ABIDE_fs-6.0.0/0050267/scripts/recon-all.log

Sat Oct  7 20:02:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050267 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050267/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050267
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-960 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   52988928   13085908    1770996          0   43433520
-/+ buffers/cache:    9555408   56519428
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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:22-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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: 2017/10/07-18:02:23-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-960  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-6.0.0/0050267

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050267/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050267/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050267/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-6.0.0/0050267/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 20:02:25 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/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-6.0.0/0050267/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 20:02:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/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-960 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 20:02:34 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.1211
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1211/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1211/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.1211/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 20:02:36 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.1211/nu0.mnc ./tmp.mri_nu_correct.mni.1211/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1211/0/ -iterations 1000 -distance 50
[ntraut@tars-960:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/] [2017-10-07 20:02:36] 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.1211/0/ ./tmp.mri_nu_correct.mni.1211/nu0.mnc ./tmp.mri_nu_correct.mni.1211/nu1.imp

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Number of iterations: 59 
CV of field change: 0.000977247
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.1211/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.1211/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.1211/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 20:03:57 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 20:03:57 CEST 2017
Ended   at Sat Oct  7 20:04:32 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 20:04:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6826, 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-6.0.0/0050267/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/transforms/talairach_avi.log 

TalAviQA: 0.97807
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 20:04:34 CEST 2017

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-960 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 20:04:34 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.2225
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2225/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2225/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.2225/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 20:04:37 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.2225/nu0.mnc ./tmp.mri_nu_correct.mni.2225/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2225/0/
[ntraut@tars-960:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/] [2017-10-07 20:04:37] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2225/0/ ./tmp.mri_nu_correct.mni.2225/nu0.mnc ./tmp.mri_nu_correct.mni.2225/nu1.imp

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Number of iterations: 48 
CV of field change: 0.00096588
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 20:05:29 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.2225/nu1.mnc ./tmp.mri_nu_correct.mni.2225/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2225/1/
[ntraut@tars-960:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/] [2017-10-07 20:05:29] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2225/1/ ./tmp.mri_nu_correct.mni.2225/nu1.mnc ./tmp.mri_nu_correct.mni.2225/nu2.imp

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Number of iterations: 13 
CV of field change: 0.000972249
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.2225/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2225/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-6.0.0/0050267/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.2225/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2225/ones.mgz 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.2225/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.2225/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.2225/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2225/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2225/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.2225/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2225/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2225/input.mean.dat 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.2225/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.2225/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2225/ones.mgz --i ./tmp.mri_nu_correct.mni.2225/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2225/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2225/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.2225/ones.mgz --i ./tmp.mri_nu_correct.mni.2225/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2225/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2225/output.mean.dat 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.2225/ones.mgz
Loading ./tmp.mri_nu_correct.mni.2225/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.2225/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.2225/nu2.mnc ./tmp.mri_nu_correct.mni.2225/nu2.mnc mul .86005670073203183891
Saving result to './tmp.mri_nu_correct.mni.2225/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.2225/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.2225/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.2225/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping ( 5, 140) to ( 3, 110)
 
 
Sat Oct  7 20:06:37 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 20:06:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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
 0.99735  -0.00570   0.00327  -11.64098;
-0.01162   0.95538   0.25362  -4.73402;
-0.00704  -0.22421   1.03434  -7.52615;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 21
Starting OpenSpline(): npoints = 21
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 74 (74), valley at 24 (24)
csf peak at 38, setting threshold to 62
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 73 (73), valley at 22 (22)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 6 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 20:08:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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=15.0
skull bounding box = (46, 39, 10) --> (208, 192, 217)
using (100, 90, 114) as brain centroid...
mean wm in atlas = 108, using box (80,71,88) --> (119, 108,139) to find MRI wm
before smoothing, mri peak at 109
robust fit to distribution - 108 +- 4.8
after smoothing, mri peak at 109, scaling input intensities by 0.991
scaling channel 0 by 0.990826
initial log_p = -4.171
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.144979 @ (0.000, 0.000, 0.000)
max log p =    -4.106580 @ (-4.545, 4.545, -4.545)
max log p =    -4.106580 @ (0.000, 0.000, 0.000)
max log p =    -4.069807 @ (1.136, -3.409, 1.136)
max log p =    -4.052326 @ (2.841, 3.977, 0.568)
max log p =    -4.052326 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, 5.1, -2.8): log p = -4.052
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.935, old_max_log_p =-4.052 (thresh=-4.0)
 1.00000   0.00000   0.00000  -0.56818;
 0.00000   1.19413   0.31997  -50.39389;
 0.00000  -0.25882   0.96593   36.50940;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.935, old_max_log_p =-3.935 (thresh=-3.9)
 1.00000   0.00000   0.00000  -0.56818;
 0.00000   1.19413   0.31997  -50.39389;
 0.00000  -0.25882   0.96593   36.50940;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.876, old_max_log_p =-3.935 (thresh=-3.9)
 1.01734   0.04300   0.01015  -11.28180;
-0.02847   1.14590   0.21125  -31.85392;
-0.00210  -0.13788   0.97331   18.00837;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.876, old_max_log_p =-3.876 (thresh=-3.9)
 1.01734   0.04300   0.01015  -11.28180;
-0.02847   1.14590   0.21125  -31.85392;
-0.00210  -0.13788   0.97331   18.00837;
 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=-3.864, old_max_log_p =-3.876 (thresh=-3.9)
 1.01625   0.06680  -0.01787  -10.17895;
-0.04524   1.14523   0.22800  -32.49273;
 0.03158  -0.15475   0.96726   16.68289;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.862, old_max_log_p =-3.864 (thresh=-3.9)
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 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
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.862 (old=-4.171)
transform before final EM align:
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 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
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.3  tol 0.000000
final transform:
 1.01543   0.06449  -0.00198  -11.58925;
-0.04569   1.14627   0.21189  -29.78816;
 0.01415  -0.13659   0.96762   17.33002;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1006.769947
mri_em_register stimesec    0.950855
mri_em_register ru_maxrss   609824
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157572
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    63
mri_em_register ru_nivcsw   1630
registration took 8 minutes and 52 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=128 y=111 z=111 r=71
      first estimation of the main basin volume: 1543588 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=109, y=92, z=77, Imax=255
      CSF=13, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=9593237573 voxels, voxel volume =1.000 
                     = 9593237573 mmm3 = 9593237.504 cm3
done.
PostAnalyze...Basin Prior
 60 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=127,y=116, z=105, r=10258 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=5, CSF_MAX=28 , nb = 43966
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1032223160
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=36 , nb = -1047627314
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=5, CSF_MAX=26 , nb = 1094909257
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=5, CSF_MAX=26 , nb = 1081408852
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1071205222
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    28,      43,        54,   69
  after  analyzing :    28,      50,        54,   54
   RIGHT_CER   
  before analyzing :    24,      38,        52,   72
  after  analyzing :    24,      47,        52,   53
   LEFT_CER    
  before analyzing :    36,      46,        53,   73
  after  analyzing :    36,      50,        53,   55
  RIGHT_BRAIN  
  before analyzing :    26,      41,        53,   68
  after  analyzing :    26,      49,        53,   53
  LEFT_BRAIN   
  before analyzing :    26,      41,        53,   69
  after  analyzing :    26,      49,        53,   54
     OTHER     
  before analyzing :    3,      3,        19,   92
  after  analyzing :    3,      17,        25,   35
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...65 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 73.306, std = 7.591

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.24, sigma = 2.05
      after  rotation: sse = 1.24, sigma = 2.05
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  1.25, its var is  1.64   
      before Erosion-Dilatation  0.01% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

