0.895     0.122     0.033       15     2.2  G&S_paracentral
 2005   1337   4453  2.819 0.551     0.134     0.033       29     2.6  G&S_subcentral
 1097    811   3689  3.012 0.801     0.184     0.062       27     2.9  G&S_transv_frontopol
 3043   2122   6970  2.863 0.799     0.121     0.030       33     3.9  G&S_cingul-Ant
 1312    935   2900  2.982 0.512     0.109     0.022       11     1.1  G&S_cingul-Mid-Ant
 1829   1261   3571  2.797 0.562     0.135     0.035       21     2.7  G&S_cingul-Mid-Post
  733    504   2380  3.215 0.855     0.165     0.050       13     1.6  G_cingul-Post-dorsal
  383    258    823  2.357 0.896     0.163     0.074       17     1.1  G_cingul-Post-ventral
 2304   1513   3685  2.167 0.707     0.161     0.046       40     4.4  G_cuneus
 2092   1527   5216  2.697 0.622     0.146     0.037       36     3.4  G_front_inf-Opercular
  405    300   1285  2.773 0.631     0.170     0.046       12     1.0  G_front_inf-Orbital
 1300    940   3742  2.840 0.819     0.167     0.060       33     3.4  G_front_inf-Triangul
 5509   3536  14847  2.988 0.743     0.141     0.050      105    11.8  G_front_middle
 7900   5201  21523  3.078 0.854     0.147     0.050      129    17.9  G_front_sup
  708    479   1589  3.184 0.830     0.136     0.042        9     1.1  G_Ins_lg&S_cent_ins
  672    449   1861  3.280 0.822     0.162     0.051       13     1.5  G_insular_short
 2381   1602   7065  3.093 0.915     0.157     0.054       47     5.3  G_occipital_middle
 1644   1130   3291  2.304 0.632     0.152     0.048       27     3.4  G_occipital_sup
 2228   1499   5543  2.924 0.640     0.151     0.043       41     4.3  G_oc-temp_lat-fusifor
 3435   2360   6287  2.237 0.725     0.171     0.056       69     7.8  G_oc-temp_med-Lingual
 1347    887   3595  2.934 0.964     0.126     0.044       18     2.3  G_oc-temp_med-Parahip
 3034   2073   7664  2.772 0.726     0.159     0.055       64     7.7  G_orbital
 4763   3106  12569  2.852 0.807     0.142     0.043       81     8.2  G_pariet_inf-Angular
 3551   2403   9416  3.015 0.724     0.142     0.041       59     6.0  G_pariet_inf-Supramar
 3246   1970   6927  2.536 0.743     0.139     0.059       55     8.2  G_parietal_sup
 2867   1601   4268  2.144 0.604     0.113     0.041       41     5.1  G_postcentral
 3562   1951   6606  2.656 0.665     0.127     0.053       49     8.2  G_precentral
 3281   2228   7933  2.767 0.662     0.127     0.028       44     3.9  G_precuneus
  744    528   1901  2.436 0.726     0.154     0.053       18     1.6  G_rectus
  572    348    749  2.305 0.851     0.079     0.031        4     0.5  G_subcallosal
  458    309    916  2.555 0.721     0.133     0.041        7     0.7  G_temp_sup-G_T_transv
 1868   1355   5352  2.904 0.834     0.152     0.060       38     4.9  G_temp_sup-Lateral
  588    481   1737  3.178 0.789     0.110     0.030        4     0.7  G_temp_sup-Plan_polar
 1048    737   2299  2.808 0.591     0.104     0.021        9     1.0  G_temp_sup-Plan_tempo
 3027   2015   9196  3.134 0.886     0.153     0.058       60     7.1  G_temporal_inf
 3776   2608  11371  3.045 0.823     0.157     0.049       87     8.6  G_temporal_middle
  387    266    570  2.507 0.526     0.082     0.009        2     0.1  Lat_Fis-ant-Horizont
  200    146    341  2.786 0.435     0.095     0.020        1     0.1  Lat_Fis-ant-Vertical
 1459    997   2268  2.669 0.474     0.106     0.021        9     1.1  Lat_Fis-post
 3614   2293   4555  1.892 0.592     0.147     0.043       68     6.2  Pole_occipital
 1719   1251   6575  3.355 0.858     0.163     0.049       30     3.9  Pole_temporal
 3110   2125   4094  2.109 0.723     0.128     0.028       33     3.5  S_calcarine
 3237   2183   3855  2.071 0.697     0.088     0.016       16     2.0  S_central
 1501   1007   2480  2.654 0.650     0.097     0.015        9     0.9  S_cingul-Marginalis
  445    296    839  3.093 0.545     0.085     0.014        1     0.3  S_circular_insula_ant
  940    640   1462  2.646 0.624     0.090     0.017        4     0.7  S_circular_insula_inf
 1501   1044   2529  2.928 0.595     0.111     0.019        8     1.3  S_circular_insula_sup
 1074    743   1782  2.671 0.494     0.102     0.018        6     0.8  S_collat_transv_ant
  392    272    545  2.424 0.424     0.126     0.022        3     0.4  S_collat_transv_post
 3154   2189   5903  2.656 0.602     0.117     0.025       30     2.9  S_front_inf
