ABIDE_fs-6.0.0/0051348/scripts/recon-all.log

Sat Oct  7 17:01:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051348 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_c/0051348/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051348
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-553 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:      65993860   50258380   15735480    1756068          0   47564700
-/+ buffers/cache:    2693680   63300180
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: 2017/10/07-15:01:48-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-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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: 2017/10/07-15:01:49-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-553  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-6.0.0/0051348

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_c/0051348/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_c/0051348/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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/MaxMun_c/0051348/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-6.0.0/0051348/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 17:01:51 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 17:02:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-553 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 17:02:01 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.10063
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10063/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10063/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.10063/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:02:03 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10063/nu0.mnc ./tmp.mri_nu_correct.mni.10063/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10063/0/ -iterations 1000 -distance 50
[ntraut@tars-553:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/] [2017-10-07 17:02:03] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10063/0/ ./tmp.mri_nu_correct.mni.10063/nu0.mnc ./tmp.mri_nu_correct.mni.10063/nu1.imp

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Number of iterations: 39 
CV of field change: 0.000982278
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.10063/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.10063/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.10063/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 17:03:06 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 17:03:06 CEST 2017
Ended   at Sat Oct  7 17:03:37 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 17:03:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4171, pval=0.0643 >= 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-6.0.0/0051348/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/talairach_avi.log 

TalAviQA: 0.97879
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 17:03:40 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-6.0.0/0051348/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-553 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 17:03:40 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.10873
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10873/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10873/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.10873/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:03:42 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10873/nu0.mnc ./tmp.mri_nu_correct.mni.10873/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10873/0/
[ntraut@tars-553:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/] [2017-10-07 17:03:42] 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.10873/0/ ./tmp.mri_nu_correct.mni.10873/nu0.mnc ./tmp.mri_nu_correct.mni.10873/nu1.imp

Processing:.................................................................Done
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Number of iterations: 39 
CV of field change: 0.000972007
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 17:04:28 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10873/nu1.mnc ./tmp.mri_nu_correct.mni.10873/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10873/1/
[ntraut@tars-553:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/] [2017-10-07 17:04:28] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.10873/1/ ./tmp.mri_nu_correct.mni.10873/nu1.mnc ./tmp.mri_nu_correct.mni.10873/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 14 
CV of field change: 0.000995407
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10873/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-6.0.0/0051348/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10873/ones.mgz 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.10873/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.10873/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.10873/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/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.10873/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/input.mean.dat 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.10873/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.10873/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10873/ones.mgz --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/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.10873/ones.mgz --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/output.mean.dat 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.10873/ones.mgz
Loading ./tmp.mri_nu_correct.mni.10873/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.10873/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.10873/nu2.mnc ./tmp.mri_nu_correct.mni.10873/nu2.mnc mul .96167811818778809197
Saving result to './tmp.mri_nu_correct.mni.10873/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.10873/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.10873/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.10873/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 (18, 147) to ( 3, 110)
 
 
Sat Oct  7 17:05:36 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 17:05:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

 mri_normalize -g 1 -mprage nu.mgz T1.mgz 

using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
 1.15435   0.02161  -0.16422   7.60110;
-0.09427   1.02657  -0.08129   11.33200;
 0.15816   0.17914   1.03470  -68.80373;
 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 = 15
Starting OpenSpline(): npoints = 15
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 106
gm peak at 73 (73), valley at 39 (39)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 72 (72), valley at 37 (37)
csf peak at 36, setting threshold to 60
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 12 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 17:07:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=6.0
skull bounding box = (56, 21, 28) --> (197, 171, 221)
using (103, 71, 125) as brain centroid...
mean wm in atlas = 108, using box (86,53,101) --> (120, 89,148) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 6.1
after smoothing, mri peak at 105, scaling input intensities by 1.029
scaling channel 0 by 1.02857
initial log_p = -4.709
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.495207 @ (9.091, 27.273, -9.091)
max log p =    -4.466466 @ (-4.545, 4.545, -4.545)
max log p =    -4.418298 @ (-6.818, -6.818, 6.818)
max log p =    -4.413081 @ (3.409, -1.136, -7.955)
max log p =    -4.408009 @ (0.568, 2.841, 5.114)
max log p =    -4.400772 @ (-1.989, -1.989, 2.557)
Found translation: (-0.3, 24.7, -7.1): log p = -4.401
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.166, old_max_log_p =-4.401 (thresh=-4.4)
 1.22567  -0.15998   0.02106  -19.72387;
 0.16136   1.21519  -0.15998   5.62621;
 0.00000   0.15011   1.14016  -41.27601;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.157, old_max_log_p =-4.166 (thresh=-4.2)
 1.13375  -0.14798   0.01948  -8.87893;
 0.14926   1.12405  -0.14798   8.36730;
 0.00000   0.15011   1.14016  -48.77601;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.157, old_max_log_p =-4.157 (thresh=-4.2)
 1.13375  -0.14798   0.01948  -8.87893;
 0.14926   1.12405  -0.14798   8.36730;
 0.00000   0.15011   1.14016  -48.77601;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.097, old_max_log_p =-4.157 (thresh=-4.2)
 1.19064  -0.20039  -0.05621  -0.60923;
 0.19287   1.16808  -0.07768  -7.55813;
 0.06316   0.06513   1.12392  -41.19419;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.097, old_max_log_p =-4.097 (thresh=-4.1)
 1.19064  -0.20039  -0.05621  -0.60923;
 0.19287   1.16808  -0.07768  -7.55813;
 0.06316   0.06513   1.12392  -41.19419;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.085, old_max_log_p =-4.097 (thresh=-4.1)
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.085, old_max_log_p =-4.085 (thresh=-4.1)
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 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
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.085 (old=-4.709)
transform before final EM align:
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 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
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.5  tol 0.000000
final transform:
 1.19087  -0.19667  -0.01949  -4.58742;
 0.19092   1.16669  -0.11455  -2.67036;
 0.03044   0.10982   1.12201  -43.22834;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    2018.600126
mri_em_register stimesec    2.287652
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   157588
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    193060
mri_em_register ru_nivcsw   7776
registration took 20 minutes and 58 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=127 y=86 z=124 r=65
      first estimation of the main basin volume: 1155728 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        12 found in the rest of the brain 
      global maximum in x=143, y=73, z=93, Imax=255
      CSF=16, 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=6854126761 voxels, voxel volume =1.000 
                     = 6854126761 mmm3 = 6854126.592 cm3
done.
PostAnalyze...Basin Prior
 34 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=126,y=96, z=119, r=9556 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=52 , nb = 43226
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1104425715
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = -1041375197
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 1088343356
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=64 , nb = 1057488526
    OTHER      CSF_MIN=0, CSF_intensity=9, CSF_MAX=82 , nb = 1078804540
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    52,      47,        45,   66
  after  analyzing :    31,      47,        47,   51
   RIGHT_CER   
  before analyzing :    5,      10,        47,   69
  after  analyzing :    5,      34,        47,   42
   LEFT_CER    
  before analyzing :    10,      19,        44,   66
  after  analyzing :    10,      35,        44,   42
  RIGHT_BRAIN  
  before analyzing :    56,      48,        45,   66
  after  analyzing :    33,      48,        48,   52
  LEFT_BRAIN   
  before analyzing :    64,      49,        44,   66
  after  analyzing :    37,      49,        49,   53
     OTHER     
  before analyzing :    82,      88,        89,   95
  after  analyzing :    82,      88,        89,   89
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...78 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.013
curvature mean = 68.877, std = 9.407