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

      mri_strip_skull: done peeling brain

Brain Size = 1927969 voxels, voxel volume = 1.000 mm3
           = 1927969 mmm3 = 1927.969 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    23.134483
mri_watershed stimesec    0.396939
mri_watershed ru_maxrss   822492
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   212963
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  3024
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1082
mri_watershed ru_nivcsw   47
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 20:17:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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=28.0
skull bounding box = (58, 51, 26) --> (196, 189, 199)
using (104, 97, 113) as brain centroid...
mean wm in atlas = 107, using box (87,80,92) --> (120, 113,134) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.2
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
initial log_p = -3.862
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.812278 @ (0.000, 0.000, 0.000)
max log p =    -3.812278 @ (0.000, 0.000, 0.000)
max log p =    -3.708219 @ (-2.273, 6.818, -2.273)
max log p =    -3.704608 @ (1.136, -1.136, -1.136)
max log p =    -3.691436 @ (-1.705, -1.705, 0.568)
max log p =    -3.691436 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, 4.0, -2.8): log p = -3.691
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.549, old_max_log_p =-3.691 (thresh=-3.7)
 1.00000   0.00000   0.00000  -2.84091;
 0.00000   1.03837   0.27823  -30.57557;
 0.00000  -0.23941   0.89348   36.30024;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.549, old_max_log_p =-3.549 (thresh=-3.5)
 1.00000   0.00000   0.00000  -2.84091;
 0.00000   1.03837   0.27823  -30.57557;
 0.00000  -0.23941   0.89348   36.30024;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.455, old_max_log_p =-3.549 (thresh=-3.5)
 0.99946   0.03421   0.00818  -5.72250;
-0.03211   1.02529   0.24515  -21.20374;
 0.00000  -0.20774   0.91865   33.60125;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.455, old_max_log_p =-3.455 (thresh=-3.5)
 1.01873   0.00090  -0.00084  -3.37500;
 0.00063   1.01851   0.27519  -27.73667;
 0.00107  -0.24570   0.92720   36.97640;
 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=-3.415, old_max_log_p =-3.455 (thresh=-3.5)
 1.01946   0.02288  -0.01983  -3.54461;
-0.01615   1.02823   0.24539  -24.07679;
 0.02612  -0.21213   0.93657   27.96510;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.415, old_max_log_p =-3.415 (thresh=-3.4)
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 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
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.415 (old=-3.862)
transform before final EM align:
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 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
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    3.9  tol 0.000000
final transform:
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    854.162147
mri_em_register stimesec    0.927858
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   158955
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    96
mri_em_register ru_nivcsw   1383
registration took 7 minutes and 25 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 20:25:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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=24.0
skull bounding box = (57, 50, 26) --> (196, 190, 199)
using (103, 97, 113) as brain centroid...
mean wm in atlas = 107, using box (86,80,92) --> (120, 114,134) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.2
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
using 246344 sample points...
INFO: compute sample coordinates transform
 1.02066   0.02291  -0.01985  -3.69727;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87430;
 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 (124, 53, 26) --> (191, 165, 197)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
1 of 4338 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 53, 26) --> (130, 160, 198)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 3973 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 141, 55) --> (174, 183, 111)
Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 137 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (82, 141, 53) --> (126, 179, 113)
Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0
0 of 93 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 127, 93) --> (144, 195, 124)
Brain_Stem: limiting intensities to 90.0 --> 132.0
0 of 110 (0.0%) samples deleted
using 8651 total control points for intensity normalization...
bias field = 0.972 +- 0.049
75 of 8650 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 53, 26) --> (191, 165, 197)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
3 of 5134 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 53, 26) --> (130, 160, 198)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
1 of 4703 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 141, 55) --> (174, 183, 111)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 224 (0.4%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (82, 141, 53) --> (126, 179, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 163 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 127, 93) --> (144, 195, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
36 of 194 (18.6%) samples deleted
using 10418 total control points for intensity normalization...
bias field = 1.039 +- 0.045
60 of 10280 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 53, 26) --> (191, 165, 197)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
3 of 5079 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 53, 26) --> (130, 160, 198)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
1 of 4755 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 141, 55) --> (174, 183, 111)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
67 of 290 (23.1%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (82, 141, 53) --> (126, 179, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
8 of 200 (4.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 127, 93) --> (144, 195, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
140 of 293 (47.8%) samples deleted
using 10617 total control points for intensity normalization...
bias field = 1.034 +- 0.040
52 of 10223 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 42 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 20:27:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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) = 1.04 (predicted orig area = 7.7)
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=0.792, neg=0, invalid=762
0001: dt=221.952000, rms=0.740 (6.454%), neg=0, invalid=762
0002: dt=203.191257, rms=0.725 (2.050%), neg=0, invalid=762
0003: dt=295.936000, rms=0.714 (1.565%), neg=0, invalid=762
0004: dt=129.472000, rms=0.710 (0.522%), neg=0, invalid=762
0005: dt=517.888000, rms=0.704 (0.910%), neg=0, invalid=762
0006: dt=129.472000, rms=0.702 (0.182%), neg=0, invalid=762
0007: dt=129.472000, rms=0.701 (0.146%), neg=0, invalid=762
0008: dt=129.472000, rms=0.700 (0.228%), neg=0, invalid=762
0009: dt=129.472000, rms=0.698 (0.275%), neg=0, invalid=762
0010: dt=129.472000, rms=0.696 (0.270%), neg=0, invalid=762
0011: dt=129.472000, rms=0.694 (0.244%), neg=0, invalid=762
0012: dt=129.472000, rms=0.693 (0.232%), neg=0, invalid=762
0013: dt=129.472000, rms=0.691 (0.199%), neg=0, invalid=762
0014: dt=129.472000, rms=0.690 (0.181%), neg=0, invalid=762
0015: dt=129.472000, rms=0.689 (0.157%), neg=0, invalid=762
0016: dt=129.472000, rms=0.688 (0.152%), neg=0, invalid=762
0017: dt=129.472000, rms=0.687 (0.163%), neg=0, invalid=762
0018: dt=129.472000, rms=0.686 (0.124%), neg=0, invalid=762
0019: dt=129.472000, rms=0.685 (0.085%), neg=0, invalid=762
0020: dt=517.888000, rms=0.685 (0.094%), neg=0, invalid=762
0021: dt=129.472000, rms=0.684 (0.062%), neg=0, invalid=762
0022: dt=129.472000, rms=0.684 (0.017%), neg=0, invalid=762
0023: dt=129.472000, rms=0.684 (0.036%), neg=0, invalid=762
0024: dt=129.472000, rms=0.684 (0.059%), neg=0, invalid=762
0025: dt=129.472000, rms=0.683 (0.064%), neg=0, invalid=762
0026: dt=129.472000, rms=0.683 (0.061%), neg=0, invalid=762
0027: dt=129.472000, rms=0.682 (0.044%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.683, neg=0, invalid=762
0028: dt=295.936000, rms=0.680 (0.425%), neg=0, invalid=762
0029: dt=369.920000, rms=0.679 (0.143%), neg=0, invalid=762
0030: dt=369.920000, rms=0.679 (0.056%), neg=0, invalid=762
0031: dt=369.920000, rms=0.677 (0.179%), neg=0, invalid=762
0032: dt=369.920000, rms=0.677 (0.129%), neg=0, invalid=762
0033: dt=369.920000, rms=0.675 (0.196%), neg=0, invalid=762
0034: dt=369.920000, rms=0.674 (0.143%), neg=0, invalid=762
0035: dt=369.920000, rms=0.673 (0.174%), neg=0, invalid=762
0036: dt=369.920000, rms=0.672 (0.103%), neg=0, invalid=762
0037: dt=369.920000, rms=0.672 (0.134%), neg=0, invalid=762
0038: dt=369.920000, rms=0.671 (0.085%), neg=0, invalid=762
0039: dt=369.920000, rms=0.670 (0.106%), neg=0, invalid=762
0040: dt=369.920000, rms=0.669 (0.123%), neg=0, invalid=762
0041: dt=369.920000, rms=0.669 (0.087%), neg=0, invalid=762
0042: dt=295.936000, rms=0.669 (0.038%), neg=0, invalid=762
0043: dt=295.936000, rms=0.669 (0.000%), neg=0, invalid=762
0044: dt=295.936000, rms=0.668 (0.026%), neg=0, invalid=762
0045: dt=295.936000, rms=0.668 (0.032%), neg=0, invalid=762
0046: dt=295.936000, rms=0.668 (0.038%), neg=0, invalid=762
0047: dt=295.936000, rms=0.668 (0.014%), neg=0, invalid=762
0048: dt=295.936000, rms=0.668 (0.020%), neg=0, invalid=762
0049: dt=295.936000, rms=0.667 (0.044%), neg=0, invalid=762
0050: dt=295.936000, rms=0.667 (0.018%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.673, neg=0, invalid=762
0051: dt=36.288000, rms=0.671 (0.265%), neg=0, invalid=762
0052: dt=103.680000, rms=0.670 (0.200%), neg=0, invalid=762
0053: dt=103.680000, rms=0.666 (0.548%), neg=0, invalid=762
0054: dt=103.680000, rms=0.661 (0.732%), neg=0, invalid=762
0055: dt=103.680000, rms=0.656 (0.704%), neg=0, invalid=762
0056: dt=103.680000, rms=0.652 (0.648%), neg=0, invalid=762
0057: dt=103.680000, rms=0.648 (0.641%), neg=0, invalid=762
0058: dt=103.680000, rms=0.644 (0.675%), neg=0, invalid=762
0059: dt=103.680000, rms=0.640 (0.537%), neg=0, invalid=762
0060: dt=103.680000, rms=0.637 (0.481%), neg=0, invalid=762
0061: dt=103.680000, rms=0.634 (0.504%), neg=0, invalid=762
0062: dt=103.680000, rms=0.631 (0.459%), neg=0, invalid=762
0063: dt=103.680000, rms=0.629 (0.291%), neg=0, invalid=762
0064: dt=103.680000, rms=0.628 (0.163%), neg=0, invalid=762
0065: dt=103.680000, rms=0.627 (0.166%), neg=0, invalid=762
0066: dt=103.680000, rms=0.626 (0.157%), neg=0, invalid=762
0067: dt=103.680000, rms=0.625 (0.113%), neg=0, invalid=762
0068: dt=103.680000, rms=0.625 (0.116%), neg=0, invalid=762
0069: dt=103.680000, rms=0.623 (0.186%), neg=0, invalid=762
0070: dt=103.680000, rms=0.623 (0.135%), neg=0, invalid=762
0071: dt=103.680000, rms=0.622 (0.106%), neg=0, invalid=762
0072: dt=103.680000, rms=0.621 (0.156%), neg=0, invalid=762
0073: dt=103.680000, rms=0.620 (0.125%), neg=0, invalid=762
0074: dt=103.680000, rms=0.620 (0.059%), neg=0, invalid=762
0075: dt=145.152000, rms=0.619 (0.084%), neg=0, invalid=762
0076: dt=103.680000, rms=0.619 (0.037%), neg=0, invalid=762
0077: dt=103.680000, rms=0.619 (0.013%), neg=0, invalid=762
0078: dt=103.680000, rms=0.619 (0.055%), neg=0, invalid=762
0079: dt=103.680000, rms=0.619 (0.001%), neg=0, invalid=762
0080: dt=103.680000, rms=0.619 (0.015%), neg=0, invalid=762
0081: dt=103.680000, rms=0.618 (0.038%), neg=0, invalid=762
0082: dt=103.680000, rms=0.618 (0.046%), neg=0, invalid=762
0083: dt=103.680000, rms=0.618 (0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.619, neg=0, invalid=762
0084: dt=98.798479, rms=0.616 (0.512%), neg=0, invalid=762
0085: dt=62.208000, rms=0.615 (0.081%), neg=0, invalid=762
0086: dt=62.208000, rms=0.615 (0.062%), neg=0, invalid=762
0087: dt=62.208000, rms=0.614 (0.066%), neg=0, invalid=762
0088: dt=62.208000, rms=0.614 (0.034%), neg=0, invalid=762
0089: dt=62.208000, rms=0.614 (-0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.642, neg=0, invalid=762
0090: dt=6.400000, rms=0.641 (0.163%), neg=0, invalid=762
0091: dt=2.000000, rms=0.641 (0.005%), neg=0, invalid=762
0092: dt=2.000000, rms=0.641 (0.002%), neg=0, invalid=762
0093: dt=2.000000, rms=0.641 (-0.020%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.641, neg=0, invalid=762
0094: dt=0.700000, rms=0.641 (0.104%), neg=0, invalid=762
0095: dt=0.175000, rms=0.641 (0.000%), neg=0, invalid=762
0096: dt=0.175000, rms=0.641 (-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=0.710, neg=0, invalid=762
0097: dt=6.113314, rms=0.684 (3.646%), neg=0, invalid=762
0098: dt=6.285714, rms=0.681 (0.433%), neg=0, invalid=762
0099: dt=2.461538, rms=0.681 (0.020%), neg=0, invalid=762
0100: dt=2.461538, rms=0.681 (0.001%), neg=0, invalid=762
0101: dt=2.461538, rms=0.681 (-0.044%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.682, neg=0, invalid=762
0102: dt=0.000000, rms=0.681 (0.075%), neg=0, invalid=762
0103: dt=0.000000, rms=0.681 (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=0.719, neg=0, invalid=762
0104: dt=0.000000, rms=0.718 (0.067%), neg=0, invalid=762
0105: dt=0.000000, rms=0.718 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.719, neg=0, invalid=762
0106: dt=0.256000, rms=0.718 (0.094%), neg=0, invalid=762
0107: dt=0.112000, rms=0.718 (0.008%), neg=0, invalid=762
0108: dt=0.112000, rms=0.718 (0.007%), neg=0, invalid=762
0109: dt=0.112000, rms=0.718 (-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=0.662, neg=0, invalid=762
0110: dt=0.720000, rms=0.647 (2.194%), neg=0, invalid=762
0111: dt=0.064000, rms=0.647 (0.078%), neg=0, invalid=762
0112: dt=0.064000, rms=0.647 (-0.067%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.647, neg=0, invalid=762
0113: dt=0.028000, rms=0.647 (0.099%), neg=0, invalid=762
0114: dt=0.004000, rms=0.647 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.14943 (25)
Left_Lateral_Ventricle (4): linear fit = 1.41 x + 0.0 (930 voxels, overlap=0.504)
Left_Lateral_Ventricle (4): linear fit = 1.41 x + 0.0 (930 voxels, peak = 28), gca=28.3
gca peak = 0.15565 (16)
mri peak = 0.17013 (25)
Right_Lateral_Ventricle (43): linear fit = 1.59 x + 0.0 (1101 voxels, overlap=0.254)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1101 voxels, peak = 25), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.08569 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1104 voxels, overlap=1.007)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1104 voxels, peak = 96), gca=96.0
gca peak = 0.20183 (93)
mri peak = 0.07284 (95)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (990 voxels, overlap=1.024)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (990 voxels, peak = 91), gca=90.7
gca peak = 0.21683 (55)
mri peak = 0.08417 (68)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1051 voxels, overlap=0.048)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1051 voxels, peak = 66), gca=66.3
gca peak = 0.30730 (58)
mri peak = 0.07256 (64)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1002 voxels, overlap=0.282)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1002 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.14050 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (77242 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (77242 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.12548 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (78174 voxels, overlap=0.719)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (78174 voxels, peak = 104), gca=103.5
gca peak = 0.14995 (59)
mri peak = 0.05017 (67)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (32946 voxels, overlap=0.285)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (32946 voxels, peak = 69), gca=69.3
gca peak = 0.15082 (58)
mri peak = 0.05206 (69)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (32701 voxels, overlap=0.245)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (32701 voxels, peak = 69), gca=69.3
gca peak = 0.14161 (67)
mri peak = 0.15132 (77)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (863 voxels, overlap=0.029)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (863 voxels, peak = 76), gca=76.0
gca peak = 0.15243 (71)
mri peak = 0.11377 (81)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (1077 voxels, overlap=0.574)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (1077 voxels, peak = 77), gca=77.0
gca peak = 0.13336 (57)
mri peak = 0.04595 (65)
Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (23699 voxels, overlap=0.186)
Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (23699 voxels, peak = 69), gca=69.3
gca peak = 0.13252 (56)
mri peak = 0.04138 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (22574 voxels, overlap=0.182)
Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (22574 voxels, peak = 69), gca=69.2
gca peak = 0.18181 (84)
mri peak = 0.11219 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9891 voxels, overlap=0.409)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9891 voxels, peak = 89), gca=89.5
gca peak = 0.20573 (83)
mri peak = 0.10621 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (8864 voxels, overlap=0.117)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (8864 voxels, peak = 90), gca=90.1
gca peak = 0.21969 (57)
mri peak = 0.10458 (71)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (534 voxels, overlap=0.051)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (534 voxels, peak = 70), gca=69.8
gca peak = 0.39313 (56)
mri peak = 0.09554 (67)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (636 voxels, overlap=0.036)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (636 voxels, peak = 67), gca=67.5
gca peak = 0.14181 (85)
mri peak = 0.07308 (92)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6578 voxels, overlap=0.851)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6578 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.07318 (91)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5635 voxels, overlap=0.651)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5635 voxels, peak = 90), gca=90.1
gca peak = 0.13399 (79)
mri peak = 0.08366 (82)
Left_Putamen (12): linear fit = 1.05 x + 0.0 (2677 voxels, overlap=0.772)
Left_Putamen (12): linear fit = 1.05 x + 0.0 (2677 voxels, peak = 83), gca=83.3
gca peak = 0.14159 (79)
mri peak = 0.08583 (82)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2936 voxels, overlap=0.760)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2936 voxels, peak = 85), gca=84.9
gca peak = 0.10025 (80)
mri peak = 0.11242 (87)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (14118 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (14118 voxels, peak = 88), gca=88.4
gca peak = 0.13281 (86)
mri peak = 0.08221 (88)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1487 voxels, overlap=0.666)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1487 voxels, peak = 92), gca=91.6
gca peak = 0.12801 (89)
mri peak = 0.08079 (87)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1515 voxels, overlap=0.703)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1515 voxels, peak = 92), gca=92.1
gca peak = 0.20494 (23)
mri peak = 0.16251 (26)
gca peak = 0.15061 (21)
mri peak = 0.15741 (26)
Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (404 voxels, overlap=0.493)
Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (404 voxels, peak = 28), gca=28.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.18 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.42 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=0.631, neg=0, invalid=762
0115: dt=96.032487, rms=0.621 (1.590%), neg=0, invalid=762
0116: dt=129.472000, rms=0.620 (0.251%), neg=0, invalid=762
0117: dt=443.904000, rms=0.617 (0.466%), neg=0, invalid=762
0118: dt=517.888000, rms=0.614 (0.417%), neg=0, invalid=762
0119: dt=129.472000, rms=0.613 (0.172%), neg=0, invalid=762
0120: dt=221.952000, rms=0.613 (0.043%), neg=0, invalid=762
0121: dt=221.952000, rms=0.612 (0.081%), neg=0, invalid=762
0122: dt=221.952000, rms=0.611 (0.154%), neg=0, invalid=762
0123: dt=221.952000, rms=0.610 (0.152%), neg=0, invalid=762
0124: dt=221.952000, rms=0.609 (0.173%), neg=0, invalid=762
0125: dt=221.952000, rms=0.609 (0.142%), neg=0, invalid=762
0126: dt=221.952000, rms=0.608 (0.091%), neg=0, invalid=762
0127: dt=221.952000, rms=0.607 (0.102%), neg=0, invalid=762
0128: dt=221.952000, rms=0.607 (0.098%), neg=0, invalid=762
0129: dt=221.952000, rms=0.606 (0.097%), neg=0, invalid=762
0130: dt=221.952000, rms=0.606 (0.112%), neg=0, invalid=762
0131: dt=221.952000, rms=0.605 (0.093%), neg=0, invalid=762
0132: dt=221.952000, rms=0.605 (0.074%), neg=0, invalid=762
0133: dt=221.952000, rms=0.604 (0.080%), neg=0, invalid=762
0134: dt=221.952000, rms=0.604 (0.071%), neg=0, invalid=762
0135: dt=221.952000, rms=0.603 (0.075%), neg=0, invalid=762
0136: dt=221.952000, rms=0.603 (0.076%), neg=0, invalid=762
0137: dt=221.952000, rms=0.602 (0.065%), neg=0, invalid=762
0138: dt=221.952000, rms=0.602 (0.057%), neg=0, invalid=762
0139: dt=221.952000, rms=0.602 (0.039%), neg=0, invalid=762
0140: dt=221.952000, rms=0.601 (0.045%), neg=0, invalid=762
0141: dt=221.952000, rms=0.601 (0.042%), neg=0, invalid=762
0142: dt=221.952000, rms=0.601 (0.055%), neg=0, invalid=762
0143: dt=221.952000, rms=0.600 (0.064%), neg=0, invalid=762
0144: dt=221.952000, rms=0.600 (0.059%), neg=0, invalid=762
0145: dt=221.952000, rms=0.600 (0.054%), neg=0, invalid=762
0146: dt=221.952000, rms=0.600 (0.051%), neg=0, invalid=762
0147: dt=221.952000, rms=0.599 (0.052%), neg=0, invalid=762
0148: dt=221.952000, rms=0.599 (0.046%), neg=0, invalid=762
0149: dt=221.952000, rms=0.599 (0.042%), neg=0, invalid=762
0150: dt=221.952000, rms=0.598 (0.037%), neg=0, invalid=762
0151: dt=221.952000, rms=0.598 (0.034%), neg=0, invalid=762
0152: dt=221.952000, rms=0.598 (0.036%), neg=0, invalid=762
0153: dt=221.952000, rms=0.598 (0.038%), neg=0, invalid=762
0154: dt=221.952000, rms=0.598 (0.027%), neg=0, invalid=762
0155: dt=221.952000, rms=0.597 (0.025%), neg=0, invalid=762
0156: dt=221.952000, rms=0.597 (0.032%), neg=0, invalid=762
0157: dt=221.952000, rms=0.597 (0.032%), neg=0, invalid=762
0158: dt=221.952000, rms=0.597 (0.016%), neg=0, invalid=762
0159: dt=221.952000, rms=0.597 (0.019%), neg=0, invalid=762
0160: dt=221.952000, rms=0.597 (0.020%), neg=0, invalid=762
0161: dt=221.952000, rms=0.597 (0.018%), neg=0, invalid=762
0162: dt=129.472000, rms=0.597 (0.004%), neg=0, invalid=762
0163: dt=129.472000, rms=0.597 (0.001%), neg=0, invalid=762
0164: dt=129.472000, rms=0.597 (0.003%), neg=0, invalid=762
0165: dt=129.472000, rms=0.597 (0.007%), neg=0, invalid=762
0166: dt=129.472000, rms=0.597 (0.005%), neg=0, invalid=762
0167: dt=129.472000, rms=0.597 (0.006%), neg=0, invalid=762
0168: dt=129.472000, rms=0.596 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.597, neg=0, invalid=762
0169: dt=369.920000, rms=0.595 (0.261%), neg=0, invalid=762
0170: dt=295.936000, rms=0.595 (0.074%), neg=0, invalid=762
0171: dt=129.472000, rms=0.595 (0.020%), neg=0, invalid=762
0172: dt=129.472000, rms=0.595 (0.015%), neg=0, invalid=762
0173: dt=129.472000, rms=0.595 (0.024%), neg=0, invalid=762
0174: dt=129.472000, rms=0.594 (0.029%), neg=0, invalid=762
0175: dt=129.472000, rms=0.594 (0.032%), neg=0, invalid=762
0176: dt=129.472000, rms=0.594 (0.032%), neg=0, invalid=762
0177: dt=129.472000, rms=0.594 (0.032%), neg=0, invalid=762
0178: dt=129.472000, rms=0.594 (0.028%), neg=0, invalid=762
0179: dt=129.472000, rms=0.593 (0.029%), neg=0, invalid=762
0180: dt=129.472000, rms=0.593 (0.026%), neg=0, invalid=762
0181: dt=129.472000, rms=0.593 (0.024%), neg=0, invalid=762
0182: dt=129.472000, rms=0.593 (0.027%), neg=0, invalid=762
0183: dt=129.472000, rms=0.593 (0.028%), neg=0, invalid=762
0184: dt=129.472000, rms=0.593 (0.026%), neg=0, invalid=762
0185: dt=129.472000, rms=0.593 (0.021%), neg=0, invalid=762
0186: dt=129.472000, rms=0.592 (0.019%), neg=0, invalid=762
0187: dt=369.920000, rms=0.592 (0.004%), neg=0, invalid=762
0188: dt=369.920000, rms=0.592 (-0.024%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.594, neg=0, invalid=762
0189: dt=66.782609, rms=0.592 (0.228%), neg=0, invalid=762
0190: dt=248.832000, rms=0.590 (0.412%), neg=0, invalid=762
0191: dt=145.152000, rms=0.586 (0.607%), neg=0, invalid=762
0192: dt=66.939929, rms=0.585 (0.237%), neg=0, invalid=762
0193: dt=145.152000, rms=0.583 (0.249%), neg=0, invalid=762
0194: dt=82.909091, rms=0.582 (0.221%), neg=0, invalid=762
0195: dt=82.944000, rms=0.581 (0.170%), neg=0, invalid=762
0196: dt=103.680000, rms=0.580 (0.167%), neg=0, invalid=762
0197: dt=77.395349, rms=0.579 (0.168%), neg=0, invalid=762
0198: dt=103.680000, rms=0.578 (0.155%), neg=0, invalid=762
0199: dt=82.944000, rms=0.577 (0.153%), neg=0, invalid=762
0200: dt=103.680000, rms=0.577 (0.130%), neg=0, invalid=762
0201: dt=82.944000, rms=0.576 (0.130%), neg=0, invalid=762
0202: dt=103.680000, rms=0.575 (0.123%), neg=0, invalid=762
0203: dt=82.944000, rms=0.575 (0.118%), neg=0, invalid=762
0204: dt=103.680000, rms=0.574 (0.118%), neg=0, invalid=762
0205: dt=62.208000, rms=0.573 (0.100%), neg=0, invalid=762
0206: dt=145.152000, rms=0.573 (0.145%), neg=0, invalid=762
0207: dt=82.944000, rms=0.572 (0.083%), neg=0, invalid=762
0208: dt=103.680000, rms=0.571 (0.098%), neg=0, invalid=762
0209: dt=82.944000, rms=0.571 (0.082%), neg=0, invalid=762
0210: dt=103.680000, rms=0.570 (0.095%), neg=0, invalid=762
0211: dt=82.944000, rms=0.570 (0.071%), neg=0, invalid=762
0212: dt=103.680000, rms=0.570 (0.087%), neg=0, invalid=762
0213: dt=36.288000, rms=0.569 (0.053%), neg=0, invalid=762
0214: dt=1327.104000, rms=0.566 (0.574%), neg=0, invalid=762
0215: dt=69.000000, rms=0.564 (0.312%), neg=0, invalid=762
0216: dt=36.288000, rms=0.564 (0.070%), neg=0, invalid=762
0217: dt=145.152000, rms=0.564 (0.061%), neg=0, invalid=762
0218: dt=103.680000, rms=0.563 (0.045%), neg=0, invalid=762
0219: dt=103.680000, rms=0.563 (0.021%), neg=0, invalid=762
0220: dt=103.680000, rms=0.563 (0.110%), neg=0, invalid=762
0221: dt=103.680000, rms=0.562 (0.108%), neg=0, invalid=762
0222: dt=103.680000, rms=0.561 (0.149%), neg=0, invalid=762
0223: dt=103.680000, rms=0.560 (0.134%), neg=0, invalid=762
0224: dt=103.680000, rms=0.559 (0.168%), neg=0, invalid=762
0225: dt=103.680000, rms=0.559 (0.154%), neg=0, invalid=762
0226: dt=103.680000, rms=0.558 (0.017%), neg=0, invalid=762
0227: dt=103.680000, rms=0.558 (0.052%), neg=0, invalid=762
0228: dt=103.680000, rms=0.558 (0.028%), neg=0, invalid=762
0229: dt=103.680000, rms=0.558 (0.039%), neg=0, invalid=762
0230: dt=0.202500, rms=0.558 (0.001%), neg=0, invalid=762
0231: dt=0.101250, rms=0.558 (0.000%), neg=0, invalid=762
0232: dt=0.007594, rms=0.558 (0.000%), neg=0, invalid=762
0233: dt=0.007594, rms=0.558 (0.000%), neg=0, invalid=762
0234: dt=0.000475, rms=0.558 (0.000%), neg=0, invalid=762
0235: dt=0.000237, rms=0.558 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.558, neg=0, invalid=762
0236: dt=145.152000, rms=0.555 (0.631%), neg=0, invalid=762
0237: dt=82.944000, rms=0.554 (0.114%), neg=0, invalid=762
0238: dt=145.152000, rms=0.553 (0.117%), neg=0, invalid=762
0239: dt=62.208000, rms=0.553 (0.060%), neg=0, invalid=762
0240: dt=145.152000, rms=0.553 (0.079%), neg=0, invalid=762
0241: dt=36.288000, rms=0.553 (0.031%), neg=0, invalid=762
0242: dt=36.288000, rms=0.552 (0.015%), neg=0, invalid=762
0243: dt=36.288000, rms=0.552 (0.029%), neg=0, invalid=762
0244: dt=36.288000, rms=0.552 (0.034%), neg=0, invalid=762
0245: dt=36.288000, rms=0.552 (0.049%), neg=0, invalid=762
0246: dt=36.288000, rms=0.552 (0.053%), neg=0, invalid=762
0247: dt=36.288000, rms=0.551 (0.053%), neg=0, invalid=762
0248: dt=36.288000, rms=0.551 (0.054%), neg=0, invalid=762
0249: dt=36.288000, rms=0.551 (0.053%), neg=0, invalid=762
0250: dt=36.288000, rms=0.550 (0.053%), neg=0, invalid=762
0251: dt=36.288000, rms=0.550 (0.054%), neg=0, invalid=762
0252: dt=36.288000, rms=0.550 (0.056%), neg=0, invalid=762
0253: dt=36.288000, rms=0.549 (0.057%), neg=0, invalid=762
0254: dt=36.288000, rms=0.549 (0.054%), neg=0, invalid=762
0255: dt=36.288000, rms=0.549 (0.052%), neg=0, invalid=762
0256: dt=36.288000, rms=0.549 (0.050%), neg=0, invalid=762
0257: dt=36.288000, rms=0.548 (0.051%), neg=0, invalid=762
0258: dt=36.288000, rms=0.548 (0.050%), neg=0, invalid=762
0259: dt=36.288000, rms=0.548 (0.050%), neg=0, invalid=762
0260: dt=36.288000, rms=0.547 (0.047%), neg=0, invalid=762
0261: dt=36.288000, rms=0.547 (0.049%), neg=0, invalid=762
0262: dt=36.288000, rms=0.547 (0.053%), neg=0, invalid=762
0263: dt=36.288000, rms=0.547 (0.055%), neg=0, invalid=762
0264: dt=36.288000, rms=0.546 (0.058%), neg=0, invalid=762
0265: dt=36.288000, rms=0.546 (0.050%), neg=0, invalid=762
0266: dt=36.288000, rms=0.546 (0.049%), neg=0, invalid=762
0267: dt=36.288000, rms=0.546 (0.043%), neg=0, invalid=762
0268: dt=36.288000, rms=0.545 (0.045%), neg=0, invalid=762
0269: dt=36.288000, rms=0.545 (0.045%), neg=0, invalid=762
0270: dt=36.288000, rms=0.545 (0.045%), neg=0, invalid=762
0271: dt=36.288000, rms=0.545 (0.043%), neg=0, invalid=762
0272: dt=36.288000, rms=0.544 (0.045%), neg=0, invalid=762
0273: dt=36.288000, rms=0.544 (0.038%), neg=0, invalid=762
0274: dt=36.288000, rms=0.544 (0.042%), neg=0, invalid=762
0275: dt=36.288000, rms=0.544 (0.037%), neg=0, invalid=762
0276: dt=36.288000, rms=0.543 (0.036%), neg=0, invalid=762
0277: dt=36.288000, rms=0.543 (0.033%), neg=0, invalid=762
0278: dt=36.288000, rms=0.543 (0.034%), neg=0, invalid=762
0279: dt=36.288000, rms=0.543 (0.034%), neg=0, invalid=762
0280: dt=36.288000, rms=0.543 (0.035%), neg=0, invalid=762
0281: dt=36.288000, rms=0.543 (0.034%), neg=0, invalid=762
0282: dt=36.288000, rms=0.542 (0.031%), neg=0, invalid=762
0283: dt=36.288000, rms=0.542 (0.031%), neg=0, invalid=762
0284: dt=36.288000, rms=0.542 (0.031%), neg=0, invalid=762
0285: dt=36.288000, rms=0.542 (0.027%), neg=0, invalid=762
0286: dt=36.288000, rms=0.542 (0.029%), neg=0, invalid=762
0287: dt=36.288000, rms=0.542 (0.028%), neg=0, invalid=762
0288: dt=36.288000, rms=0.541 (0.028%), neg=0, invalid=762
0289: dt=36.288000, rms=0.541 (0.028%), neg=0, invalid=762
0290: dt=36.288000, rms=0.541 (0.027%), neg=0, invalid=762
0291: dt=36.288000, rms=0.541 (0.027%), neg=0, invalid=762
0292: dt=36.288000, rms=0.541 (0.025%), neg=0, invalid=762
0293: dt=36.288000, rms=0.541 (0.024%), neg=0, invalid=762
0294: dt=414.720000, rms=0.541 (0.012%), neg=0, invalid=762
0295: dt=414.720000, rms=0.541 (-0.394%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.547, neg=0, invalid=762
0296: dt=25.230769, rms=0.545 (0.264%), neg=0, invalid=762
0297: dt=44.800000, rms=0.544 (0.307%), neg=0, invalid=762
0298: dt=32.000000, rms=0.542 (0.328%), neg=0, invalid=762
0299: dt=0.175000, rms=0.542 (0.002%), neg=0, invalid=762
0300: dt=0.175000, rms=0.542 (0.001%), neg=0, invalid=762
0301: dt=0.043750, rms=0.542 (0.001%), neg=0, invalid=762
0302: dt=0.021875, rms=0.542 (0.000%), neg=0, invalid=762
0303: dt=0.002344, rms=0.542 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.542, neg=0, invalid=762
0304: dt=61.538462, rms=0.537 (0.921%), neg=0, invalid=762
0305: dt=31.776224, rms=0.535 (0.400%), neg=0, invalid=762
0306: dt=32.000000, rms=0.534 (0.229%), neg=0, invalid=762
0307: dt=44.800000, rms=0.533 (0.233%), neg=0, invalid=762
0308: dt=25.600000, rms=0.532 (0.219%), neg=0, invalid=762
0309: dt=44.800000, rms=0.530 (0.237%), neg=0, invalid=762
0310: dt=32.000000, rms=0.530 (0.150%), neg=0, invalid=762
0311: dt=38.400000, rms=0.529 (0.168%), neg=0, invalid=762
0312: dt=25.600000, rms=0.528 (0.148%), neg=0, invalid=762
0313: dt=44.800000, rms=0.527 (0.181%), neg=0, invalid=762
0314: dt=32.000000, rms=0.526 (0.113%), neg=0, invalid=762
0315: dt=32.000000, rms=0.526 (0.132%), neg=0, invalid=762
0316: dt=32.000000, rms=0.525 (0.111%), neg=0, invalid=762
0317: dt=32.000000, rms=0.524 (0.114%), neg=0, invalid=762
0318: dt=32.000000, rms=0.524 (0.106%), neg=0, invalid=762
0319: dt=32.000000, rms=0.523 (0.102%), neg=0, invalid=762
0320: dt=32.000000, rms=0.523 (0.097%), neg=0, invalid=762
0321: dt=32.000000, rms=0.522 (0.082%), neg=0, invalid=762
0322: dt=32.000000, rms=0.522 (0.097%), neg=0, invalid=762
0323: dt=32.000000, rms=0.522 (0.080%), neg=0, invalid=762
0324: dt=32.000000, rms=0.521 (0.089%), neg=0, invalid=762
0325: dt=32.000000, rms=0.521 (0.069%), neg=0, invalid=762
0326: dt=32.000000, rms=0.520 (0.077%), neg=0, invalid=762
0327: dt=25.600000, rms=0.520 (0.066%), neg=0, invalid=762
0328: dt=38.400000, rms=0.520 (0.072%), neg=0, invalid=762
0329: dt=25.600000, rms=0.519 (0.066%), neg=0, invalid=762
0330: dt=32.000000, rms=0.519 (0.056%), neg=0, invalid=762
0331: dt=32.000000, rms=0.519 (0.071%), neg=0, invalid=762
0332: dt=25.600000, rms=0.518 (0.050%), neg=0, invalid=762
0333: dt=25.600000, rms=0.518 (0.061%), neg=0, invalid=762
0334: dt=25.600000, rms=0.518 (0.089%), neg=0, invalid=762
0335: dt=25.600000, rms=0.517 (0.128%), neg=0, invalid=762
0336: dt=25.600000, rms=0.516 (0.148%), neg=0, invalid=762
0337: dt=25.600000, rms=0.515 (0.174%), neg=0, invalid=762
0338: dt=25.600000, rms=0.514 (0.188%), neg=0, invalid=762
0339: dt=25.600000, rms=0.513 (0.193%), neg=0, invalid=762
0340: dt=25.600000, rms=0.512 (0.198%), neg=0, invalid=762
0341: dt=25.600000, rms=0.511 (0.199%), neg=0, invalid=762
0342: dt=25.600000, rms=0.510 (0.198%), neg=0, invalid=762
0343: dt=25.600000, rms=0.509 (0.187%), neg=0, invalid=762
0344: dt=25.600000, rms=0.508 (0.172%), neg=0, invalid=762
0345: dt=25.600000, rms=0.508 (0.157%), neg=0, invalid=762
0346: dt=25.600000, rms=0.507 (0.138%), neg=0, invalid=762
0347: dt=25.600000, rms=0.506 (0.130%), neg=0, invalid=762
0348: dt=25.600000, rms=0.506 (0.125%), neg=0, invalid=762
0349: dt=25.600000, rms=0.505 (0.108%), neg=0, invalid=762
0350: dt=25.600000, rms=0.505 (0.096%), neg=0, invalid=762
0351: dt=25.600000, rms=0.504 (0.094%), neg=0, invalid=762
0352: dt=25.600000, rms=0.504 (0.082%), neg=0, invalid=762
0353: dt=25.600000, rms=0.503 (0.069%), neg=0, invalid=762
0354: dt=25.600000, rms=0.503 (0.061%), neg=0, invalid=762
0355: dt=25.600000, rms=0.503 (0.076%), neg=0, invalid=762
0356: dt=25.600000, rms=0.502 (0.061%), neg=0, invalid=762
0357: dt=25.600000, rms=0.502 (0.063%), neg=0, invalid=762
0358: dt=25.600000, rms=0.502 (0.052%), neg=0, invalid=762
0359: dt=25.600000, rms=0.501 (0.056%), neg=0, invalid=762
0360: dt=25.600000, rms=0.501 (0.053%), neg=0, invalid=762
0361: dt=25.600000, rms=0.501 (0.044%), neg=0, invalid=762
0362: dt=25.600000, rms=0.501 (0.043%), neg=0, invalid=762
0363: dt=25.600000, rms=0.501 (0.044%), neg=0, invalid=762
0364: dt=25.600000, rms=0.500 (0.038%), neg=0, invalid=762
0365: dt=25.600000, rms=0.500 (0.038%), neg=0, invalid=762
0366: dt=25.600000, rms=0.500 (0.038%), neg=0, invalid=762
0367: dt=25.600000, rms=0.500 (0.038%), neg=0, invalid=762
0368: dt=25.600000, rms=0.500 (0.038%), neg=0, invalid=762
0369: dt=25.600000, rms=0.499 (0.035%), neg=0, invalid=762
0370: dt=25.600000, rms=0.499 (0.027%), neg=0, invalid=762
0371: dt=25.600000, rms=0.499 (0.030%), neg=0, invalid=762
0372: dt=25.600000, rms=0.499 (0.031%), neg=0, invalid=762
0373: dt=25.600000, rms=0.499 (0.028%), neg=0, invalid=762
0374: dt=25.600000, rms=0.499 (0.026%), neg=0, invalid=762
0375: dt=25.600000, rms=0.499 (0.030%), neg=0, invalid=762
0376: dt=25.600000, rms=0.498 (0.027%), neg=0, invalid=762
0377: dt=25.600000, rms=0.498 (0.021%), neg=0, invalid=762
0378: dt=25.600000, rms=0.498 (0.025%), neg=0, invalid=762
0379: dt=25.600000, rms=0.498 (0.028%), neg=0, invalid=762
0380: dt=25.600000, rms=0.498 (0.021%), neg=0, invalid=762
0381: dt=25.600000, rms=0.498 (0.017%), neg=0, invalid=762
0382: dt=38.400000, rms=0.498 (0.007%), neg=0, invalid=762
0383: dt=38.400000, rms=0.498 (-0.035%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.514, neg=0, invalid=762
0384: dt=0.000000, rms=0.514 (0.067%), neg=0, invalid=762
0385: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762
0386: dt=0.150000, rms=0.514 (-0.020%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.514, neg=0, invalid=762
0387: dt=0.000000, rms=0.514 (0.067%), neg=0, invalid=762
0388: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762
0389: dt=0.150000, rms=0.514 (-0.019%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.547, neg=0, invalid=762
0390: dt=1.024000, rms=0.546 (0.340%), neg=0, invalid=762
0391: dt=0.028000, rms=0.546 (0.002%), neg=0, invalid=762
0392: dt=0.028000, rms=0.546 (0.000%), neg=0, invalid=762
0393: dt=0.028000, rms=0.546 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.546, neg=0, invalid=762
0394: dt=0.448000, rms=0.545 (0.145%), neg=0, invalid=762
0395: dt=0.384000, rms=0.545 (0.020%), neg=0, invalid=762
0396: dt=0.384000, rms=0.545 (-0.009%), 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=0.507, neg=0, invalid=762
0397: dt=0.448000, rms=0.494 (2.455%), neg=0, invalid=762
0398: dt=0.448000, rms=0.492 (0.414%), neg=0, invalid=762
0399: dt=0.448000, rms=0.491 (0.239%), neg=0, invalid=762
0400: dt=0.448000, rms=0.490 (0.128%), neg=0, invalid=762
0401: dt=0.448000, rms=0.490 (0.100%), neg=0, invalid=762
0402: dt=0.448000, rms=0.490 (0.063%), neg=0, invalid=762
0403: dt=0.448000, rms=0.489 (0.059%), neg=0, invalid=762
0404: dt=0.448000, rms=0.489 (0.035%), neg=0, invalid=762
0405: dt=0.448000, rms=0.489 (0.042%), neg=0, invalid=762
0406: dt=0.448000, rms=0.489 (0.052%), neg=0, invalid=762
0407: dt=0.224000, rms=0.489 (0.011%), neg=0, invalid=762
0408: dt=0.224000, rms=0.489 (0.017%), neg=0, invalid=762
0409: dt=0.224000, rms=0.488 (0.023%), neg=0, invalid=762
0410: dt=0.224000, rms=0.488 (0.025%), neg=0, invalid=762
0411: dt=0.224000, rms=0.488 (0.024%), neg=0, invalid=762
0412: dt=0.192000, rms=0.488 (0.002%), neg=0, invalid=762
0413: dt=0.192000, rms=0.488 (0.003%), neg=0, invalid=762
0414: dt=0.192000, rms=0.488 (0.003%), neg=0, invalid=762
0415: dt=0.192000, rms=0.488 (0.003%), neg=0, invalid=762
0416: dt=0.192000, rms=0.488 (0.004%), neg=0, invalid=762
0417: dt=0.192000, rms=0.488 (0.005%), neg=0, invalid=762
0418: dt=0.192000, rms=0.488 (0.006%), neg=0, invalid=762
0419: dt=0.192000, rms=0.488 (0.008%), neg=0, invalid=762
0420: dt=0.192000, rms=0.488 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
0421: dt=0.320000, rms=0.484 (0.973%), neg=0, invalid=762
0422: dt=0.448000, rms=0.481 (0.510%), neg=0, invalid=762
0423: dt=0.448000, rms=0.481 (0.102%), neg=0, invalid=762
0424: dt=0.448000, rms=0.481 (0.039%), neg=0, invalid=762
0425: dt=0.448000, rms=0.481 (0.016%), neg=0, invalid=762
0426: dt=0.448000, rms=0.481 (0.004%), neg=0, invalid=762
0427: dt=0.448000, rms=0.480 (0.011%), neg=0, invalid=762
0428: dt=0.448000, rms=0.480 (0.006%), neg=0, invalid=762
0429: dt=0.256000, rms=0.480 (0.004%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
0430: dt=0.000000, rms=0.478 (0.098%), neg=0, invalid=762
0431: dt=0.000000, rms=0.478 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
0432: dt=129.472000, rms=0.478 (0.114%), neg=0, invalid=762
0433: dt=369.920000, rms=0.478 (0.035%), neg=0, invalid=762
0434: dt=369.920000, rms=0.478 (-0.377%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
0435: dt=0.006010, rms=0.478 (0.100%), neg=0, invalid=762
0436: dt=0.000000, rms=0.478 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
0437: dt=103.680000, rms=0.477 (0.273%), neg=0, invalid=762
0438: dt=36.288000, rms=0.477 (0.100%), neg=0, invalid=762
0439: dt=36.288000, rms=0.477 (0.044%), neg=0, invalid=762
0440: dt=36.288000, rms=0.476 (0.068%), neg=0, invalid=762
0441: dt=36.288000, rms=0.476 (0.084%), neg=0, invalid=762
0442: dt=36.288000, rms=0.476 (0.090%), neg=0, invalid=762
0443: dt=36.288000, rms=0.475 (0.088%), neg=0, invalid=762
0444: dt=36.288000, rms=0.475 (0.073%), neg=0, invalid=762
0445: dt=145.152000, rms=0.475 (0.026%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.475, neg=0, invalid=762
0446: dt=11.200000, rms=0.474 (0.225%), neg=0, invalid=762
0447: dt=11.200000, rms=0.474 (0.054%), neg=0, invalid=762
0448: dt=11.200000, rms=0.474 (0.029%), neg=0, invalid=762
0449: dt=11.200000, rms=0.474 (-0.020%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.474, neg=0, invalid=762
0450: dt=51.256637, rms=0.470 (0.955%), neg=0, invalid=762
0451: dt=25.149560, rms=0.468 (0.366%), neg=0, invalid=762
0452: dt=32.000000, rms=0.467 (0.172%), neg=0, invalid=762
0453: dt=32.000000, rms=0.467 (0.162%), neg=0, invalid=762
0454: dt=32.000000, rms=0.465 (0.353%), neg=0, invalid=762
0455: dt=32.000000, rms=0.464 (0.232%), neg=0, invalid=762
0456: dt=32.000000, rms=0.462 (0.476%), neg=0, invalid=762
0457: dt=32.000000, rms=0.460 (0.242%), neg=0, invalid=762
0458: dt=32.000000, rms=0.459 (0.372%), neg=0, invalid=762
0459: dt=32.000000, rms=0.458 (0.113%), neg=0, invalid=762
0460: dt=32.000000, rms=0.457 (0.307%), neg=0, invalid=762
0461: dt=32.000000, rms=0.456 (0.120%), neg=0, invalid=762
0462: dt=32.000000, rms=0.456 (0.162%), neg=0, invalid=762
0463: dt=32.000000, rms=0.455 (0.091%), neg=0, invalid=762
0464: dt=32.000000, rms=0.455 (0.122%), neg=0, invalid=762
0465: dt=32.000000, rms=0.454 (0.101%), neg=0, invalid=762
0466: dt=11.200000, rms=0.454 (0.069%), neg=0, invalid=762
0467: dt=11.200000, rms=0.454 (0.026%), neg=0, invalid=762
0468: dt=11.200000, rms=0.454 (0.005%), neg=0, invalid=762
0469: dt=11.200000, rms=0.454 (0.007%), neg=0, invalid=762
0470: dt=11.200000, rms=0.454 (0.010%), neg=0, invalid=762
0471: dt=11.200000, rms=0.454 (0.005%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.458, neg=0, invalid=762
0472: dt=0.000270, rms=0.458 (0.098%), neg=0, invalid=762
0473: dt=0.000000, rms=0.458 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.458, neg=0, invalid=762
0474: dt=1.728000, rms=0.458 (0.107%), neg=0, invalid=762
0475: dt=1.008000, rms=0.458 (0.004%), neg=0, invalid=762
0476: dt=1.008000, rms=0.458 (0.001%), neg=0, invalid=762
0477: dt=1.008000, rms=0.458 (-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=0.465, neg=0, invalid=762
0478: dt=0.448000, rms=0.465 (0.135%), neg=0, invalid=762
0479: dt=0.112000, rms=0.465 (0.003%), neg=0, invalid=762
0480: dt=0.112000, rms=0.465 (0.001%), neg=0, invalid=762
0481: dt=0.112000, rms=0.465 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.465, neg=0, invalid=762
0482: dt=1.792000, rms=0.463 (0.387%), neg=0, invalid=762
0483: dt=1.280000, rms=0.463 (0.045%), neg=0, invalid=762
0484: dt=1.280000, rms=0.463 (0.002%), neg=0, invalid=762
0485: dt=1.280000, rms=0.463 (-0.083%), 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=0.458, neg=0, invalid=762
iter 0, gcam->neg = 342
after 13 iterations, nbhd size=1, neg = 0
0486: dt=2.082108, rms=0.433 (5.476%), neg=0, invalid=762
0487: dt=0.064000, rms=0.433 (0.042%), neg=0, invalid=762
0488: dt=0.064000, rms=0.433 (-0.023%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0489: dt=0.112000, rms=0.433 (0.228%), neg=0, invalid=762
0490: dt=0.007000, rms=0.433 (0.003%), neg=0, invalid=762
0491: dt=0.007000, rms=0.433 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0492: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0493: dt=27.744000, rms=0.421 (0.002%), neg=0, invalid=762
0494: dt=8.092000, rms=0.421 (0.000%), neg=0, invalid=762
0495: dt=8.092000, rms=0.421 (0.000%), neg=0, invalid=762
0496: dt=8.092000, rms=0.421 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0497: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0498: dt=62.208000, rms=0.421 (0.032%), neg=0, invalid=762
0499: dt=145.152000, rms=0.421 (0.042%), neg=0, invalid=762
0500: dt=36.288000, rms=0.421 (0.008%), neg=0, invalid=762
0501: dt=36.288000, rms=0.420 (0.007%), neg=0, invalid=762
0502: dt=36.288000, rms=0.420 (0.012%), neg=0, invalid=762
0503: dt=36.288000, rms=0.420 (0.015%), neg=0, invalid=762
0504: dt=36.288000, rms=0.420 (0.015%), neg=0, invalid=762
0505: dt=36.288000, rms=0.420 (0.012%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0506: dt=2.800000, rms=0.421 (0.008%), neg=0, invalid=762
0507: dt=1.200000, rms=0.421 (0.001%), neg=0, invalid=762
0508: dt=1.200000, rms=0.421 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0509: dt=114.758621, rms=0.418 (0.620%), neg=0, invalid=762
0510: dt=25.600000, rms=0.417 (0.207%), neg=0, invalid=762
0511: dt=25.600000, rms=0.417 (0.060%), neg=0, invalid=762
0512: dt=25.600000, rms=0.417 (0.084%), neg=0, invalid=762
0513: dt=25.600000, rms=0.416 (0.123%), neg=0, invalid=762
0514: dt=25.600000, rms=0.416 (0.138%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0515: dt=25.600000, rms=0.415 (0.141%), neg=0, invalid=762
0516: dt=25.600000, rms=0.414 (0.141%), neg=0, invalid=762
0517: dt=25.600000, rms=0.414 (0.121%), neg=0, invalid=762
0518: dt=25.600000, rms=0.414 (0.108%), neg=0, invalid=762
0519: dt=44.800000, rms=0.413 (0.012%), neg=0, invalid=762
0520: dt=44.800000, rms=0.413 (0.015%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0521: dt=44.800000, rms=0.413 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 4 iterations, nbhd size=0, neg = 0
0522: dt=44.800000, rms=0.413 (0.022%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0523: dt=44.800000, rms=0.413 (0.039%), neg=0, invalid=762
0524: dt=44.800000, rms=0.413 (0.042%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0525: dt=44.800000, rms=0.413 (0.044%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 9 iterations, nbhd size=1, neg = 0
0526: dt=44.800000, rms=0.412 (0.046%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 4 iterations, nbhd size=0, neg = 0
0527: dt=44.800000, rms=0.412 (0.059%), neg=0, invalid=762
0528: dt=44.800000, rms=0.412 (0.067%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0529: dt=44.800000, rms=0.412 (0.070%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 2 iterations, nbhd size=0, neg = 0
0530: dt=44.800000, rms=0.411 (0.062%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0531: dt=0.000176, rms=0.415 (0.000%), neg=0, invalid=762
0532: dt=0.000000, 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
0533: dt=3.250000, rms=0.415 (0.014%), neg=0, invalid=762
0534: dt=2.304000, rms=0.415 (0.004%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0535: dt=2.304000, rms=0.415 (0.003%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0536: dt=2.304000, rms=0.415 (-0.009%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
0537: dt=0.000050, rms=0.422 (0.000%), neg=0, invalid=762
0538: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
0539: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762
0540: dt=0.100000, rms=0.422 (-0.008%), 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=0.411, neg=0, invalid=762
iter 0, gcam->neg = 395
after 14 iterations, nbhd size=1, neg = 0
0541: dt=1.280000, rms=0.403 (1.855%), neg=0, invalid=762
0542: dt=0.000020, rms=0.403 (0.000%), neg=0, invalid=762
0543: dt=0.000020, rms=0.403 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.403, neg=0, invalid=762
0544: dt=0.112000, rms=0.402 (0.125%), neg=0, invalid=762
0545: dt=0.112000, rms=0.402 (0.073%), neg=0, invalid=762
0546: dt=0.112000, rms=0.402 (0.060%), neg=0, invalid=762
0547: dt=0.112000, rms=0.402 (0.045%), neg=0, invalid=762
0548: dt=0.112000, rms=0.402 (-0.018%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 24 minutes and 8 seconds.
mri_ca_register utimesec    9538.921863
mri_ca_register stimesec    8.086770
mri_ca_register ru_maxrss   1338224
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4991265
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63528
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3988
mri_ca_register ru_nivcsw   11916
FSRUNTIME@ mri_ca_register  2.4023 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 22:51:14 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-960
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-6.0.0/0050267/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 7.71
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 = 0.16173 (25)
Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (369 voxels, overlap=0.547)
Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (369 voxels, peak = 24), gca=23.9
gca peak = 0.17677 (13)
mri peak = 0.16860 (25)
Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (778 voxels, overlap=0.243)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (778 voxels, peak = 24), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.11592 (97)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (716 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (716 voxels, peak = 96), gca=96.4
gca peak = 0.16930 (96)
mri peak = 0.13793 (94)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (821 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (821 voxels, peak = 94), gca=93.6
gca peak = 0.24553 (55)
mri peak = 0.09609 (67)
Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (1288 voxels, overlap=0.064)
Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (1288 voxels, peak = 65), gca=64.6
gca peak = 0.30264 (59)
mri peak = 0.09228 (64)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (1094 voxels, overlap=0.132)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (1094 voxels, peak = 67), gca=67.0
gca peak = 0.07580 (103)
mri peak = 0.15023 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58369 voxels, overlap=0.595)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58369 voxels, peak = 104), gca=103.5
gca peak = 0.07714 (104)
mri peak = 0.13549 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63879 voxels, overlap=0.658)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63879 voxels, peak = 103), gca=103.5
gca peak = 0.09712 (58)
mri peak = 0.05201 (67)
Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (41687 voxels, overlap=0.447)
Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (41687 voxels, peak = 68), gca=67.6
gca peak = 0.11620 (58)
mri peak = 0.05497 (68)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (40741 voxels, overlap=0.432)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (40741 voxels, peak = 68), gca=67.6
gca peak = 0.30970 (66)
mri peak = 0.12665 (81)
Right_Caudate (50): linear fit = 1.17 x + 0.0 (1054 voxels, overlap=0.016)
Right_Caudate (50): linear fit = 1.17 x + 0.0 (1054 voxels, peak = 78), gca=77.5
gca peak = 0.15280 (69)
mri peak = 0.13499 (80)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (963 voxels, overlap=0.503)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (963 voxels, peak = 73), gca=73.5
gca peak = 0.13902 (56)
mri peak = 0.05213 (68)
Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (26447 voxels, overlap=0.331)
Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (26447 voxels, peak = 67), gca=67.5
gca peak = 0.14777 (55)
mri peak = 0.05040 (68)
Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (25947 voxels, overlap=0.227)
Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (25947 voxels, peak = 68), gca=68.5
gca peak = 0.16765 (84)
mri peak = 0.17167 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (6438 voxels, overlap=0.530)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (6438 voxels, peak = 88), gca=87.8
gca peak = 0.18739 (84)
mri peak = 0.14488 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6466 voxels, overlap=0.326)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6466 voxels, peak = 90), gca=90.3
gca peak = 0.29869 (57)
mri peak = 0.12081 (71)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (760 voxels, overlap=0.053)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (760 voxels, peak = 69), gca=69.3
gca peak = 0.33601 (57)
mri peak = 0.10468 (69)
Right_Amygdala (54): linear fit = 1.22 x + 0.0 (810 voxels, overlap=0.046)
Right_Amygdala (54): linear fit = 1.22 x + 0.0 (810 voxels, peak = 69), gca=69.3
gca peak = 0.11131 (90)
mri peak = 0.07890 (91)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5879 voxels, overlap=0.877)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5879 voxels, peak = 93), gca=93.1
gca peak = 0.11793 (83)
mri peak = 0.07601 (91)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5568 voxels, overlap=0.754)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5568 voxels, peak = 90), gca=90.1
gca peak = 0.08324 (81)
mri peak = 0.11054 (82)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (2048 voxels, overlap=0.630)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (2048 voxels, peak = 84), gca=83.8
gca peak = 0.10360 (77)
mri peak = 0.09683 (84)
Right_Putamen (51): linear fit = 1.07 x + 0.0 (2207 voxels, overlap=0.546)
Right_Putamen (51): linear fit = 1.07 x + 0.0 (2207 voxels, peak = 82), gca=82.0
gca peak = 0.08424 (78)
mri peak = 0.11237 (87)
Brain_Stem (16): linear fit = 1.08 x + 0.0 (15786 voxels, overlap=0.414)
Brain_Stem (16): linear fit = 1.08 x + 0.0 (15786 voxels, peak = 84), gca=83.9
gca peak = 0.12631 (89)
mri peak = 0.08492 (93)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1905 voxels, overlap=0.784)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1905 voxels, peak = 95), gca=94.8
gca peak = 0.14500 (87)
mri peak = 0.07749 (93)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1893 voxels, overlap=0.863)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1893 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.14836 (22)
gca peak = 0.19357 (14)
mri peak = 0.16120 (26)
Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (487 voxels, overlap=0.210)
Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (487 voxels, peak = 23), gca=22.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.18 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.35 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15914 (22)
mri peak = 0.16173 (25)
Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (369 voxels, overlap=0.808)
Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (369 voxels, peak = 24), gca=23.7
gca peak = 0.13759 (19)
mri peak = 0.16860 (25)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (778 voxels, overlap=0.409)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (778 voxels, peak = 23), gca=22.5
gca peak = 0.25980 (97)
mri peak = 0.11592 (97)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (716 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (716 voxels, peak = 96), gca=95.5
gca peak = 0.20240 (94)
mri peak = 0.13793 (94)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (821 voxels, overlap=1.005)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (821 voxels, peak = 95), gca=95.4
gca peak = 0.23579 (65)
mri peak = 0.09609 (67)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1288 voxels, overlap=1.005)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1288 voxels, peak = 65), gca=65.0
gca peak = 0.27654 (64)
mri peak = 0.09228 (64)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1094 voxels, overlap=1.004)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1094 voxels, peak = 63), gca=63.0
gca peak = 0.07871 (103)
mri peak = 0.15023 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58369 voxels, overlap=0.616)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58369 voxels, peak = 103), gca=103.0
gca peak = 0.08042 (104)
mri peak = 0.13549 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63879 voxels, overlap=0.638)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (63879 voxels, peak = 104), gca=104.0
gca peak = 0.08266 (66)
mri peak = 0.05201 (67)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (41687 voxels, overlap=0.956)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (41687 voxels, peak = 66), gca=66.0
gca peak = 0.09789 (68)
mri peak = 0.05497 (68)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (40741 voxels, overlap=0.961)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (40741 voxels, peak = 68), gca=68.0
gca peak = 0.23086 (78)
mri peak = 0.12665 (81)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1054 voxels, overlap=0.999)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1054 voxels, peak = 78), gca=78.0
gca peak = 0.12832 (73)
mri peak = 0.13499 (80)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, overlap=0.833)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, peak = 73), gca=73.0
gca peak = 0.12063 (67)
mri peak = 0.05213 (68)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (26447 voxels, overlap=0.996)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (26447 voxels, peak = 66), gca=66.0
gca peak = 0.12462 (68)
mri peak = 0.05040 (68)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (25947 voxels, overlap=0.985)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (25947 voxels, peak = 67), gca=67.0
gca peak = 0.15161 (88)
mri peak = 0.17167 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6438 voxels, overlap=0.840)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6438 voxels, peak = 88), gca=88.0
gca peak = 0.14937 (90)
mri peak = 0.14488 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6466 voxels, overlap=0.857)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6466 voxels, peak = 90), gca=89.6
gca peak = 0.28070 (69)
mri peak = 0.12081 (71)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (760 voxels, overlap=1.012)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (760 voxels, peak = 69), gca=69.0
gca peak = 0.29387 (69)
mri peak = 0.10468 (69)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (810 voxels, overlap=1.000)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (810 voxels, peak = 69), gca=69.0
gca peak = 0.11202 (93)
mri peak = 0.07890 (91)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5879 voxels, overlap=0.959)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5879 voxels, peak = 93), gca=92.5
gca peak = 0.10388 (90)
mri peak = 0.07601 (91)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5568 voxels, overlap=0.960)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5568 voxels, peak = 90), gca=89.6
gca peak = 0.08284 (84)
mri peak = 0.11054 (82)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (2048 voxels, overlap=0.774)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (2048 voxels, peak = 85), gca=85.3
gca peak = 0.09474 (82)
mri peak = 0.09683 (84)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2207 voxels, overlap=0.812)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2207 voxels, peak = 83), gca=83.2
gca peak = 0.08828 (84)
mri peak = 0.11237 (87)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (15786 voxels, overlap=0.703)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (15786 voxels, peak = 84), gca=83.6
gca peak = 0.11658 (95)
mri peak = 0.08492 (93)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1905 voxels, overlap=0.862)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1905 voxels, peak = 93), gca=92.6
gca peak = 0.14658 (91)
mri peak = 0.07749 (93)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1893 voxels, overlap=0.943)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1893 voxels, peak = 90), gca=89.6
gca peak = 0.12947 (34)
mri peak = 0.14836 (22)
gca peak = 0.15119 (20)
mri peak = 0.16120 (26)
Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (487 voxels, overlap=0.569)
Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (487 voxels, peak = 24), gca=24.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.17373 (37)
gca peak Left_Thalamus = 0.36646 (101)
gca peak Third_Ventricle = 0.12947 (34)
gca peak CSF = 0.19061 (49)
gca peak Left_Accumbens_area = 0.58279 (66)
gca peak Left_undetermined = 0.98573 (27)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11914 (35)
gca peak Right_Inf_Lat_Vent = 0.21147 (27)
gca peak Right_Accumbens_area = 0.29771 (76)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14509 (37)
gca peak Fifth_Ventricle = 0.75707 (42)
gca peak WM_hypointensities = 0.08402 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.70889 (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 1.16 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
95113 voxels changed in iteration 0 of unlikely voxel relabeling
598 voxels changed in iteration 1 of unlikely voxel relabeling
15 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
65707 gm and wm labels changed (%30 to gray, %70 to white out of all changed labels)
445 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 84099 changed. image ll: -2.144, PF=0.500
pass 2: 22944 changed. image ll: -2.143, PF=0.500
pass 3: 6209 changed.
pass 4: 2299 changed.
69839 voxels changed in iteration 0 of unlikely voxel relabeling
500 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8487 voxels changed in iteration 0 of unlikely voxel relabeling
174 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
7537 voxels changed in iteration 0 of unlikely voxel relabeling
64 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
5897 voxels changed in iteration 0 of unlikely voxel relabeling
34 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    4252.241561
mri_ca_label stimesec    1.434781
mri_ca_label ru_maxrss   2108288
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   719978
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63520
mri_ca_label ru_oublock  520
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    248
mri_ca_label ru_nivcsw   6783
auto-labeling took 70 minutes and 9 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/transforms/cc_up.lta 0050267 