 2082   1457   3549  2.684 0.528     0.106     0.025       16     2.1  S_front_middle
 2608   1826   4925  2.890 0.550     0.100     0.018       16     1.9  S_front_sup
  650    440   1079  3.025 0.524     0.111     0.023        4     0.5  S_interm_prim-Jensen
 4438   3089   6975  2.454 0.487     0.093     0.016       24     2.8  S_intrapariet&P_trans
  823    601   1180  2.226 0.365     0.110     0.018        5     0.6  S_oc_middle&Lunatus
 1910   1342   2884  2.508 0.550     0.123     0.025       17     2.0  S_oc_sup&transversal
  673    460   1250  3.118 0.470     0.090     0.017        3     0.4  S_occipital_ant
 1265    862   1900  2.717 0.562     0.109     0.019       10     0.9  S_oc-temp_lat
 2205   1572   3498  2.498 0.493     0.105     0.019       14     1.7  S_oc-temp_med&Lingual
  386    267    516  2.169 0.500     0.113     0.026        3     0.3  S_orbital_lateral
  620    465    868  2.172 0.528     0.134     0.026        7     0.6  S_orbital_med-olfact
 1533   1066   2892  2.740 0.617     0.137     0.032       21     1.9  S_orbital-H_Shaped
 2479   1677   4103  2.696 0.698     0.110     0.022       19     2.3  S_parieto_occipital
 1449    926   1713  2.260 0.719     0.136     0.025       23     1.2  S_pericallosal
 3680   2527   5404  2.423 0.546     0.099     0.019       25     2.9  S_postcentral
 2305   1614   3817  2.573 0.562     0.110     0.022       18     2.1  S_precentral-inf-part
 1657   1145   2828  2.897 0.440     0.104     0.017        8     1.3  S_precentral-sup-part
  353    258    763  3.337 0.843     0.105     0.014        2     0.2  S_suborbital
 1384    982   2777  2.977 0.546     0.116     0.026       10     1.3  S_subparietal
 1403    974   2326  2.795 0.560     0.105     0.022        8     1.2  S_temporal_inf
 7934   5614  15315  3.004 0.612     0.105     0.018       51     5.9  S_temporal_sup
  346    242    588  3.235 0.719     0.136     0.018        3     0.3  S_temporal_transverse
PIDs (25267 25270) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 08:35:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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 08:35:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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 25327 of (25327 25330) to complete...
Waiting for PID 25330 of (25327 25330) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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...
1309 labels changed using aseg
relabeling using gibbs priors...
000:   2284 changed, 153035 examined...
001:    501 changed, 10461 examined...
002:    143 changed, 2879 examined...
003:     47 changed, 877 examined...
004:     22 changed, 301 examined...
005:      7 changed, 150 examined...
006:      9 changed, 40 examined...
007:      4 changed, 51 examined...
008:      4 changed, 24 examined...
009:      3 changed, 22 examined...
010:      3 changed, 15 examined...
011:      2 changed, 19 examined...
012:      1 changed, 14 examined...
013:      1 changed, 7 examined...
014:      0 changed, 7 examined...
156 labels changed using aseg
000: 61 total segments, 28 labels (262 vertices) changed
001: 35 total segments, 2 labels (4 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 10 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
901 vertices marked for relabeling...
901 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050310 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...
1418 labels changed using aseg
relabeling using gibbs priors...
000:   2188 changed, 155154 examined...
001:    484 changed, 10088 examined...
002:    128 changed, 2810 examined...
003:     51 changed, 765 examined...
004:     20 changed, 303 examined...
005:      9 changed, 112 examined...
006:      7 changed, 61 examined...
007:      6 changed, 41 examined...
008:      8 changed, 25 examined...
009:      3 changed, 31 examined...
010:      0 changed, 21 examined...
142 labels changed using aseg
000: 65 total segments, 32 labels (220 vertices) changed
001: 35 total segments, 2 labels (3 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
746 vertices marked for relabeling...
746 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.
PIDs (25327 25330) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 08:35:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 08:35:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 rh white 