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 7.87, sigma = 12.16
      after  rotation: sse = 7.87, sigma = 12.16
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  8.66, its var is 10.83   
      before Erosion-Dilatation  8.49% of inacurate vertices
      after  Erosion-Dilatation 13.27% 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...43 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1602451 voxels, voxel volume = 1.000 mm3
           = 1602451 mmm3 = 1602.451 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    29.319542
mri_watershed stimesec    0.447931
mri_watershed ru_maxrss   818064
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   211392
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  4544
mri_watershed ru_oublock  2728
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1846
mri_watershed ru_nivcsw   1143
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 17:29:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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=21.9
skull bounding box = (62, 29, 37) --> (189, 146, 211)
using (104, 68, 124) as brain centroid...
mean wm in atlas = 107, using box (88,54,103) --> (119, 82,145) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 5.8
after smoothing, mri peak at 105, scaling input intensities by 1.019
scaling channel 0 by 1.01905
initial log_p = -4.512
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.172519 @ (-9.091, 27.273, -9.091)
max log p =    -4.016878 @ (13.636, -4.545, -4.545)
max log p =    -3.914818 @ (-2.273, 2.273, 2.273)
max log p =    -3.914818 @ (0.000, 0.000, 0.000)
max log p =    -3.912988 @ (-0.568, -3.977, -0.568)
max log p =    -3.912988 @ (0.000, 0.000, 0.000)
Found translation: (1.7, 21.0, -11.9): log p = -3.913
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.747, old_max_log_p =-3.913 (thresh=-3.9)
 1.06549  -0.14148  -0.01831   9.56794;
 0.13796   1.05700  -0.13912   14.50175;
 0.03125   0.11662   0.91709  -17.56709;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.747, old_max_log_p =-3.747 (thresh=-3.7)
 1.06549  -0.14148  -0.01831   9.56794;
 0.13796   1.05700  -0.13912   14.50175;
 0.03125   0.11662   0.91709  -17.56709;
 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=-3.606, old_max_log_p =-3.747 (thresh=-3.7)
 1.12398  -0.15605  -0.05065   5.54722;
 0.13548   1.05776  -0.13706   16.61471;
 0.06947   0.11593   0.96848  -30.30967;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.592, old_max_log_p =-3.606 (thresh=-3.6)
 1.10004  -0.18067  -0.01250   6.38888;
 0.16741   1.04245  -0.20063   21.64808;
 0.04214   0.19343   0.97656  -35.28300;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.584, old_max_log_p =-3.592 (thresh=-3.6)
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.584, old_max_log_p =-3.584 (thresh=-3.6)
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.584, old_max_log_p =-3.584 (thresh=-3.6)
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 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
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.584 (old=-4.512)
transform before final EM align:
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 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
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.0  tol 0.000000
final transform:
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1523.550385
mri_em_register stimesec    2.091682
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158952
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    13415
mri_em_register ru_nivcsw   5596
registration took 13 minutes and 15 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 17:42:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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=21.9
skull bounding box = (62, 29, 37) --> (189, 146, 211)
using (104, 68, 124) as brain centroid...
mean wm in atlas = 107, using box (88,54,103) --> (119, 82,145) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 5.8
after smoothing, mri peak at 105, scaling input intensities by 1.019
scaling channel 0 by 1.01905
using 246344 sample points...
INFO: compute sample coordinates transform
 1.10694  -0.11683  -0.05557   4.51488;
 0.09651   1.05813  -0.16529   24.88750;
 0.07125   0.15034   0.96326  -33.22721;
 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 (121, 31, 36) --> (187, 145, 208)
Left_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0
0 of 14 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 33, 39) --> (131, 151, 211)
Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0
0 of 12 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 108, 53) --> (173, 146, 110)
Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0
0 of 7 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 109, 53) --> (128, 150, 113)
Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0
2 of 18 (11.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 105, 85) --> (146, 168, 124)
Brain_Stem: limiting intensities to 104.0 --> 132.0
9 of 10 (90.0%) samples deleted
using 61 total control points for intensity normalization...
bias field = 0.854 +- 0.081
0 of 50 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (121, 31, 36) --> (187, 145, 208)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 128 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 33, 39) --> (131, 151, 211)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 108 (0.9%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 108, 53) --> (173, 146, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
18 of 59 (30.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 109, 53) --> (128, 150, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
36 of 53 (67.9%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 105, 85) --> (146, 168, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
41 of 104 (39.4%) samples deleted
using 452 total control points for intensity normalization...
bias field = 0.998 +- 0.103
0 of 348 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (121, 31, 36) --> (187, 145, 208)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 252 (0.4%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 33, 39) --> (131, 151, 211)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
10 of 255 (3.9%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 108, 53) --> (173, 146, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
38 of 68 (55.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 109, 53) --> (128, 150, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
74 of 96 (77.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 105, 85) --> (146, 168, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
111 of 169 (65.7%) samples deleted
using 840 total control points for intensity normalization...
bias field = 1.012 +- 0.070
0 of 604 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 51 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 17:44:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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) = 1.17 (predicted orig area = 6.8)
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=0.814, neg=0, invalid=762
0001: dt=221.952000, rms=0.738 (9.411%), neg=0, invalid=762
0002: dt=156.505747, rms=0.721 (2.269%), neg=0, invalid=762
0003: dt=226.513089, rms=0.711 (1.410%), neg=0, invalid=762
0004: dt=129.472000, rms=0.706 (0.618%), neg=0, invalid=762
0005: dt=295.936000, rms=0.703 (0.507%), neg=0, invalid=762
0006: dt=129.472000, rms=0.700 (0.333%), neg=0, invalid=762
0007: dt=129.472000, rms=0.699 (0.156%), neg=0, invalid=762
0008: dt=129.472000, rms=0.698 (0.133%), neg=0, invalid=762
0009: dt=129.472000, rms=0.697 (0.208%), neg=0, invalid=762
0010: dt=129.472000, rms=0.695 (0.265%), neg=0, invalid=762
0011: dt=129.472000, rms=0.694 (0.214%), neg=0, invalid=762
0012: dt=129.472000, rms=0.692 (0.216%), neg=0, invalid=762
0013: dt=129.472000, rms=0.691 (0.206%), neg=0, invalid=762
0014: dt=129.472000, rms=0.689 (0.187%), neg=0, invalid=762
0015: dt=129.472000, rms=0.688 (0.181%), neg=0, invalid=762
0016: dt=129.472000, rms=0.687 (0.167%), neg=0, invalid=762
0017: dt=129.472000, rms=0.686 (0.176%), neg=0, invalid=762
0018: dt=129.472000, rms=0.685 (0.158%), neg=0, invalid=762
0019: dt=129.472000, rms=0.684 (0.148%), neg=0, invalid=762
0020: dt=129.472000, rms=0.683 (0.135%), neg=0, invalid=762
0021: dt=129.472000, rms=0.682 (0.108%), neg=0, invalid=762
0022: dt=129.472000, rms=0.681 (0.095%), neg=0, invalid=762
0023: dt=517.888000, rms=0.681 (0.051%), neg=0, invalid=762
0024: dt=517.888000, rms=0.680 (0.101%), neg=0, invalid=762
0025: dt=517.888000, rms=0.680 (-1.591%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.681, neg=0, invalid=762
0026: dt=110.976000, rms=0.679 (0.222%), neg=0, invalid=762
0027: dt=92.480000, rms=0.679 (0.016%), neg=0, invalid=762
0028: dt=92.480000, rms=0.679 (0.022%), neg=0, invalid=762
0029: dt=92.480000, rms=0.679 (0.026%), neg=0, invalid=762
0030: dt=92.480000, rms=0.678 (0.043%), neg=0, invalid=762
0031: dt=92.480000, rms=0.678 (0.069%), neg=0, invalid=762
0032: dt=92.480000, rms=0.677 (0.090%), neg=0, invalid=762
0033: dt=92.480000, rms=0.677 (0.092%), neg=0, invalid=762
0034: dt=92.480000, rms=0.676 (0.080%), neg=0, invalid=762
0035: dt=92.480000, rms=0.676 (0.063%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.680, neg=0, invalid=762
0036: dt=92.307692, rms=0.675 (0.775%), neg=0, invalid=762
0037: dt=267.310751, rms=0.661 (1.974%), neg=0, invalid=762
0038: dt=48.905660, rms=0.658 (0.538%), neg=0, invalid=762
0039: dt=497.664000, rms=0.651 (1.078%), neg=0, invalid=762
0040: dt=77.913043, rms=0.644 (1.103%), neg=0, invalid=762
0041: dt=31.104000, rms=0.643 (0.042%), neg=0, invalid=762
0042: dt=31.104000, rms=0.643 (0.031%), neg=0, invalid=762
0043: dt=31.104000, rms=0.643 (0.066%), neg=0, invalid=762
0044: dt=31.104000, rms=0.642 (0.116%), neg=0, invalid=762
0045: dt=31.104000, rms=0.641 (0.189%), neg=0, invalid=762
0046: dt=31.104000, rms=0.639 (0.240%), neg=0, invalid=762
0047: dt=31.104000, rms=0.638 (0.255%), neg=0, invalid=762
0048: dt=31.104000, rms=0.636 (0.263%), neg=0, invalid=762
0049: dt=31.104000, rms=0.634 (0.256%), neg=0, invalid=762
0050: dt=31.104000, rms=0.633 (0.245%), neg=0, invalid=762
0051: dt=31.104000, rms=0.631 (0.235%), neg=0, invalid=762
0052: dt=31.104000, rms=0.630 (0.229%), neg=0, invalid=762
0053: dt=31.104000, rms=0.628 (0.220%), neg=0, invalid=762
0054: dt=31.104000, rms=0.627 (0.197%), neg=0, invalid=762
0055: dt=31.104000, rms=0.626 (0.184%), neg=0, invalid=762
0056: dt=31.104000, rms=0.625 (0.167%), neg=0, invalid=762
0057: dt=31.104000, rms=0.624 (0.159%), neg=0, invalid=762
0058: dt=31.104000, rms=0.623 (0.157%), neg=0, invalid=762
0059: dt=31.104000, rms=0.622 (0.141%), neg=0, invalid=762
0060: dt=31.104000, rms=0.621 (0.123%), neg=0, invalid=762
0061: dt=31.104000, rms=0.621 (0.116%), neg=0, invalid=762
0062: dt=145.152000, rms=0.620 (0.042%), neg=0, invalid=762
0063: dt=145.152000, rms=0.620 (-0.158%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.621, neg=0, invalid=762
0064: dt=66.237762, rms=0.619 (0.324%), neg=0, invalid=762
0065: dt=82.944000, rms=0.619 (0.085%), neg=0, invalid=762
0066: dt=82.944000, rms=0.618 (0.054%), neg=0, invalid=762
0067: dt=82.944000, rms=0.618 (0.076%), neg=0, invalid=762
0068: dt=82.944000, rms=0.618 (0.017%), neg=0, invalid=762