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-6.0.0/0050267/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/norm.mgz
42249 voxels in left wm, 72450 in right wm, xrange [121, 131]
searching rotation angles z=[-8  6], y=[-8  6]

searching scale 1 Z rot -8.3  
searching scale 1 Z rot -8.0  
searching scale 1 Z rot -7.8  
searching scale 1 Z rot -7.5  
searching scale 1 Z rot -7.3  
searching scale 1 Z rot -7.0  
searching scale 1 Z rot -6.8  
searching scale 1 Z rot -6.5  
searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.0  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.2  global minimum found at slice 127.0, rotations (-0.77, -1.51)
final transformation (x=127.0, yr=-0.773, zr=-1.507):
 0.99956   0.02631  -0.01348  -0.01437;
-0.02630   0.99965   0.00035   36.33584;
 0.01349  -0.00000   0.99991   20.29668;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 132] in xformed coordinates
best xformed slice 129
cc center is found at 129 95 106
eigenvectors:
 0.00159  -0.00775   0.99997;
-0.09394  -0.99555  -0.00757;
 0.99558  -0.09392  -0.00231;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.0 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 00:02:24 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 00:02:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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...
1274 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 74 (74), valley at 31 (31)
csf peak at 38, setting threshold to 62
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 74 (74), valley at 19 (19)
csf peak at 38, setting threshold to 62
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 16 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 00:05:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1879417 voxels in mask (pct= 11.20)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 00:05:43 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 103.6 +- 6.9 [79.0 --> 125.0]
GM (74.0) : 72.3 +- 10.2 [30.0 --> 95.0]
setting bottom of white matter range to 82.5
setting top of gray matter range to 92.7
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...
11902 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4587 filled
2866 bright non-wm voxels segmented.
5000 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 0.51 minutes
reading wm segmentation from wm.seg.mgz...
199 voxels added to wm to prevent paths from MTL structures to cortex
3024 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 33342 voxels turned on, 62648 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  21 found -  21 modified     |    TOTAL:  21
pass   2 (xy+):   0 found -  21 modified     |    TOTAL:  21
pass   1 (xy-):  24 found -  24 modified     |    TOTAL:  45
pass   2 (xy-):   0 found -  24 modified     |    TOTAL:  45
pass   1 (yz+):  29 found -  29 modified     |    TOTAL:  74
pass   2 (yz+):   0 found -  29 modified     |    TOTAL:  74
pass   1 (yz-):  34 found -  34 modified     |    TOTAL: 108
pass   2 (yz-):   0 found -  34 modified     |    TOTAL: 108
pass   1 (xz+):  19 found -  19 modified     |    TOTAL: 127
pass   2 (xz+):   0 found -  19 modified     |    TOTAL: 127
pass   1 (xz-):  30 found -  30 modified     |    TOTAL: 157
pass   2 (xz-):   0 found -  30 modified     |    TOTAL: 157
Iteration Number : 1
pass   1 (+++):  38 found -  38 modified     |    TOTAL:  38
pass   2 (+++):   0 found -  38 modified     |    TOTAL:  38
pass   1 (+++):  43 found -  43 modified     |    TOTAL:  81
pass   2 (+++):   0 found -  43 modified     |    TOTAL:  81
pass   1 (+++):  56 found -  56 modified     |    TOTAL: 137
pass   2 (+++):   0 found -  56 modified     |    TOTAL: 137
pass   1 (+++):  27 found -  27 modified     |    TOTAL: 164
pass   2 (+++):   0 found -  27 modified     |    TOTAL: 164
Iteration Number : 1
pass   1 (++): 224 found - 224 modified     |    TOTAL: 224
pass   2 (++):   0 found - 224 modified     |    TOTAL: 224
pass   1 (+-): 187 found - 187 modified     |    TOTAL: 411
pass   2 (+-):   2 found - 189 modified     |    TOTAL: 413
pass   3 (+-):   0 found - 189 modified     |    TOTAL: 413
pass   1 (--): 160 found - 160 modified     |    TOTAL: 573
pass   2 (--):   1 found - 161 modified     |    TOTAL: 574
pass   3 (--):   0 found - 161 modified     |    TOTAL: 574
pass   1 (-+): 172 found - 172 modified     |    TOTAL: 746
pass   2 (-+):   0 found - 172 modified     |    TOTAL: 746
Iteration Number : 2
pass   1 (xy+):  11 found -  11 modified     |    TOTAL:  11
pass   2 (xy+):   0 found -  11 modified     |    TOTAL:  11
pass   1 (xy-):   8 found -   8 modified     |    TOTAL:  19
pass   2 (xy-):   0 found -   8 modified     |    TOTAL:  19
pass   1 (yz+):   7 found -   7 modified     |    TOTAL:  26
pass   2 (yz+):   0 found -   7 modified     |    TOTAL:  26
pass   1 (yz-):  17 found -  17 modified     |    TOTAL:  43
pass   2 (yz-):   0 found -  17 modified     |    TOTAL:  43
pass   1 (xz+):   8 found -   8 modified     |    TOTAL:  51
pass   2 (xz+):   0 found -   8 modified     |    TOTAL:  51
pass   1 (xz-):  11 found -  11 modified     |    TOTAL:  62
pass   2 (xz-):   0 found -  11 modified     |    TOTAL:  62
Iteration Number : 2
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   3
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   5
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   5
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   9
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   9
Iteration Number : 2
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (--):   6 found -   6 modified     |    TOTAL:  11
pass   2 (--):   0 found -   6 modified     |    TOTAL:  11
pass   1 (-+):   3 found -   3 modified     |    TOTAL:  14
pass   2 (-+):   0 found -   3 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-):   4 found -   4 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   5
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   8
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 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (--):   0 found -   0 modified     |    TOTAL:   3
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   4
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-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 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 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1168 (out of 662670: 0.176257)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 00:08:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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
 1.02066   0.02291  -0.01985  -3.69728;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87431;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.02066   0.02291  -0.01985  -3.69728;
-0.01613   1.02703   0.24510  -23.90878;
 0.02615  -0.21238   0.93767   27.87431;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1081 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75)
no need to search
using seed (126, 122, 146), TAL = (2.0, 18.0, 6.0)
talairach voxel to voxel transform
 0.97886  -0.01665   0.02508   2.52208;
 0.02077   0.92340  -0.24093   28.86992;
-0.02259   0.20961   1.01121  -23.25864;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  122,  146) --> (2.0, 18.0, 6.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (2.00, 18.00, 6.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 18.00, 6.00) SRC: (109.87, 108.59, 147.51)
search lh wm seed point around talairach space (-16.00, 18.00, 6.00), SRC: (145.11, 109.34, 146.70)
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 00:08:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-):   4 found -   4 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   5
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   8
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   8
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  10
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  12
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  12
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  14
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  14
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 17 (out of 319566: 0.005320)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 30: 1272 vertices, 1370 faces
slice 40: 7342 vertices, 7631 faces
slice 50: 17945 vertices, 18353 faces
slice 60: 30620 vertices, 31110 faces
slice 70: 43793 vertices, 44260 faces
slice 80: 57988 vertices, 58484 faces
slice 90: 72198 vertices, 72669 faces
slice 100: 85782 vertices, 86243 faces
slice 110: 99377 vertices, 99816 faces
slice 120: 111848 vertices, 112325 faces
slice 130: 124230 vertices, 124744 faces
slice 140: 136864 vertices, 137284 faces
slice 150: 146965 vertices, 147385 faces
slice 160: 155991 vertices, 156333 faces
slice 170: 164315 vertices, 164655 faces
slice 180: 171035 vertices, 171320 faces
slice 190: 176216 vertices, 176410 faces
slice 200: 177310 vertices, 177378 faces
slice 210: 177310 vertices, 177378 faces
slice 220: 177310 vertices, 177378 faces
slice 230: 177310 vertices, 177378 faces
slice 240: 177310 vertices, 177378 faces
slice 250: 177310 vertices, 177378 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...
   177310 voxel in cpt #1: X=-68 [v=177310,e=532134,f=354756] located at (-27.740252, -24.502193, 17.730404)
For the whole surface: X=-68 [v=177310,e=532134,f=354756]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 00:08:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
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 = 3 (out of 316763: 0.000947)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 30: 490 vertices, 552 faces
slice 40: 4831 vertices, 5044 faces
slice 50: 13479 vertices, 13856 faces
slice 60: 25048 vertices, 25455 faces
slice 70: 37942 vertices, 38399 faces
slice 80: 51043 vertices, 51515 faces
slice 90: 64401 vertices, 64849 faces
slice 100: 78671 vertices, 79180 faces
slice 110: 92457 vertices, 92916 faces
slice 120: 105762 vertices, 106245 faces
slice 130: 118563 vertices, 119036 faces
slice 140: 130524 vertices, 130948 faces
slice 150: 141269 vertices, 141651 faces
slice 160: 150716 vertices, 151073 faces
slice 170: 158971 vertices, 159306 faces
slice 180: 166725 vertices, 167028 faces
slice 190: 173106 vertices, 173362 faces
slice 200: 176126 vertices, 176204 faces
slice 210: 176126 vertices, 176204 faces
slice 220: 176126 vertices, 176204 faces
slice 230: 176126 vertices, 176204 faces
slice 240: 176126 vertices, 176204 faces
slice 250: 176126 vertices, 176204 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...
   176126 voxel in cpt #1: X=-78 [v=176126,e=528612,f=352408] located at (29.936506, -19.969278, 18.993687)
For the whole surface: X=-78 [v=176126,e=528612,f=352408]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 00:09:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 00:09:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

Waiting for PID 14202 of (14202 14205) to complete...
Waiting for PID 14205 of (14202 14205) 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 (14202 14205) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 00:09:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 00:09:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

Waiting for PID 14251 of (14251 14254) to complete...
Waiting for PID 14254 of (14251 14254) 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 = 49.8 mm, total surface area = 92187 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.159 (target=0.015)   
step 005: RMS=0.120 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.061 (target=0.015)   
step 030: RMS=0.055 (target=0.015)   
step 035: RMS=0.051 (target=0.015)   
step 040: RMS=0.048 (target=0.015)   
step 045: RMS=0.046 (target=0.015)   
step 050: RMS=0.045 (target=0.015)   
step 055: RMS=0.045 (target=0.015)   
step 060: RMS=0.044 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    55.415575
mris_inflate stimesec    0.176973
mris_inflate ru_maxrss   257940
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36828
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  12496
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5267
mris_inflate ru_nivcsw   4810

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 49.6 mm, total surface area = 91077 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.161 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.080 (target=0.015)   
step 020: RMS=0.069 (target=0.015)   
step 025: RMS=0.063 (target=0.015)   
step 030: RMS=0.058 (target=0.015)   
step 035: RMS=0.054 (target=0.015)   
step 040: RMS=0.051 (target=0.015)   
step 045: RMS=0.050 (target=0.015)   
step 050: RMS=0.049 (target=0.015)   
step 055: RMS=0.049 (target=0.015)   
step 060: RMS=0.048 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    55.610545
mris_inflate stimesec    0.157975
mris_inflate ru_maxrss   256440
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36963
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12392
mris_inflate ru_oublock  12408
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    6801
mris_inflate ru_nivcsw   5847
PIDs (14251 14254) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 00:10:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 00:10:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

Waiting for PID 14339 of (14339 14343) to complete...
Waiting for PID 14343 of (14339 14343) 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 0.87 +- 0.53 (0.00-->8.23) (max @ vno 80308 --> 80329)
face area 0.02 +- 0.03 (-0.39-->0.58)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.281...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.620, avgs=0
005/300: dt: 0.9000, rms radial error=176.361, avgs=0
010/300: dt: 0.9000, rms radial error=175.804, avgs=0
015/300: dt: 0.9000, rms radial error=175.074, avgs=0
020/300: dt: 0.9000, rms radial error=174.242, avgs=0
025/300: dt: 0.9000, rms radial error=173.352, avgs=0
030/300: dt: 0.9000, rms radial error=172.430, avgs=0
035/300: dt: 0.9000, rms radial error=171.492, avgs=0
040/300: dt: 0.9000, rms radial error=170.546, avgs=0
045/300: dt: 0.9000, rms radial error=169.596, avgs=0
050/300: dt: 0.9000, rms radial error=168.648, avgs=0
055/300: dt: 0.9000, rms radial error=167.702, avgs=0
060/300: dt: 0.9000, rms radial error=166.760, avgs=0
065/300: dt: 0.9000, rms radial error=165.821, avgs=0
070/300: dt: 0.9000, rms radial error=164.887, avgs=0
075/300: dt: 0.9000, rms radial error=163.958, avgs=0
080/300: dt: 0.9000, rms radial error=163.034, avgs=0
085/300: dt: 0.9000, rms radial error=162.114, avgs=0
090/300: dt: 0.9000, rms radial error=161.200, avgs=0
095/300: dt: 0.9000, rms radial error=160.290, avgs=0
100/300: dt: 0.9000, rms radial error=159.385, avgs=0
105/300: dt: 0.9000, rms radial error=158.485, avgs=0
110/300: dt: 0.9000, rms radial error=157.590, avgs=0
115/300: dt: 0.9000, rms radial error=156.700, avgs=0
120/300: dt: 0.9000, rms radial error=155.814, avgs=0
125/300: dt: 0.9000, rms radial error=154.933, avgs=0
130/300: dt: 0.9000, rms radial error=154.056, avgs=0
135/300: dt: 0.9000, rms radial error=153.184, avgs=0
140/300: dt: 0.9000, rms radial error=152.318, avgs=0
145/300: dt: 0.9000, rms radial error=151.457, avgs=0
150/300: dt: 0.9000, rms radial error=150.602, avgs=0
155/300: dt: 0.9000, rms radial error=149.751, avgs=0
160/300: dt: 0.9000, rms radial error=148.905, avgs=0
165/300: dt: 0.9000, rms radial error=148.063, avgs=0
170/300: dt: 0.9000, rms radial error=147.226, avgs=0
175/300: dt: 0.9000, rms radial error=146.394, avgs=0
180/300: dt: 0.9000, rms radial error=145.567, avgs=0
185/300: dt: 0.9000, rms radial error=144.744, avgs=0
190/300: dt: 0.9000, rms radial error=143.926, avgs=0
195/300: dt: 0.9000, rms radial error=143.114, avgs=0
200/300: dt: 0.9000, rms radial error=142.307, avgs=0
205/300: dt: 0.9000, rms radial error=141.505, avgs=0
210/300: dt: 0.9000, rms radial error=140.707, avgs=0
215/300: dt: 0.9000, rms radial error=139.914, avgs=0
220/300: dt: 0.9000, rms radial error=139.125, avgs=0
225/300: dt: 0.9000, rms radial error=138.341, avgs=0
230/300: dt: 0.9000, rms radial error=137.561, avgs=0
235/300: dt: 0.9000, rms radial error=136.785, avgs=0
240/300: dt: 0.9000, rms radial error=136.014, avgs=0
245/300: dt: 0.9000, rms radial error=135.247, avgs=0
250/300: dt: 0.9000, rms radial error=134.484, avgs=0
255/300: dt: 0.9000, rms radial error=133.725, avgs=0
260/300: dt: 0.9000, rms radial error=132.971, avgs=0
265/300: dt: 0.9000, rms radial error=132.220, avgs=0
270/300: dt: 0.9000, rms radial error=131.474, avgs=0
275/300: dt: 0.9000, rms radial error=130.732, avgs=0
280/300: dt: 0.9000, rms radial error=129.995, avgs=0
285/300: dt: 0.9000, rms radial error=129.261, avgs=0
290/300: dt: 0.9000, rms radial error=128.532, avgs=0
295/300: dt: 0.9000, rms radial error=127.806, avgs=0
300/300: dt: 0.9000, rms radial error=127.085, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 21449.37
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
epoch 2 (K=40.0), pass 1, starting sse = 3854.59
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
epoch 3 (K=160.0), pass 1, starting sse = 449.53
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00383
epoch 4 (K=640.0), pass 1, starting sse = 35.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/11 = 0.00902
final distance error %28.90
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    340.058303
mris_sphere stimesec    0.249962
mris_sphere ru_maxrss   258136
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   36875
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  12480
mris_sphere ru_oublock  12520
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8231
mris_sphere ru_nivcsw   24641
FSRUNTIME@ mris_sphere  0.0945 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 0.87 +- 0.54 (0.00-->7.35) (max @ vno 125711 --> 127034)
face area 0.02 +- 0.03 (-0.24-->0.74)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.280...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.740, avgs=0
005/300: dt: 0.9000, rms radial error=176.478, avgs=0
010/300: dt: 0.9000, rms radial error=175.917, avgs=0
015/300: dt: 0.9000, rms radial error=175.181, avgs=0
020/300: dt: 0.9000, rms radial error=174.343, avgs=0
025/300: dt: 0.9000, rms radial error=173.446, avgs=0
030/300: dt: 0.9000, rms radial error=172.517, avgs=0
035/300: dt: 0.9000, rms radial error=171.571, avgs=0
040/300: dt: 0.9000, rms radial error=170.618, avgs=0
045/300: dt: 0.9000, rms radial error=169.663, avgs=0
050/300: dt: 0.9000, rms radial error=168.709, avgs=0
055/300: dt: 0.9000, rms radial error=167.758, avgs=0
060/300: dt: 0.9000, rms radial error=166.811, avgs=0
065/300: dt: 0.9000, rms radial error=165.868, avgs=0
070/300: dt: 0.9000, rms radial error=164.932, avgs=0
075/300: dt: 0.9000, rms radial error=164.004, avgs=0
080/300: dt: 0.9000, rms radial error=163.080, avgs=0
085/300: dt: 0.9000, rms radial error=162.161, avgs=0
090/300: dt: 0.9000, rms radial error=161.248, avgs=0
095/300: dt: 0.9000, rms radial error=160.339, avgs=0
100/300: dt: 0.9000, rms radial error=159.436, avgs=0
105/300: dt: 0.9000, rms radial error=158.538, avgs=0
110/300: dt: 0.9000, rms radial error=157.645, avgs=0
115/300: dt: 0.9000, rms radial error=156.756, avgs=0
120/300: dt: 0.9000, rms radial error=155.873, avgs=0
125/300: dt: 0.9000, rms radial error=154.994, avgs=0
130/300: dt: 0.9000, rms radial error=154.121, avgs=0
135/300: dt: 0.9000, rms radial error=153.252, avgs=0
140/300: dt: 0.9000, rms radial error=152.388, avgs=0
145/300: dt: 0.9000, rms radial error=151.529, avgs=0
150/300: dt: 0.9000, rms radial error=150.675, avgs=0
155/300: dt: 0.9000, rms radial error=149.825, avgs=0
160/300: dt: 0.9000, rms radial error=148.980, avgs=0
165/300: dt: 0.9000, rms radial error=148.140, avgs=0
170/300: dt: 0.9000, rms radial error=147.305, avgs=0
175/300: dt: 0.9000, rms radial error=146.474, avgs=0
180/300: dt: 0.9000, rms radial error=145.648, avgs=0
185/300: dt: 0.9000, rms radial error=144.826, avgs=0
190/300: dt: 0.9000, rms radial error=144.010, avgs=0
195/300: dt: 0.9000, rms radial error=143.197, avgs=0
200/300: dt: 0.9000, rms radial error=142.389, avgs=0
205/300: dt: 0.9000, rms radial error=141.586, avgs=0
210/300: dt: 0.9000, rms radial error=140.787, avgs=0
215/300: dt: 0.9000, rms radial error=139.993, avgs=0
220/300: dt: 0.9000, rms radial error=139.204, avgs=0
225/300: dt: 0.9000, rms radial error=138.419, avgs=0
230/300: dt: 0.9000, rms radial error=137.639, avgs=0
235/300: dt: 0.9000, rms radial error=136.863, avgs=0
240/300: dt: 0.9000, rms radial error=136.092, avgs=0
245/300: dt: 0.9000, rms radial error=135.325, avgs=0
250/300: dt: 0.9000, rms radial error=134.563, avgs=0
255/300: dt: 0.9000, rms radial error=133.806, avgs=0
260/300: dt: 0.9000, rms radial error=133.054, avgs=0
265/300: dt: 0.9000, rms radial error=132.305, avgs=0
270/300: dt: 0.9000, rms radial error=131.552, avgs=0
275/300: dt: 0.9000, rms radial error=130.816, avgs=0
280/300: dt: 0.9000, rms radial error=130.074, avgs=0
285/300: dt: 0.9000, rms radial error=129.343, avgs=0
290/300: dt: 0.9000, rms radial error=128.617, avgs=0
295/300: dt: 0.9000, rms radial error=127.896, avgs=0
300/300: dt: 0.9000, rms radial error=127.176, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 21343.58
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 2 (K=40.0), pass 1, starting sse = 3863.98
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00000
epoch 3 (K=160.0), pass 1, starting sse = 450.69
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00359
epoch 4 (K=640.0), pass 1, starting sse = 35.74
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00665
final distance error %28.92
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    340.097297
mris_sphere stimesec    0.251961
mris_sphere ru_maxrss   256648
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   36502
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12432
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8361
mris_sphere ru_nivcsw   24908
FSRUNTIME@ mris_sphere  0.0945 hours 1 threads
PIDs (14339 14343) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 00:15:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 00:15:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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