Waiting for PID 25387 of (25387 25390) to complete...
Waiting for PID 25390 of (25387 25390) 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 0050310 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315041
Total vertex volume 311966 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 2109   1412   4484  3.097 0.611     0.121     0.025       23     2.0  caudalanteriorcingulate
 3703   2495   8085  2.978 0.685     0.107     0.026       29     3.8  caudalmiddlefrontal
 3269   2300   5231  2.032 0.592     0.151     0.048       64     6.8  cuneus
  630    435   1394  2.357 0.902     0.153     0.054       11     1.4  entorhinal
 5012   3514  11077  2.827 0.703     0.137     0.036       69     7.5  fusiform
 9064   6036  17862  2.611 0.704     0.126     0.038      120    14.4  inferiorparietal
 6334   4367  16554  2.885 0.835     0.137     0.045      102    12.1  inferiortemporal
 1606   1108   3149  2.743 0.794     0.135     0.034       20     2.3  isthmuscingulate
 8777   5781  15229  2.316 0.669     0.139     0.039      140    14.1  lateraloccipital
 4833   3255  10777  2.818 0.807     0.150     0.053       84    10.8  lateralorbitofrontal
 5114   3713   8940  2.315 0.735     0.165     0.043       83     9.6  lingual
 2131   1523   5081  2.769 0.880     0.152     0.056       46     5.3  medialorbitofrontal
 6671   4805  17371  2.849 0.723     0.142     0.041      111    11.4  middletemporal
 1051    696   2248  2.920 0.745     0.106     0.025       13     0.9  parahippocampal
 3081   2113   6815  2.862 0.794     0.115     0.024       25     3.0  paracentral
 3061   2174   7163  2.903 0.512     0.125     0.030       42     3.8  parsopercularis
 1133    812   3033  2.975 0.686     0.139     0.031       16     1.3  parsorbitalis
 2628   1869   6275  2.832 0.639     0.128     0.032       31     3.6  parstriangularis
 2606   1808   3059  1.775 0.533     0.147     0.038       38     4.3  pericalcarine
 8564   5559  13508  2.278 0.746     0.108     0.026       80     8.8  postcentral
 2463   1648   4923  2.883 0.746     0.128     0.028       27     2.7  posteriorcingulate
 8425   5332  15927  2.786 0.672     0.111     0.033       82    11.9  precentral
 5943   4189  13074  2.774 0.632     0.127     0.032       77     7.8  precuneus
 1639   1124   3414  2.920 0.824     0.121     0.035       25     2.4  rostralanteriorcingulate
 6800   4686  16774  2.923 0.720     0.130     0.033       91     9.2  rostralmiddlefrontal
12458   8571  32698  3.110 0.794     0.138     0.041      173    21.5  superiorfrontal
 8657   5735  15389  2.395 0.610     0.119     0.034      110    12.9  superiorparietal
 7536   5350  18409  2.828 0.755     0.119     0.033       92    10.6  superiortemporal
 7277   4985  16021  2.924 0.631     0.128     0.030       91     9.0  supramarginal
  734    508   1467  2.545 0.476     0.154     0.047       13     1.5  transversetemporal
 2872   1977   6537  3.327 0.771     0.121     0.030       25     3.6  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 0050310 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 315565
Total vertex volume 311618 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1224    842   2754  2.905 0.635     0.142     0.029       20     1.4  caudalanteriorcingulate
 5148   3311  10332  2.832 0.654     0.123     0.040       64     8.9  caudalmiddlefrontal
 3071   2023   5023  2.318 0.651     0.149     0.039       47     4.9  cuneus
  560    398   1671  3.038 0.727     0.120     0.039        7     0.7  entorhinal
 4360   3032   8894  2.669 0.659     0.138     0.036       61     6.6  fusiform
11122   7500  24518  2.847 0.729     0.123     0.032      127    14.4  inferiorparietal
 5816   3897  14945  3.016 0.810     0.132     0.042       82     9.8  inferiortemporal
 1382    938   2950  2.666 0.935     0.124     0.035       24     1.7  isthmuscingulate
 7514   4982  13543  2.362 0.753     0.144     0.045      136    14.1  lateraloccipital
 4535   3098   9839  2.738 0.740     0.149     0.047       80     9.2  lateralorbitofrontal
 5510   3850   9608  2.286 0.715     0.156     0.047       91    10.7  lingual
 2050   1445   4706  2.723 0.866     0.132     0.039       32     3.1  medialorbitofrontal
 7386   5201  18952  3.056 0.753     0.138     0.036      115    12.2  middletemporal
 1101    697   2378  2.897 0.799     0.091     0.021        7     0.8  parahippocampal
 3028   1990   6053  2.760 0.717     0.113     0.027       27     3.5  paracentral
 3132   2210   6503  2.640 0.621     0.127     0.032       38     4.4  parsopercularis
  970    679   2496  2.840 0.725     0.140     0.039       21     1.5  parsorbitalis
 2606   1877   6137  2.732 0.698     0.141     0.041       44     4.6  parstriangularis
 2738   1837   2918  1.733 0.527     0.138     0.031       33     3.5  pericalcarine
 8389   5277  13039  2.239 0.707     0.109     0.030       89    10.7  postcentral
 2255   1539   4833  2.835 0.720     0.142     0.034       30     3.3  posteriorcingulate
 8689   5562  15828  2.647 0.593     0.118     0.034       91    12.2  precentral
 6905   4709  14114  2.751 0.679     0.122     0.028       76     7.8  precuneus
 1203    831   2556  2.700 0.896     0.116     0.026       12     1.4  rostralanteriorcingulate
 6876   4706  15985  2.829 0.696     0.130     0.035       98     9.9  rostralmiddlefrontal
14046   9599  34949  2.985 0.783     0.136     0.042      193    26.0  superiorfrontal
 8292   5549  15098  2.411 0.621     0.121     0.038       99    13.1  superiorparietal
 7056   5073  17408  2.986 0.731     0.121     0.034       80    10.3  superiortemporal
 7466   5062  16423  2.885 0.698     0.122     0.030       86     9.0  supramarginal
  495    333    944  2.654 0.719     0.148     0.042        8     0.8  transversetemporal
 2959   2003   6219  3.107 0.721     0.129     0.032       32     3.8  insula
PIDs (25387 25390) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 08:36:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 pctsurfcon --s 0050310 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 08:36:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts

 pctsurfcon --s 0050310 --rh-only 

Waiting for PID 25448 of (25448 25458) to complete...
Waiting for PID 25458 of (25448 25458) to complete...

 pctsurfcon --s 0050310 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts/pctsurfcon.log
Sun Oct  8 08:36:07 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-6.0.0/0050310/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-948 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-6.0.0/0050310/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25448/lh.wm.mgh --regheader 0050310 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 75758
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25448/lh.wm.mgh
Dim: 153035 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25448/lh.gm.mgh --projfrac 0.3 --regheader 0050310 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 91470
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25448/lh.gm.mgh
Dim: 153035 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25448/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25448/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.w-g.pct.mgh --annot 0050310 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/lh.w-g.pct.mgh --annot 0050310 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/lh.w-g.pct.mgh
Vertex Area is 0.681915 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 0050310 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/scripts/pctsurfcon.log
Sun Oct  8 08:36:07 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-6.0.0/0050310/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-948 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-6.0.0/0050310/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25458/rh.wm.mgh --regheader 0050310 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 76613
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25458/rh.wm.mgh
Dim: 155154 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25458/rh.gm.mgh --projfrac 0.3 --regheader 0050310 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 92086
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25458/rh.gm.mgh
Dim: 155154 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25458/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/tmp.pctsurfcon.25458/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.w-g.pct.mgh --annot 0050310 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.w-g.pct.mgh --annot 0050310 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.w-g.pct.mgh
Vertex Area is 0.676292 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 (25448 25458) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 08:36:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2480 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2297 voxels changed to hypointensity...
4936 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 08:36:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310

 mri_aparc2aseg --s 0050310 --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 08:36:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310

 mri_aparc2aseg --s 0050310 --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 08:36:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310

 mri_aparc2aseg --s 0050310 --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 25620 of (25620 25623 25626) to complete...
Waiting for PID 25623 of (25620 25623 25626) to complete...
Waiting for PID 25626 of (25620 25623 25626) to complete...