0069: dt=82.944000, rms=0.617 (0.036%), neg=0, invalid=762
0070: dt=82.944000, rms=0.617 (0.040%), neg=0, invalid=762
0071: dt=82.944000, rms=0.617 (0.051%), neg=0, invalid=762
0072: dt=82.944000, rms=0.617 (0.009%), neg=0, invalid=762
0073: dt=82.944000, rms=0.616 (0.057%), neg=0, invalid=762
0074: dt=62.208000, rms=0.616 (0.027%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.635, neg=0, invalid=762
0075: dt=4.800000, rms=0.634 (0.107%), neg=0, invalid=762
0076: dt=2.000000, rms=0.634 (0.003%), neg=0, invalid=762
0077: dt=2.000000, rms=0.634 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.634, neg=0, invalid=762
0078: dt=0.000000, rms=0.634 (0.080%), neg=0, invalid=762
0079: dt=0.000000, rms=0.634 (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=0.686, neg=0, invalid=762
0080: dt=5.775862, rms=0.670 (2.228%), neg=0, invalid=762
0081: dt=2.880000, rms=0.670 (0.085%), neg=0, invalid=762
0082: dt=2.880000, rms=0.670 (-0.015%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.670, neg=0, invalid=762
0083: dt=0.000000, rms=0.670 (0.064%), neg=0, invalid=762
0084: dt=0.000000, rms=0.670 (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=0.722, neg=0, invalid=762
0085: dt=0.448000, rms=0.720 (0.208%), neg=0, invalid=762
0086: dt=1.024000, rms=0.719 (0.189%), neg=0, invalid=762
0087: dt=1.024000, rms=0.717 (0.299%), neg=0, invalid=762
0088: dt=1.024000, rms=0.716 (0.161%), neg=0, invalid=762
0089: dt=1.024000, rms=0.716 (-0.259%), neg=0, invalid=762
0090: dt=1.792000, rms=0.715 (0.130%), neg=0, invalid=762
0091: dt=1.792000, rms=0.713 (0.188%), neg=0, invalid=762
0092: dt=0.000000, rms=0.713 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.714, neg=0, invalid=762
0093: dt=0.448000, rms=0.713 (0.103%), neg=0, invalid=762
0094: dt=1.024000, rms=0.713 (0.030%), neg=0, invalid=762
0095: dt=1.024000, rms=0.713 (0.030%), neg=0, invalid=762
0096: dt=1.024000, rms=0.713 (-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=0.680, neg=0, invalid=762
0097: dt=0.804555, rms=0.664 (2.366%), neg=0, invalid=762
0098: dt=0.080000, rms=0.663 (0.142%), neg=0, invalid=762
0099: dt=0.080000, rms=0.663 (-0.075%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.663, neg=0, invalid=762
0100: dt=0.028000, rms=0.663 (0.092%), neg=0, invalid=762
0101: dt=0.020000, rms=0.663 (0.005%), neg=0, invalid=762
0102: dt=0.020000, rms=0.663 (-0.004%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.12091 (24)
Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (1031 voxels, overlap=0.812)
Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (1031 voxels, peak = 23), gca=22.9
gca peak = 0.15565 (16)
mri peak = 0.11057 (25)
Right_Lateral_Ventricle (43): linear fit = 1.48 x + 0.0 (1180 voxels, overlap=0.471)
Right_Lateral_Ventricle (43): linear fit = 1.48 x + 0.0 (1180 voxels, peak = 24), gca=23.6
gca peak = 0.26829 (96)
mri peak = 0.07828 (93)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (622 voxels, overlap=0.740)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (622 voxels, peak = 92), gca=91.7
gca peak = 0.20183 (93)
mri peak = 0.07371 (92)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (526 voxels, overlap=0.679)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (526 voxels, peak = 89), gca=88.8
gca peak = 0.21683 (55)
mri peak = 0.09206 (71)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (641 voxels, overlap=0.141)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (641 voxels, peak = 66), gca=66.3
gca peak = 0.30730 (58)
mri peak = 0.07674 (67)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (625 voxels, overlap=0.284)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (625 voxels, peak = 68), gca=67.6
gca peak = 0.11430 (101)
mri peak = 0.06924 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52326 voxels, overlap=0.809)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52326 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.07337 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (50225 voxels, overlap=0.779)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (50225 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.04646 (70)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (18533 voxels, overlap=0.157)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (18533 voxels, peak = 71), gca=70.5
gca peak = 0.15082 (58)
mri peak = 0.04856 (70)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (19732 voxels, overlap=0.245)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (19732 voxels, peak = 69), gca=69.3
gca peak = 0.14161 (67)
mri peak = 0.08449 (76)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (721 voxels, overlap=0.562)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (721 voxels, peak = 75), gca=74.7
gca peak = 0.15243 (71)
mri peak = 0.08067 (76)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (721 voxels, overlap=0.963)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (721 voxels, peak = 73), gca=73.5
gca peak = 0.13336 (57)
mri peak = 0.05754 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (22326 voxels, overlap=0.442)
Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (22326 voxels, peak = 66), gca=66.4
gca peak = 0.13252 (56)
mri peak = 0.05292 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (23979 voxels, overlap=0.670)
Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (23979 voxels, peak = 64), gca=63.6
gca peak = 0.18181 (84)
mri peak = 0.05431 (86)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7501 voxels, overlap=0.929)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7501 voxels, peak = 86), gca=86.1
gca peak = 0.20573 (83)
mri peak = 0.05678 (83)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7261 voxels, overlap=0.978)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7261 voxels, peak = 82), gca=81.8
gca peak = 0.21969 (57)
mri peak = 0.08513 (62)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (321 voxels, overlap=0.484)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (321 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.07977 (63)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (345 voxels, overlap=0.648)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (345 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.05426 (89)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4628 voxels, overlap=0.923)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4628 voxels, peak = 87), gca=87.1
gca peak = 0.11978 (83)
mri peak = 0.05723 (89)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4097 voxels, overlap=0.852)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4097 voxels, peak = 88), gca=87.6
gca peak = 0.13399 (79)
mri peak = 0.07389 (79)
Left_Putamen (12): linear fit = 1.05 x + 0.0 (1637 voxels, overlap=0.864)
Left_Putamen (12): linear fit = 1.05 x + 0.0 (1637 voxels, peak = 83), gca=83.3
gca peak = 0.14159 (79)
mri peak = 0.06844 (79)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (1878 voxels, overlap=0.913)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (1878 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.09480 (82)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8537 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8537 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.07640 (89)
Right_VentralDC (60): linear fit = 1.04 x + 0.0 (753 voxels, overlap=0.728)
Right_VentralDC (60): linear fit = 1.04 x + 0.0 (753 voxels, peak = 90), gca=89.9
gca peak = 0.12801 (89)
mri peak = 0.07967 (89)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (810 voxels, overlap=0.850)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (810 voxels, peak = 91), gca=91.2
gca peak = 0.20494 (23)
mri peak = 1.00000 (40)
gca peak = 0.15061 (21)
mri peak = 0.08803 (25)
Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (395 voxels, overlap=0.654)
Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (395 voxels, peak = 24), gca=24.5
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 1.17 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.26 x + 0.0
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.655, neg=0, invalid=762
0103: dt=92.480000, rms=0.647 (1.195%), neg=0, invalid=762
0104: dt=129.472000, rms=0.645 (0.307%), neg=0, invalid=762
0105: dt=369.920000, rms=0.643 (0.370%), neg=0, invalid=762
0106: dt=295.936000, rms=0.642 (0.203%), neg=0, invalid=762
0107: dt=73.984000, rms=0.641 (0.110%), neg=0, invalid=762
0108: dt=1479.680000, rms=0.638 (0.530%), neg=0, invalid=762
0109: dt=92.480000, rms=0.637 (0.082%), neg=0, invalid=762
0110: dt=369.920000, rms=0.637 (0.078%), neg=0, invalid=762
0111: dt=369.920000, rms=0.635 (0.227%), neg=0, invalid=762
0112: dt=32.368000, rms=0.635 (0.014%), neg=0, invalid=762
0113: dt=32.368000, rms=0.635 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.635, neg=0, invalid=762
0114: dt=55.488000, rms=0.635 (0.074%), neg=0, invalid=762
0115: dt=92.480000, rms=0.635 (0.017%), neg=0, invalid=762
0116: dt=92.480000, rms=0.635 (0.032%), neg=0, invalid=762
0117: dt=92.480000, rms=0.634 (0.043%), neg=0, invalid=762
0118: dt=92.480000, rms=0.634 (0.052%), neg=0, invalid=762
0119: dt=92.480000, rms=0.634 (0.058%), neg=0, invalid=762
0120: dt=92.480000, rms=0.633 (0.068%), neg=0, invalid=762
0121: dt=92.480000, rms=0.633 (0.063%), neg=0, invalid=762
0122: dt=92.480000, rms=0.633 (0.053%), neg=0, invalid=762
0123: dt=92.480000, rms=0.632 (0.046%), neg=0, invalid=762
0124: dt=92.480000, rms=0.632 (0.055%), neg=0, invalid=762
0125: dt=92.480000, rms=0.631 (0.070%), neg=0, invalid=762
0126: dt=92.480000, rms=0.631 (0.090%), neg=0, invalid=762
0127: dt=92.480000, rms=0.630 (0.096%), neg=0, invalid=762
0128: dt=92.480000, rms=0.630 (0.083%), neg=0, invalid=762
0129: dt=92.480000, rms=0.629 (0.066%), neg=0, invalid=762
0130: dt=92.480000, rms=0.629 (0.047%), neg=0, invalid=762
0131: dt=92.480000, rms=0.629 (0.039%), neg=0, invalid=762
0132: dt=92.480000, rms=0.628 (0.044%), neg=0, invalid=762
0133: dt=92.480000, rms=0.628 (0.049%), neg=0, invalid=762
0134: dt=92.480000, rms=0.628 (0.050%), neg=0, invalid=762
0135: dt=92.480000, rms=0.628 (0.050%), neg=0, invalid=762
0136: dt=92.480000, rms=0.627 (0.045%), neg=0, invalid=762
0137: dt=92.480000, rms=0.627 (0.043%), neg=0, invalid=762
0138: dt=92.480000, rms=0.627 (0.046%), neg=0, invalid=762
0139: dt=92.480000, rms=0.626 (0.053%), neg=0, invalid=762
0140: dt=92.480000, rms=0.626 (0.056%), neg=0, invalid=762
0141: dt=92.480000, rms=0.626 (0.055%), neg=0, invalid=762
0142: dt=92.480000, rms=0.625 (0.044%), neg=0, invalid=762
0143: dt=92.480000, rms=0.625 (0.040%), neg=0, invalid=762
0144: dt=92.480000, rms=0.625 (0.038%), neg=0, invalid=762
0145: dt=92.480000, rms=0.625 (0.037%), neg=0, invalid=762
0146: dt=92.480000, rms=0.624 (0.037%), neg=0, invalid=762
0147: dt=92.480000, rms=0.624 (0.037%), neg=0, invalid=762
0148: dt=92.480000, rms=0.624 (0.036%), neg=0, invalid=762
0149: dt=92.480000, rms=0.624 (0.033%), neg=0, invalid=762
0150: dt=92.480000, rms=0.624 (0.034%), neg=0, invalid=762
0151: dt=92.480000, rms=0.623 (0.038%), neg=0, invalid=762
0152: dt=92.480000, rms=0.623 (0.037%), neg=0, invalid=762
0153: dt=92.480000, rms=0.623 (0.032%), neg=0, invalid=762
0154: dt=92.480000, rms=0.623 (0.030%), neg=0, invalid=762
0155: dt=92.480000, rms=0.623 (0.029%), neg=0, invalid=762
0156: dt=92.480000, rms=0.622 (0.032%), neg=0, invalid=762