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

#@# Fix Topology lh Sun Oct  8 00:15:46 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050267 lh 

#@# Fix Topology rh Sun Oct  8 00:15:46 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050267 rh 

Waiting for PID 14615 of (14615 14618) to complete...
Waiting for PID 14618 of (14615 14618) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050267 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=-68 (nv=177310, nf=354756, ne=532134, g=35)
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...
9716 ambiguous faces found in tessellation
segmenting defects...
43 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 6 into 5
      -merging segment 10 into 7
      -merging segment 27 into 18
      -merging segment 36 into 35
39 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3501  (-4.6750)
      -vertex     loglikelihood: -6.0141  (-3.0071)
      -normal dot loglikelihood: -3.5891  (-3.5891)
      -quad curv  loglikelihood: -6.1382  (-3.0691)
      Total Loglikelihood : -25.0915

CORRECTING DEFECT 0 (vertices=96, convex hull=131, v0=12419)
After retessellation of defect 0 (v0=12419), euler #=-38 (171743,513858,342077) : difference with theory (-36) = 2 

CORRECTING DEFECT 1 (vertices=360, convex hull=252, v0=15202)
After retessellation of defect 1 (v0=15202), euler #=-37 (171910,514487,342540) : difference with theory (-35) = 2 

CORRECTING DEFECT 2 (vertices=28, convex hull=26, v0=23159)
After retessellation of defect 2 (v0=23159), euler #=-36 (171914,514507,342557) : difference with theory (-34) = 2 

CORRECTING DEFECT 3 (vertices=7, convex hull=30, v0=25113)
After retessellation of defect 3 (v0=25113), euler #=-35 (171917,514525,342573) : difference with theory (-33) = 2 

CORRECTING DEFECT 4 (vertices=29, convex hull=10, v0=29954)
After retessellation of defect 4 (v0=29954), euler #=-34 (171917,514527,342576) : difference with theory (-32) = 2 

CORRECTING DEFECT 5 (vertices=48, convex hull=34, v0=31430)
After retessellation of defect 5 (v0=31430), euler #=-32 (171925,514565,342608) : difference with theory (-31) = 1 

CORRECTING DEFECT 6 (vertices=30, convex hull=37, v0=42884)
After retessellation of defect 6 (v0=42884), euler #=-30 (171927,514587,342630) : difference with theory (-30) = 0 

CORRECTING DEFECT 7 (vertices=882, convex hull=154, v0=44029)
After retessellation of defect 7 (v0=44029), euler #=-29 (172003,514899,342867) : difference with theory (-29) = 0 

CORRECTING DEFECT 8 (vertices=20, convex hull=31, v0=45991)
After retessellation of defect 8 (v0=45991), euler #=-28 (172005,514915,342882) : difference with theory (-28) = 0 

CORRECTING DEFECT 9 (vertices=302, convex hull=219, v0=64575)
After retessellation of defect 9 (v0=64575), euler #=-27 (172097,515299,343175) : difference with theory (-27) = 0 

CORRECTING DEFECT 10 (vertices=153, convex hull=106, v0=66107)
After retessellation of defect 10 (v0=66107), euler #=-26 (172133,515452,343293) : difference with theory (-26) = 0 

CORRECTING DEFECT 11 (vertices=58, convex hull=44, v0=70632)
After retessellation of defect 11 (v0=70632), euler #=-25 (172146,515504,343333) : difference with theory (-25) = 0 

CORRECTING DEFECT 12 (vertices=36, convex hull=59, v0=70911)
After retessellation of defect 12 (v0=70911), euler #=-24 (172162,515575,343389) : difference with theory (-24) = 0 

CORRECTING DEFECT 13 (vertices=45, convex hull=32, v0=80055)
After retessellation of defect 13 (v0=80055), euler #=-23 (172175,515626,343428) : difference with theory (-23) = 0 

CORRECTING DEFECT 14 (vertices=9, convex hull=30, v0=83432)
After retessellation of defect 14 (v0=83432), euler #=-22 (172177,515644,343445) : difference with theory (-22) = 0 

CORRECTING DEFECT 15 (vertices=7, convex hull=13, v0=83935)
After retessellation of defect 15 (v0=83935), euler #=-21 (172178,515649,343450) : difference with theory (-21) = 0 

CORRECTING DEFECT 16 (vertices=1340, convex hull=661, v0=93638)
XL defect detected...
After retessellation of defect 16 (v0=93638), euler #=-21 (172605,517316,344690) : difference with theory (-20) = 1 

CORRECTING DEFECT 17 (vertices=45, convex hull=42, v0=94721)
After retessellation of defect 17 (v0=94721), euler #=-20 (172614,517353,344719) : difference with theory (-19) = 1 

CORRECTING DEFECT 18 (vertices=12, convex hull=26, v0=97684)
After retessellation of defect 18 (v0=97684), euler #=-19 (172617,517370,344734) : difference with theory (-18) = 1 

CORRECTING DEFECT 19 (vertices=17, convex hull=30, v0=100696)
After retessellation of defect 19 (v0=100696), euler #=-18 (172618,517383,344747) : difference with theory (-17) = 1 

CORRECTING DEFECT 20 (vertices=71, convex hull=32, v0=106850)
After retessellation of defect 20 (v0=106850), euler #=-17 (172623,517410,344770) : difference with theory (-16) = 1 

CORRECTING DEFECT 21 (vertices=29, convex hull=30, v0=110861)
After retessellation of defect 21 (v0=110861), euler #=-16 (172627,517430,344787) : difference with theory (-15) = 1 

CORRECTING DEFECT 22 (vertices=35, convex hull=64, v0=112357)
After retessellation of defect 22 (v0=112357), euler #=-15 (172639,517492,344838) : difference with theory (-14) = 1 

CORRECTING DEFECT 23 (vertices=22, convex hull=50, v0=115143)
After retessellation of defect 23 (v0=115143), euler #=-14 (172649,517539,344876) : difference with theory (-13) = 1 

CORRECTING DEFECT 24 (vertices=11, convex hull=37, v0=115313)
After retessellation of defect 24 (v0=115313), euler #=-13 (172653,517568,344902) : difference with theory (-12) = 1 

CORRECTING DEFECT 25 (vertices=12, convex hull=33, v0=123589)
After retessellation of defect 25 (v0=123589), euler #=-12 (172658,517595,344925) : difference with theory (-11) = 1 

CORRECTING DEFECT 26 (vertices=75, convex hull=81, v0=123869)
After retessellation of defect 26 (v0=123869), euler #=-11 (172686,517715,345018) : difference with theory (-10) = 1 

CORRECTING DEFECT 27 (vertices=8, convex hull=21, v0=124066)
After retessellation of defect 27 (v0=124066), euler #=-10 (172689,517734,345035) : difference with theory (-9) = 1 

CORRECTING DEFECT 28 (vertices=542, convex hull=122, v0=124196)
After retessellation of defect 28 (v0=124196), euler #=-9 (172737,517933,345187) : difference with theory (-8) = 1 

CORRECTING DEFECT 29 (vertices=148, convex hull=104, v0=125576)
After retessellation of defect 29 (v0=125576), euler #=-8 (172760,518052,345284) : difference with theory (-7) = 1 

CORRECTING DEFECT 30 (vertices=905, convex hull=261, v0=126515)
After retessellation of defect 30 (v0=126515), euler #=-7 (172942,518718,345769) : difference with theory (-6) = 1 

CORRECTING DEFECT 31 (vertices=9, convex hull=20, v0=126951)
After retessellation of defect 31 (v0=126951), euler #=-6 (172943,518726,345777) : difference with theory (-5) = 1 

CORRECTING DEFECT 32 (vertices=73, convex hull=50, v0=129627)
After retessellation of defect 32 (v0=129627), euler #=-4 (172954,518779,345821) : difference with theory (-4) = 0 

CORRECTING DEFECT 33 (vertices=26, convex hull=41, v0=132449)
After retessellation of defect 33 (v0=132449), euler #=-3 (172957,518800,345840) : difference with theory (-3) = 0 

CORRECTING DEFECT 34 (vertices=37, convex hull=31, v0=133212)
After retessellation of defect 34 (v0=133212), euler #=-2 (172965,518832,345865) : difference with theory (-2) = 0 

CORRECTING DEFECT 35 (vertices=11, convex hull=24, v0=136292)
After retessellation of defect 35 (v0=136292), euler #=-1 (172968,518848,345879) : difference with theory (-1) = 0 

CORRECTING DEFECT 36 (vertices=34, convex hull=34, v0=144986)
After retessellation of defect 36 (v0=144986), euler #=0 (172975,518883,345908) : difference with theory (0) = 0 

CORRECTING DEFECT 37 (vertices=6, convex hull=24, v0=159560)
After retessellation of defect 37 (v0=159560), euler #=1 (172976,518894,345919) : difference with theory (1) = 0 

CORRECTING DEFECT 38 (vertices=27, convex hull=65, v0=165630)
After retessellation of defect 38 (v0=165630), euler #=2 (172987,518955,345970) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.02-->8.14) (max @ vno 23503 --> 29708)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.02-->8.14) (max @ vno 23503 --> 29708)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
137 mutations (39.3%), 212 crossovers (60.7%), 97 vertices were eliminated
building final representation...
4323 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=172987, nf=345970, ne=518955, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 33.1 minutes
0 defective edges
removing intersecting faces
000: 311 intersecting
001: 6 intersecting
mris_fix_topology utimesec    1988.228743
mris_fix_topology stimesec    0.258960
mris_fix_topology ru_maxrss   560948
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   62496
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23040
mris_fix_topology ru_oublock  16576
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    569
mris_fix_topology ru_nivcsw   5285
FSRUNTIME@ mris_fix_topology lh  0.5523 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050267 rh

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-78 (nv=176126, nf=352408, ne=528612, g=40)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
9229 ambiguous faces found in tessellation
segmenting defects...
52 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 39 into 36
51 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3935  (-4.6967)
      -vertex     loglikelihood: -5.9752  (-2.9876)
      -normal dot loglikelihood: -3.5551  (-3.5551)
      -quad curv  loglikelihood: -6.5496  (-3.2748)
      Total Loglikelihood : -25.4734

CORRECTING DEFECT 0 (vertices=48, convex hull=70, v0=27497)
After retessellation of defect 0 (v0=27497), euler #=-46 (170789,510907,340072) : difference with theory (-48) = -2 

CORRECTING DEFECT 1 (vertices=16, convex hull=25, v0=52773)
After retessellation of defect 1 (v0=52773), euler #=-45 (170790,510920,340085) : difference with theory (-47) = -2 

CORRECTING DEFECT 2 (vertices=45, convex hull=31, v0=58595)
After retessellation of defect 2 (v0=58595), euler #=-44 (170796,510948,340108) : difference with theory (-46) = -2 

CORRECTING DEFECT 3 (vertices=729, convex hull=234, v0=61486)
After retessellation of defect 3 (v0=61486), euler #=-43 (170923,511437,340471) : difference with theory (-45) = -2 

CORRECTING DEFECT 4 (vertices=16, convex hull=21, v0=71232)
After retessellation of defect 4 (v0=71232), euler #=-42 (170925,511450,340483) : difference with theory (-44) = -2 

CORRECTING DEFECT 5 (vertices=6, convex hull=29, v0=76881)
After retessellation of defect 5 (v0=76881), euler #=-41 (170927,511463,340495) : difference with theory (-43) = -2 

CORRECTING DEFECT 6 (vertices=112, convex hull=145, v0=77134)
After retessellation of defect 6 (v0=77134), euler #=-40 (170963,511638,340635) : difference with theory (-42) = -2 

CORRECTING DEFECT 7 (vertices=258, convex hull=257, v0=80711)
After retessellation of defect 7 (v0=80711), euler #=-39 (171028,511955,340888) : difference with theory (-41) = -2 

CORRECTING DEFECT 8 (vertices=33, convex hull=21, v0=82641)
After retessellation of defect 8 (v0=82641), euler #=-38 (171031,511972,340903) : difference with theory (-40) = -2 

CORRECTING DEFECT 9 (vertices=7, convex hull=27, v0=86858)
After retessellation of defect 9 (v0=86858), euler #=-37 (171032,511984,340915) : difference with theory (-39) = -2 

CORRECTING DEFECT 10 (vertices=8, convex hull=27, v0=88365)
After retessellation of defect 10 (v0=88365), euler #=-36 (171033,511996,340927) : difference with theory (-38) = -2 

CORRECTING DEFECT 11 (vertices=31, convex hull=45, v0=92277)
After retessellation of defect 11 (v0=92277), euler #=-35 (171042,512039,340962) : difference with theory (-37) = -2 

CORRECTING DEFECT 12 (vertices=993, convex hull=504, v0=93417)
XL defect detected...
After retessellation of defect 12 (v0=93417), euler #=-37 (171429,513495,342029) : difference with theory (-36) = 1 

CORRECTING DEFECT 13 (vertices=15, convex hull=32, v0=94480)
After retessellation of defect 13 (v0=94480), euler #=-36 (171436,513526,342054) : difference with theory (-35) = 1 

CORRECTING DEFECT 14 (vertices=62, convex hull=26, v0=100410)
After retessellation of defect 14 (v0=100410), euler #=-35 (171440,513545,342070) : difference with theory (-34) = 1 

CORRECTING DEFECT 15 (vertices=26, convex hull=59, v0=100414)
After retessellation of defect 15 (v0=100414), euler #=-34 (171450,513602,342118) : difference with theory (-33) = 1 

CORRECTING DEFECT 16 (vertices=81, convex hull=62, v0=101262)
After retessellation of defect 16 (v0=101262), euler #=-33 (171459,513654,342162) : difference with theory (-32) = 1 

CORRECTING DEFECT 17 (vertices=29, convex hull=29, v0=104814)
After retessellation of defect 17 (v0=104814), euler #=-32 (171464,513677,342181) : difference with theory (-31) = 1 

CORRECTING DEFECT 18 (vertices=125, convex hull=149, v0=105785)
After retessellation of defect 18 (v0=105785), euler #=-31 (171525,513931,342375) : difference with theory (-30) = 1 

CORRECTING DEFECT 19 (vertices=13, convex hull=32, v0=106512)
After retessellation of defect 19 (v0=106512), euler #=-30 (171527,513946,342389) : difference with theory (-29) = 1 

CORRECTING DEFECT 20 (vertices=12, convex hull=35, v0=106544)
After retessellation of defect 20 (v0=106544), euler #=-29 (171533,513976,342414) : difference with theory (-28) = 1 

CORRECTING DEFECT 21 (vertices=23, convex hull=48, v0=111677)
After retessellation of defect 21 (v0=111677), euler #=-28 (171546,514032,342458) : difference with theory (-27) = 1 

CORRECTING DEFECT 22 (vertices=51, convex hull=38, v0=111796)
After retessellation of defect 22 (v0=111796), euler #=-27 (171557,514079,342495) : difference with theory (-26) = 1 

CORRECTING DEFECT 23 (vertices=37, convex hull=51, v0=112271)
After retessellation of defect 23 (v0=112271), euler #=-26 (171575,514149,342548) : difference with theory (-25) = 1 

CORRECTING DEFECT 24 (vertices=9, convex hull=20, v0=113482)
After retessellation of defect 24 (v0=113482), euler #=-25 (171577,514161,342559) : difference with theory (-24) = 1 

CORRECTING DEFECT 25 (vertices=18, convex hull=26, v0=114864)
After retessellation of defect 25 (v0=114864), euler #=-24 (171579,514176,342573) : difference with theory (-23) = 1 

CORRECTING DEFECT 26 (vertices=64, convex hull=27, v0=116774)
After retessellation of defect 26 (v0=116774), euler #=-23 (171588,514212,342601) : difference with theory (-22) = 1 

CORRECTING DEFECT 27 (vertices=36, convex hull=24, v0=117424)
After retessellation of defect 27 (v0=117424), euler #=-22 (171589,514223,342612) : difference with theory (-21) = 1 

CORRECTING DEFECT 28 (vertices=40, convex hull=68, v0=118171)
After retessellation of defect 28 (v0=118171), euler #=-21 (171605,514299,342673) : difference with theory (-20) = 1 

CORRECTING DEFECT 29 (vertices=59, convex hull=28, v0=118246)
After retessellation of defect 29 (v0=118246), euler #=-20 (171611,514328,342697) : difference with theory (-19) = 1 

CORRECTING DEFECT 30 (vertices=8, convex hull=26, v0=118421)
After retessellation of defect 30 (v0=118421), euler #=-19 (171613,514341,342709) : difference with theory (-18) = 1 

CORRECTING DEFECT 31 (vertices=26, convex hull=56, v0=121786)
After retessellation of defect 31 (v0=121786), euler #=-18 (171627,514405,342760) : difference with theory (-17) = 1 

CORRECTING DEFECT 32 (vertices=76, convex hull=64, v0=121891)
After retessellation of defect 32 (v0=121891), euler #=-17 (171643,514481,342821) : difference with theory (-16) = 1 

CORRECTING DEFECT 33 (vertices=8, convex hull=27, v0=122381)
After retessellation of defect 33 (v0=122381), euler #=-16 (171644,514493,342833) : difference with theory (-15) = 1 

CORRECTING DEFECT 34 (vertices=43, convex hull=79, v0=124159)
After retessellation of defect 34 (v0=124159), euler #=-15 (171660,514574,342899) : difference with theory (-14) = 1 

CORRECTING DEFECT 35 (vertices=8, convex hull=26, v0=124409)
After retessellation of defect 35 (v0=124409), euler #=-14 (171661,514582,342907) : difference with theory (-13) = 1 

CORRECTING DEFECT 36 (vertices=108, convex hull=113, v0=125638)
After retessellation of defect 36 (v0=125638), euler #=-12 (171698,514743,343033) : difference with theory (-12) = 0 

CORRECTING DEFECT 37 (vertices=42, convex hull=60, v0=125904)
After retessellation of defect 37 (v0=125904), euler #=-11 (171715,514820,343094) : difference with theory (-11) = 0 

CORRECTING DEFECT 38 (vertices=60, convex hull=34, v0=129487)
After retessellation of defect 38 (v0=129487), euler #=-10 (171724,514859,343125) : difference with theory (-10) = 0 

CORRECTING DEFECT 39 (vertices=16, convex hull=43, v0=132390)
After retessellation of defect 39 (v0=132390), euler #=-9 (171730,514893,343154) : difference with theory (-9) = 0 

CORRECTING DEFECT 40 (vertices=27, convex hull=28, v0=133620)
After retessellation of defect 40 (v0=133620), euler #=-8 (171732,514907,343167) : difference with theory (-8) = 0 

CORRECTING DEFECT 41 (vertices=24, convex hull=59, v0=134514)
After retessellation of defect 41 (v0=134514), euler #=-7 (171741,514959,343211) : difference with theory (-7) = 0 

CORRECTING DEFECT 42 (vertices=81, convex hull=81, v0=134732)
After retessellation of defect 42 (v0=134732), euler #=-6 (171768,515076,343302) : difference with theory (-6) = 0 

CORRECTING DEFECT 43 (vertices=13, convex hull=25, v0=134945)
After retessellation of defect 43 (v0=134945), euler #=-5 (171770,515091,343316) : difference with theory (-5) = 0 

CORRECTING DEFECT 44 (vertices=344, convex hull=190, v0=137033)
After retessellation of defect 44 (v0=137033), euler #=-4 (171862,515457,343591) : difference with theory (-4) = 0 

CORRECTING DEFECT 45 (vertices=146, convex hull=51, v0=159061)
After retessellation of defect 45 (v0=159061), euler #=-3 (171875,515519,343641) : difference with theory (-3) = 0 

CORRECTING DEFECT 46 (vertices=58, convex hull=33, v0=162115)
After retessellation of defect 46 (v0=162115), euler #=-2 (171879,515540,343659) : difference with theory (-2) = 0 

CORRECTING DEFECT 47 (vertices=142, convex hull=32, v0=164822)
After retessellation of defect 47 (v0=164822), euler #=-1 (171887,515573,343685) : difference with theory (-1) = 0 

CORRECTING DEFECT 48 (vertices=1018, convex hull=106, v0=166302)
After retessellation of defect 48 (v0=166302), euler #=0 (171934,515763,343829) : difference with theory (0) = 0 

CORRECTING DEFECT 49 (vertices=12, convex hull=35, v0=173135)
After retessellation of defect 49 (v0=173135), euler #=1 (171935,515777,343843) : difference with theory (1) = 0 

CORRECTING DEFECT 50 (vertices=88, convex hull=58, v0=175514)
After retessellation of defect 50 (v0=175514), euler #=2 (171943,515823,343882) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.04-->12.22) (max @ vno 63804 --> 80118)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.04-->12.22) (max @ vno 63804 --> 80118)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
209 mutations (37.6%), 347 crossovers (62.4%), 192 vertices were eliminated
building final representation...
4183 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=171943, nf=343882, ne=515823, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 39.8 minutes
0 defective edges
removing intersecting faces
000: 414 intersecting
001: 14 intersecting
002: 3 intersecting
mris_fix_topology utimesec    2387.450052
mris_fix_topology stimesec    0.266959
mris_fix_topology ru_maxrss   549556
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   60232
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23040
mris_fix_topology ru_oublock  16560
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    540
mris_fix_topology ru_nivcsw   3905
FSRUNTIME@ mris_fix_topology rh  0.6630 hours 1 threads
PIDs (14615 14618) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 172987 - 518955 + 345970 = 2 --> 0 holes
      F =2V-4:          345970 = 345974-4 (0)
      2E=3F:            1037910 = 1037910 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 171943 - 515823 + 343882 = 2 --> 0 holes
      F =2V-4:          343882 = 343886-4 (0)
      2E=3F:            1031646 = 1031646 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 57 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 58 intersecting
001: 3 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:55:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050267 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:55:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050267 rh 

Waiting for PID 16245 of (16245 16248) to complete...
Waiting for PID 16248 of (16245 16248) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050267 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-6.0.0/0050267/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
37009 bright wm thresholded.
3041 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.orig...
computing class statistics...
border white:    327838 voxels (1.95%)
border gray      383327 voxels (2.28%)
WM (102.0): 101.2 +- 7.6 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70)
setting MAX_BORDER_WHITE to 113.6 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 53.8 (was 40)
setting MAX_GRAY to 98.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->3.99) (max @ vno 171802 --> 171818)
face area 0.28 +- 0.12 (0.00-->2.88)
mean absolute distance = 0.64 +- 0.79
6097 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=74+-6.1
mean inside = 97.1, mean outside = 79.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=84.3, 90 (90) missing vertices, mean dist 0.3 [0.5 (%38.3)->0.7 (%61.7))]
%75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.24 (0.07-->6.25) (max @ vno 172029 --> 66151)
face area 0.28 +- 0.13 (0.00-->3.41)
mean absolute distance = 0.30 +- 0.46
4025 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3496349.5, rms=9.131
001: dt: 0.5000, sse=1990729.1, rms=6.257 (31.474%)
002: dt: 0.5000, sse=1407527.5, rms=4.670 (25.363%)
003: dt: 0.5000, sse=1167589.4, rms=3.839 (17.792%)
004: dt: 0.5000, sse=1058780.6, rms=3.386 (11.791%)
005: dt: 0.5000, sse=1024056.2, rms=3.220 (4.919%)
006: dt: 0.5000, sse=1000363.7, rms=3.112 (3.341%)
rms = 3.10, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=1002672.3, rms=3.098 (0.465%)
008: dt: 0.2500, sse=818043.1, rms=1.935 (37.547%)
009: dt: 0.2500, sse=787783.9, rms=1.660 (14.177%)
010: dt: 0.2500, sse=780801.8, rms=1.596 (3.874%)
rms = 1.55, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=775661.9, rms=1.551 (2.833%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=773085.4, rms=1.521 (1.943%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=87.4, 75 (15) missing vertices, mean dist -0.2 [0.3 (%78.1)->0.2 (%21.9))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.05-->6.70) (max @ vno 172029 --> 66151)
face area 0.34 +- 0.16 (0.00-->4.57)
mean absolute distance = 0.21 +- 0.30
4808 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1473180.4, rms=4.276
013: dt: 0.5000, sse=1108438.4, rms=2.688 (37.145%)
rms = 2.76, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=1009101.0, rms=2.080 (22.588%)
015: dt: 0.2500, sse=954277.8, rms=1.631 (21.594%)
016: dt: 0.2500, sse=940277.3, rms=1.432 (12.195%)
017: dt: 0.2500, sse=926733.9, rms=1.357 (5.281%)
rms = 1.32, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=926771.1, rms=1.316 (2.967%)
rms = 1.29, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=922409.2, rms=1.285 (2.350%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=89.4, 69 (11) missing vertices, mean dist -0.1 [0.2 (%73.5)->0.2 (%26.5))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.07-->6.85) (max @ vno 172029 --> 66151)
face area 0.33 +- 0.15 (0.00-->4.60)
mean absolute distance = 0.17 +- 0.25
3840 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1098032.0, rms=2.804
020: dt: 0.5000, sse=1023921.2, rms=2.304 (17.856%)
rms = 2.60, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=922162.9, rms=1.583 (31.267%)
022: dt: 0.2500, sse=889808.4, rms=1.247 (21.209%)
023: dt: 0.2500, sse=881939.7, rms=1.162 (6.832%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=883653.4, rms=1.152 (0.859%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=877478.7, rms=1.119 (2.850%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=90.0, 76 (9) missing vertices, mean dist -0.0 [0.2 (%56.9)->0.2 (%43.1))]
%93 local maxima, % 3 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-6.0.0/0050267/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=883764.8, rms=1.355
rms = 1.35, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=894807.4, rms=1.353 (0.129%)
027: dt: 0.2500, sse=859280.8, rms=1.059 (21.724%)
028: dt: 0.2500, sse=847371.3, rms=0.891 (15.905%)
rms = 0.94, time step reduction 2 of 3 to 0.125...
rms = 0.87, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=844536.1, rms=0.865 (2.836%)
positioning took 0.6 minutes
generating cortex label...
15 non-cortical segments detected
only using segment with 8276 vertices
erasing segment 1 (vno[0] = 95158)
erasing segment 2 (vno[0] = 103614)
erasing segment 3 (vno[0] = 106079)
erasing segment 4 (vno[0] = 111983)
erasing segment 5 (vno[0] = 121408)
erasing segment 6 (vno[0] = 124101)
erasing segment 7 (vno[0] = 124288)
erasing segment 8 (vno[0] = 125300)
erasing segment 9 (vno[0] = 125529)
erasing segment 10 (vno[0] = 126359)
erasing segment 11 (vno[0] = 127560)
erasing segment 12 (vno[0] = 133209)
erasing segment 13 (vno[0] = 139069)
erasing segment 14 (vno[0] = 172776)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.area
vertex spacing 0.88 +- 0.24 (0.03-->6.90) (max @ vno 66151 --> 172029)
face area 0.33 +- 0.15 (0.00-->4.59)
refinement took 6.4 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050267 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-6.0.0/0050267/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
37009 bright wm thresholded.
3041 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.orig...
computing class statistics...
border white:    327838 voxels (1.95%)
border gray      383327 voxels (2.28%)
WM (102.0): 101.2 +- 7.6 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70)
setting MAX_BORDER_WHITE to 113.6 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 52.8 (was 40)
setting MAX_GRAY to 98.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.02-->4.80) (max @ vno 63804 --> 170885)
face area 0.28 +- 0.12 (0.00-->6.70)
mean absolute distance = 0.65 +- 0.80
5573 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=73+-7.0
mean inside = 97.2, mean outside = 79.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=84.2, 96 (96) missing vertices, mean dist 0.3 [0.5 (%37.8)->0.7 (%62.2))]
%78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.09-->7.33) (max @ vno 170828 --> 69300)
face area 0.28 +- 0.13 (0.00-->6.47)
mean absolute distance = 0.31 +- 0.45
4258 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3553658.5, rms=9.242
001: dt: 0.5000, sse=2041211.9, rms=6.398 (30.773%)
002: dt: 0.5000, sse=1428079.9, rms=4.769 (25.469%)
003: dt: 0.5000, sse=1174322.2, rms=3.891 (18.401%)
004: dt: 0.5000, sse=1053421.6, rms=3.391 (12.843%)
005: dt: 0.5000, sse=1009563.2, rms=3.192 (5.883%)
006: dt: 0.5000, sse=983752.5, rms=3.065 (3.984%)
rms = 3.05, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=987208.8, rms=3.050 (0.467%)
008: dt: 0.2500, sse=809622.0, rms=1.899 (37.737%)
009: dt: 0.2500, sse=776814.9, rms=1.627 (14.340%)
010: dt: 0.2500, sse=771920.2, rms=1.559 (4.187%)
rms = 1.52, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=766999.6, rms=1.522 (2.377%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=764004.1, rms=1.489 (2.172%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=87.3, 114 (32) missing vertices, mean dist -0.2 [0.3 (%78.4)->0.2 (%21.6))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.08-->8.16) (max @ vno 170828 --> 69300)
face area 0.35 +- 0.16 (0.00-->9.16)
mean absolute distance = 0.21 +- 0.32
4275 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1487885.1, rms=4.339
013: dt: 0.5000, sse=1102091.2, rms=2.639 (39.191%)
rms = 2.66, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=1000030.1, rms=2.035 (22.891%)
015: dt: 0.2500, sse=949135.2, rms=1.552 (23.706%)
016: dt: 0.2500, sse=929074.5, rms=1.369 (11.791%)
017: dt: 0.2500, sse=920574.0, rms=1.309 (4.380%)
rms = 1.28, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=930499.4, rms=1.282 (2.081%)
rms = 1.26, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=917457.3, rms=1.258 (1.891%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=89.3, 131 (19) missing vertices, mean dist -0.1 [0.2 (%73.3)->0.2 (%26.7))]
%92 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.04-->8.62) (max @ vno 170828 --> 69300)
face area 0.33 +- 0.16 (0.00-->9.45)
mean absolute distance = 0.18 +- 0.27
4239 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1085848.5, rms=2.757
020: dt: 0.5000, sse=1008912.8, rms=2.274 (17.516%)
rms = 2.55, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=936438.8, rms=1.577 (30.653%)
022: dt: 0.2500, sse=888915.6, rms=1.265 (19.813%)
023: dt: 0.2500, sse=881524.4, rms=1.179 (6.784%)
rms = 1.18, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=881186.6, rms=1.177 (0.129%)
rms = 1.14, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=877713.7, rms=1.139 (3.218%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 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
mean border=89.9, 126 (13) missing vertices, mean dist -0.0 [0.2 (%56.9)->0.2 (%43.1))]
%93 local maxima, % 3 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-6.0.0/0050267/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=886426.2, rms=1.397
rms = 1.38, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=892210.4, rms=1.375 (1.579%)
027: dt: 0.2500, sse=867422.2, rms=1.099 (20.115%)
028: dt: 0.2500, sse=846903.2, rms=0.933 (15.050%)
rms = 0.99, time step reduction 2 of 3 to 0.125...
rms = 0.91, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=845063.5, rms=0.907 (2.817%)
positioning took 0.6 minutes
generating cortex label...
14 non-cortical segments detected
only using segment with 7619 vertices
erasing segment 1 (vno[0] = 90532)
erasing segment 2 (vno[0] = 91780)
erasing segment 3 (vno[0] = 96677)
erasing segment 4 (vno[0] = 98051)
erasing segment 5 (vno[0] = 116474)
erasing segment 6 (vno[0] = 117774)
erasing segment 7 (vno[0] = 118803)
erasing segment 8 (vno[0] = 119607)
erasing segment 9 (vno[0] = 119962)
erasing segment 10 (vno[0] = 121178)
erasing segment 11 (vno[0] = 121277)
erasing segment 12 (vno[0] = 122493)
erasing segment 13 (vno[0] = 123855)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.area
vertex spacing 0.88 +- 0.25 (0.03-->8.98) (max @ vno 69300 --> 170828)
face area 0.33 +- 0.15 (0.00-->9.61)
refinement took 6.4 minutes
PIDs (16245 16248) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 01:02:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 01:02:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