 mri_aparc2aseg --s 0050310 --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 0050310
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/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-6.0.0/0050310/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 7.12
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 62
rescaling Left_Lateral_Ventricle from 13 --> 20
rescaling Left_Inf_Lat_Vent from 34 --> 28
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 65
rescaling Left_Thalamus from 94 --> 100
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 75
rescaling Left_Pallidum from 98 --> 92
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 59
rescaling Left_Amygdala from 56 --> 64
rescaling CSF from 32 --> 36
rescaling Left_Accumbens_area from 62 --> 58
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 62
rescaling Right_Lateral_Ventricle from 13 --> 15
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 63
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 71
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 59
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 69
rescaling Right_VentralDC from 86 --> 91
rescaling Fifth_Ventricle from 40 --> 32
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 618039
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 123 changed.
pass 2: 10 changed.
pass 3: 6 changed.
pass 4: 2 changed.
pass 5: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050310 --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 0050310
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/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-6.0.0/0050310/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 7.12
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 62
rescaling Left_Lateral_Ventricle from 13 --> 20
rescaling Left_Inf_Lat_Vent from 34 --> 28
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 65
rescaling Left_Thalamus from 94 --> 100
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 75
rescaling Left_Pallidum from 98 --> 92
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 59
rescaling Left_Amygdala from 56 --> 64
rescaling CSF from 32 --> 36
rescaling Left_Accumbens_area from 62 --> 58
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 62
rescaling Right_Lateral_Ventricle from 13 --> 15
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 63
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 71
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 59
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 69
rescaling Right_VentralDC from 86 --> 91
rescaling Fifth_Ventricle from 40 --> 32
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 617801
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 123 changed.
pass 2: 10 changed.
pass 3: 6 changed.
pass 4: 2 changed.
pass 5: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050310 --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 0050310
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/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-6.0.0/0050310/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 7.12
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 62
rescaling Left_Lateral_Ventricle from 13 --> 20
rescaling Left_Inf_Lat_Vent from 34 --> 28
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 65
rescaling Left_Thalamus from 94 --> 100
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 75
rescaling Left_Pallidum from 98 --> 92
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 59
rescaling Left_Amygdala from 56 --> 64
rescaling CSF from 32 --> 36
rescaling Left_Accumbens_area from 62 --> 58
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 62
rescaling Right_Lateral_Ventricle from 13 --> 15
rescaling Right_Inf_Lat_Vent from 25 --> 25
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 63
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 71
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 59
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 69
rescaling Right_VentralDC from 86 --> 91
rescaling Fifth_Ventricle from 40 --> 32
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 617801
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 123 changed.
pass 2: 10 changed.
pass 3: 6 changed.
pass 4: 2 changed.
pass 5: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (25620 25623 25626) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 08:44:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri

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

Sun Oct  8 08:44:51 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-6.0.0/0050310/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-948 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-6.0.0/0050310/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-948
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 08:44:51 CEST 2017 
Ended   at Sun Oct  8 08:44:57 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 08:44:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310

 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 0050310 


$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 0050310 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1581221 mm^3    (det: 1.232026 )
Computing euler number
orig.nofix lheno = -170, rheno = -198
orig.nofix lhholes =   86, rhholes = 100
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
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 08:46:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310

 mri_aparc2aseg --s 0050310 --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 0050310
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-6.0.0/0050310/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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-6.0.0/0050310/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 6848 vertices from left hemi
Ripped 7121 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-6.0.0/0050310/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 = 1074269
Used brute-force search on 31 voxels
Fixing Parahip LH WM
  Found 14 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 2.000000
     4 k 1.000000
     5 k 1372.000000
     6 k 1.000000
     7 k 1.000000
     8 k 22.000000
     9 k 1.000000
     10 k 2.000000
     11 k 1.000000
     12 k 1.000000
     13 k 2.000000
Fixing Parahip RH WM
  Found 7 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 2.000000
     3 k 18.000000
     4 k 4.000000
     5 k 1454.000000
     6 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050310 --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 0050310 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-948
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1581221 mm^3    (det: 1.232026 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
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-6.0.0/0050310/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 08:55:57 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 26438 of (26438 26444 26450 26456 26462) to complete...
Waiting for PID 26444 of (26438 26444 26450 26456 26462) to complete...
Waiting for PID 26450 of (26438 26444 26450 26456 26462) to complete...
Waiting for PID 26456 of (26438 26444 26450 26456 26462) to complete...
Waiting for PID 26462 of (26438 26444 26450 26456 26462) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 522
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4651
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1219
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9128
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 240
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4317
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 536
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6519
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 839
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6623
mri_label2label: Done

PIDs (26438 26444 26450 26456 26462) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 26532 of (26532 26538 26544 26550) to complete...
Waiting for PID 26538 of (26532 26538 26544 26550) to complete...
Waiting for PID 26544 of (26532 26538 26544 26550) to complete...
Waiting for PID 26550 of (26532 26538 26544 26550) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 405
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4475
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1896
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15485
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 794
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4975
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1008
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4430
mri_label2label: Done