0157: dt=92.480000, rms=0.622 (0.033%), neg=0, invalid=762
0158: dt=92.480000, rms=0.622 (0.031%), neg=0, invalid=762
0159: dt=92.480000, rms=0.622 (0.026%), neg=0, invalid=762
0160: dt=92.480000, rms=0.622 (0.024%), neg=0, invalid=762
0161: dt=92.480000, rms=0.622 (0.020%), neg=0, invalid=762
0162: dt=2071.552000, rms=0.621 (0.044%), neg=0, invalid=762
0163: dt=23.120000, rms=0.621 (-0.006%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.622, neg=0, invalid=762
0164: dt=160.603774, rms=0.616 (0.939%), neg=0, invalid=762
0165: dt=129.665944, rms=0.609 (1.128%), neg=0, invalid=762
0166: dt=76.000000, rms=0.606 (0.464%), neg=0, invalid=762
0167: dt=92.790831, rms=0.603 (0.504%), neg=0, invalid=762
0168: dt=68.491228, rms=0.601 (0.356%), neg=0, invalid=762
0169: dt=124.416000, rms=0.599 (0.414%), neg=0, invalid=762
0170: dt=36.288000, rms=0.597 (0.276%), neg=0, invalid=762
0171: dt=580.608000, rms=0.591 (1.069%), neg=0, invalid=762
0172: dt=55.560440, rms=0.587 (0.658%), neg=0, invalid=762
0173: dt=103.680000, rms=0.586 (0.178%), neg=0, invalid=762
0174: dt=69.019608, rms=0.585 (0.176%), neg=0, invalid=762
0175: dt=103.680000, rms=0.584 (0.147%), neg=0, invalid=762
0176: dt=72.186047, rms=0.583 (0.158%), neg=0, invalid=762
0177: dt=103.680000, rms=0.582 (0.127%), neg=0, invalid=762
0178: dt=65.422222, rms=0.581 (0.152%), neg=0, invalid=762
0179: dt=103.680000, rms=0.581 (0.116%), neg=0, invalid=762
0180: dt=82.944000, rms=0.580 (0.131%), neg=0, invalid=762
0181: dt=62.208000, rms=0.579 (0.100%), neg=0, invalid=762
0182: dt=145.152000, rms=0.578 (0.158%), neg=0, invalid=762
0183: dt=36.288000, rms=0.578 (0.087%), neg=0, invalid=762
0184: dt=580.608000, rms=0.575 (0.530%), neg=0, invalid=762
0185: dt=36.288000, rms=0.574 (0.181%), neg=0, invalid=762
0186: dt=331.776000, rms=0.573 (0.163%), neg=0, invalid=762
0187: dt=36.288000, rms=0.572 (0.147%), neg=0, invalid=762
0188: dt=145.152000, rms=0.571 (0.095%), neg=0, invalid=762
0189: dt=82.944000, rms=0.571 (0.080%), neg=0, invalid=762
0190: dt=62.208000, rms=0.571 (0.046%), neg=0, invalid=762
0191: dt=62.208000, rms=0.570 (0.052%), neg=0, invalid=762
0192: dt=62.208000, rms=0.570 (0.078%), neg=0, invalid=762
0193: dt=62.208000, rms=0.569 (0.110%), neg=0, invalid=762
0194: dt=62.208000, rms=0.569 (0.138%), neg=0, invalid=762
0195: dt=62.208000, rms=0.568 (0.168%), neg=0, invalid=762
0196: dt=62.208000, rms=0.567 (0.176%), neg=0, invalid=762
0197: dt=62.208000, rms=0.566 (0.186%), neg=0, invalid=762
0198: dt=62.208000, rms=0.565 (0.186%), neg=0, invalid=762
0199: dt=62.208000, rms=0.564 (0.166%), neg=0, invalid=762
0200: dt=62.208000, rms=0.563 (0.162%), neg=0, invalid=762
0201: dt=62.208000, rms=0.562 (0.165%), neg=0, invalid=762
0202: dt=62.208000, rms=0.561 (0.173%), neg=0, invalid=762
0203: dt=62.208000, rms=0.560 (0.156%), neg=0, invalid=762
0204: dt=62.208000, rms=0.560 (0.021%), neg=0, invalid=762
0205: dt=62.208000, rms=0.560 (0.028%), neg=0, invalid=762
0206: dt=62.208000, rms=0.559 (0.044%), neg=0, invalid=762
0207: dt=62.208000, rms=0.559 (0.051%), neg=0, invalid=762
0208: dt=62.208000, rms=0.559 (0.059%), neg=0, invalid=762
0209: dt=62.208000, rms=0.558 (0.061%), neg=0, invalid=762
0210: dt=62.208000, rms=0.558 (0.076%), neg=0, invalid=762
0211: dt=62.208000, rms=0.558 (0.080%), neg=0, invalid=762
0212: dt=62.208000, rms=0.557 (0.091%), neg=0, invalid=762
0213: dt=31.104000, rms=0.557 (0.008%), neg=0, invalid=762
0214: dt=31.104000, rms=0.557 (0.008%), neg=0, invalid=762
0215: dt=1.944000, rms=0.557 (0.000%), neg=0, invalid=762
0216: dt=0.015187, rms=0.557 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.557, neg=0, invalid=762
0217: dt=103.680000, rms=0.556 (0.317%), neg=0, invalid=762
0218: dt=145.152000, rms=0.554 (0.236%), neg=0, invalid=762
0219: dt=36.288000, rms=0.554 (0.074%), neg=0, invalid=762
0220: dt=103.680000, rms=0.554 (0.034%), neg=0, invalid=762
0221: dt=103.680000, rms=0.553 (0.117%), neg=0, invalid=762
0222: dt=103.680000, rms=0.553 (0.111%), neg=0, invalid=762
0223: dt=103.680000, rms=0.552 (0.076%), neg=0, invalid=762
0224: dt=103.680000, rms=0.551 (0.143%), neg=0, invalid=762
0225: dt=103.680000, rms=0.551 (0.136%), neg=0, invalid=762
0226: dt=103.680000, rms=0.550 (0.103%), neg=0, invalid=762
0227: dt=103.680000, rms=0.549 (0.109%), neg=0, invalid=762
0228: dt=103.680000, rms=0.549 (0.133%), neg=0, invalid=762
0229: dt=103.680000, rms=0.548 (0.142%), neg=0, invalid=762
0230: dt=103.680000, rms=0.547 (0.121%), neg=0, invalid=762
0231: dt=103.680000, rms=0.547 (0.127%), neg=0, invalid=762
0232: dt=103.680000, rms=0.546 (0.129%), neg=0, invalid=762
0233: dt=103.680000, rms=0.545 (0.109%), neg=0, invalid=762
0234: dt=103.680000, rms=0.545 (0.105%), neg=0, invalid=762
0235: dt=103.680000, rms=0.544 (0.097%), neg=0, invalid=762
0236: dt=103.680000, rms=0.544 (0.096%), neg=0, invalid=762
0237: dt=103.680000, rms=0.543 (0.087%), neg=0, invalid=762
0238: dt=103.680000, rms=0.543 (0.071%), neg=0, invalid=762
0239: dt=103.680000, rms=0.542 (0.089%), neg=0, invalid=762
0240: dt=103.680000, rms=0.542 (0.085%), neg=0, invalid=762
0241: dt=103.680000, rms=0.541 (0.085%), neg=0, invalid=762
0242: dt=103.680000, rms=0.541 (0.092%), neg=0, invalid=762
0243: dt=103.680000, rms=0.540 (0.108%), neg=0, invalid=762
0244: dt=103.680000, rms=0.540 (0.102%), neg=0, invalid=762
0245: dt=103.680000, rms=0.539 (0.081%), neg=0, invalid=762
0246: dt=103.680000, rms=0.539 (0.083%), neg=0, invalid=762
0247: dt=103.680000, rms=0.538 (0.074%), neg=0, invalid=762
0248: dt=103.680000, rms=0.538 (0.072%), neg=0, invalid=762
0249: dt=103.680000, rms=0.538 (0.068%), neg=0, invalid=762
0250: dt=103.680000, rms=0.537 (0.068%), neg=0, invalid=762
0251: dt=103.680000, rms=0.537 (0.057%), neg=0, invalid=762
0252: dt=103.680000, rms=0.537 (0.046%), neg=0, invalid=762
0253: dt=103.680000, rms=0.537 (0.036%), neg=0, invalid=762
0254: dt=103.680000, rms=0.536 (0.049%), neg=0, invalid=762
0255: dt=103.680000, rms=0.536 (0.065%), neg=0, invalid=762
0256: dt=103.680000, rms=0.536 (0.046%), neg=0, invalid=762
0257: dt=103.680000, rms=0.535 (0.042%), neg=0, invalid=762
0258: dt=103.680000, rms=0.535 (0.006%), neg=0, invalid=762
0259: dt=103.680000, rms=0.535 (0.001%), neg=0, invalid=762
0260: dt=36.288000, rms=0.535 (0.010%), neg=0, invalid=762
0261: dt=36.288000, rms=0.535 (0.002%), neg=0, invalid=762
0262: dt=36.288000, rms=0.535 (0.001%), neg=0, invalid=762
0263: dt=18.144000, rms=0.535 (0.004%), neg=0, invalid=762
0264: dt=18.144000, rms=0.535 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.545, neg=0, invalid=762
0265: dt=32.000000, rms=0.543 (0.362%), neg=0, invalid=762
0266: dt=90.612245, rms=0.539 (0.620%), neg=0, invalid=762
0267: dt=44.800000, rms=0.537 (0.392%), neg=0, invalid=762
0268: dt=32.000000, rms=0.535 (0.374%), neg=0, invalid=762
0269: dt=32.000000, rms=0.534 (0.197%), neg=0, invalid=762
0270: dt=38.400000, rms=0.533 (0.241%), neg=0, invalid=762
0271: dt=25.600000, rms=0.532 (0.161%), neg=0, invalid=762
0272: dt=44.800000, rms=0.531 (0.225%), neg=0, invalid=762
0273: dt=25.600000, rms=0.530 (0.141%), neg=0, invalid=762
0274: dt=44.800000, rms=0.529 (0.205%), neg=0, invalid=762
0275: dt=25.600000, rms=0.528 (0.118%), neg=0, invalid=762
0276: dt=32.000000, rms=0.527 (0.149%), neg=0, invalid=762
0277: dt=8.000000, rms=0.527 (0.037%), neg=0, invalid=762
0278: dt=0.125000, rms=0.527 (0.002%), neg=0, invalid=762
0279: dt=0.031250, rms=0.527 (0.000%), neg=0, invalid=762
0280: dt=0.000977, rms=0.527 (0.000%), neg=0, invalid=762
0281: dt=0.000684, rms=0.527 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0282: dt=44.800000, rms=0.525 (0.519%), neg=0, invalid=762
0283: dt=44.800000, rms=0.523 (0.292%), neg=0, invalid=762
0284: dt=38.400000, rms=0.523 (0.104%), neg=0, invalid=762
0285: dt=44.800000, rms=0.522 (0.183%), neg=0, invalid=762
0286: dt=25.600000, rms=0.521 (0.087%), neg=0, invalid=762
0287: dt=76.800000, rms=0.521 (0.182%), neg=0, invalid=762
0288: dt=24.436364, rms=0.520 (0.109%), neg=0, invalid=762
0289: dt=44.800000, rms=0.519 (0.133%), neg=0, invalid=762
0290: dt=32.000000, rms=0.519 (0.077%), neg=0, invalid=762
0291: dt=38.400000, rms=0.518 (0.092%), neg=0, invalid=762
0292: dt=25.600000, rms=0.518 (0.058%), neg=0, invalid=762
0293: dt=44.800000, rms=0.518 (0.102%), neg=0, invalid=762
0294: dt=25.600000, rms=0.517 (0.043%), neg=0, invalid=762
0295: dt=25.600000, rms=0.517 (0.078%), neg=0, invalid=762
0296: dt=25.600000, rms=0.516 (0.095%), neg=0, invalid=762
0297: dt=25.600000, rms=0.516 (0.134%), neg=0, invalid=762
0298: dt=25.600000, rms=0.515 (0.152%), neg=0, invalid=762
0299: dt=25.600000, rms=0.514 (0.184%), neg=0, invalid=762
0300: dt=25.600000, rms=0.513 (0.187%), neg=0, invalid=762
0301: dt=25.600000, rms=0.512 (0.187%), neg=0, invalid=762
0302: dt=25.600000, rms=0.511 (0.184%), neg=0, invalid=762
0303: dt=25.600000, rms=0.510 (0.189%), neg=0, invalid=762
0304: dt=25.600000, rms=0.509 (0.183%), neg=0, invalid=762
0305: dt=25.600000, rms=0.508 (0.180%), neg=0, invalid=762
0306: dt=25.600000, rms=0.508 (0.037%), neg=0, invalid=762
0307: dt=25.600000, rms=0.508 (0.034%), neg=0, invalid=762
0308: dt=25.600000, rms=0.508 (0.040%), neg=0, invalid=762
0309: dt=25.600000, rms=0.508 (0.043%), neg=0, invalid=762
0310: dt=12.800000, rms=0.507 (0.011%), neg=0, invalid=762
0311: dt=3.200000, rms=0.507 (0.002%), neg=0, invalid=762
0312: dt=2.800000, rms=0.507 (0.002%), neg=0, invalid=762
0313: dt=0.350000, rms=0.507 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.526, neg=0, invalid=762
0314: dt=0.000000, rms=0.525 (0.084%), neg=0, invalid=762
0315: dt=0.000000, rms=0.525 (0.000%), neg=0, invalid=762
0316: dt=0.150000, rms=0.525 (-0.014%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.526, neg=0, invalid=762
0317: dt=0.000000, rms=0.525 (0.084%), neg=0, invalid=762
0318: dt=0.000000, rms=0.525 (0.000%), neg=0, invalid=762
0319: dt=0.150000, rms=0.525 (-0.016%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.562, neg=0, invalid=762
0320: dt=1.024000, rms=0.560 (0.367%), neg=0, invalid=762
0321: dt=0.112000, rms=0.560 (0.007%), neg=0, invalid=762
0322: dt=0.112000, rms=0.560 (0.002%), neg=0, invalid=762
0323: dt=0.112000, rms=0.560 (-0.008%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.560, neg=0, invalid=762
0324: dt=0.448000, rms=0.559 (0.145%), neg=0, invalid=762
0325: dt=0.384000, rms=0.559 (0.021%), neg=0, invalid=762
0326: dt=0.384000, rms=0.559 (-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=0.515, neg=0, invalid=762
0327: dt=0.448000, rms=0.501 (2.543%), neg=0, invalid=762
0328: dt=0.448000, rms=0.499 (0.557%), neg=0, invalid=762
0329: dt=0.448000, rms=0.497 (0.336%), neg=0, invalid=762
0330: dt=0.448000, rms=0.496 (0.203%), neg=0, invalid=762
0331: dt=0.458333, rms=0.495 (0.153%), neg=0, invalid=762
0332: dt=0.448000, rms=0.495 (0.109%), neg=0, invalid=762
0333: dt=0.448000, rms=0.494 (0.088%), neg=0, invalid=762
0334: dt=0.448000, rms=0.494 (0.070%), neg=0, invalid=762
0335: dt=0.448000, rms=0.494 (0.057%), neg=0, invalid=762
0336: dt=0.448000, rms=0.493 (0.046%), neg=0, invalid=762
0337: dt=0.448000, rms=0.493 (0.040%), neg=0, invalid=762
0338: dt=0.448000, rms=0.493 (0.068%), neg=0, invalid=762
0339: dt=0.448000, rms=0.493 (0.026%), neg=0, invalid=762
0340: dt=0.448000, rms=0.492 (0.043%), neg=0, invalid=762
0341: dt=0.448000, rms=0.492 (0.018%), neg=0, invalid=762
0342: dt=0.448000, rms=0.492 (0.026%), neg=0, invalid=762