Waiting for PID 16607 of (16607 16610) to complete...
Waiting for PID 16610 of (16607 16610) 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 (16607 16610) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 01:02:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 01:02:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 16653 of (16653 16656) to complete...
Waiting for PID 16656 of (16653 16656) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 50.1 mm, total surface area = 102667 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.177 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.043 (target=0.015)   
step 035: RMS=0.036 (target=0.015)   
step 040: RMS=0.032 (target=0.015)   
step 045: RMS=0.028 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 1.0 minutes
mris_inflate utimesec    60.027874
mris_inflate stimesec    0.144977
mris_inflate ru_maxrss   251900
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36467
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  13536
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2261
mris_inflate ru_nivcsw   4499

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 49.6 mm, total surface area = 101876 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.180 (target=0.015)   
step 005: RMS=0.126 (target=0.015)   
step 010: RMS=0.094 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.047 (target=0.015)   
step 035: RMS=0.040 (target=0.015)   
step 040: RMS=0.035 (target=0.015)   
step 045: RMS=0.032 (target=0.015)   
step 050: RMS=0.029 (target=0.015)   
step 055: RMS=0.027 (target=0.015)   
step 060: RMS=0.025 (target=0.015)   
inflation complete.
inflation took 1.0 minutes
mris_inflate utimesec    60.250840
mris_inflate stimesec    0.138978
mris_inflate ru_maxrss   250612
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36144
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12096
mris_inflate ru_oublock  13456
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2258
mris_inflate ru_nivcsw   4818
PIDs (16653 16656) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 01:03:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 01:03:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 16766 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16769 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16772 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16775 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16778 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16781 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16784 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16787 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16790 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16793 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16797 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...
Waiting for PID 16800 of (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 4.654*4pi (58.487) --> -4 handles
ICI = 196.2, FI = 2323.7, variation=35640.445
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
244 vertices thresholded to be in k1 ~ [-0.29 0.37], k2 ~ [-0.09 0.05]
total integrated curvature = 0.531*4pi (6.677) --> 0 handles
ICI = 1.6, FI = 11.4, variation=188.428
180 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
171 vertices thresholded to be in [-0.14 0.19]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.023
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 9.458*4pi (118.848) --> -8 handles
ICI = 209.5, FI = 2451.7, variation=37615.245
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
239 vertices thresholded to be in k1 ~ [-0.23 0.61], k2 ~ [-0.10 0.08]
total integrated curvature = 0.547*4pi (6.875) --> 0 handles
ICI = 1.6, FI = 10.2, variation=175.082
192 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
157 vertices thresholded to be in [-0.11 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.021
done.
PIDs (16766 16769 16772 16775 16778 16781 16784 16787 16790 16793 16797 16800) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 01:05:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050267 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      [ 0050267/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                      [ 286 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.495054
WARN:    S explicit min:                          0.000000	vertex = 28

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 01:05:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050267 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      [ 0050267/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                      [ 320 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.004873
WARN:    S explicit min:                          0.000000	vertex = 143
#--------------------------------------------
#@# Sphere lh Sun Oct  8 01:05:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 01:05:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 16947 of (16947 16950) to complete...
Waiting for PID 16950 of (16947 16950) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0.264...
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 %20.72
pass 1: epoch 2 of 3 starting distance error %20.66
unfolding complete - removing small folds...
starting distance error %20.60
removing remaining folds...
final distance error %20.61
MRISunfold() return, current seed 1234
-01: dt=0.0000, 238 negative triangles
176: dt=0.9900, 238 negative triangles
177: dt=0.9900, 111 negative triangles
178: dt=0.9900, 82 negative triangles
179: dt=0.9900, 71 negative triangles
180: dt=0.9900, 73 negative triangles
181: dt=0.9900, 71 negative triangles
182: dt=0.9900, 62 negative triangles
183: dt=0.9900, 50 negative triangles
184: dt=0.9900, 57 negative triangles
185: dt=0.9900, 54 negative triangles
186: dt=0.9900, 49 negative triangles
187: dt=0.9900, 45 negative triangles
188: dt=0.9900, 40 negative triangles
189: dt=0.9900, 41 negative triangles
190: dt=0.9900, 40 negative triangles
191: dt=0.9900, 38 negative triangles
192: dt=0.9900, 34 negative triangles
193: dt=0.9900, 38 negative triangles
194: dt=0.9900, 33 negative triangles
195: dt=0.9900, 35 negative triangles
196: dt=0.9900, 39 negative triangles
197: dt=0.9900, 37 negative triangles
198: dt=0.9900, 31 negative triangles
199: dt=0.9900, 35 negative triangles
200: dt=0.9900, 32 negative triangles
201: dt=0.9900, 28 negative triangles
202: dt=0.9900, 28 negative triangles
203: dt=0.9900, 33 negative triangles
204: dt=0.9900, 32 negative triangles
205: dt=0.9900, 25 negative triangles
206: dt=0.9900, 28 negative triangles
207: dt=0.9900, 22 negative triangles
208: dt=0.9900, 22 negative triangles
209: dt=0.9900, 23 negative triangles
210: dt=0.9900, 28 negative triangles
211: dt=0.9900, 23 negative triangles
212: dt=0.9900, 16 negative triangles
213: dt=0.9900, 13 negative triangles
214: dt=0.9900, 12 negative triangles
215: dt=0.9900, 11 negative triangles
216: dt=0.9900, 8 negative triangles
217: dt=0.9900, 9 negative triangles
218: dt=0.9900, 7 negative triangles
219: dt=0.9900, 3 negative triangles
220: dt=0.9900, 3 negative triangles
221: dt=0.9900, 3 negative triangles
222: dt=0.9900, 2 negative triangles
223: dt=0.9900, 2 negative triangles
224: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.27 hours
mris_sphere utimesec    4564.109149
mris_sphere stimesec    2.000695
mris_sphere ru_maxrss   350928
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   61366
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12240
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    137737
mris_sphere ru_nivcsw   376896
FSRUNTIME@ mris_sphere  1.2683 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0.263...
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 %21.30
pass 1: epoch 2 of 3 starting distance error %21.16
unfolding complete - removing small folds...
starting distance error %21.07
removing remaining folds...
final distance error %21.08
MRISunfold() return, current seed 1234
-01: dt=0.0000, 533 negative triangles
171: dt=0.9900, 533 negative triangles
172: dt=0.9900, 412 negative triangles
173: dt=0.9900, 376 negative triangles
174: dt=0.9900, 370 negative triangles
175: dt=0.9900, 350 negative triangles
176: dt=0.9900, 353 negative triangles
177: dt=0.9900, 334 negative triangles
178: dt=0.9900, 308 negative triangles
179: dt=0.9900, 294 negative triangles
180: dt=0.9900, 293 negative triangles
181: dt=0.9900, 279 negative triangles
182: dt=0.9900, 282 negative triangles
183: dt=0.9900, 285 negative triangles
184: dt=0.9900, 292 negative triangles
185: dt=0.9900, 283 negative triangles
186: dt=0.9900, 270 negative triangles
187: dt=0.9900, 270 negative triangles
188: dt=0.9900, 250 negative triangles
189: dt=0.9900, 262 negative triangles
190: dt=0.9900, 248 negative triangles
191: dt=0.9900, 265 negative triangles
192: dt=0.9900, 248 negative triangles
193: dt=0.9900, 243 negative triangles
194: dt=0.9900, 236 negative triangles
195: dt=0.9900, 233 negative triangles
196: dt=0.9900, 230 negative triangles
197: dt=0.9900, 229 negative triangles
198: dt=0.9900, 215 negative triangles
199: dt=0.9900, 217 negative triangles
200: dt=0.9900, 195 negative triangles
201: dt=0.9900, 207 negative triangles
202: dt=0.9900, 209 negative triangles
203: dt=0.9900, 200 negative triangles
204: dt=0.9900, 195 negative triangles
205: dt=0.9900, 195 negative triangles
206: dt=0.9900, 196 negative triangles
207: dt=0.9900, 176 negative triangles
208: dt=0.9900, 181 negative triangles
209: dt=0.9900, 203 negative triangles
210: dt=0.9900, 189 negative triangles
211: dt=0.9900, 168 negative triangles
212: dt=0.9900, 179 negative triangles
213: dt=0.9900, 177 negative triangles
214: dt=0.9900, 188 negative triangles
215: dt=0.9900, 177 negative triangles
216: dt=0.9900, 172 negative triangles
217: dt=0.9900, 167 negative triangles
218: dt=0.9900, 167 negative triangles
219: dt=0.9900, 152 negative triangles
220: dt=0.9900, 163 negative triangles
221: dt=0.9900, 158 negative triangles
222: dt=0.9900, 153 negative triangles
223: dt=0.9900, 153 negative triangles
224: dt=0.9900, 149 negative triangles
225: dt=0.9900, 141 negative triangles
226: dt=0.9900, 143 negative triangles
227: dt=0.9900, 143 negative triangles
228: dt=0.9900, 146 negative triangles
229: dt=0.9900, 134 negative triangles
230: dt=0.9900, 138 negative triangles
231: dt=0.9900, 134 negative triangles
232: dt=0.9900, 140 negative triangles
233: dt=0.9900, 128 negative triangles
234: dt=0.9900, 126 negative triangles
235: dt=0.9900, 134 negative triangles
236: dt=0.9900, 125 negative triangles
237: dt=0.9900, 127 negative triangles
238: dt=0.9900, 129 negative triangles
239: dt=0.9900, 122 negative triangles
240: dt=0.9900, 120 negative triangles
241: dt=0.9900, 125 negative triangles
242: dt=0.9900, 121 negative triangles
243: dt=0.9900, 121 negative triangles
244: dt=0.9900, 124 negative triangles
245: dt=0.9900, 121 negative triangles
246: dt=0.9900, 120 negative triangles
247: dt=0.9900, 116 negative triangles
248: dt=0.9900, 119 negative triangles
249: dt=0.9900, 117 negative triangles
250: dt=0.9900, 111 negative triangles
251: dt=0.9900, 117 negative triangles
252: dt=0.9900, 112 negative triangles
253: dt=0.9900, 102 negative triangles
254: dt=0.9900, 105 negative triangles
255: dt=0.9900, 105 negative triangles
256: dt=0.9900, 114 negative triangles
257: dt=0.9900, 106 negative triangles
258: dt=0.9900, 108 negative triangles
259: dt=0.9900, 101 negative triangles
260: dt=0.9900, 111 negative triangles
261: dt=0.9900, 106 negative triangles
262: dt=0.9900, 106 negative triangles
263: dt=0.9900, 105 negative triangles
264: dt=0.9900, 97 negative triangles
265: dt=0.9900, 97 negative triangles
266: dt=0.9900, 99 negative triangles
267: dt=0.9900, 94 negative triangles
268: dt=0.9900, 91 negative triangles
269: dt=0.9900, 100 negative triangles
270: dt=0.9900, 93 negative triangles
271: dt=0.9900, 84 negative triangles
272: dt=0.9900, 88 negative triangles
273: dt=0.9900, 87 negative triangles
274: dt=0.9900, 87 negative triangles
275: dt=0.9900, 80 negative triangles
276: dt=0.9900, 80 negative triangles
277: dt=0.9900, 80 negative triangles
278: dt=0.9900, 77 negative triangles
279: dt=0.9900, 79 negative triangles
280: dt=0.9900, 75 negative triangles
281: dt=0.9900, 71 negative triangles
282: dt=0.9900, 75 negative triangles
283: dt=0.9900, 70 negative triangles
284: dt=0.9900, 65 negative triangles
285: dt=0.9900, 69 negative triangles
286: dt=0.9900, 67 negative triangles
287: dt=0.9900, 66 negative triangles
288: dt=0.9900, 66 negative triangles
289: dt=0.9900, 66 negative triangles
290: dt=0.9900, 68 negative triangles
291: dt=0.9900, 65 negative triangles
292: dt=0.9900, 65 negative triangles
293: dt=0.9900, 68 negative triangles
294: dt=0.9405, 67 negative triangles
295: dt=0.9405, 67 negative triangles
296: dt=0.9405, 66 negative triangles
297: dt=0.9405, 70 negative triangles
298: dt=0.9405, 63 negative triangles
299: dt=0.9405, 67 negative triangles
300: dt=0.9405, 66 negative triangles
301: dt=0.9405, 59 negative triangles
302: dt=0.9405, 60 negative triangles
303: dt=0.9405, 63 negative triangles
304: dt=0.9405, 62 negative triangles
305: dt=0.9405, 60 negative triangles
306: dt=0.9405, 62 negative triangles
307: dt=0.9405, 60 negative triangles
308: dt=0.9405, 62 negative triangles
309: dt=0.9405, 63 negative triangles
310: dt=0.9405, 63 negative triangles
311: dt=0.8935, 63 negative triangles
312: dt=0.8935, 65 negative triangles
313: dt=0.8935, 62 negative triangles
314: dt=0.8935, 62 negative triangles
315: dt=0.8935, 63 negative triangles
316: dt=0.8935, 60 negative triangles
317: dt=0.8935, 59 negative triangles
318: dt=0.8935, 64 negative triangles
319: dt=0.8935, 60 negative triangles
320: dt=0.8935, 59 negative triangles
321: dt=0.8488, 62 negative triangles
322: dt=0.8488, 59 negative triangles
323: dt=0.8488, 60 negative triangles
324: dt=0.8488, 62 negative triangles
325: dt=0.8488, 62 negative triangles
326: dt=0.8488, 63 negative triangles
327: dt=0.8488, 66 negative triangles
328: dt=0.8488, 62 negative triangles
329: dt=0.8488, 63 negative triangles
330: dt=0.8488, 61 negative triangles
331: dt=0.8488, 58 negative triangles
332: dt=0.8488, 58 negative triangles
333: dt=0.8488, 64 negative triangles
334: dt=0.8488, 62 negative triangles
335: dt=0.8488, 61 negative triangles
336: dt=0.8488, 61 negative triangles
337: dt=0.8488, 59 negative triangles
338: dt=0.8488, 61 negative triangles
339: dt=0.8488, 62 negative triangles
340: dt=0.8488, 66 negative triangles
341: dt=0.8064, 61 negative triangles
342: dt=0.8064, 62 negative triangles
343: dt=0.8064, 65 negative triangles
344: dt=0.8064, 62 negative triangles
345: dt=0.8064, 58 negative triangles
346: dt=0.8064, 63 negative triangles
347: dt=0.8064, 62 negative triangles
348: dt=0.8064, 60 negative triangles
349: dt=0.8064, 59 negative triangles
350: dt=0.8064, 62 negative triangles
351: dt=0.7660, 60 negative triangles
352: dt=0.7660, 61 negative triangles
353: dt=0.7660, 64 negative triangles
354: dt=0.7660, 59 negative triangles
355: dt=0.7660, 59 negative triangles
356: dt=0.7660, 61 negative triangles
357: dt=0.7660, 58 negative triangles
358: dt=0.7660, 55 negative triangles
359: dt=0.7660, 62 negative triangles
360: dt=0.7660, 63 negative triangles
361: dt=0.7660, 58 negative triangles
362: dt=0.7660, 59 negative triangles
363: dt=0.7660, 59 negative triangles
364: dt=0.7660, 60 negative triangles
365: dt=0.7660, 64 negative triangles
366: dt=0.7660, 59 negative triangles
367: dt=0.7660, 59 negative triangles
368: dt=0.7277, 60 negative triangles
369: dt=0.7277, 59 negative triangles
370: dt=0.7277, 57 negative triangles
371: dt=0.7277, 60 negative triangles
372: dt=0.7277, 57 negative triangles
373: dt=0.7277, 58 negative triangles
374: dt=0.7277, 55 negative triangles
375: dt=0.7277, 58 negative triangles
376: dt=0.7277, 56 negative triangles
377: dt=0.7277, 60 negative triangles
378: dt=0.6914, 58 negative triangles
379: dt=0.6914, 59 negative triangles
380: dt=0.6914, 57 negative triangles
381: dt=0.6914, 60 negative triangles
382: dt=0.6914, 56 negative triangles
383: dt=0.6914, 54 negative triangles
384: dt=0.6914, 59 negative triangles
385: dt=0.6914, 59 negative triangles
386: dt=0.6914, 53 negative triangles
387: dt=0.6914, 58 negative triangles
388: dt=0.6914, 61 negative triangles
389: dt=0.6914, 57 negative triangles
390: dt=0.6914, 55 negative triangles
391: dt=0.6914, 55 negative triangles
392: dt=0.6914, 57 negative triangles
393: dt=0.6914, 57 negative triangles
394: dt=0.6914, 53 negative triangles
395: dt=0.6914, 59 negative triangles
396: dt=0.6568, 58 negative triangles
397: dt=0.6568, 58 negative triangles
398: dt=0.6568, 60 negative triangles
399: dt=0.6568, 56 negative triangles
400: dt=0.6568, 59 negative triangles
401: dt=0.6568, 58 negative triangles
402: dt=0.6568, 53 negative triangles
403: dt=0.6568, 58 negative triangles
404: dt=0.6568, 57 negative triangles
405: dt=0.6568, 58 negative triangles
406: dt=0.6239, 55 negative triangles
407: dt=0.6239, 58 negative triangles
408: dt=0.6239, 55 negative triangles
409: dt=0.6239, 54 negative triangles
410: dt=0.6239, 53 negative triangles
411: dt=0.6239, 55 negative triangles
412: dt=0.6239, 52 negative triangles
413: dt=0.6239, 51 negative triangles
414: dt=0.6239, 50 negative triangles
415: dt=0.6239, 50 negative triangles
416: dt=0.6239, 49 negative triangles
417: dt=0.6239, 48 negative triangles
418: dt=0.6239, 44 negative triangles
419: dt=0.6239, 47 negative triangles
420: dt=0.6239, 49 negative triangles
421: dt=0.6239, 47 negative triangles
422: dt=0.6239, 46 negative triangles
423: dt=0.6239, 45 negative triangles
424: dt=0.6239, 45 negative triangles
425: dt=0.6239, 47 negative triangles
426: dt=0.6239, 45 negative triangles
427: dt=0.6239, 46 negative triangles
428: dt=0.5927, 45 negative triangles
429: dt=0.5927, 42 negative triangles
430: dt=0.5927, 46 negative triangles
431: dt=0.5927, 45 negative triangles
432: dt=0.5927, 46 negative triangles
433: dt=0.5927, 47 negative triangles
434: dt=0.5927, 42 negative triangles
435: dt=0.5927, 43 negative triangles
436: dt=0.5927, 39 negative triangles
437: dt=0.5927, 42 negative triangles
438: dt=0.5927, 42 negative triangles
439: dt=0.5927, 38 negative triangles
440: dt=0.5927, 37 negative triangles
441: dt=0.5927, 33 negative triangles
442: dt=0.5927, 39 negative triangles
443: dt=0.5927, 36 negative triangles
444: dt=0.5927, 36 negative triangles
445: dt=0.5927, 33 negative triangles
446: dt=0.5927, 31 negative triangles
447: dt=0.5927, 28 negative triangles
448: dt=0.5927, 28 negative triangles
449: dt=0.5927, 30 negative triangles
450: dt=0.5927, 28 negative triangles
451: dt=0.5927, 28 negative triangles
452: dt=0.5927, 28 negative triangles
453: dt=0.5927, 23 negative triangles
454: dt=0.5927, 26 negative triangles
455: dt=0.5927, 23 negative triangles
456: dt=0.5927, 26 negative triangles
457: dt=0.5927, 22 negative triangles
458: dt=0.5927, 23 negative triangles
459: dt=0.5927, 23 negative triangles
460: dt=0.5927, 20 negative triangles
461: dt=0.5927, 19 negative triangles
462: dt=0.5927, 21 negative triangles
463: dt=0.5927, 18 negative triangles
464: dt=0.5927, 16 negative triangles
465: dt=0.5927, 19 negative triangles
466: dt=0.5927, 15 negative triangles
467: dt=0.5927, 16 negative triangles
468: dt=0.5927, 19 negative triangles
469: dt=0.5927, 16 negative triangles
470: dt=0.5927, 14 negative triangles
471: dt=0.5927, 14 negative triangles
472: dt=0.5927, 15 negative triangles
473: dt=0.5927, 13 negative triangles
474: dt=0.5927, 14 negative triangles
475: dt=0.5927, 14 negative triangles
476: dt=0.5927, 12 negative triangles
477: dt=0.5927, 10 negative triangles
478: dt=0.5927, 8 negative triangles
479: dt=0.5927, 7 negative triangles
480: dt=0.5927, 11 negative triangles
481: dt=0.5927, 7 negative triangles
482: dt=0.5927, 8 negative triangles
483: dt=0.5927, 5 negative triangles
484: dt=0.5927, 6 negative triangles
485: dt=0.5927, 3 negative triangles
486: dt=0.5927, 4 negative triangles
487: dt=0.5927, 2 negative triangles
488: dt=0.5927, 2 negative triangles
489: dt=0.5927, 2 negative triangles
490: dt=0.5927, 2 negative triangles
491: dt=0.5927, 3 negative triangles
492: dt=0.5927, 3 negative triangles
493: dt=0.5927, 1 negative triangles
494: dt=0.5927, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.39 hours
mris_sphere utimesec    5427.869838
mris_sphere stimesec    1.997696
mris_sphere ru_maxrss   353204
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   61927
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12312
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    128335
mris_sphere ru_nivcsw   387238
FSRUNTIME@ mris_sphere  1.3917 hours 1 threads
PIDs (16947 16950) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 02:28:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 02:28:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 25441 of (25441 25444) to complete...
Waiting for PID 25444 of (25441 25444) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 5.491
curvature mean = 0.027, std = 0.817
curvature mean = 0.025, std = 0.828
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 427892.3, tmin=1.2954
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 312164.2, tmin=2.6335
  d=16.00 min @ (0.00, 0.00, -4.00) sse = 305287.3, tmin=3.9931
  d=8.00 min @ (0.00, 0.00, 2.00) sse = 296545.4, tmin=5.3622
  d=4.00 min @ (0.00, 1.00, -1.00) sse = 295719.1, tmin=6.7359
  d=2.00 min @ (-0.50, -0.50, 0.50) sse = 294702.3, tmin=8.1202
  d=1.00 min @ (0.25, 0.00, 0.00) sse = 294628.3, tmin=9.5221
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  10.92 min
curvature mean = -0.015, std = 0.807
curvature mean = 0.010, std = 0.926
curvature mean = -0.026, std = 0.810
curvature mean = 0.003, std = 0.967
curvature mean = -0.029, std = 0.810
curvature mean = 0.001, std = 0.985
2 Reading smoothwm
curvature mean = -0.026, std = 0.303
curvature mean = 0.034, std = 0.241
curvature mean = 0.071, std = 0.307
curvature mean = 0.030, std = 0.300
curvature mean = 0.037, std = 0.498
curvature mean = 0.029, std = 0.327
curvature mean = 0.022, std = 0.642
curvature mean = 0.029, std = 0.339
curvature mean = 0.008, std = 0.758
MRISregister() return, current seed 0
-01: dt=0.0000, 117 negative triangles
129: dt=0.9900, 117 negative triangles
130: dt=0.9900, 106 negative triangles
131: dt=0.9900, 103 negative triangles
132: dt=0.9900, 97 negative triangles
133: dt=0.9900, 86 negative triangles
134: dt=0.9900, 82 negative triangles
135: dt=0.9900, 80 negative triangles
136: dt=0.9900, 67 negative triangles
137: dt=0.9900, 62 negative triangles
138: dt=0.9900, 57 negative triangles
139: dt=0.9900, 66 negative triangles
140: dt=0.9900, 60 negative triangles
141: dt=0.9900, 63 negative triangles
142: dt=0.9900, 58 negative triangles
143: dt=0.9900, 47 negative triangles
144: dt=0.9900, 45 negative triangles
145: dt=0.9900, 49 negative triangles
146: dt=0.9900, 48 negative triangles
147: dt=0.9900, 44 negative triangles
148: dt=0.9900, 46 negative triangles
149: dt=0.9900, 48 negative triangles
150: dt=0.9900, 39 negative triangles
151: dt=0.9900, 42 negative triangles
152: dt=0.9900, 40 negative triangles
153: dt=0.9900, 31 negative triangles
154: dt=0.9900, 35 negative triangles
155: dt=0.9900, 27 negative triangles
156: dt=0.9900, 27 negative triangles
157: dt=0.9900, 29 negative triangles
158: dt=0.9900, 27 negative triangles
159: dt=0.9900, 21 negative triangles
160: dt=0.9900, 15 negative triangles
161: dt=0.9900, 19 negative triangles
162: dt=0.9900, 18 negative triangles
163: dt=0.9900, 12 negative triangles
164: dt=0.9900, 7 negative triangles
165: dt=0.9900, 6 negative triangles
166: dt=0.9900, 6 negative triangles
167: dt=0.9900, 4 negative triangles
168: dt=0.9900, 3 negative triangles
169: dt=0.9900, 3 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.78 hours
mris_register utimesec    6457.850257
mris_register stimesec    5.857109
mris_register ru_maxrss   306688
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   44437
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  12176
mris_register ru_oublock  12264
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    431413
mris_register ru_nivcsw   289007
FSRUNTIME@ mris_register  1.7758 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 5.581
curvature mean = 0.016, std = 0.808
curvature mean = 0.024, std = 0.835
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 438434.8, tmin=1.2840
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 344446.0, tmin=2.6103
  d=16.00 min @ (0.00, 4.00, 4.00) sse = 309642.8, tmin=3.9597
  d=8.00 min @ (-2.00, -2.00, 0.00) sse = 301837.6, tmin=5.3352
  d=4.00 min @ (1.00, 0.00, -1.00) sse = 299343.1, tmin=6.7228
  d=2.00 min @ (0.00, 0.00, 0.50) sse = 298598.7, tmin=8.1143
  d=0.50 min @ (0.12, 0.12, 0.00) sse = 298542.9, tmin=10.8985
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  10.90 min
curvature mean = -0.014, std = 0.804
curvature mean = 0.008, std = 0.932
curvature mean = -0.024, std = 0.806
curvature mean = 0.002, std = 0.971
curvature mean = -0.026, std = 0.804
curvature mean = 0.000, std = 0.987
2 Reading smoothwm
curvature mean = -0.029, std = 0.756
curvature mean = 0.030, std = 0.236
curvature mean = 0.031, std = 0.125
curvature mean = 0.027, std = 0.294
curvature mean = 0.017, std = 0.205
curvature mean = 0.026, std = 0.320
curvature mean = 0.010, std = 0.269
curvature mean = 0.026, std = 0.332
curvature mean = 0.004, std = 0.331
MRISregister() return, current seed 0
-01: dt=0.0000, 212 negative triangles
131: dt=0.9900, 212 negative triangles
expanding nbhd size to 1
132: dt=0.9900, 238 negative triangles
133: dt=0.9900, 199 negative triangles
134: dt=0.9900, 181 negative triangles
135: dt=0.9900, 170 negative triangles
136: dt=0.9900, 166 negative triangles
137: dt=0.9900, 163 negative triangles
138: dt=0.9900, 153 negative triangles
139: dt=0.9900, 144 negative triangles
140: dt=0.9900, 128 negative triangles
141: dt=0.9900, 113 negative triangles
142: dt=0.9900, 109 negative triangles
143: dt=0.9900, 116 negative triangles
144: dt=0.9900, 102 negative triangles
145: dt=0.9900, 97 negative triangles
146: dt=0.9900, 85 negative triangles
147: dt=0.9900, 76 negative triangles
148: dt=0.9900, 79 negative triangles
149: dt=0.9900, 68 negative triangles
150: dt=0.9900, 63 negative triangles
151: dt=0.9900, 61 negative triangles
152: dt=0.9900, 64 negative triangles
153: dt=0.9900, 59 negative triangles
154: dt=0.9900, 56 negative triangles
155: dt=0.9900, 53 negative triangles
156: dt=0.9900, 56 negative triangles
157: dt=0.9900, 50 negative triangles
158: dt=0.9900, 50 negative triangles
159: dt=0.9900, 40 negative triangles
160: dt=0.9900, 38 negative triangles
161: dt=0.9900, 37 negative triangles
162: dt=0.9900, 37 negative triangles
163: dt=0.9900, 36 negative triangles
164: dt=0.9900, 33 negative triangles
165: dt=0.9900, 31 negative triangles
166: dt=0.9900, 26 negative triangles
167: dt=0.9900, 27 negative triangles
168: dt=0.9900, 23 negative triangles
169: dt=0.9900, 21 negative triangles
170: dt=0.9900, 19 negative triangles
171: dt=0.9900, 19 negative triangles
172: dt=0.9900, 16 negative triangles
173: dt=0.9900, 11 negative triangles
174: dt=0.9900, 9 negative triangles
175: dt=0.9900, 12 negative triangles
176: dt=0.9900, 9 negative triangles
177: dt=0.9900, 8 negative triangles
178: dt=0.9900, 5 negative triangles
179: dt=0.9900, 4 negative triangles
180: dt=0.9900, 5 negative triangles
181: dt=0.9900, 3 negative triangles
182: dt=0.9900, 4 negative triangles
183: dt=0.9900, 1 negative triangles
184: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.74 hours
mris_register utimesec    6268.754004
mris_register stimesec    5.547156
mris_register ru_maxrss   303344
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   42944
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  12096
mris_register ru_oublock  12200
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    416188
mris_register ru_nivcsw   290459
FSRUNTIME@ mris_register  1.7425 hours 1 threads
PIDs (25441 25444) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 04:15:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 04:15:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