PIDs (26532 26538 26544 26550) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 26595 of (26595 26601 26607 26613 26619) to complete...
Waiting for PID 26601 of (26595 26601 26607 26613 26619) to complete...
Waiting for PID 26607 of (26595 26601 26607 26613 26619) to complete...
Waiting for PID 26613 of (26595 26601 26607 26613 26619) to complete...
Waiting for PID 26619 of (26595 26601 26607 26613 26619) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1986
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6627
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 3540
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11654
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 647
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2665
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 181
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1471
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 148
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1347
mri_label2label: Done

PIDs (26595 26601 26607 26613 26619) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 26827 of (26827 26833 26839 26845 26851) to complete...
Waiting for PID 26833 of (26827 26833 26839 26845 26851) to complete...
Waiting for PID 26839 of (26827 26833 26839 26845 26851) to complete...
Waiting for PID 26845 of (26827 26833 26839 26845 26851) to complete...
Waiting for PID 26851 of (26827 26833 26839 26845 26851) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 189
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1203
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 298
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2390
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 120
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1624
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 109
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2105
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 376
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2695
mri_label2label: Done

PIDs (26827 26833 26839 26845 26851) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 26893 of (26893 26899 26905 26911) to complete...
Waiting for PID 26899 of (26893 26899 26905 26911) to complete...
Waiting for PID 26905 of (26893 26899 26905 26911) to complete...
Waiting for PID 26911 of (26893 26899 26905 26911) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 95
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1644
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1061
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8096
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 455
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2367
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 409
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1560
mri_label2label: Done

PIDs (26893 26899 26905 26911) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 26962 of (26962 26968 26974 26980 26986) to complete...
Waiting for PID 26968 of (26962 26968 26974 26980 26986) to complete...
Waiting for PID 26974 of (26962 26968 26974 26980 26986) to complete...
Waiting for PID 26980 of (26962 26968 26974 26980 26986) to complete...
Waiting for PID 26986 of (26962 26968 26974 26980 26986) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1456
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4861
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 1532
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4866
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 155
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 668
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 89
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 559
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 153035
Number of reverse mapping hits = 50
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 500
mri_label2label: Done

PIDs (26962 26968 26974 26980 26986) completed and logs appended.

 mris_label2annot --s 0050310 --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-6.0.0/0050310/label
cmdline mris_label2annot --s 0050310 --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-948
machine  x86_64
user     ntraut

subject 0050310
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-6.0.0/0050310/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 104882 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050310 --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-6.0.0/0050310/label
cmdline mris_label2annot --s 0050310 --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-948
machine  x86_64
user     ntraut

subject 0050310
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-6.0.0/0050310/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 124300 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 315041
Total vertex volume 311966 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1402    787   2087  2.100 0.686     0.126     0.041       20     2.4  BA1_exvivo
 5371   3520   8899  2.507 0.609     0.099     0.019       38     4.3  BA2_exvivo
 1252    827   1320  2.058 0.538     0.127     0.023       11     1.1  BA3a_exvivo
 2616   1779   4032  2.089 0.897     0.091     0.018       17     1.8  BA3b_exvivo
 2058   1278   4211  2.794 0.759     0.110     0.040       19     4.5  BA4a_exvivo
 1500    981   2612  2.857 0.554     0.085     0.020        7     1.1  BA4p_exvivo
10333   6790  23774  2.997 0.780     0.125     0.039      118    16.6  BA6_exvivo
 3017   2127   6965  2.824 0.561     0.125     0.032       40     3.9  BA44_exvivo
 3364   2428   8197  2.778 0.678     0.128     0.032       43     4.5  BA45_exvivo
 4310   2987   5273  1.737 0.504     0.153     0.042       69     8.0  V1_exvivo
 9199   6350  15259  2.232 0.642     0.161     0.047      174    19.0  V2_exvivo
 2332   1578   4735  2.555 0.686     0.136     0.041       34     3.8  MT_exvivo
  637    421   1429  2.515 0.826     0.136     0.051        9     1.3  perirhinal_exvivo
  762    564   2266  2.962 0.954     0.152     0.048       12     1.6  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 0050310 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 315041
Total vertex volume 311966 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
  972    490   1381  2.142 0.702     0.118     0.038       13     1.6  BA1_exvivo
 2015   1301   3222  2.369 0.630     0.087     0.016       12     1.3  BA2_exvivo
 1110    718   1083  2.019 0.474     0.128     0.023       10     0.9  BA3a_exvivo
 1484   1043   1684  1.544 0.471     0.077     0.012        5     0.7  BA3b_exvivo
 2004   1234   3832  2.852 0.712     0.105     0.039       18     4.1  BA4a_exvivo
 1113    761   1970  2.736 0.570     0.080     0.018        4     0.6  BA4p_exvivo
 6157   3893  13456  2.920 0.800     0.127     0.044       72    11.2  BA6_exvivo
 1985   1435   4830  2.849 0.521     0.129     0.036       30     3.0  BA44_exvivo
 1428   1032   4142  2.948 0.702     0.148     0.042       27     2.3  BA45_exvivo
 4575   3153   5701  1.762 0.510     0.153     0.042       72     8.4  V1_exvivo
 4552   3178   7268  2.169 0.667     0.167     0.051       87    10.2  V2_exvivo
  600    410   1303  2.598 0.631     0.133     0.024        7     0.7  MT_exvivo
  352    217    741  2.409 0.919     0.143     0.064        7     0.9  perirhinal_exvivo
  388    290    868  2.666 0.848     0.123     0.028        3     0.5  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 08:59:22 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 27126 of (27126 27132 27138 27144 27150) to complete...
Waiting for PID 27132 of (27126 27132 27138 27144 27150) to complete...
Waiting for PID 27138 of (27126 27132 27138 27144 27150) to complete...
Waiting for PID 27144 of (27126 27132 27138 27144 27150) to complete...
Waiting for PID 27150 of (27126 27132 27138 27144 27150) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 711
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4673
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 963
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7650
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 187
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4167
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 537
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5059
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 767
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6514
mri_label2label: Done