0343: dt=0.448000, rms=0.492 (0.038%), neg=0, invalid=762
0344: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762
0345: dt=0.448000, rms=0.492 (-0.001%), neg=0, invalid=762
0346: dt=0.256000, rms=0.492 (0.003%), neg=0, invalid=762
0347: dt=0.448000, rms=0.492 (0.008%), neg=0, invalid=762
0348: dt=0.256000, rms=0.492 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
0349: dt=0.384000, rms=0.487 (1.051%), neg=0, invalid=762
0350: dt=0.448000, rms=0.486 (0.292%), neg=0, invalid=762
0351: dt=0.448000, rms=0.485 (0.054%), neg=0, invalid=762
0352: dt=0.448000, rms=0.485 (0.022%), neg=0, invalid=762
0353: dt=0.448000, rms=0.485 (0.005%), neg=0, invalid=762
0354: dt=0.448000, rms=0.485 (0.007%), neg=0, invalid=762
0355: dt=0.448000, rms=0.485 (-0.009%), 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=0.484, neg=0, invalid=762
0356: dt=-0.009615, rms=0.483 (0.098%), neg=0, invalid=762
0357: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
0358: dt=0.000000, rms=0.483 (0.098%), neg=0, invalid=762
0359: dt=0.000000, rms=0.483 (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=0.484, neg=0, invalid=762
0360: dt=31.104000, rms=0.483 (0.154%), neg=0, invalid=762
0361: dt=20.736000, rms=0.483 (0.010%), neg=0, invalid=762
0362: dt=20.736000, rms=0.483 (0.004%), neg=0, invalid=762
0363: dt=20.736000, rms=0.483 (-0.024%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0364: dt=75.392670, rms=0.482 (0.333%), neg=0, invalid=762
0365: dt=80.372093, rms=0.481 (0.232%), neg=0, invalid=762
0366: dt=80.372093, rms=0.481 (-0.179%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.481, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0367: dt=30.997389, rms=0.478 (0.669%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0368: dt=38.400000, rms=0.476 (0.314%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0369: dt=23.787611, rms=0.476 (0.111%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0370: dt=23.787611, rms=0.475 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0371: dt=23.787611, rms=0.475 (0.071%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0372: dt=23.787611, rms=0.475 (0.039%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0373: dt=44.800000, rms=0.474 (0.088%), neg=0, invalid=762
0374: dt=11.200000, rms=0.474 (0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.475, neg=0, invalid=762
0375: dt=53.807407, rms=0.469 (1.206%), neg=0, invalid=762
0376: dt=30.537143, rms=0.467 (0.488%), neg=0, invalid=762
0377: dt=25.600000, rms=0.466 (0.206%), neg=0, invalid=762
0378: dt=25.600000, rms=0.465 (0.183%), neg=0, invalid=762
0379: dt=25.600000, rms=0.464 (0.216%), neg=0, invalid=762
0380: dt=25.600000, rms=0.463 (0.203%), neg=0, invalid=762
0381: dt=25.600000, rms=0.462 (0.177%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0382: dt=25.600000, rms=0.461 (0.180%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0383: dt=25.600000, rms=0.460 (0.153%), neg=0, invalid=762
0384: dt=25.600000, rms=0.460 (0.138%), neg=0, invalid=762
0385: dt=25.600000, rms=0.459 (0.165%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0386: dt=25.600000, rms=0.458 (0.162%), neg=0, invalid=762
0387: dt=25.600000, rms=0.458 (0.171%), neg=0, invalid=762
0388: dt=25.600000, rms=0.457 (0.139%), neg=0, invalid=762
0389: dt=25.600000, rms=0.456 (0.136%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0390: dt=25.600000, rms=0.456 (0.117%), neg=0, invalid=762
0391: dt=25.600000, rms=0.455 (0.092%), neg=0, invalid=762
0392: dt=19.200000, rms=0.455 (0.031%), neg=0, invalid=762
0393: dt=19.200000, rms=0.455 (0.014%), neg=0, invalid=762
0394: dt=19.200000, rms=0.455 (0.013%), neg=0, invalid=762
0395: dt=19.200000, rms=0.455 (0.015%), neg=0, invalid=762
0396: dt=19.200000, rms=0.455 (0.009%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0397: dt=0.000141, rms=0.459 (0.104%), neg=0, invalid=762
0398: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0399: dt=1.008000, rms=0.459 (0.107%), neg=0, invalid=762
0400: dt=0.576000, rms=0.459 (0.002%), neg=0, invalid=762
0401: dt=0.576000, rms=0.459 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.468, neg=0, invalid=762
0402: dt=0.448000, rms=0.467 (0.158%), neg=0, invalid=762
0403: dt=0.384000, rms=0.467 (0.015%), neg=0, invalid=762
0404: dt=0.384000, rms=0.467 (-0.011%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.467, neg=0, invalid=762
0405: dt=1.536000, rms=0.466 (0.315%), neg=0, invalid=762
0406: dt=0.768000, rms=0.466 (0.024%), neg=0, invalid=762
0407: dt=0.768000, rms=0.466 (-0.003%), 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=0.459, neg=0, invalid=762
iter 0, gcam->neg = 521
after 12 iterations, nbhd size=1, neg = 0
0408: dt=2.000000, rms=0.434 (5.363%), neg=0, invalid=762
0409: dt=0.028000, rms=0.434 (0.026%), neg=0, invalid=762
0410: dt=0.028000, rms=0.434 (0.001%), neg=0, invalid=762
0411: dt=0.028000, rms=0.434 (-0.030%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.435, neg=0, invalid=762
0412: dt=0.096000, rms=0.434 (0.198%), neg=0, invalid=762
0413: dt=0.006000, rms=0.434 (-0.001%), 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=0.422, neg=0, invalid=762
0414: dt=2.023000, rms=0.422 (0.000%), neg=0, invalid=762
0415: dt=0.090313, rms=0.422 (0.000%), neg=0, invalid=762
0416: dt=0.090313, 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
0417: dt=23.120000, rms=0.422 (0.001%), neg=0, invalid=762
0418: dt=6.936000, rms=0.422 (0.000%), neg=0, invalid=762
0419: dt=6.936000, rms=0.422 (-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=0.422, neg=0, invalid=762
0420: 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
0421: dt=36.288000, rms=0.422 (0.020%), neg=0, invalid=762
0422: dt=82.944000, rms=0.422 (0.017%), neg=0, invalid=762
0423: dt=82.944000, rms=0.422 (0.024%), neg=0, invalid=762
0424: dt=82.944000, rms=0.422 (0.021%), neg=0, invalid=762
0425: dt=82.944000, rms=0.422 (0.007%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
0426: dt=2.800000, rms=0.422 (0.013%), neg=0, invalid=762
0427: dt=2.400000, rms=0.422 (0.004%), neg=0, invalid=762
0428: dt=2.400000, rms=0.422 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0429: dt=102.400000, rms=0.420 (0.601%), neg=0, invalid=762
0430: dt=20.817204, rms=0.419 (0.165%), neg=0, invalid=762
0431: dt=20.817204, rms=0.419 (0.055%), neg=0, invalid=762
0432: dt=20.817204, rms=0.419 (0.062%), neg=0, invalid=762
0433: dt=20.817204, rms=0.418 (0.091%), neg=0, invalid=762
0434: dt=20.817204, rms=0.418 (0.109%), neg=0, invalid=762
0435: dt=20.817204, rms=0.417 (0.136%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0436: dt=20.817204, rms=0.417 (0.128%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0437: dt=20.817204, rms=0.416 (0.104%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0438: dt=20.817204, rms=0.416 (0.094%), neg=0, invalid=762
0439: dt=44.800000, rms=0.416 (0.017%), neg=0, invalid=762
0440: dt=44.800000, rms=0.416 (0.020%), neg=0, invalid=762
0441: dt=44.800000, rms=0.416 (0.037%), neg=0, invalid=762
0442: dt=44.800000, rms=0.415 (0.048%), neg=0, invalid=762
0443: dt=44.800000, rms=0.415 (0.046%), neg=0, invalid=762
0444: dt=44.800000, rms=0.415 (0.060%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0445: dt=44.800000, rms=0.415 (0.068%), neg=0, invalid=762
0446: dt=44.800000, rms=0.414 (0.068%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0447: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0448: dt=6.800000, rms=0.417 (0.056%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0449: dt=12.750000, rms=0.417 (0.064%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 11 iterations, nbhd size=1, neg = 0
0450: dt=49.116279, rms=0.416 (0.257%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0451: dt=20.645161, rms=0.415 (0.178%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 11 iterations, nbhd size=1, neg = 0
0452: dt=20.645161, rms=0.415 (-0.124%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0453: dt=0.000050, rms=0.420 (0.000%), neg=0, invalid=762
0454: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0455: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.412, neg=0, invalid=762
iter 0, gcam->neg = 402
after 15 iterations, nbhd size=1, neg = 0
0456: dt=1.280000, rms=0.404 (2.032%), neg=0, invalid=762
0457: dt=0.000023, rms=0.404 (0.000%), neg=0, invalid=762
0458: dt=0.000023, rms=0.404 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.404, neg=0, invalid=762
0459: dt=0.112000, rms=0.403 (0.126%), neg=0, invalid=762
0460: dt=0.112000, rms=0.403 (0.066%), neg=0, invalid=762
0461: dt=0.112000, rms=0.403 (0.047%), neg=0, invalid=762
0462: dt=0.112000, rms=0.403 (0.017%), neg=0, invalid=762
0463: dt=0.112000, rms=0.403 (-0.063%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 17 minutes and 4 seconds.
mri_ca_register utimesec    9062.624271
mri_ca_register stimesec    10.716370
mri_ca_register ru_maxrss   1348772
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4691929
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63720
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    8322
mri_ca_register ru_nivcsw   35807
FSRUNTIME@ mri_ca_register  2.2843 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 20:01:28 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-553
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-6.0.0/0051348/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.83
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 = 0.09618 (23)
Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (2614 voxels, overlap=0.944)
Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (2614 voxels, peak = 24), gca=24.5
gca peak = 0.17677 (13)
mri peak = 0.11519 (25)
Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (2414 voxels, overlap=0.414)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2414 voxels, peak = 23), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.09058 (93)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (543 voxels, overlap=1.013)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (543 voxels, peak = 92), gca=91.7
gca peak = 0.16930 (96)
mri peak = 0.10084 (92)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (476 voxels, overlap=1.014)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (476 voxels, peak = 93), gca=92.6
gca peak = 0.24553 (55)
mri peak = 0.09346 (67)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (687 voxels, overlap=0.164)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (687 voxels, peak = 66), gca=66.3
gca peak = 0.30264 (59)
mri peak = 0.08206 (67)
Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (715 voxels, overlap=0.437)
Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (715 voxels, peak = 69), gca=69.3
gca peak = 0.07580 (103)
mri peak = 0.07576 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27031 voxels, overlap=0.784)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27031 voxels, peak = 106), gca=105.6
gca peak = 0.07714 (104)
mri peak = 0.08048 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28977 voxels, overlap=0.704)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28977 voxels, peak = 107), gca=106.6
gca peak = 0.09712 (58)
mri peak = 0.05035 (69)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (27068 voxels, overlap=0.357)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (27068 voxels, peak = 69), gca=68.7
gca peak = 0.11620 (58)