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

Waiting for PID 1706 of (1706 1709) to complete...
Waiting for PID 1709 of (1706 1709) 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 (1706 1709) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 04:15:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 04:15:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 1755 of (1755 1758) to complete...
Waiting for PID 1758 of (1755 1758) 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 (1755 1758) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 04:15:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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 04:15:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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 1805 of (1805 1808) to complete...
Waiting for PID 1808 of (1805 1808) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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...
1772 labels changed using aseg
relabeling using gibbs priors...
000:   3811 changed, 172987 examined...
001:    944 changed, 15724 examined...
002:    260 changed, 5139 examined...
003:     78 changed, 1518 examined...
004:     23 changed, 491 examined...
005:      8 changed, 122 examined...
006:      8 changed, 45 examined...
007:      2 changed, 43 examined...
008:      0 changed, 7 examined...
295 labels changed using aseg
000: 135 total segments, 90 labels (355 vertices) changed
001: 44 total segments, 1 labels (4 vertices) changed
002: 43 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 17 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2439 vertices marked for relabeling...
2439 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 18 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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...
1294 labels changed using aseg
relabeling using gibbs priors...
000:   3217 changed, 171943 examined...
001:    779 changed, 13989 examined...
002:    174 changed, 4445 examined...
003:     57 changed, 1071 examined...
004:     26 changed, 336 examined...
005:     15 changed, 164 examined...
006:      4 changed, 92 examined...
007:      5 changed, 25 examined...
008:      6 changed, 28 examined...
009:      0 changed, 22 examined...
134 labels changed using aseg
000: 92 total segments, 53 labels (195 vertices) changed
001: 41 total segments, 2 labels (2 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 12 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2220 vertices marked for relabeling...
2220 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 18 seconds.
PIDs (1805 1808) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 04:15:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050267 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 04:15:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050267 rh 

Waiting for PID 1860 of (1860 1863) to complete...
Waiting for PID 1863 of (1860 1863) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050267 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-6.0.0/0050267/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
37009 bright wm thresholded.
3041 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.orig...
computing class statistics...
border white:    327838 voxels (1.95%)
border gray      383327 voxels (2.28%)
WM (102.0): 101.2 +- 7.6 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70)
setting MAX_BORDER_WHITE to 113.6 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 53.8 (was 40)
setting MAX_GRAY to 98.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=74+-6.1
mean inside = 97.1, mean outside = 79.5
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 0.88 +- 0.24 (0.03-->6.90) (max @ vno 66151 --> 172029)
face area 0.32 +- 0.15 (0.00-->4.55)
mean absolute distance = 0.56 +- 0.75
4017 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 30 points - only 0.00% unknown
deleting segment 3 with 67 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 140 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 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 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
deleting segment 11 with 16 points - only 0.00% unknown
deleting segment 12 with 72 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
mean border=84.1, 136 (136) missing vertices, mean dist 0.4 [0.7 (%12.4)->0.5 (%87.6))]
%73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.09-->7.12) (max @ vno 172029 --> 66151)
face area 0.32 +- 0.15 (0.00-->4.50)
mean absolute distance = 0.30 +- 0.45
3566 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2630729.5, rms=7.382
001: dt: 0.5000, sse=1416677.5, rms=4.256 (42.342%)
002: dt: 0.5000, sse=1119914.2, rms=3.064 (28.011%)
003: dt: 0.5000, sse=1091693.1, rms=2.940 (4.056%)
004: dt: 0.5000, sse=1052615.0, rms=2.743 (6.697%)
rms = 2.92, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=940891.2, rms=1.966 (28.324%)
006: dt: 0.2500, sse=900580.1, rms=1.615 (17.863%)
007: dt: 0.2500, sse=890754.4, rms=1.520 (5.893%)
rms = 1.49, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=888617.8, rms=1.492 (1.823%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=885878.1, rms=1.460 (2.116%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 27 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 48 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 4 with 8 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 74 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 7 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 11 points - only 0.00% unknown
deleting segment 11 with 71 points - only 0.00% unknown
mean border=87.3, 68 (18) missing vertices, mean dist -0.2 [0.3 (%79.0)->0.2 (%21.0))]
%86 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.09-->7.17) (max @ vno 172029 --> 66151)
face area 0.35 +- 0.16 (0.00-->5.06)
mean absolute distance = 0.21 +- 0.31
4743 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1478346.8, rms=4.258
010: dt: 0.5000, sse=1118206.0, rms=2.621 (38.432%)
rms = 2.66, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=1010681.4, rms=2.005 (23.533%)
012: dt: 0.2500, sse=955593.8, rms=1.514 (24.487%)
013: dt: 0.2500, sse=934104.2, rms=1.310 (13.472%)
014: dt: 0.2500, sse=941803.6, rms=1.248 (4.744%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=927998.8, rms=1.225 (1.812%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=932087.9, rms=1.200 (2.082%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 29 points - only 0.00% unknown
deleting segment 1 with 54 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 89 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 7 points - only 0.00% unknown
deleting segment 6 with 36 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 69 points - only 0.00% unknown
mean border=89.3, 46 (6) missing vertices, mean dist -0.1 [0.2 (%74.0)->0.2 (%26.0))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.08-->7.22) (max @ vno 172029 --> 66151)
face area 0.33 +- 0.16 (0.00-->4.93)
mean absolute distance = 0.17 +- 0.25
3768 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1106913.5, rms=2.791
017: dt: 0.5000, sse=1033220.0, rms=2.278 (18.375%)
rms = 2.55, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=927672.2, rms=1.548 (32.042%)
019: dt: 0.2500, sse=901064.1, rms=1.206 (22.131%)
020: dt: 0.2500, sse=886244.9, rms=1.118 (7.303%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=884686.9, rms=1.114 (0.283%)
rms = 1.08, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=882109.4, rms=1.082 (2.929%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 29 points - only 0.00% unknown
deleting segment 1 with 58 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 96 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 38 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 69 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
mean border=90.0, 74 (5) missing vertices, mean dist -0.0 [0.2 (%57.4)->0.2 (%42.6))]
%93 local maxima, % 3 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-6.0.0/0050267/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=889225.8, rms=1.340
rms = 1.35, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=862201.9, rms=0.998 (25.542%)
024: dt: 0.2500, sse=852710.6, rms=0.828 (17.062%)
rms = 0.84, time step reduction 2 of 3 to 0.125...
rms = 0.83, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=851591.9, rms=0.826 (0.229%)
positioning took 0.6 minutes
generating cortex label...
17 non-cortical segments detected
only using segment with 8274 vertices
erasing segment 1 (vno[0] = 72893)
erasing segment 2 (vno[0] = 72908)
erasing segment 3 (vno[0] = 95158)
erasing segment 4 (vno[0] = 106062)
erasing segment 5 (vno[0] = 111983)
erasing segment 6 (vno[0] = 119739)
erasing segment 7 (vno[0] = 122730)
erasing segment 8 (vno[0] = 122756)
erasing segment 9 (vno[0] = 124101)
erasing segment 10 (vno[0] = 125300)
erasing segment 11 (vno[0] = 125529)
erasing segment 12 (vno[0] = 126359)
erasing segment 13 (vno[0] = 127560)
erasing segment 14 (vno[0] = 133209)
erasing segment 15 (vno[0] = 139069)
erasing segment 16 (vno[0] = 172776)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.area
vertex spacing 0.88 +- 0.25 (0.03-->7.18) (max @ vno 66151 --> 172029)
face area 0.33 +- 0.16 (0.00-->4.86)
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 25 points - only 0.00% unknown
deleting segment 2 with 20 points - only 0.00% unknown
deleting segment 3 with 20 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 6 with 13 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.8, 150 (150) missing vertices, mean dist 1.4 [0.2 (%0.0)->3.0 (%100.0))]
%12 local maxima, %32 large gradients and %52 min vals, 281 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=26629484.0, rms=27.847
001: dt: 0.0500, sse=23286070.0, rms=25.981 (6.700%)
002: dt: 0.0500, sse=20930828.0, rms=24.582 (5.386%)
003: dt: 0.0500, sse=19158236.0, rms=23.474 (4.508%)
004: dt: 0.0500, sse=17751316.0, rms=22.555 (3.913%)
005: dt: 0.0500, sse=16589720.0, rms=21.768 (3.492%)
006: dt: 0.0500, sse=15602392.0, rms=21.075 (3.182%)
007: dt: 0.0500, sse=14743965.0, rms=20.454 (2.948%)
008: dt: 0.0500, sse=13985572.0, rms=19.889 (2.763%)
009: dt: 0.0500, sse=13306523.0, rms=19.369 (2.615%)
010: dt: 0.0500, sse=12693658.0, rms=18.887 (2.487%)
positioning took 1.2 minutes
mean border=62.6, 106 (70) missing vertices, mean dist 1.2 [0.1 (%0.0)->2.5 (%100.0))]
%13 local maxima, %33 large gradients and %51 min vals, 266 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=13572022.0, rms=19.573
011: dt: 0.0500, sse=13010820.0, rms=19.137 (2.226%)
012: dt: 0.0500, sse=12497174.0, rms=18.729 (2.131%)
013: dt: 0.0500, sse=12024324.0, rms=18.346 (2.048%)
014: dt: 0.0500, sse=11588002.0, rms=17.985 (1.969%)
015: dt: 0.0500, sse=11184419.0, rms=17.644 (1.895%)
016: dt: 0.0500, sse=10810378.0, rms=17.322 (1.824%)
017: dt: 0.0500, sse=10463318.0, rms=17.018 (1.756%)
018: dt: 0.0500, sse=10139935.0, rms=16.729 (1.696%)
019: dt: 0.0500, sse=9838475.0, rms=16.456 (1.636%)
020: dt: 0.0500, sse=9556397.0, rms=16.195 (1.582%)
positioning took 1.2 minutes
mean border=62.6, 117 (56) missing vertices, mean dist 1.0 [0.1 (%0.4)->2.2 (%99.6))]
%13 local maxima, %33 large gradients and %50 min vals, 261 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=9650104.0, rms=16.289
021: dt: 0.0500, sse=9382826.0, rms=16.039 (1.530%)
022: dt: 0.0500, sse=9132115.0, rms=15.802 (1.480%)
023: dt: 0.0500, sse=8895988.0, rms=15.575 (1.437%)
024: dt: 0.0500, sse=8673229.0, rms=15.358 (1.395%)
025: dt: 0.0500, sse=8462529.0, rms=15.149 (1.358%)
026: dt: 0.0500, sse=8262416.5, rms=14.948 (1.326%)
027: dt: 0.0500, sse=8071807.0, rms=14.754 (1.297%)
028: dt: 0.0500, sse=7889471.0, rms=14.566 (1.274%)
029: dt: 0.0500, sse=7714138.0, rms=14.383 (1.258%)
030: dt: 0.0500, sse=7545072.5, rms=14.204 (1.244%)
positioning took 1.2 minutes
mean border=62.5, 153 (47) missing vertices, mean dist 0.9 [0.1 (%3.8)->2.0 (%96.2))]
%14 local maxima, %33 large gradients and %50 min vals, 227 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=7634192.0, rms=14.299
031: dt: 0.5000, sse=6403483.5, rms=12.930 (9.573%)
032: dt: 0.5000, sse=5482113.0, rms=11.796 (8.776%)
033: dt: 0.5000, sse=4735720.5, rms=10.789 (8.535%)
034: dt: 0.5000, sse=4093420.0, rms=9.838 (8.817%)
035: dt: 0.5000, sse=3507591.8, rms=8.884 (9.694%)
036: dt: 0.5000, sse=2961384.5, rms=7.893 (11.154%)
037: dt: 0.5000, sse=2486466.5, rms=6.920 (12.323%)
038: dt: 0.5000, sse=2134943.2, rms=6.102 (11.828%)
039: dt: 0.5000, sse=1903091.1, rms=5.497 (9.907%)
040: dt: 0.5000, sse=1767031.1, rms=5.107 (7.101%)
041: dt: 0.5000, sse=1686917.6, rms=4.864 (4.754%)
042: dt: 0.5000, sse=1646593.8, rms=4.735 (2.662%)
043: dt: 0.5000, sse=1615541.5, rms=4.634 (2.121%)
044: dt: 0.5000, sse=1595616.1, rms=4.567 (1.442%)
rms = 4.54, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1586810.2, rms=4.537 (0.669%)
046: dt: 0.2500, sse=1474435.9, rms=4.094 (9.771%)
047: dt: 0.2500, sse=1440777.1, rms=3.967 (3.090%)
rms = 3.98, time step reduction 2 of 3 to 0.125...
rms = 3.93, time step reduction 3 of 3 to 0.062...
048: dt: 0.1250, sse=1431449.6, rms=3.928 (0.979%)
positioning took 3.2 minutes
mean border=61.7, 3671 (13) missing vertices, mean dist 0.1 [0.2 (%46.9)->0.5 (%53.1))]
%23 local maxima, %26 large gradients and %46 min vals, 181 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=1727423.0, rms=4.217
049: dt: 0.5000, sse=1677695.8, rms=4.050 (3.948%)
050: dt: 0.5000, sse=1637189.0, rms=3.925 (3.083%)
rms = 4.07, time step reduction 1 of 3 to 0.250...
051: dt: 0.2500, sse=1521337.4, rms=3.397 (13.448%)
052: dt: 0.2500, sse=1493097.9, rms=3.247 (4.426%)
rms = 3.26, time step reduction 2 of 3 to 0.125...
053: dt: 0.1250, sse=1482279.2, rms=3.191 (1.726%)
054: dt: 0.1250, sse=1468415.1, rms=3.118 (2.294%)
rms = 3.10, time step reduction 3 of 3 to 0.062...
055: dt: 0.1250, sse=1465506.5, rms=3.103 (0.483%)
positioning took 1.8 minutes
mean border=61.1, 3827 (12) missing vertices, mean dist 0.1 [0.2 (%43.3)->0.4 (%56.7))]
%34 local maxima, %16 large gradients and %45 min vals, 165 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=1513666.0, rms=3.340
rms = 3.74, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1485882.0, rms=3.204 (4.061%)
rms = 3.19, time step reduction 2 of 3 to 0.125...
057: dt: 0.2500, sse=1481865.1, rms=3.190 (0.453%)
rms = 3.14, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1472977.5, rms=3.142 (1.494%)
positioning took 0.9 minutes
mean border=60.6, 7502 (12) missing vertices, mean dist 0.0 [0.2 (%44.5)->0.3 (%55.5))]
%36 local maxima, %13 large gradients and %43 min vals, 164 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-6.0.0/0050267/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1491448.6, rms=3.225
rms = 3.45, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1472373.1, rms=3.133 (2.848%)
060: dt: 0.2500, sse=1456647.5, rms=3.075 (1.863%)
rms = 3.07, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1452855.9, rms=3.066 (0.290%)
062: dt: 0.1250, sse=1432826.2, rms=2.960 (3.453%)
rms = 2.93, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1426514.5, rms=2.932 (0.936%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.area.pial
vertex spacing 1.00 +- 0.43 (0.06-->6.39) (max @ vno 146609 --> 145682)
face area 0.39 +- 0.31 (0.00-->9.87)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 172987 vertices processed
25000 of 172987 vertices processed
50000 of 172987 vertices processed
75000 of 172987 vertices processed
100000 of 172987 vertices processed
125000 of 172987 vertices processed
150000 of 172987 vertices processed
0 of 172987 vertices processed
25000 of 172987 vertices processed
50000 of 172987 vertices processed
75000 of 172987 vertices processed
100000 of 172987 vertices processed
125000 of 172987 vertices processed
150000 of 172987 vertices processed
thickness calculation complete, 416:1100 truncations.
38135 vertices at 0 distance
121921 vertices at 1 distance
106323 vertices at 2 distance
44615 vertices at 3 distance
14835 vertices at 4 distance
4806 vertices at 5 distance
1495 vertices at 6 distance
506 vertices at 7 distance
200 vertices at 8 distance
68 vertices at 9 distance
40 vertices at 10 distance
27 vertices at 11 distance
24 vertices at 12 distance
28 vertices at 13 distance
27 vertices at 14 distance
30 vertices at 15 distance
27 vertices at 16 distance
20 vertices at 17 distance
14 vertices at 18 distance
21 vertices at 19 distance
28 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.thickness
positioning took 19.5 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050267 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-6.0.0/0050267/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
37009 bright wm thresholded.
3041 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.orig...
computing class statistics...
border white:    327838 voxels (1.95%)
border gray      383327 voxels (2.28%)
WM (102.0): 101.2 +- 7.6 [70.0 --> 110.0]
GM (76.0) : 75.6 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70)
setting MAX_BORDER_WHITE to 113.6 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 52.8 (was 40)
setting MAX_GRAY to 98.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=73+-7.0
mean inside = 97.2, mean outside = 79.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.25 (0.03-->8.98) (max @ vno 69300 --> 170828)
face area 0.33 +- 0.15 (0.00-->9.55)
mean absolute distance = 0.58 +- 0.76
4239 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 69 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 14 points - only 0.00% unknown
deleting segment 4 with 108 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 6 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 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 5 points - only 0.00% unknown
deleting segment 10 with 42 points - only 0.00% unknown
deleting segment 11 with 8 points - only 0.00% unknown
deleting segment 12 with 25 points - only 0.00% unknown
mean border=83.9, 170 (170) missing vertices, mean dist 0.4 [0.7 (%12.7)->0.6 (%87.3))]
%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 +- 0.25 (0.09-->8.40) (max @ vno 170828 --> 69300)
face area 0.33 +- 0.15 (0.00-->9.14)
mean absolute distance = 0.32 +- 0.45
3874 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2675012.0, rms=7.490
001: dt: 0.5000, sse=1433859.9, rms=4.317 (42.361%)
002: dt: 0.5000, sse=1127192.5, rms=3.073 (28.824%)
003: dt: 0.5000, sse=1082291.9, rms=2.891 (5.908%)
004: dt: 0.5000, sse=1044487.0, rms=2.703 (6.507%)
rms = 2.86, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=936177.6, rms=1.953 (27.750%)
006: dt: 0.2500, sse=907775.1, rms=1.602 (17.990%)
007: dt: 0.2500, sse=889948.7, rms=1.506 (5.979%)
rms = 1.48, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=887914.5, rms=1.480 (1.709%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=884114.3, rms=1.450 (2.024%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 64 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 10 points - only 0.00% unknown
deleting segment 3 with 91 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 9 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 17 points - only 0.00% unknown
deleting segment 9 with 24 points - only 0.00% unknown
mean border=87.2, 109 (36) missing vertices, mean dist -0.2 [0.3 (%79.9)->0.2 (%20.1))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.25 (0.02-->8.58) (max @ vno 170828 --> 69300)
face area 0.35 +- 0.17 (0.00-->11.99)
mean absolute distance = 0.21 +- 0.32
5094 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1514141.1, rms=4.392
010: dt: 0.5000, sse=1124038.2, rms=2.614 (40.486%)
rms = 2.59, time step reduction 1 of 3 to 0.250...
011: dt: 0.5000, sse=1095293.9, rms=2.586 (1.063%)
012: dt: 0.2500, sse=951845.2, rms=1.467 (43.270%)
013: dt: 0.2500, sse=932927.4, rms=1.267 (13.645%)
rms = 1.24, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=935822.2, rms=1.238 (2.286%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=924761.4, rms=1.199 (3.168%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 64 points - only 0.00% unknown
deleting segment 1 with 9 points - only 0.00% unknown
deleting segment 2 with 11 points - only 0.00% unknown
deleting segment 3 with 101 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 24 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
deleting segment 9 with 24 points - only 0.00% unknown
mean border=89.3, 114 (23) missing vertices, mean dist -0.1 [0.2 (%73.7)->0.2 (%26.3))]
%92 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.10-->8.64) (max @ vno 170828 --> 69300)
face area 0.33 +- 0.16 (0.00-->11.95)
mean absolute distance = 0.18 +- 0.27
4295 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1091618.6, rms=2.758
016: dt: 0.5000, sse=1014544.8, rms=2.259 (18.108%)
rms = 2.52, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=923168.7, rms=1.555 (31.174%)
018: dt: 0.2500, sse=893497.8, rms=1.227 (21.091%)
019: dt: 0.2500, sse=885193.4, rms=1.144 (6.787%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
rms = 1.13, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=883407.2, rms=1.127 (1.437%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 65 points - only 0.00% unknown
deleting segment 1 with 9 points - only 0.00% unknown
deleting segment 2 with 11 points - only 0.00% unknown
deleting segment 3 with 153 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 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
deleting segment 8 with 22 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 25 points - only 0.00% unknown
mean border=89.9, 124 (15) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))]
%93 local maxima, % 3 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-6.0.0/0050267/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=893066.5, rms=1.390
rms = 1.43, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=866207.4, rms=1.045 (24.802%)
022: dt: 0.2500, sse=869985.1, rms=0.859 (17.831%)
rms = 0.88, time step reduction 2 of 3 to 0.125...
rms = 0.85, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=854141.2, rms=0.852 (0.816%)
positioning took 0.6 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7567 vertices
erasing segment 1 (vno[0] = 90532)
erasing segment 2 (vno[0] = 91795)
erasing segment 3 (vno[0] = 96677)
erasing segment 4 (vno[0] = 98051)
erasing segment 5 (vno[0] = 104724)
erasing segment 6 (vno[0] = 116474)
erasing segment 7 (vno[0] = 117774)
erasing segment 8 (vno[0] = 119607)
erasing segment 9 (vno[0] = 119962)
erasing segment 10 (vno[0] = 121277)
erasing segment 11 (vno[0] = 122493)
erasing segment 12 (vno[0] = 123855)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.area
vertex spacing 0.89 +- 0.26 (0.03-->8.66) (max @ vno 69300 --> 170828)
face area 0.33 +- 0.16 (0.00-->11.94)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
deleting segment 1 with 44 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
deleting segment 4 with 11 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 14 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.3, 181 (181) missing vertices, mean dist 1.3 [0.1 (%0.0)->3.1 (%100.0))]
%11 local maxima, %30 large gradients and %55 min vals, 204 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=27225032.0, rms=28.241
001: dt: 0.0500, sse=23898606.0, rms=26.403 (6.508%)
002: dt: 0.0500, sse=21538504.0, rms=25.017 (5.250%)
003: dt: 0.0500, sse=19757238.0, rms=23.918 (4.395%)
004: dt: 0.0500, sse=18341000.0, rms=23.006 (3.812%)
005: dt: 0.0500, sse=17169798.0, rms=22.224 (3.400%)
006: dt: 0.0500, sse=16173035.0, rms=21.536 (3.097%)
007: dt: 0.0500, sse=15304303.0, rms=20.918 (2.871%)
008: dt: 0.0500, sse=14536100.0, rms=20.355 (2.689%)
009: dt: 0.0500, sse=13846713.0, rms=19.837 (2.547%)
010: dt: 0.0500, sse=13222583.0, rms=19.355 (2.427%)
positioning took 1.2 minutes
mean border=62.1, 162 (109) missing vertices, mean dist 1.2 [0.1 (%0.0)->2.6 (%100.0))]
%12 local maxima, %31 large gradients and %54 min vals, 177 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=14163462.0, rms=20.076
011: dt: 0.0500, sse=13589560.0, rms=19.640 (2.175%)
012: dt: 0.0500, sse=13063946.0, rms=19.231 (2.081%)
013: dt: 0.0500, sse=12578991.0, rms=18.846 (2.002%)
014: dt: 0.0500, sse=12131291.0, rms=18.483 (1.924%)
015: dt: 0.0500, sse=11716413.0, rms=18.141 (1.854%)
016: dt: 0.0500, sse=11330757.0, rms=17.816 (1.789%)
017: dt: 0.0500, sse=10972138.0, rms=17.509 (1.724%)
018: dt: 0.0500, sse=10638070.0, rms=17.218 (1.663%)
019: dt: 0.0500, sse=10326089.0, rms=16.941 (1.606%)
020: dt: 0.0500, sse=10034670.0, rms=16.679 (1.550%)
positioning took 1.2 minutes
mean border=62.1, 165 (82) missing vertices, mean dist 1.0 [0.1 (%0.4)->2.3 (%99.6))]
%12 local maxima, %31 large gradients and %54 min vals, 175 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=10133390.0, rms=16.774
021: dt: 0.0500, sse=9857049.0, rms=16.523 (1.499%)
022: dt: 0.0500, sse=9597883.0, rms=16.284 (1.449%)
023: dt: 0.0500, sse=9353375.0, rms=16.054 (1.408%)
024: dt: 0.0500, sse=9122824.0, rms=15.835 (1.366%)
025: dt: 0.0500, sse=8904658.0, rms=15.625 (1.329%)
026: dt: 0.0500, sse=8698056.0, rms=15.422 (1.293%)
027: dt: 0.0500, sse=8500801.0, rms=15.227 (1.268%)
028: dt: 0.0500, sse=8311973.0, rms=15.037 (1.245%)
029: dt: 0.0500, sse=8130664.0, rms=14.853 (1.227%)
030: dt: 0.0500, sse=7955862.5, rms=14.673 (1.213%)
positioning took 1.2 minutes
mean border=62.0, 175 (68) missing vertices, mean dist 0.9 [0.1 (%3.3)->2.1 (%96.7))]
%12 local maxima, %31 large gradients and %53 min vals, 152 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=8034151.5, rms=14.755
031: dt: 0.5000, sse=6761425.0, rms=13.378 (9.333%)
032: dt: 0.5000, sse=5775443.0, rms=12.198 (8.817%)
033: dt: 0.5000, sse=4956710.5, rms=11.124 (8.810%)
034: dt: 0.5000, sse=4237428.0, rms=10.083 (9.356%)
035: dt: 0.5000, sse=3601859.5, rms=9.067 (10.075%)
036: dt: 0.5000, sse=3050655.2, rms=8.082 (10.862%)
037: dt: 0.5000, sse=2589903.0, rms=7.160 (11.405%)
038: dt: 0.5000, sse=2247679.2, rms=6.389 (10.776%)
039: dt: 0.5000, sse=2014248.9, rms=5.808 (9.098%)
040: dt: 0.5000, sse=1871444.9, rms=5.418 (6.714%)
041: dt: 0.5000, sse=1788223.1, rms=5.180 (4.381%)
042: dt: 0.5000, sse=1738389.5, rms=5.028 (2.944%)
043: dt: 0.5000, sse=1707477.4, rms=4.934 (1.862%)
044: dt: 0.5000, sse=1685757.0, rms=4.863 (1.435%)
rms = 4.83, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1675384.1, rms=4.832 (0.655%)
046: dt: 0.2500, sse=1564426.2, rms=4.419 (8.535%)
047: dt: 0.2500, sse=1529555.2, rms=4.297 (2.758%)
rms = 4.30, time step reduction 2 of 3 to 0.125...
048: dt: 0.2500, sse=1530420.8, rms=4.296 (0.020%)
049: dt: 0.1250, sse=1506456.0, rms=4.205 (2.138%)
rms = 4.19, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1501262.1, rms=4.185 (0.463%)
positioning took 3.6 minutes
mean border=61.3, 4217 (18) missing vertices, mean dist 0.1 [0.2 (%47.1)->0.6 (%52.9))]
%21 local maxima, %24 large gradients and %49 min vals, 116 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=1746220.1, rms=4.294
051: dt: 0.5000, sse=1704977.0, rms=4.167 (2.938%)
052: dt: 0.5000, sse=1660768.9, rms=4.037 (3.124%)
rms = 4.15, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1547937.9, rms=3.538 (12.363%)
054: dt: 0.2500, sse=1521423.2, rms=3.403 (3.820%)
rms = 3.40, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1520624.5, rms=3.399 (0.127%)
056: dt: 0.1250, sse=1493188.1, rms=3.261 (4.039%)
rms = 3.23, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1487129.5, rms=3.233 (0.862%)
positioning took 1.8 minutes
mean border=60.8, 4372 (11) missing vertices, mean dist 0.1 [0.1 (%44.7)->0.4 (%55.3))]
%30 local maxima, %16 large gradients and %48 min vals, 132 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=1530555.4, rms=3.424
rms = 3.82, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1504292.9, rms=3.300 (3.641%)
rms = 3.30, time step reduction 2 of 3 to 0.125...
rms = 3.28, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1500616.2, rms=3.282 (0.549%)
positioning took 0.8 minutes
mean border=60.4, 7649 (11) missing vertices, mean dist 0.1 [0.1 (%42.9)->0.3 (%57.1))]
%32 local maxima, %13 large gradients and %47 min vals, 126 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-6.0.0/0050267/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1526017.8, rms=3.399
rms = 3.64, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1500395.6, rms=3.282 (3.454%)
061: dt: 0.2500, sse=1484663.2, rms=3.226 (1.679%)
rms = 3.22, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1480412.2, rms=3.217 (0.307%)
063: dt: 0.1250, sse=1459931.5, rms=3.113 (3.219%)
rms = 3.09, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1454331.1, rms=3.090 (0.743%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.area.pial
vertex spacing 1.00 +- 0.44 (0.08-->9.52) (max @ vno 67977 --> 170868)
face area 0.39 +- 0.31 (0.00-->12.36)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 171943 vertices processed
25000 of 171943 vertices processed
50000 of 171943 vertices processed
75000 of 171943 vertices processed
100000 of 171943 vertices processed
125000 of 171943 vertices processed
150000 of 171943 vertices processed
0 of 171943 vertices processed
25000 of 171943 vertices processed
50000 of 171943 vertices processed
75000 of 171943 vertices processed
100000 of 171943 vertices processed
125000 of 171943 vertices processed
150000 of 171943 vertices processed
thickness calculation complete, 540:1092 truncations.
35625 vertices at 0 distance
116780 vertices at 1 distance
106745 vertices at 2 distance
47227 vertices at 3 distance
16315 vertices at 4 distance
5431 vertices at 5 distance
1968 vertices at 6 distance
645 vertices at 7 distance
256 vertices at 8 distance
165 vertices at 9 distance
91 vertices at 10 distance
79 vertices at 11 distance
43 vertices at 12 distance
42 vertices at 13 distance
31 vertices at 14 distance
24 vertices at 15 distance
23 vertices at 16 distance
13 vertices at 17 distance
10 vertices at 18 distance
4 vertices at 19 distance
5 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.thickness
positioning took 19.4 minutes
PIDs (1860 1863) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 04:35:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label
Total face volume 321013
Total vertex volume 317157 (mask=0)
#@# 0050267 lh 317157
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 04:35:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label
Total face volume 323031
Total vertex volume 319815 (mask=0)
#@# 0050267 rh 319815
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 04:35:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 