PIDs (27126 27132 27138 27144 27150) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 27193 of (27193 27199 27209 27215) to complete...
Waiting for PID 27199 of (27193 27199 27209 27215) to complete...
Waiting for PID 27209 of (27193 27199 27209 27215) to complete...
Waiting for PID 27215 of (27193 27199 27209 27215) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 246
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4719
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 2049
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14305
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 2098
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 9010
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 1645
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7000
mri_label2label: Done

PIDs (27193 27199 27209 27215) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 27285 of (27285 27291 27297 27303 27309) to complete...
Waiting for PID 27291 of (27285 27291 27297 27303 27309) to complete...
Waiting for PID 27297 of (27285 27291 27297 27303 27309) to complete...
Waiting for PID 27303 of (27285 27291 27297 27303 27309) to complete...
Waiting for PID 27309 of (27285 27291 27297 27303 27309) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 2188
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6915
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 3281
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11297
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 523
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2455
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 166
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1204
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 101
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 853
mri_label2label: Done

PIDs (27285 27291 27297 27303 27309) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27359 of (27359 27365 27371 27377 27383) to complete...
Waiting for PID 27365 of (27359 27365 27371 27377 27383) to complete...
Waiting for PID 27371 of (27359 27365 27371 27377 27383) to complete...
Waiting for PID 27377 of (27359 27365 27371 27377 27383) to complete...
Waiting for PID 27383 of (27359 27365 27371 27377 27383) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 212
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1088
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 291
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2979
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 52
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1750
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 241
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2424
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 187
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1575
mri_label2label: Done

PIDs (27359 27365 27371 27377 27383) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27448 of (27448 27454 27460 27466) to complete...
Waiting for PID 27454 of (27448 27454 27460 27466) to complete...
Waiting for PID 27460 of (27448 27454 27460 27466) to complete...
Waiting for PID 27466 of (27448 27454 27460 27466) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 64
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1553
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 1294
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8253
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 378
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1390
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 252
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1430
mri_label2label: Done

PIDs (27448 27454 27460 27466) 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 0050310 --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 0050310 --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 0050310 --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 0050310 --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 0050310 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 27531 of (27531 27537 27543 27549 27555) to complete...
Waiting for PID 27537 of (27531 27537 27543 27549 27555) to complete...
Waiting for PID 27543 of (27531 27537 27543 27549 27555) to complete...
Waiting for PID 27549 of (27531 27537 27543 27549 27555) to complete...
Waiting for PID 27555 of (27531 27537 27543 27549 27555) 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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 1513
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4745
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 1680
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5117
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 34
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 302
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 798
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 0050310 --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 = 0050310
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-6.0.0/0050310/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 155154
Number of reverse mapping hits = 41
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 332
mri_label2label: Done

PIDs (27531 27537 27543 27549 27555) completed and logs appended.