mri peak = 0.04936 (69)
Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (27048 voxels, overlap=0.321)
Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (27048 voxels, peak = 69), gca=68.7
gca peak = 0.30970 (66)
mri peak = 0.07407 (80)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (982 voxels, overlap=0.380)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (982 voxels, peak = 76), gca=75.6
gca peak = 0.15280 (69)
mri peak = 0.07643 (76)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (942 voxels, overlap=1.006)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (942 voxels, peak = 71), gca=70.7
gca peak = 0.13902 (56)
mri peak = 0.06089 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (27656 voxels, overlap=0.608)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (27656 voxels, peak = 65), gca=64.7
gca peak = 0.14777 (55)
mri peak = 0.05835 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (30163 voxels, overlap=0.721)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (30163 voxels, peak = 64), gca=63.5
gca peak = 0.16765 (84)
mri peak = 0.07768 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4480 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4480 voxels, peak = 86), gca=86.1
gca peak = 0.18739 (84)
mri peak = 0.08056 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, peak = 84), gca=83.6
gca peak = 0.29869 (57)
mri peak = 0.10170 (70)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (349 voxels, overlap=0.216)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (349 voxels, peak = 68), gca=67.5
gca peak = 0.33601 (57)
mri peak = 0.07832 (67)
Right_Amygdala (54): linear fit = 1.16 x + 0.0 (357 voxels, overlap=0.561)
Right_Amygdala (54): linear fit = 1.16 x + 0.0 (357 voxels, peak = 66), gca=66.4
gca peak = 0.11131 (90)
mri peak = 0.06315 (84)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4166 voxels, overlap=0.997)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4166 voxels, peak = 88), gca=87.8
gca peak = 0.11793 (83)
mri peak = 0.05907 (83)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4116 voxels, overlap=0.921)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4116 voxels, peak = 88), gca=87.6
gca peak = 0.08324 (81)
mri peak = 0.07483 (80)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1522 voxels, overlap=0.758)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1522 voxels, peak = 85), gca=84.6
gca peak = 0.10360 (77)
mri peak = 0.06543 (82)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1821 voxels, overlap=0.810)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1821 voxels, peak = 81), gca=81.2
gca peak = 0.08424 (78)
mri peak = 0.08595 (84)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (8165 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (8165 voxels, peak = 83), gca=83.1
gca peak = 0.12631 (89)
mri peak = 0.07374 (89)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (881 voxels, overlap=0.807)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (881 voxels, peak = 91), gca=91.2
gca peak = 0.14500 (87)
mri peak = 0.07743 (89)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (928 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (928 voxels, peak = 88), gca=88.3
gca peak = 0.14975 (24)
mri peak = 0.07166 (19)
gca peak = 0.19357 (14)
mri peak = 0.09845 (22)
Fourth_Ventricle (15): linear fit = 1.52 x + 0.0 (578 voxels, overlap=0.735)
Fourth_Ventricle (15): linear fit = 1.52 x + 0.0 (578 voxels, peak = 21), gca=21.4
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 1.02 x + 0.0
estimating mean csf scale to be 1.36 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.13931 (25)
mri peak = 0.09618 (23)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2614 voxels, overlap=0.862)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2614 voxels, peak = 25), gca=25.4
gca peak = 0.13758 (19)
mri peak = 0.11519 (25)
Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (2414 voxels, overlap=0.742)
Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (2414 voxels, peak = 22), gca=21.6
gca peak = 0.26757 (90)
mri peak = 0.09058 (93)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (543 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (543 voxels, peak = 91), gca=91.3
gca peak = 0.18617 (93)
mri peak = 0.10084 (92)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (476 voxels, overlap=1.009)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (476 voxels, peak = 93), gca=92.5
gca peak = 0.27943 (67)
mri peak = 0.09346 (67)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (687 voxels, overlap=1.003)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (687 voxels, peak = 66), gca=66.0
gca peak = 0.29154 (66)
mri peak = 0.08206 (67)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (715 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (715 voxels, peak = 66), gca=66.0
gca peak = 0.07614 (105)
mri peak = 0.07576 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27031 voxels, overlap=0.864)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27031 voxels, peak = 104), gca=104.5
gca peak = 0.07686 (107)
mri peak = 0.08048 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28977 voxels, overlap=0.807)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28977 voxels, peak = 106), gca=106.5
gca peak = 0.08206 (69)
mri peak = 0.05035 (69)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27068 voxels, overlap=0.962)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27068 voxels, peak = 69), gca=69.0
gca peak = 0.09961 (69)
mri peak = 0.04936 (69)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (27048 voxels, overlap=0.956)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (27048 voxels, peak = 69), gca=69.0
gca peak = 0.24442 (76)
mri peak = 0.07407 (80)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (982 voxels, overlap=1.005)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (982 voxels, peak = 76), gca=76.0
gca peak = 0.15167 (70)
mri peak = 0.07643 (76)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (942 voxels, overlap=1.005)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (942 voxels, peak = 69), gca=69.0
gca peak = 0.12579 (65)
mri peak = 0.06089 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27656 voxels, overlap=0.995)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27656 voxels, peak = 65), gca=65.0
gca peak = 0.13049 (63)
mri peak = 0.05835 (64)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30163 voxels, overlap=0.990)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30163 voxels, peak = 62), gca=62.1
gca peak = 0.15819 (86)
mri peak = 0.07768 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4480 voxels, overlap=0.985)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4480 voxels, peak = 86), gca=85.6
gca peak = 0.15632 (83)
mri peak = 0.08056 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, overlap=0.980)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, peak = 83), gca=82.6
gca peak = 0.29148 (69)
mri peak = 0.10170 (70)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (349 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (349 voxels, peak = 69), gca=69.0
gca peak = 0.34643 (66)
mri peak = 0.07832 (67)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (357 voxels, overlap=1.015)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (357 voxels, peak = 66), gca=66.0
gca peak = 0.11483 (86)
mri peak = 0.06315 (84)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4166 voxels, overlap=0.973)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4166 voxels, peak = 87), gca=87.3
gca peak = 0.10619 (85)
mri peak = 0.05907 (83)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4116 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4116 voxels, peak = 83), gca=82.9
gca peak = 0.07460 (79)
mri peak = 0.07483 (80)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1522 voxels, overlap=0.884)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1522 voxels, peak = 79), gca=78.6
gca peak = 0.08162 (81)
mri peak = 0.06543 (82)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1821 voxels, overlap=0.957)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1821 voxels, peak = 81), gca=80.6
gca peak = 0.07275 (83)
mri peak = 0.08595 (84)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (8165 voxels, overlap=0.726)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (8165 voxels, peak = 84), gca=84.2
gca peak = 0.11391 (86)
mri peak = 0.07374 (89)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (881 voxels, overlap=0.831)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (881 voxels, peak = 84), gca=83.8
gca peak = 0.16107 (87)
mri peak = 0.07743 (89)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (928 voxels, overlap=0.933)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (928 voxels, peak = 87), gca=86.6
gca peak = 0.12335 (35)
mri peak = 0.07166 (19)
gca peak = 0.14598 (22)
mri peak = 0.09845 (22)
Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (578 voxels, overlap=0.835)
Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (578 voxels, peak = 25), gca=24.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.14952 (38)
gca peak Left_Thalamus = 0.64095 (104)
gca peak Third_Ventricle = 0.12335 (35)
gca peak CSF = 0.18746 (49)
gca peak Left_Accumbens_area = 0.73514 (64)
gca peak Left_undetermined = 0.96707 (28)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12577 (35)
gca peak Right_Inf_Lat_Vent = 0.24202 (28)
gca peak Right_Accumbens_area = 0.29837 (74)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14507 (37)
gca peak Fifth_Ventricle = 0.75707 (42)
gca peak WM_hypointensities = 0.07984 (78)
gca peak non_WM_hypointensities = 0.07502 (56)
gca peak Optic_Chiasm = 0.70948 (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 1.09 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
85735 voxels changed in iteration 0 of unlikely voxel relabeling
369 voxels changed in iteration 1 of unlikely voxel relabeling
11 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
61499 gm and wm labels changed (%34 to gray, %66 to white out of all changed labels)
454 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 85068 changed. image ll: -2.107, PF=0.500
pass 2: 20626 changed. image ll: -2.105, PF=0.500
pass 3: 5426 changed.
pass 4: 1722 changed.
48787 voxels changed in iteration 0 of unlikely voxel relabeling
481 voxels changed in iteration 1 of unlikely voxel relabeling
22 voxels changed in iteration 2 of unlikely voxel relabeling
2 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
8522 voxels changed in iteration 0 of unlikely voxel relabeling
177 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
6345 voxels changed in iteration 0 of unlikely voxel relabeling
71 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
4833 voxels changed in iteration 0 of unlikely voxel relabeling
23 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3762.974940
mri_ca_label stimesec    2.082683
mri_ca_label ru_maxrss   2093732
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   743105
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63712
mri_ca_label ru_oublock  488
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    351
mri_ca_label ru_nivcsw   7278
auto-labeling took 61 minutes and 56 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/cc_up.lta 0051348 