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 = 210
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/ribbon.mgz
mris_volmask took 19.38 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 04:54:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 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 0050267 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 04:54:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 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 0050267 rh pial 

Waiting for PID 3613 of (3613 3616 3619 3622) to complete...
Waiting for PID 3616 of (3613 3616 3619 3622) to complete...
Waiting for PID 3619 of (3613 3616 3619 3622) to complete...
Waiting for PID 3622 of (3613 3616 3619 3622) 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 0050267 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 321013
Total vertex volume 317157 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1565   1087   2812  2.745 0.464     0.119     0.021       15     1.3  bankssts
 1161    746   1750  2.448 0.593     0.109     0.023       14     1.0  caudalanteriorcingulate
 3763   2504   7829  2.714 0.547     0.118     0.022       40     3.2  caudalmiddlefrontal
 2248   1431   2872  1.955 0.486     0.137     0.029       31     2.6  cuneus
  929    629   2603  3.179 0.882     0.133     0.044       12     1.6  entorhinal
 6316   4188  13267  2.811 0.497     0.121     0.025       74     6.8  fusiform
 9401   6169  18017  2.636 0.496     0.117     0.024      132     8.7  inferiorparietal
 7293   4741  14913  2.694 0.665     0.128     0.035      128    11.0  inferiortemporal
 2107   1352   3670  2.389 0.944     0.121     0.024       28     1.7  isthmuscingulate
10394   6592  16293  2.252 0.510     0.132     0.028      138    11.5  lateraloccipital
 5241   3448  10347  2.742 0.676     0.128     0.033       72     6.7  lateralorbitofrontal
 5330   3425   7652  2.160 0.559     0.129     0.029       66     6.3  lingual
 3481   2241   6719  2.670 0.685     0.122     0.033       50     4.4  medialorbitofrontal
 6273   4281  14739  2.891 0.667     0.123     0.024       95     5.9  middletemporal
 1264    840   2881  3.007 0.561     0.103     0.018       13     0.8  parahippocampal
 2425   1543   4592  2.711 0.584     0.110     0.020       20     1.9  paracentral
 3733   2489   8319  2.890 0.497     0.119     0.024       41     3.4  parsopercularis
 1673   1070   3849  2.891 0.636     0.138     0.035       26     2.4  parsorbitalis
 2971   1997   6495  2.791 0.462     0.122     0.022       36     2.6  parstriangularis
 2060   1371   2276  1.948 0.429     0.118     0.025       20     2.1  pericalcarine
 7133   4334  10102  2.068 0.578     0.106     0.026       69     7.7  postcentral
 2138   1416   4117  2.626 0.799     0.143     0.032       42     2.6  posteriorcingulate
 8366   5210  15289  2.689 0.544     0.109     0.023       79     7.8  precentral
 8141   5355  14539  2.578 0.464     0.125     0.024      103     7.6  precuneus
 1829   1156   3806  2.862 0.474     0.130     0.033       39     2.0  rostralanteriorcingulate
13648   9086  26087  2.558 0.489     0.133     0.029      200    16.0  rostralmiddlefrontal
14182   9539  31768  2.894 0.559     0.125     0.027      173    15.6  superiorfrontal
 9839   6421  17207  2.419 0.479     0.125     0.025      125    10.3  superiorparietal
 7197   4752  16137  3.017 0.765     0.108     0.020       73     6.0  superiortemporal
 6298   4142  12312  2.740 0.519     0.130     0.028       86     6.7  supramarginal
  522    335   1450  3.100 0.430     0.150     0.041       11     0.8  frontalpole
  847    577   3096  3.820 0.614     0.133     0.037       11     1.3  temporalpole
  963    558   1418  2.379 0.459     0.134     0.060       20     2.6  transversetemporal
 3693   2424   7885  3.307 0.756     0.118     0.033       41     4.6  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050267 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 321013
Total vertex volume 317157 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1565    996   2812  2.745 0.464     0.114     0.026       17     1.8  bankssts
 1161    793   1750  2.448 0.593     0.122     0.037       31     1.1  caudalanteriorcingulate
 3763   3125   7829  2.714 0.547     0.138     0.029       52     5.0  caudalmiddlefrontal
 2248   1611   2872  1.955 0.486     0.128     0.027       30     2.7  cuneus
  929   1064   2603  3.179 0.882     0.187     0.047       11     2.1  entorhinal
 6316   5245  13267  2.811 0.497     0.142     0.034       78     9.9  fusiform
 9401   7545  18017  2.636 0.496     0.135     0.030      115    12.2  inferiorparietal
 7293   6140  14913  2.694 0.665     0.151     0.039      141    14.2  inferiortemporal
 2107   1670   3670  2.389 0.944     0.147     0.037       41     3.4  isthmuscingulate
10394   7884  16293  2.252 0.510     0.137     0.031      158    14.6  lateraloccipital
 5241   4024  10347  2.742 0.676     0.145     0.037       91     9.1  lateralorbitofrontal
 5330   3873   7652  2.160 0.559     0.133     0.033       70     7.8  lingual
 3481   2821   6719  2.670 0.685     0.150     0.039       53     5.8  medialorbitofrontal
 6273   5618  14739  2.891 0.667     0.144     0.030       84     8.4  middletemporal
 1264   1122   2881  3.007 0.561     0.145     0.033       14     1.9  parahippocampal
 2425   1866   4592  2.711 0.584     0.127     0.030       34     3.2  paracentral
 3733   3159   8319  2.890 0.497     0.143     0.033       60     5.8  parsopercularis
 1673   1561   3849  2.891 0.636     0.154     0.033       17     2.3  parsorbitalis
 2971   2557   6495  2.791 0.462     0.152     0.033       42     4.6  parstriangularis
 2060   1072   2276  1.948 0.429     0.101     0.027       43     2.5  pericalcarine
 7133   5456  10102  2.068 0.578     0.128     0.029       72     9.8  postcentral
 2138   1640   4117  2.626 0.799     0.139     0.038       36     3.3  posteriorcingulate
 8366   6037  15289  2.689 0.544     0.115     0.026      110     9.4  precentral
 8141   5940  14539  2.578 0.464     0.130     0.031      119    10.8  precuneus
 1829   1592   3806  2.862 0.474     0.156     0.043       42     3.5  rostralanteriorcingulate
13648  11120  26087  2.558 0.489     0.152     0.036      199    22.6  rostralmiddlefrontal
14182  12124  31768  2.894 0.559     0.144     0.038      204    25.5  superiorfrontal
 9839   7710  17207  2.419 0.479     0.133     0.030      129    13.6  superiorparietal
 7197   5884  16137  3.017 0.765     0.138     0.031       94    10.3  superiortemporal
 6298   4792  12312  2.740 0.519     0.140     0.039      202    11.6  supramarginal
  522    600   1450  3.100 0.430     0.205     0.039       13     1.0  frontalpole
  847   1073   3096  3.820 0.614     0.210     0.048       18     2.2  temporalpole
  963    666   1418  2.379 0.459     0.129     0.037       12     1.6  transversetemporal
 3693   2184   7885  3.307 0.756     0.137     0.050      106     6.8  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 0050267 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 323031
Total vertex volume 319815 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1356    925   2362  2.600 0.456     0.115     0.022       12     1.2  bankssts
 1350    912   2934  2.744 0.686     0.129     0.019       23     1.0  caudalanteriorcingulate
 3815   2506   8367  2.942 0.583     0.110     0.020       36     3.0  caudalmiddlefrontal
 2999   1901   4276  2.010 0.492     0.158     0.038       55     4.5  cuneus
  799    542   2719  3.541 0.805     0.130     0.057       11     1.8  entorhinal
 5368   3581  10749  2.846 0.559     0.120     0.026       66     5.3  fusiform
 9818   6568  19134  2.637 0.477     0.119     0.024      129     9.2  inferiorparietal
 7512   4883  16409  2.842 0.623     0.127     0.036      125    11.1  inferiortemporal
 1790   1138   3148  2.393 0.807     0.131     0.028       27     1.9  isthmuscingulate
 9873   6366  16314  2.304 0.498     0.134     0.029      129    11.8  lateraloccipital
 5182   3442  10036  2.755 0.596     0.140     0.039       84     8.4  lateralorbitofrontal
 5744   3704   8327  2.097 0.641     0.142     0.033       86     8.5  lingual
 3829   2556   7347  2.610 0.670     0.139     0.039       79     6.5  medialorbitofrontal
 6708   4654  16699  3.090 0.587     0.124     0.024       93     6.3  middletemporal
 1110    744   2606  3.100 0.602     0.116     0.023       16     0.9  parahippocampal
 2521   1609   4486  2.580 0.474     0.111     0.020       22     1.9  paracentral
 3010   2053   6206  2.806 0.407     0.120     0.025       34     2.9  parsopercularis
 1816   1168   3999  2.880 0.611     0.146     0.041       34     3.1  parsorbitalis
 3357   2190   6938  2.724 0.491     0.128     0.026       47     3.5  parstriangularis
 2844   1868   2988  1.794 0.422     0.122     0.029       29     3.1  pericalcarine
 7152   4415  10126  2.112 0.614     0.114     0.027       77     7.6  postcentral
 2180   1432   4255  2.686 0.651     0.141     0.026       38     2.4  posteriorcingulate
 9456   5871  17869  2.747 0.542     0.110     0.023      104     8.4  precentral
 7534   4956  13435  2.581 0.474     0.130     0.027       96     8.0  precuneus
 1027    671   2253  2.854 0.714     0.124     0.025       15     1.0  rostralanteriorcingulate
13482   8734  26495  2.662 0.525     0.130     0.029      198    15.9  rostralmiddlefrontal
13519   9109  30870  2.983 0.551     0.127     0.029      165    15.7  superiorfrontal
 9089   5996  16210  2.419 0.469     0.122     0.022      108     8.1  superiorparietal
 6331   4145  14563  3.136 0.575     0.113     0.023       68     5.6  superiortemporal
 6797   4455  13155  2.723 0.496     0.129     0.026       90     7.3  supramarginal
  649    368   1202  2.557 0.647     0.150     0.068       17     2.0  frontalpole
  824    573   3045  3.875 0.854     0.150     0.039       14     1.4  temporalpole
  647    400   1142  2.387 0.800     0.121     0.051       12     1.2  transversetemporal
 4460   2946   9139  3.085 0.837     0.123     0.041       60     6.3  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 0050267 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 323031
Total vertex volume 319815 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1356    886   2362  2.600 0.456     0.129     0.032       23     2.0  bankssts
 1350   1210   2934  2.744 0.686     0.172     0.048       63     2.7  caudalanteriorcingulate
 3815   3111   8367  2.942 0.583     0.129     0.028       47     4.9  caudalmiddlefrontal
 2999   2471   4276  2.010 0.492     0.155     0.037       61     5.0  cuneus
  799    994   2719  3.541 0.805     0.192     0.052       32     1.7  entorhinal
 5368   3946  10749  2.846 0.559     0.134     0.034       95     8.0  fusiform
 9818   7754  19134  2.637 0.477     0.132     0.031      138    14.2  inferiorparietal
 7512   6602  16409  2.842 0.623     0.148     0.035      100    12.5  inferiortemporal
 1790   1456   3148  2.393 0.807     0.142     0.036       28     2.5  isthmuscingulate
 9873   7719  16314  2.304 0.498     0.137     0.032      129    13.9  lateraloccipital
 5182   3873  10036  2.755 0.596     0.146     0.042      100     9.3  lateralorbitofrontal
 5744   4365   8327  2.097 0.641     0.133     0.031       90     8.4  lingual
 3829   3156   7347  2.610 0.670     0.151     0.044       79     7.6  medialorbitofrontal
 6708   6041  16699  3.090 0.587     0.145     0.029       89     8.8  middletemporal
 1110    907   2606  3.100 0.602     0.146     0.036       20     1.8  parahippocampal
 2521   1860   4486  2.580 0.474     0.121     0.029       33     3.1  paracentral
 3010   2419   6206  2.806 0.407     0.147     0.039       45     5.1  parsopercularis
 1816   1562   3999  2.880 0.611     0.148     0.032       23     2.6  parsorbitalis
 3357   2857   6938  2.724 0.491     0.151     0.033       50     5.2  parstriangularis
 2844   1593   2988  1.794 0.422     0.114     0.031       57     3.7  pericalcarine
 7152   5369  10126  2.112 0.614     0.131     0.032       83    10.1  postcentral
 2180   1731   4255  2.686 0.651     0.151     0.038       38     3.6  posteriorcingulate
 9456   6951  17869  2.747 0.542     0.123     0.030      145    12.7  precentral
 7534   5375  13435  2.581 0.474     0.131     0.032      118    10.0  precuneus
 1027    896   2253  2.854 0.714     0.165     0.039       21     1.8  rostralanteriorcingulate
13482  11092  26495  2.662 0.525     0.151     0.037      206    22.6  rostralmiddlefrontal
13519  11212  30870  2.983 0.551     0.141     0.037      236    21.0  superiorfrontal
 9089   7186  16210  2.419 0.469     0.132     0.032      160    14.3  superiorparietal
 6331   5190  14563  3.136 0.575     0.145     0.034       94     9.8  superiortemporal
 6797   5225  13155  2.723 0.496     0.139     0.035       97    10.6  supramarginal
  649    563   1202  2.557 0.647     0.142     0.034        6     0.9  frontalpole
  824    988   3045  3.875 0.854     0.185     0.039       12     1.4  temporalpole
  647    561   1142  2.387 0.800     0.147     0.043        7     1.3  transversetemporal
 4460   2780   9139  3.085 0.837     0.149     0.049      107    10.3  insula
PIDs (3613 3616 3619 3622) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 04:56:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 04:56:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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 3723 of (3723 3726) to complete...
Waiting for PID 3726 of (3723 3726) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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...
24 labels changed using aseg
relabeling using gibbs priors...
000:  11745 changed, 172987 examined...
001:   2825 changed, 45123 examined...
002:    845 changed, 14584 examined...
003:    359 changed, 4714 examined...
004:    195 changed, 2081 examined...
005:     96 changed, 1068 examined...
006:     44 changed, 547 examined...
007:     25 changed, 256 examined...
008:     12 changed, 142 examined...
009:      4 changed, 64 examined...
010:      2 changed, 23 examined...
011:      2 changed, 13 examined...
012:      1 changed, 16 examined...
013:      0 changed, 6 examined...
5 labels changed using aseg
000: 316 total segments, 229 labels (3326 vertices) changed
001: 97 total segments, 12 labels (28 vertices) changed
002: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 64 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1546 vertices marked for relabeling...
1546 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 23 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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...
13 labels changed using aseg
relabeling using gibbs priors...
000:  11315 changed, 171943 examined...
001:   2713 changed, 44509 examined...
002:    775 changed, 14038 examined...
003:    356 changed, 4441 examined...
004:    154 changed, 1994 examined...
005:     91 changed, 889 examined...
006:     51 changed, 520 examined...
007:     32 changed, 270 examined...
008:     15 changed, 168 examined...
009:      4 changed, 84 examined...
010:      0 changed, 25 examined...
0 labels changed using aseg
000: 319 total segments, 230 labels (3302 vertices) changed
001: 104 total segments, 16 labels (77 vertices) changed
002: 88 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 47 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1443 vertices marked for relabeling...
1443 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 23 seconds.
PIDs (3723 3726) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 04:56:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 04:56:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 rh white 

Waiting for PID 3901 of (3901 3904) to complete...
Waiting for PID 3904 of (3901 3904) 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 0050267 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 321013
Total vertex volume 317157 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1969   1355   3976  2.682 0.478     0.145     0.032       32     2.8  G&S_frontomargin
 2213   1462   4194  2.521 0.508     0.136     0.025       27     2.3  G&S_occipital_inf
 2032   1170   3673  2.618 0.660     0.113     0.026       20     2.2  G&S_paracentral
 1412    953   2880  2.601 0.342     0.133     0.026       22     1.3  G&S_subcentral
 1054    702   2700  2.846 0.508     0.150     0.034       24     1.5  G&S_transv_frontopol
 2667   1761   5208  2.825 0.393     0.117     0.025       37     2.4  G&S_cingul-Ant
 1730   1160   3157  2.731 0.377     0.097     0.017       13     1.1  G&S_cingul-Mid-Ant
 1674   1129   3274  2.896 0.459     0.137     0.033       25     2.0  G&S_cingul-Mid-Post
  827    543   2322  3.242 0.665     0.149     0.030       19     1.0  G_cingul-Post-dorsal
  347    226    757  2.709 0.850     0.122     0.033        5     0.3  G_cingul-Post-ventral
 1957   1227   2648  1.894 0.512     0.139     0.032       29     2.5  G_cuneus
 2192   1405   5749  3.065 0.464     0.132     0.030       32     2.4  G_front_inf-Opercular
  658    403   1827  3.250 0.349     0.131     0.030       11     0.8  G_front_inf-Orbital
 1892   1236   4935  2.911 0.448     0.133     0.027       30     1.9  G_front_inf-Triangul
 7595   4930  17407  2.732 0.554     0.139     0.032      132     9.6  G_front_middle
 9770   6421  24627  3.027 0.569     0.134     0.032      145    12.3  G_front_sup
  862    541   1840  3.373 0.807     0.140     0.048       16     1.7  G_Ins_lg&S_cent_ins
  742    459   2442  3.888 0.611     0.118     0.044       12     1.1  G_insular_short
 3731   2291   7967  2.675 0.468     0.137     0.031       77     4.3  G_occipital_middle
 1587    973   2730  2.320 0.538     0.138     0.037       24     2.5  G_occipital_sup
 2763   1776   6307  2.835 0.510     0.127     0.029       46     3.4  G_oc-temp_lat-fusifor
 3745   2319   5543  2.079 0.589     0.138     0.035       57     5.2  G_oc-temp_med-Lingual
 1610   1073   4541  3.244 0.718     0.119     0.032       18     2.0  G_oc-temp_med-Parahip
 3701   2319   8219  2.754 0.743     0.140     0.042       66     5.9  G_orbital
 3363   2086   7686  2.876 0.530     0.129     0.031       70     3.8  G_pariet_inf-Angular
 3300   2158   7467  2.823 0.547     0.138     0.031       57     3.9  G_pariet_inf-Supramar
 3475   2243   7551  2.614 0.511     0.129     0.025       53     3.4  G_parietal_sup
 3097   1660   4298  2.087 0.517     0.106     0.034       35     4.6  G_postcentral
 3485   1985   7737  2.965 0.520     0.102     0.025       36     3.4  G_precentral
 4327   2789   8794  2.674 0.449     0.136     0.032       77     5.5  G_precuneus
 1088    676   2336  2.559 0.644     0.132     0.039       23     1.7  G_rectus
  891    572   1700  2.847 0.836     0.109     0.043       10     1.2  G_subcallosal
  832    466   1338  2.438 0.456     0.117     0.045       15     1.6  G_temp_sup-G_T_transv
 2549   1589   7334  3.235 0.771     0.136     0.032       45     3.3  G_temp_sup-Lateral
 1030    710   3051  3.966 0.677     0.104     0.021        6     0.9  G_temp_sup-Plan_polar
 1134    757   2350  2.765 0.508     0.094     0.017        9     0.8  G_temp_sup-Plan_tempo
 3904   2402   9139  2.729 0.745     0.137     0.049      100     8.3  G_temporal_inf
 3472   2360   9621  3.009 0.626     0.137     0.029       72     3.9  G_temporal_middle
  365    250    570  2.594 0.295     0.095     0.010        2     0.1  Lat_Fis-ant-Horizont
  741    526   1155  2.759 0.425     0.109     0.016        4     0.6  Lat_Fis-ant-Vertical
 1305    897   1766  2.546 0.437     0.125     0.034       13     1.9  Lat_Fis-post
 2518   1506   3291  1.938 0.408     0.141     0.034       38     3.4  Pole_occipital
 2048   1382   6286  3.369 0.698     0.136     0.034       27     2.9  Pole_temporal
 2748   1869   3266  2.075 0.509     0.117     0.023       26     2.5  S_calcarine
 3154   2129   3427  1.861 0.502     0.105     0.020       21     2.4  S_central
 1116    794   1699  2.306 0.376     0.096     0.015        6     0.6  S_cingul-Marginalis
  563    383   1083  3.264 0.590     0.097     0.018        2     0.5  S_circular_insula_ant
 1563   1059   2840  3.197 0.706     0.088     0.013        7     0.7  S_circular_insula_inf
 2072   1373   3361  2.984 0.426     0.105     0.019       11     1.7  S_circular_insula_sup
 1173    819   2168  2.792 0.494     0.105     0.017        7     0.7  S_collat_transv_ant
  504    334    702  2.062 0.325     0.134     0.019        7     0.4  S_collat_transv_post
 3395   2363   5744  2.495 0.376     0.111     0.019       29     2.6  S_front_inf
 1872   1255   2766  2.287 0.359     0.119     0.024       22     1.7  S_front_middle
 3818   2666   6365  2.429 0.400     0.111     0.020       31     3.3  S_front_sup
  220    155    573  3.524 0.586     0.138     0.028        2     0.3  S_interm_prim-Jensen
 3999   2710   5800  2.382 0.394     0.111     0.017       31     2.9  S_intrapariet&P_trans
 1409    969   1846  2.100 0.455     0.123     0.023       11     1.4  S_oc_middle&Lunatus
 1860   1242   2409  2.143 0.329     0.118     0.023       16     1.6  S_oc_sup&transversal
 1157    778   1846  2.475 0.385     0.106     0.018        9     0.7  S_occipital_ant
 1443    982   2194  2.566 0.361     0.114     0.022       10     1.3  S_oc-temp_lat
 2876   1968   4656  2.640 0.392     0.113     0.020       20     2.4  S_oc-temp_med&Lingual
  568    380    800  2.378 0.476     0.132     0.027        6     0.6  S_orbital_lateral
  782    542   1014  2.178 0.438     0.121     0.022        7     0.7  S_orbital_med-olfact
 2084   1437   3812  2.735 0.556     0.123     0.028       22     2.3  S_orbital-H_Shaped
 2965   1931   4173  2.384 0.425     0.115     0.020       25     2.4  S_parieto_occipital
 1780   1093   1787  1.853 0.868     0.121     0.022       27     1.5  S_pericallosal
 3284   2167   4349  2.211 0.373     0.115     0.022       31     2.7  S_postcentral
 1710   1132   2531  2.562 0.413     0.119     0.021       16     1.5  S_precentral-inf-part
 1515   1051   2391  2.543 0.343     0.103     0.015       10     0.9  S_precentral-sup-part
 1053    704   1674  2.689 0.580     0.120     0.023       12     1.0  S_suborbital
 1577   1095   2687  2.599 0.456     0.121     0.021       13     1.5  S_subparietal
 2461   1696   3563  2.473 0.468     0.101     0.012       14     1.3  S_temporal_inf
 7611   5219  12645  2.582 0.439     0.105     0.017       59     5.2  S_temporal_sup
  448    305    593  2.231 0.451     0.117     0.015        4     0.3  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050267 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 323031
Total vertex volume 319815 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1582   1016   2854  2.528 0.486     0.138     0.041       28     2.6  G&S_frontomargin
 1731   1147   3384  2.496 0.498     0.131     0.026       22     1.8  G&S_occipital_inf
 1710    981   2778  2.367 0.532     0.111     0.023       16     1.7  G&S_paracentral
 1904   1250   3803  2.788 0.492     0.135     0.036       28     2.5  G&S_subcentral
 1672   1028   3450  2.616 0.653     0.149     0.047       39     3.3  G&S_transv_frontopol
 4170   2856   8754  2.958 0.533     0.131     0.028       58     4.5  G&S_cingul-Ant
 1813   1271   3631  2.857 0.386     0.108     0.018       17     1.3  G&S_cingul-Mid-Ant
 1985   1328   3913  2.747 0.456     0.131     0.027       26     2.2  G&S_cingul-Mid-Post
  752    471   2025  3.158 0.520     0.155     0.036       17     1.1  G_cingul-Post-dorsal
  449    283    998  2.604 0.638     0.151     0.035       10     0.6  G_cingul-Post-ventral
 2781   1747   3862  1.941 0.513     0.153     0.037       50     4.1  G_cuneus
 2105   1394   5346  3.018 0.414     0.130     0.030       33     2.2  G_front_inf-Opercular
  563    333   1391  2.973 0.421     0.147     0.035       15     0.7  G_front_inf-Orbital
 1798   1132   4187  2.808 0.529     0.142     0.032       33     2.5  G_front_inf-Triangul
 6105   3779  16001  3.006 0.620     0.134     0.029      109     7.3  G_front_middle
 8286   5516  21595  3.073 0.581     0.133     0.033      123    11.0  G_front_sup
  651    430   1675  3.397 0.849     0.146     0.063       14     1.8  G_Ins_lg&S_cent_ins
 1113    699   2696  2.959 0.934     0.148     0.047       27     2.1  G_insular_short
 3163   2040   7206  2.689 0.515     0.145     0.032       60     3.8  G_occipital_middle
 1376    889   2362  2.243 0.546     0.124     0.032       18     1.5  G_occipital_sup
 2131   1369   5006  2.921 0.657     0.132     0.033       37     2.7  G_oc-temp_lat-fusifor
 3617   2297   5484  2.032 0.710     0.150     0.040       62     6.2  G_oc-temp_med-Lingual
 1450    960   4596  3.456 0.755     0.133     0.044       25     2.5  G_oc-temp_med-Parahip
 4070   2642   9326  2.784 0.680     0.153     0.049       88     7.8  G_orbital
 3518   2249   8345  2.806 0.541     0.140     0.035       71     4.8  G_pariet_inf-Angular
 3642   2319   8394  2.893 0.500     0.139     0.029       64     4.3  G_pariet_inf-Supramar
 3842   2452   8066  2.588 0.439     0.125     0.026       58     4.1  G_parietal_sup
 2740   1473   3840  2.088 0.537     0.113     0.031       33     3.5  G_postcentral
 3678   2029   8206  2.917 0.537     0.105     0.027       57     3.5  G_precentral
 3230   2097   6887  2.690 0.452     0.137     0.029       50     3.7  G_precuneus
  929    601   2144  2.518 0.821     0.144     0.046       24     1.9  G_rectus
  721    424   1017  2.163 0.819     0.103     0.089       15     2.1  G_subcallosal
  559    337   1162  2.598 0.777     0.121     0.052       11     1.1  G_temp_sup-G_T_transv
 2168   1396   6234  3.351 0.551     0.134     0.034       34     2.7  G_temp_sup-Lateral
 1125    735   2869  3.646 0.729     0.106     0.028        8     1.1  G_temp_sup-Plan_polar
  970    646   1911  2.791 0.399     0.102     0.018        8     0.7  G_temp_sup-Plan_tempo
 4700   2967  11260  2.855 0.698     0.140     0.043      101     8.2  G_temporal_inf
 3748   2598  11218  3.267 0.585     0.135     0.029       69     4.2  G_temporal_middle
  495    342    832  2.621 0.422     0.104     0.013        3     0.2  Lat_Fis-ant-Horizont
  190    140    324  2.628 0.477     0.113     0.019        1     0.1  Lat_Fis-ant-Vertical
 1636   1074   2329  2.718 0.497     0.120     0.026       14     1.7  Lat_Fis-post
 4079   2526   5746  2.006 0.466     0.138     0.035       57     5.9  Pole_occipital
 2226   1472   6849  3.366 0.696     0.137     0.039       39     3.4  Pole_temporal
 2900   1951   3407  2.009 0.538     0.126     0.027       32     3.0  S_calcarine
 3268   2244   3692  1.954 0.561     0.114     0.021       24     2.7  S_central
 1154    806   1911  2.563 0.478     0.111     0.021        9     0.8  S_cingul-Marginalis
  712    474   1196  3.120 0.485     0.122     0.026        5     0.8  S_circular_insula_ant
 1423    961   2710  3.363 0.659     0.087     0.015        5     0.9  S_circular_insula_inf
 1598   1077   2543  2.902 0.406     0.106     0.018        8     1.3  S_circular_insula_sup
 1507   1028   2503  2.865 0.477     0.097     0.018        8     1.2  S_collat_transv_ant
  643    429    846  2.198 0.443     0.132     0.023        6     0.7  S_collat_transv_post
 3306   2215   5236  2.473 0.360     0.115     0.021       31     2.7  S_front_inf
 3278   2234   4952  2.535 0.345     0.117     0.022       28     3.1  S_front_middle
 3514   2390   6524  2.778 0.463     0.106     0.020       26     2.6  S_front_sup
  482    336    735  2.346 0.414     0.111     0.017        3     0.4  S_interm_prim-Jensen
 3674   2518   5598  2.325 0.401     0.113     0.018       36     2.5  S_intrapariet&P_trans
 1363    922   1701  2.189 0.353     0.118     0.021       11     1.2  S_oc_middle&Lunatus
 1327    898   1865  2.197 0.445     0.111     0.019        9     1.1  S_oc_sup&transversal
 1253    844   2029  2.491 0.363     0.117     0.019       12     1.0  S_occipital_ant
 1273    907   2126  2.806 0.404     0.111     0.020        8     1.1  S_oc-temp_lat
 2480   1685   3853  2.681 0.533     0.111     0.018       19     1.8  S_oc-temp_med&Lingual
  688    471    961  2.432 0.345     0.132     0.032        6     0.8  S_orbital_lateral
  839    587   1196  2.435 0.450     0.118     0.025        9     1.0  S_orbital_med-olfact
 2000   1338   3608  2.821 0.429     0.131     0.029       22     2.4  S_orbital-H_Shaped
 3126   2075   4314  2.340 0.442     0.126     0.023       34     2.9  S_parieto_occipital
 1758   1059   1733  1.944 0.697     0.131     0.018       30     1.2  S_pericallosal
 2997   2015   4179  2.335 0.399     0.110     0.019       22     2.2  S_postcentral
 2252   1562   4010  2.714 0.333     0.106     0.016       15     1.7  S_precentral-inf-part
 1764   1201   2560  2.525 0.374     0.106     0.017       12     1.3  S_precentral-sup-part
  472    331    762  2.969 0.577     0.156     0.019        7     0.4  S_suborbital
 1773   1194   2935  2.566 0.379     0.124     0.027       18     1.9  S_subparietal
 1901   1342   2944  2.641 0.373     0.104     0.014       11     1.1  S_temporal_inf
 7669   5295  12750  2.635 0.393     0.107     0.017       60     5.5  S_temporal_sup
  386    262    477  2.368 0.479     0.125     0.014        3     0.2  S_temporal_transverse
PIDs (3901 3904) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 04:57:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 04:57:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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 3974 of (3974 3977) to complete...
Waiting for PID 3977 of (3974 3977) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050267 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...
1689 labels changed using aseg
relabeling using gibbs priors...
000:   2350 changed, 172987 examined...
001:    508 changed, 10988 examined...
002:    150 changed, 2980 examined...
003:     49 changed, 864 examined...
004:     16 changed, 297 examined...
005:      7 changed, 109 examined...
006:      4 changed, 43 examined...
007:      3 changed, 23 examined...
008:      1 changed, 21 examined...
009:      1 changed, 5 examined...
010:      0 changed, 9 examined...
188 labels changed using aseg
000: 58 total segments, 25 labels (184 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1180 vertices marked for relabeling...
1180 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 0050267 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...
1416 labels changed using aseg
relabeling using gibbs priors...
000:   2371 changed, 171943 examined...
001:    571 changed, 10856 examined...
002:    175 changed, 3158 examined...
003:     64 changed, 1017 examined...
004:     20 changed, 381 examined...
005:     11 changed, 130 examined...
006:      1 changed, 58 examined...
007:      0 changed, 5 examined...
148 labels changed using aseg
000: 66 total segments, 33 labels (197 vertices) changed
001: 35 total segments, 2 labels (8 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1241 vertices marked for relabeling...
1241 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 18 seconds.
PIDs (3974 3977) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 04:57:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 04:57:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 rh white 