 mris_label2annot --s 0050310 --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-6.0.0/0050310/label
cmdline mris_label2annot --s 0050310 --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-948
machine  x86_64
user     ntraut

subject 0050310
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-6.0.0/0050310/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 107097 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050310 --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-6.0.0/0050310/label
cmdline mris_label2annot --s 0050310 --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-948
machine  x86_64
user     ntraut

subject 0050310
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-6.0.0/0050310/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 128039 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/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 0050310 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 315565
Total vertex volume 311618 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
 1226    673   2064  2.255 0.590     0.146     0.054       23     3.1  BA1_exvivo
 4097   2661   6297  2.471 0.557     0.094     0.019       24     3.2  BA2_exvivo
 1105    771   1218  2.037 0.486     0.133     0.028       10     1.1  BA3a_exvivo
 2417   1506   3051  1.735 0.644     0.097     0.030       26     3.1  BA3b_exvivo
 1789   1135   3512  2.844 0.747     0.110     0.029       14     2.3  BA4a_exvivo
 1221    828   2019  2.577 0.639     0.088     0.021        7     1.0  BA4p_exvivo
 9502   5972  19435  2.799 0.733     0.131     0.049      126    21.3  BA6_exvivo
 5235   3676  10742  2.668 0.603     0.126     0.029       63     6.2  BA44_exvivo
 5067   3553  12121  2.765 0.713     0.136     0.037       79     8.0  BA45_exvivo
 4674   3114   5627  1.782 0.585     0.148     0.037       79     7.4  V1_exvivo
 8576   5764  14266  2.274 0.677     0.154     0.047      140    16.4  V2_exvivo
 2113   1438   4648  2.857 0.780     0.129     0.038       31     3.6  MT_exvivo
  646    430   1940  3.160 0.705     0.113     0.040        8     0.9  perirhinal_exvivo
  389    292   1174  3.092 0.988     0.128     0.034        3     0.5  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050310 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050310/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 315565
Total vertex volume 311618 (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) = 1581221 mm^3    (det: 1.232026 )
lhCtxGM: 309184.153 309021.000  diff=  163.2  pctdiff= 0.053
rhCtxGM: 309756.464 309208.000  diff=  548.5  pctdiff= 0.177
lhCtxWM: 228360.675 228811.500  diff= -450.8  pctdiff=-0.197
rhCtxWM: 229233.873 230217.500  diff= -983.6  pctdiff=-0.429
SubCortGMVol  63002.000
SupraTentVol  1151149.165 (1148703.000) diff=2446.165 pctdiff=0.212
SupraTentVolNotVent  1142709.165 (1140263.000) diff=2446.165 pctdiff=0.214
BrainSegVol  1292045.000 (1289517.000) diff=2528.000 pctdiff=0.196
BrainSegVolNotVent  1280342.000 (1279476.165) diff=865.835 pctdiff=0.068
BrainSegVolNotVent  1280342.000
CerebellumVol 139936.000
VentChorVol    8440.000
3rd4th5thCSF   3263.000
CSFVol   735.000, OptChiasmVol   143.000
MaskVol 1622526.000
  879    464   1351  2.179 0.586     0.130     0.044       14     1.8  BA1_exvivo
 2294   1475   3722  2.389 0.512     0.085     0.017       11     1.7  BA2_exvivo
 1008    688    974  1.996 0.456     0.133     0.027       10     1.0  BA3a_exvivo
 1824   1157   1868  1.547 0.493     0.083     0.020       11     1.4  BA3b_exvivo
 1137    726   2367  2.922 0.786     0.129     0.041       13     2.0  BA4a_exvivo
 1004    686   1732  2.715 0.536     0.080     0.017        4     0.6  BA4p_exvivo
 6275   3881  11928  2.729 0.709     0.133     0.052       85    14.7  BA6_exvivo
 1257    923   3022  2.591 0.724     0.152     0.039       24     2.5  BA44_exvivo
 1238    914   3451  2.868 0.703     0.129     0.035       16     1.6  BA45_exvivo
 4474   3000   5246  1.764 0.565     0.145     0.036       65     6.7  V1_exvivo
 4808   3175   7590  2.154 0.617     0.160     0.051       91    10.1  V2_exvivo
  246    177    765  3.244 0.510     0.108     0.024        2     0.2  MT_exvivo
  416    257   1291  3.266 0.731     0.099     0.033        5     0.5  perirhinal_exvivo
  255    206    697  3.201 1.003     0.128     0.030        2     0.3  entorhinal_exvivo

Started at Sat Oct 7 23:29:49 CEST 2017 
Ended   at Sun Oct 8 09:02:48 CEST 2017
#@#%# recon-all-run-time-hours 9.550
recon-all -s 0050310 finished without error at Sun Oct  8 09:02:48 CEST 2017