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-6.0.0/0051348/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/norm.mgz
97373 voxels in left wm, 102901 in right wm, xrange [115, 134]
searching rotation angles z=[ 2 16], y=[-9  5]

searching scale 1 Z rot 1.7  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.7  
searching scale 1 Z rot 6.9  
searching scale 1 Z rot 7.2  
searching scale 1 Z rot 7.4  
searching scale 1 Z rot 7.7  
searching scale 1 Z rot 7.9  
searching scale 1 Z rot 8.2  
searching scale 1 Z rot 8.4  
searching scale 1 Z rot 8.7  
searching scale 1 Z rot 8.9  
searching scale 1 Z rot 9.2  
searching scale 1 Z rot 9.4  
searching scale 1 Z rot 9.7  
searching scale 1 Z rot 9.9  
searching scale 1 Z rot 10.2  
searching scale 1 Z rot 10.4  
searching scale 1 Z rot 10.7  
searching scale 1 Z rot 10.9  
searching scale 1 Z rot 11.2  
searching scale 1 Z rot 11.4  
searching scale 1 Z rot 11.7  
searching scale 1 Z rot 11.9  
searching scale 1 Z rot 12.2  
searching scale 1 Z rot 12.4  
searching scale 1 Z rot 12.7  
searching scale 1 Z rot 12.9  
searching scale 1 Z rot 13.2  
searching scale 1 Z rot 13.4  
searching scale 1 Z rot 13.7  
searching scale 1 Z rot 13.9  
searching scale 1 Z rot 14.2  
searching scale 1 Z rot 14.4  
searching scale 1 Z rot 14.7  
searching scale 1 Z rot 14.9  
searching scale 1 Z rot 15.2  
searching scale 1 Z rot 15.4  global minimum found at slice 123.2, rotations (-2.01, 8.66)
final transformation (x=123.2, yr=-2.008, zr=8.656):
 0.98800  -0.15051  -0.03463   21.84634;
 0.15042   0.98861  -0.00527   35.97475;
 0.03503  -0.00000   0.99939  -0.24051;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 129
cc center is found at 129 75 124
eigenvectors:
-0.00218  -0.00035   1.00000;
 0.36356  -0.93157   0.00047;
 0.93157   0.36356   0.00216;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aseg.auto.mgz...
corpus callosum segmentation took 2.5 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 21:05:56 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 21:05:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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...
1791 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 107
gm peak at 73 (73), valley at 29 (29)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 71 (71), valley at 31 (31)
csf peak at 36, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 31 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 21:09:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1569126 voxels in mask (pct=  9.35)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 21:09:30 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): 103.9 +- 6.9 [79.0 --> 125.0]
GM (72.0) : 70.0 +- 9.3 [30.0 --> 95.0]
setting bottom of white matter range to 79.3
setting top of gray matter range to 88.5
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
21923 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5506 filled
610 bright non-wm voxels segmented.
9130 diagonally connected voxels added...
white matter segmentation took 1.7 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.55 minutes
reading wm segmentation from wm.seg.mgz...
622 voxels added to wm to prevent paths from MTL structures to cortex
3325 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 58961 voxels turned on, 26453 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  39 found -  39 modified     |    TOTAL:  39
pass   2 (xy+):   0 found -  39 modified     |    TOTAL:  39
pass   1 (xy-):  44 found -  44 modified     |    TOTAL:  83
pass   2 (xy-):   0 found -  44 modified     |    TOTAL:  83
pass   1 (yz+):  53 found -  53 modified     |    TOTAL: 136
pass   2 (yz+):   0 found -  53 modified     |    TOTAL: 136
pass   1 (yz-):  44 found -  44 modified     |    TOTAL: 180
pass   2 (yz-):   0 found -  44 modified     |    TOTAL: 180
pass   1 (xz+):  43 found -  43 modified     |    TOTAL: 223
pass   2 (xz+):   0 found -  43 modified     |    TOTAL: 223
pass   1 (xz-):  39 found -  39 modified     |    TOTAL: 262
pass   2 (xz-):   0 found -  39 modified     |    TOTAL: 262
Iteration Number : 1
pass   1 (+++):  66 found -  66 modified     |    TOTAL:  66
pass   2 (+++):   0 found -  66 modified     |    TOTAL:  66
pass   1 (+++): 104 found - 104 modified     |    TOTAL: 170
pass   2 (+++):   0 found - 104 modified     |    TOTAL: 170
pass   1 (+++):  73 found -  73 modified     |    TOTAL: 243
pass   2 (+++):   0 found -  73 modified     |    TOTAL: 243
pass   1 (+++):  61 found -  61 modified     |    TOTAL: 304
pass   2 (+++):   0 found -  61 modified     |    TOTAL: 304
Iteration Number : 1
pass   1 (++): 365 found - 365 modified     |    TOTAL: 365
pass   2 (++):   0 found - 365 modified     |    TOTAL: 365
pass   1 (+-): 349 found - 349 modified     |    TOTAL: 714
pass   2 (+-):   1 found - 350 modified     |    TOTAL: 715
pass   3 (+-):   0 found - 350 modified     |    TOTAL: 715
pass   1 (--): 261 found - 261 modified     |    TOTAL: 976
pass   2 (--):   0 found - 261 modified     |    TOTAL: 976
pass   1 (-+): 316 found - 316 modified     |    TOTAL: 1292
pass   2 (-+):   0 found - 316 modified     |    TOTAL: 1292
Iteration Number : 2
pass   1 (xy+):  32 found -  32 modified     |    TOTAL:  32
pass   2 (xy+):   0 found -  32 modified     |    TOTAL:  32
pass   1 (xy-):  23 found -  23 modified     |    TOTAL:  55
pass   2 (xy-):   0 found -  23 modified     |    TOTAL:  55
pass   1 (yz+):  32 found -  32 modified     |    TOTAL:  87
pass   2 (yz+):   0 found -  32 modified     |    TOTAL:  87
pass   1 (yz-):  38 found -  38 modified     |    TOTAL: 125
pass   2 (yz-):   0 found -  38 modified     |    TOTAL: 125
pass   1 (xz+):  40 found -  40 modified     |    TOTAL: 165
pass   2 (xz+):   0 found -  40 modified     |    TOTAL: 165
pass   1 (xz-):  42 found -  42 modified     |    TOTAL: 207
pass   2 (xz-):   0 found -  42 modified     |    TOTAL: 207
Iteration Number : 2
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  16
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  16
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  26
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  26
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  36
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  36
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  46
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  46
Iteration Number : 2
pass   1 (++):  18 found -  18 modified     |    TOTAL:  18
pass   2 (++):   0 found -  18 modified     |    TOTAL:  18
pass   1 (+-):  18 found -  18 modified     |    TOTAL:  36
pass   2 (+-):   0 found -  18 modified     |    TOTAL:  36
pass   1 (--):  10 found -  10 modified     |    TOTAL:  46
pass   2 (--):   0 found -  10 modified     |    TOTAL:  46
pass   1 (-+):  13 found -  13 modified     |    TOTAL:  59
pass   2 (-+):   0 found -  13 modified     |    TOTAL:  59
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz+):   7 found -   7 modified     |    TOTAL:  12
pass   2 (yz+):   0 found -   7 modified     |    TOTAL:  12
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  16
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  16
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  19
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  19
pass   1 (xz-):   8 found -   8 modified     |    TOTAL:  27
pass   2 (xz-):   0 found -   8 modified     |    TOTAL:  27
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 (++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+-):   4 found -   4 modified     |    TOTAL:   8
pass   2 (+-):   0 found -   4 modified     |    TOTAL:   8
pass   1 (--):   2 found -   2 modified     |    TOTAL:  10
pass   2 (--):   0 found -   2 modified     |    TOTAL:  10
pass   1 (-+):   5 found -   5 modified     |    TOTAL:  15
pass   2 (-+):   0 found -   5 modified     |    TOTAL:  15
Iteration Number : 4
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   5
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 = 2218 (out of 506982: 0.437491)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 21:11:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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
 1.10694  -0.11683  -0.05557   4.51487;
 0.09651   1.05813  -0.16529   24.88748;
 0.07125   0.15034   0.96326  -33.22720;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.10694  -0.11683  -0.05557   4.51487;
 0.09651   1.05813  -0.16529   24.88748;
 0.07125   0.15034   0.96326  -33.22720;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1888 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 108, 84), TAL = (1.0, -44.0, 20.0)
talairach voxel to voxel transform
 0.89135   0.08894   0.06669  -4.02203;
-0.08942   0.91365   0.15162  -17.29690;
-0.05197  -0.14918   1.00954   37.49169;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  108,  84) --> (1.0, -44.0, 20.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (1.00, -44.00, 20.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, -44.00, 20.00) SRC: (108.34, 84.37, 100.52)
search lh wm seed point around talairach space (-17.00, -44.00, 20.00), SRC: (140.43, 81.15, 98.65)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 21:12:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy-):   0 found -   7 modified     |    TOTAL:   7
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:  11
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:  11
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:  12
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:  12
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  15
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  15
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  17
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  17
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 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   5
pass   1 (--):   0 found -   0 modified     |    TOTAL:   5
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 23 (out of 249465: 0.009220)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 758 vertices, 835 faces
slice 50: 5212 vertices, 5403 faces
slice 60: 12128 vertices, 12392 faces
slice 70: 20621 vertices, 20953 faces
slice 80: 31026 vertices, 31414 faces
slice 90: 42561 vertices, 43001 faces
slice 100: 54980 vertices, 55528 faces
slice 110: 68985 vertices, 69548 faces
slice 120: 83680 vertices, 84282 faces
slice 130: 97696 vertices, 98335 faces
slice 140: 110287 vertices, 110917 faces
slice 150: 121039 vertices, 121639 faces
slice 160: 130249 vertices, 130870 faces
slice 170: 139387 vertices, 139994 faces
slice 180: 146447 vertices, 146976 faces
slice 190: 152290 vertices, 152829 faces
slice 200: 157246 vertices, 157700 faces
slice 210: 158764 vertices, 159108 faces
slice 220: 158764 vertices, 159108 faces
slice 230: 158764 vertices, 159108 faces
slice 240: 158764 vertices, 159108 faces
slice 250: 158764 vertices, 159108 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...
   158764 voxel in cpt #1: X=-344 [v=158764,e=477324,f=318216] located at (-22.184683, -10.576838, 45.570080)
For the whole surface: X=-344 [v=158764,e=477324,f=318216]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 21:12:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   9
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   2 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 = 12 (out of 243199: 0.004934)
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 50: 2070 vertices, 2233 faces
slice 60: 7445 vertices, 7668 faces
slice 70: 14539 vertices, 14800 faces
slice 80: 23078 vertices, 23457 faces
slice 90: 33633 vertices, 34067 faces
slice 100: 45557 vertices, 45994 faces
slice 110: 57848 vertices, 58340 faces
slice 120: 71660 vertices, 72211 faces
slice 130: 85280 vertices, 85855 faces
slice 140: 99795 vertices, 100465 faces
slice 150: 112081 vertices, 112657 faces
slice 160: 121869 vertices, 122374 faces
slice 170: 130685 vertices, 131226 faces
slice 180: 139306 vertices, 139795 faces
slice 190: 146471 vertices, 146965 faces
slice 200: 152245 vertices, 152670 faces
slice 210: 154026 vertices, 154320 faces
slice 220: 154026 vertices, 154320 faces
slice 230: 154026 vertices, 154320 faces
slice 240: 154026 vertices, 154320 faces
slice 250: 154026 vertices, 154320 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...
   154026 voxel in cpt #1: X=-294 [v=154026,e=462960,f=308640] located at (28.407425, -4.730974, 37.019054)
For the whole surface: X=-294 [v=154026,e=462960,f=308640]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 21:12:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 21:12:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