Waiting for PID 4023 of (4023 4026) to complete...
Waiting for PID 4026 of (4023 4026) 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 0050267 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 321013
Total vertex volume 317157 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 2342   1526   4683  2.731 0.609     0.104     0.022       27     1.8  caudalanteriorcingulate
 4023   2673   8223  2.696 0.540     0.116     0.021       42     3.4  caudalmiddlefrontal
 3331   2117   4701  2.090 0.500     0.130     0.026       42     3.6  cuneus
  813    551   2455  3.255 0.845     0.133     0.045       10     1.5  entorhinal
 5776   3842  11797  2.778 0.469     0.118     0.024       68     5.8  fusiform
 9312   6092  17744  2.644 0.491     0.120     0.025      134     9.0  inferiorparietal
 7227   4693  15105  2.713 0.676     0.130     0.036      128    11.4  inferiortemporal
 2098   1350   3630  2.396 0.917     0.121     0.024       28     1.7  isthmuscingulate
10478   6628  16375  2.253 0.512     0.134     0.028      141    11.7  lateraloccipital
 5956   3943  11634  2.704 0.705     0.136     0.038       89     8.9  lateralorbitofrontal
 5367   3450   7727  2.156 0.557     0.128     0.029       66     6.3  lingual
 2862   1827   5558  2.685 0.727     0.121     0.034       42     3.7  medialorbitofrontal
 8082   5538  18090  2.827 0.632     0.119     0.022      110     7.1  middletemporal
 1329    876   3029  3.004 0.559     0.103     0.019       14     0.9  parahippocampal
 3008   1929   5905  2.745 0.557     0.109     0.020       25     2.3  paracentral
 3592   2378   7943  2.893 0.495     0.122     0.025       42     3.4  parsopercularis
 1422    924   3256  3.049 0.427     0.125     0.025       18     1.4  parsorbitalis
 3676   2456   7514  2.731 0.479     0.120     0.022       41     3.2  parstriangularis
 2018   1342   2226  1.952 0.426     0.117     0.025       19     2.0  pericalcarine
 8094   4948  11281  2.100 0.581     0.111     0.027       83     8.9  postcentral
 2310   1528   4393  2.640 0.798     0.142     0.032       44     2.7  posteriorcingulate
 8190   5094  15007  2.699 0.541     0.110     0.023       78     7.7  precentral
 7833   5184  14199  2.585 0.474     0.128     0.025      102     7.7  precuneus
 2262   1458   4429  2.803 0.473     0.126     0.030       41     2.3  rostralanteriorcingulate
10271   6807  20334  2.588 0.508     0.131     0.029      148    11.6  rostralmiddlefrontal
15542  10441  34145  2.825 0.571     0.131     0.029      211    18.3  superiorfrontal
 7988   5231  14112  2.429 0.480     0.122     0.024       99     8.2  superiorparietal
 9431   6238  21916  3.076 0.785     0.114     0.024      105     9.6  superiortemporal
 5776   3818  11476  2.750 0.521     0.129     0.027       79     5.9  supramarginal
  922    538   1369  2.400 0.431     0.130     0.048       16     1.8  transversetemporal
 3103   2030   6903  3.357 0.704     0.111     0.029       32     3.4  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 0050267 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 323031
Total vertex volume 319815 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1454    985   3128  2.748 0.668     0.129     0.020       25     1.1  caudalanteriorcingulate
 3871   2555   8498  2.936 0.590     0.111     0.020       38     3.0  caudalmiddlefrontal
 3587   2296   4954  1.983 0.462     0.152     0.034       61     4.9  cuneus
  786    532   2765  3.582 0.811     0.136     0.059       12     1.9  entorhinal
 4795   3214   9266  2.829 0.564     0.119     0.025       56     4.7  fusiform
 9593   6413  18717  2.636 0.481     0.120     0.024      127     9.2  inferiorparietal
 7978   5203  17803  2.847 0.618     0.127     0.036      134    11.7  inferiortemporal
 1804   1150   3153  2.383 0.800     0.129     0.027       26     1.9  isthmuscingulate
 9954   6401  16577  2.313 0.512     0.134     0.029      130    11.8  lateraloccipital
 6262   4078  11957  2.676 0.614     0.141     0.042      105    10.8  lateralorbitofrontal
 5593   3615   8168  2.111 0.638     0.141     0.032       82     7.4  lingual
 2857   1892   5382  2.552 0.756     0.136     0.045       56     4.8  medialorbitofrontal
 7882   5444  18568  3.016 0.587     0.123     0.024      103     7.1  middletemporal
 1246    824   2848  3.035 0.665     0.121     0.031       20     1.7  parahippocampal
 2695   1722   4971  2.626 0.512     0.109     0.020       23     2.0  paracentral
 3493   2373   7426  2.814 0.420     0.126     0.026       43     3.7  parsopercularis
 1605   1017   3519  2.943 0.595     0.143     0.039       30     2.8  parsorbitalis
 3579   2297   7001  2.670 0.487     0.132     0.027       53     4.0  parstriangularis
 2827   1858   2957  1.784 0.424     0.124     0.030       30     3.2  pericalcarine
 7923   4930  11505  2.149 0.615     0.115     0.026       85     8.4  postcentral
 2277   1493   4462  2.692 0.646     0.142     0.027       39     2.5  posteriorcingulate
 9048   5601  17366  2.765 0.542     0.110     0.024      100     8.1  precentral
 7584   4982  13704  2.594 0.458     0.129     0.027       98     8.1  precuneus
 1403    925   2834  2.813 0.702     0.119     0.029       20     1.8  rostralanteriorcingulate
 9532   6199  18670  2.691 0.489     0.126     0.026      129     9.7  rostralmiddlefrontal
17875  11932  39007  2.881 0.582     0.129     0.031      247    22.1  superiorfrontal
 7631   5040  13758  2.428 0.457     0.121     0.023       92     6.9  superiorparietal
 8202   5405  19319  3.143 0.692     0.118     0.026       92     8.2  superiortemporal
 6575   4307  12730  2.727 0.499     0.128     0.026       86     7.0  supramarginal
  633    397   1156  2.467 0.803     0.125     0.052       12     1.2  transversetemporal
 3409   2307   7647  3.301 0.711     0.125     0.034       46     4.8  insula
PIDs (4023 4026) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 04:58:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 pctsurfcon --s 0050267 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 04:58:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts

 pctsurfcon --s 0050267 --rh-only 

Waiting for PID 4094 of (4094 4106) to complete...
Waiting for PID 4106 of (4094 4106) to complete...

 pctsurfcon --s 0050267 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts/pctsurfcon.log
Sun Oct  8 04:58:47 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-6.0.0/0050267/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-960 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-6.0.0/0050267/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4094/lh.wm.mgh --regheader 0050267 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 92060
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4094/lh.wm.mgh
Dim: 172987 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4094/lh.gm.mgh --projfrac 0.3 --regheader 0050267 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 114652
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4094/lh.gm.mgh
Dim: 172987 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4094/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4094/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.w-g.pct.mgh --annot 0050267 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/lh.w-g.pct.mgh --annot 0050267 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/lh.w-g.pct.mgh
Vertex Area is 0.653811 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 0050267 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/scripts/pctsurfcon.log
Sun Oct  8 04:58:47 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-6.0.0/0050267/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-960 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-6.0.0/0050267/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4106/rh.wm.mgh --regheader 0050267 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 91603
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4106/rh.wm.mgh
Dim: 171943 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4106/rh.gm.mgh --projfrac 0.3 --regheader 0050267 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 113607
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4106/rh.gm.mgh
Dim: 171943 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4106/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/tmp.pctsurfcon.4106/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.w-g.pct.mgh --annot 0050267 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.w-g.pct.mgh --annot 0050267 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.w-g.pct.mgh
Vertex Area is 0.655737 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 (4094 4106) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 04:58:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1768 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1970 voxels changed to hypointensity...
3727 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 04:59:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267

 mri_aparc2aseg --s 0050267 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 04:59:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267

 mri_aparc2aseg --s 0050267 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 04:59:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267

 mri_aparc2aseg --s 0050267 --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 4266 of (4266 4269 4272) to complete...
Waiting for PID 4269 of (4266 4269 4272) to complete...
Waiting for PID 4272 of (4266 4269 4272) to complete...

 mri_aparc2aseg --s 0050267 --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 0050267
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/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-6.0.0/0050267/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 7.71
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 24
rescaling Left_Inf_Lat_Vent from 34 --> 36
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 66
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 39
rescaling Fourth_Ventricle from 22 --> 24
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 63
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 67
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 78
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 96
rescaling Right_Hippocampus from 53 --> 65
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 76
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  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 = 632478
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 138 changed.
pass 2: 12 changed.
pass 3: 4 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050267 --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 0050267
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/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-6.0.0/0050267/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 7.71
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 24
rescaling Left_Inf_Lat_Vent from 34 --> 36
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 66
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 39
rescaling Fourth_Ventricle from 22 --> 24
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 63
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 67
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 78
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 96
rescaling Right_Hippocampus from 53 --> 65
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 76
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  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 = 632461
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 138 changed.
pass 2: 12 changed.
pass 3: 4 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050267 --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 0050267
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/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-6.0.0/0050267/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 7.71
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 24
rescaling Left_Inf_Lat_Vent from 34 --> 36
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 66
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 39
rescaling Fourth_Ventricle from 22 --> 24
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 63
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 67
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 78
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 96
rescaling Right_Hippocampus from 53 --> 65
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 76
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  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 = 632461
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 138 changed.
pass 2: 12 changed.
pass 3: 4 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (4266 4269 4272) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 05:07:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri

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

Sun Oct  8 05:07:27 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-6.0.0/0050267/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-960 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-6.0.0/0050267/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-960
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 05:07:27 CEST 2017 
Ended   at Sun Oct  8 05:07:33 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 05:07:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267

 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 0050267 


$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 0050267 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1869144 mm^3    (det: 1.042245 )
Computing euler number
orig.nofix lheno =  -68, rheno = -78
orig.nofix lhholes =   35, rhholes = 40
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 05:09:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267

 mri_aparc2aseg --s 0050267 --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 0050267
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-6.0.0/0050267/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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-6.0.0/0050267/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8563 vertices from left hemi
Ripped 7995 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-6.0.0/0050267/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 = 1181510
Used brute-force search on 115 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1953.000000
     3 k 1.000000
     4 k 2.000000
     5 k 4.000000
Fixing Parahip RH WM
  Found 7 clusters
     0 k 2.000000
     1 k 1.000000
     2 k 1.000000
     3 k 10.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1832.000000
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 0050267 --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 0050267 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-960
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1869144 mm^3    (det: 1.042245 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
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-6.0.0/0050267/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 05:18:44 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 5328 of (5328 5334 5340 5345 5351) to complete...
Waiting for PID 5334 of (5328 5334 5340 5345 5351) to complete...
Waiting for PID 5340 of (5328 5334 5340 5345 5351) to complete...
Waiting for PID 5345 of (5328 5334 5340 5345 5351) to complete...
Waiting for PID 5351 of (5328 5334 5340 5345 5351) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 709
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4838
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 971
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8880
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 189
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4266
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 601
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6584
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1030
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6814
mri_label2label: Done

PIDs (5328 5334 5340 5345 5351) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 5404 of (5404 5410 5416 5422) to complete...
Waiting for PID 5410 of (5404 5410 5416 5422) to complete...
Waiting for PID 5416 of (5404 5410 5416 5422) to complete...
Waiting for PID 5422 of (5404 5410 5416 5422) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 503
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4573
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 2367
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15956
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1027
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 5208
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 2348
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 5770
mri_label2label: Done

PIDs (5404 5410 5416 5422) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 5510 of (5510 5516 5522 5528 5534) to complete...
Waiting for PID 5516 of (5510 5516 5522 5528 5534) to complete...
Waiting for PID 5522 of (5510 5516 5522 5528 5534) to complete...
Waiting for PID 5528 of (5510 5516 5522 5528 5534) to complete...
Waiting for PID 5534 of (5510 5516 5522 5528 5534) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1585
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6226
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 3604
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11718
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1356
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 3374
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 199
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1489
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 226
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1425
mri_label2label: Done

PIDs (5510 5516 5522 5528 5534) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 5599 of (5599 5605 5611 5616 5623) to complete...
Waiting for PID 5605 of (5599 5605 5611 5616 5623) to complete...
Waiting for PID 5611 of (5599 5605 5611 5616 5623) to complete...
Waiting for PID 5616 of (5599 5605 5611 5616 5623) to complete...
Waiting for PID 5623 of (5599 5605 5611 5616 5623) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 282
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1296
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 238
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2330
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 69
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1573
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2136
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 421
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2740
mri_label2label: Done

PIDs (5599 5605 5611 5616 5623) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 5715 of (5715 5721 5727 5730) to complete...
Waiting for PID 5721 of (5715 5721 5727 5730) to complete...
Waiting for PID 5727 of (5715 5721 5727 5730) to complete...
Waiting for PID 5730 of (5715 5721 5727 5730) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 83
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1632
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1269
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8304
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 522
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2434
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 963
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 2114
mri_label2label: Done

PIDs (5715 5721 5727 5730) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 5776 of (5776 5782 5788 5793 5798) to complete...
Waiting for PID 5782 of (5776 5782 5788 5793 5798) to complete...
Waiting for PID 5788 of (5776 5782 5788 5793 5798) to complete...
Waiting for PID 5793 of (5776 5782 5788 5793 5798) to complete...
Waiting for PID 5798 of (5776 5782 5788 5793 5798) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1094
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4499
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 1603
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4937
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 396
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 909
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 73
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 543
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 172987
Number of reverse mapping hits = 96
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 546
mri_label2label: Done

PIDs (5776 5782 5788 5793 5798) completed and logs appended.

 mris_label2annot --s 0050267 --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-6.0.0/0050267/label
cmdline mris_label2annot --s 0050267 --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-960
machine  x86_64
user     ntraut

subject 0050267
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-6.0.0/0050267/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 122223 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050267 --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-6.0.0/0050267/label
cmdline mris_label2annot --s 0050267 --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-960
machine  x86_64
user     ntraut

subject 0050267
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-6.0.0/0050267/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 143505 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 321013
Total vertex volume 317157 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1634    818   2327  2.129 0.544     0.115     0.046       23     3.4  BA1_exvivo
 4336   2801   6314  2.259 0.418     0.115     0.021       43     3.7  BA2_exvivo
 1097    737   1030  1.828 0.388     0.145     0.031       12     1.3  BA3a_exvivo
 2593   1648   3553  1.881 0.642     0.102     0.021       22     2.2  BA3b_exvivo
 2103   1196   4058  2.911 0.455     0.098     0.022       17     1.8  BA4a_exvivo
 1412    917   2046  2.364 0.422     0.093     0.020        8     1.1  BA4p_exvivo
11542   7563  25669  2.876 0.568     0.118     0.026      123    12.0  BA6_exvivo
 3020   1990   6301  2.823 0.518     0.124     0.025       36     3.0  BA44_exvivo
 5057   3362  10840  2.692 0.485     0.125     0.025       67     4.8  BA45_exvivo
 3677   2421   4317  1.872 0.474     0.126     0.028       42     4.2  V1_exvivo
 9479   5945  12922  2.035 0.478     0.137     0.031      131    11.7  V2_exvivo
 3246   2117   5752  2.560 0.414     0.125     0.023       43     3.0  MT_exvivo
  686    460   2118  3.460 0.696     0.093     0.022        5     0.5  perirhinal_exvivo
  882    621   2126  2.912 0.676     0.123     0.031        8     1.2  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050267 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 321013
Total vertex volume 317157 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1081    501   1479  2.114 0.578     0.111     0.053       16     2.8  BA1_exvivo
 1701   1055   2461  2.248 0.362     0.105     0.019       14     1.3  BA2_exvivo
  967    650    852  1.806 0.403     0.156     0.034       11     1.3  BA3a_exvivo
 1510    983   1563  1.511 0.364     0.081     0.015        8     0.8  BA3b_exvivo
 2072   1171   3759  2.831 0.482     0.090     0.021       15     1.7  BA4a_exvivo
 1055    712   1487  2.283 0.391     0.095     0.020        6     0.7  BA4p_exvivo
 6638   4278  15040  2.899 0.583     0.120     0.029       73     7.8  BA6_exvivo
 2114   1397   4349  2.862 0.520     0.126     0.026       25     2.1  BA44_exvivo
 2104   1359   4834  2.776 0.472     0.126     0.026       28     2.0  BA45_exvivo
 3927   2591   4623  1.862 0.469     0.124     0.028       43     4.4  V1_exvivo
 4602   2812   5932  1.963 0.444     0.145     0.035       72     6.1  V2_exvivo
  898    566   1767  2.718 0.442     0.117     0.018       10     0.7  MT_exvivo
  336    238   1153  3.686 0.620     0.077     0.015        1     0.2  perirhinal_exvivo
  477    323   1339  3.198 0.686     0.124     0.037        5     0.7  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 05:22:17 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 5988 of (5988 5994 6000 6005 6012) to complete...
Waiting for PID 5994 of (5988 5994 6000 6005 6012) to complete...
Waiting for PID 6000 of (5988 5994 6000 6005 6012) to complete...
Waiting for PID 6005 of (5988 5994 6000 6005 6012) to complete...
Waiting for PID 6012 of (5988 5994 6000 6005 6012) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 701
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4663
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 832
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7519
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 220
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4200
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 420
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4942
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 936
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6683
mri_label2label: Done

PIDs (5988 5994 6000 6005 6012) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 6104 of (6104 6110 6116 6121) to complete...
Waiting for PID 6110 of (6104 6110 6116 6121) to complete...
Waiting for PID 6116 of (6104 6110 6116 6121) to complete...
Waiting for PID 6121 of (6104 6110 6116 6121) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 582
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5055
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 2071
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14327
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 2538
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 9450
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 2953
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 8308
mri_label2label: Done

PIDs (6104 6110 6116 6121) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 6169 of (6169 6175 6181 6187 6193) to complete...
Waiting for PID 6175 of (6169 6175 6181 6187 6193) to complete...
Waiting for PID 6181 of (6169 6175 6181 6187 6193) to complete...
Waiting for PID 6187 of (6169 6175 6181 6187 6193) to complete...
Waiting for PID 6193 of (6169 6175 6181 6187 6193) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 2455
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 7182
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 4094
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12110
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 1387
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 3319
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 171
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1209
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 117
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 869
mri_label2label: Done

PIDs (6169 6175 6181 6187 6193) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 6255 of (6255 6261 6267 6271 6278) to complete...
Waiting for PID 6261 of (6255 6261 6267 6271 6278) to complete...
Waiting for PID 6267 of (6255 6261 6267 6271 6278) to complete...
Waiting for PID 6271 of (6255 6261 6267 6271 6278) to complete...
Waiting for PID 6278 of (6255 6261 6267 6271 6278) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 243
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1119
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 247
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2935
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1769
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 147
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2330
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 266
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1654
mri_label2label: Done

PIDs (6255 6261 6267 6271 6278) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 6323 of (6323 6329 6335 6341) to complete...
Waiting for PID 6329 of (6323 6329 6335 6341) to complete...
Waiting for PID 6335 of (6323 6329 6335 6341) to complete...
Waiting for PID 6341 of (6323 6329 6335 6341) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 186
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1675
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 1066
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8025
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 444
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1456
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 648
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1826
mri_label2label: Done

PIDs (6323 6329 6335 6341) 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 0050267 --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 0050267 --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 0050267 --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 0050267 --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 0050267 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 6397 of (6397 6403 6409 6414 6421) to complete...
Waiting for PID 6403 of (6397 6403 6409 6414 6421) to complete...
Waiting for PID 6409 of (6397 6403 6409 6414 6421) to complete...
Waiting for PID 6414 of (6397 6403 6409 6414 6421) to complete...
Waiting for PID 6421 of (6397 6403 6409 6414 6421) 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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 1704
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4936
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 1886
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5323
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 232
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 500
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 115
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 809
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 0050267 --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 = 0050267
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-6.0.0/0050267/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 171943
Number of reverse mapping hits = 43
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 334
mri_label2label: Done

PIDs (6397 6403 6409 6414 6421) completed and logs appended.

 mris_label2annot --s 0050267 --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-6.0.0/0050267/label
cmdline mris_label2annot --s 0050267 --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-960
machine  x86_64
user     ntraut

subject 0050267
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-6.0.0/0050267/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 119501 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050267 --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-6.0.0/0050267/label
cmdline mris_label2annot --s 0050267 --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-960
machine  x86_64
user     ntraut

subject 0050267
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-6.0.0/0050267/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 143430 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/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 0050267 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 323031
Total vertex volume 319815 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
 1343    645   1965  2.154 0.555     0.118     0.036       20     2.1  BA1_exvivo
 3668   2370   5567  2.322 0.434     0.109     0.020       30     3.1  BA2_exvivo
 1140    787   1115  1.882 0.427     0.146     0.032       13     1.3  BA3a_exvivo
 2161   1392   2533  1.712 0.499     0.110     0.023       18     2.0  BA3b_exvivo
 2111   1186   3733  2.655 0.464     0.094     0.020       15     1.6  BA4a_exvivo
 1467    952   2192  2.436 0.416     0.093     0.017        7     1.0  BA4p_exvivo
 9834   6422  22297  2.917 0.585     0.120     0.028      124    11.4  BA6_exvivo
 5255   3516  10640  2.849 0.428     0.118     0.023       57     4.8  BA44_exvivo
 6549   4307  13982  2.752 0.508     0.135     0.030       99     7.6  BA45_exvivo
 4899   3116   5743  1.818 0.469     0.135     0.034       66     6.8  V1_exvivo
 9640   6208  14027  2.084 0.532     0.142     0.033      140    12.5  V2_exvivo
 3280   2203   5760  2.498 0.422     0.119     0.021       37     2.6  MT_exvivo
  667    458   2359  3.450 0.816     0.129     0.054       10     1.5  perirhinal_exvivo
  428    297   1226  3.092 0.626     0.149     0.039       11     0.8  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 0050267 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050267/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 323031
Total vertex volume 319815 (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) = 1869144 mm^3    (det: 1.042245 )
lhCtxGM: 316049.611 315378.000  diff=  671.6  pctdiff= 0.213
rhCtxGM: 318302.408 317434.000  diff=  868.4  pctdiff= 0.273
lhCtxWM: 276935.603 277331.500  diff= -395.9  pctdiff=-0.143
rhCtxWM: 274772.824 275646.500  diff= -873.7  pctdiff=-0.318
SubCortGMVol  68125.000
SupraTentVol  1266536.447 (1263428.000) diff=3108.447 pctdiff=0.245
SupraTentVolNotVent  1257068.447 (1253960.000) diff=3108.447 pctdiff=0.247
BrainSegVol  1430523.000 (1427537.000) diff=2986.000 pctdiff=0.209
BrainSegVolNotVent  1417162.000 (1417368.447) diff=-206.447 pctdiff=-0.015
BrainSegVolNotVent  1417162.000
CerebellumVol 163138.000
VentChorVol    9468.000
3rd4th5thCSF   3893.000
CSFVol   907.000, OptChiasmVol    64.000
MaskVol 1920482.000
  896    418   1160  2.005 0.591     0.121     0.044       15     1.7  BA1_exvivo
 2014   1239   3105  2.303 0.429     0.100     0.019       17     1.4  BA2_exvivo
 1014    709    925  1.874 0.390     0.148     0.031       11     1.2  BA3a_exvivo
 1629   1108   1669  1.514 0.306     0.107     0.020       13     1.3  BA3b_exvivo
 1331    739   2356  2.631 0.477     0.101     0.021       10     1.1  BA4a_exvivo
 1279    830   1956  2.472 0.406     0.095     0.018        7     0.9  BA4p_exvivo
 6337   4088  14207  2.897 0.610     0.121     0.029       85     7.6  BA6_exvivo
 1374    940   3011  2.887 0.396     0.133     0.030       19     1.7  BA44_exvivo
 1727   1151   3994  2.811 0.507     0.131     0.029       26     2.0  BA45_exvivo
 4673   2977   5393  1.816 0.468     0.134     0.033       62     6.5  V1_exvivo
 5048   3224   6679  1.886 0.450     0.144     0.036       75     7.2  V2_exvivo
  497    320   1012  2.637 0.313     0.131     0.026        7     0.4  MT_exvivo
  423    290   1454  3.415 0.834     0.132     0.060        7     1.3  perirhinal_exvivo
  271    189   1017  3.347 0.625     0.153     0.039        8     0.4  entorhinal_exvivo

Started at Sat Oct 7 20:02:22 CEST 2017 
Ended   at Sun Oct 8 05:25:47 CEST 2017
#@#%# recon-all-run-time-hours 9.390
recon-all -s 0050267 finished without error at Sun Oct  8 05:25:47 CEST 2017