Waiting for PID 28760 of (28760 28763) to complete...
Waiting for PID 28763 of (28760 28763) 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 (28760 28763) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 21:12:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 21:12:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

Waiting for PID 28811 of (28811 28814) to complete...
Waiting for PID 28814 of (28811 28814) 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 = 47.9 mm, total surface area = 79608 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.179 (target=0.015)   
step 005: RMS=0.139 (target=0.015)   
step 010: RMS=0.113 (target=0.015)   
step 015: RMS=0.101 (target=0.015)   
step 020: RMS=0.093 (target=0.015)   
step 025: RMS=0.088 (target=0.015)   
step 030: RMS=0.083 (target=0.015)   
step 035: RMS=0.081 (target=0.015)   
step 040: RMS=0.079 (target=0.015)   
step 045: RMS=0.078 (target=0.015)   
step 050: RMS=0.076 (target=0.015)   
step 055: RMS=0.076 (target=0.015)   
step 060: RMS=0.075 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    49.802428
mris_inflate stimesec    0.116982
mris_inflate ru_maxrss   233884
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34391
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11200
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2053
mris_inflate ru_nivcsw   3496

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 46.7 mm, total surface area = 77385 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.177 (target=0.015)   
step 005: RMS=0.136 (target=0.015)   
step 010: RMS=0.111 (target=0.015)   
step 015: RMS=0.100 (target=0.015)   
step 020: RMS=0.094 (target=0.015)   
step 025: RMS=0.090 (target=0.015)   
step 030: RMS=0.086 (target=0.015)   
step 035: RMS=0.082 (target=0.015)   
step 040: RMS=0.078 (target=0.015)   
step 045: RMS=0.076 (target=0.015)   
step 050: RMS=0.075 (target=0.015)   
step 055: RMS=0.073 (target=0.015)   
step 060: RMS=0.072 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    48.837575
mris_inflate stimesec    0.112982
mris_inflate ru_maxrss   226636
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33089
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10848
mris_inflate ru_oublock  10864
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2310
mris_inflate ru_nivcsw   3540
PIDs (28811 28814) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 21:13:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 21:13:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

Waiting for PID 28866 of (28866 28870) to complete...
Waiting for PID 28870 of (28866 28870) 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 0.90 +- 0.60 (0.00-->7.90) (max @ vno 61838 --> 63181)
face area 0.02 +- 0.03 (-0.35-->0.53)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.292...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.239, avgs=0
005/300: dt: 0.9000, rms radial error=176.982, avgs=0
010/300: dt: 0.9000, rms radial error=176.432, avgs=0
015/300: dt: 0.9000, rms radial error=175.708, avgs=0
020/300: dt: 0.9000, rms radial error=174.883, avgs=0
025/300: dt: 0.9000, rms radial error=174.001, avgs=0
030/300: dt: 0.9000, rms radial error=173.087, avgs=0
035/300: dt: 0.9000, rms radial error=172.151, avgs=0
040/300: dt: 0.9000, rms radial error=171.207, avgs=0
045/300: dt: 0.9000, rms radial error=170.260, avgs=0
050/300: dt: 0.9000, rms radial error=169.313, avgs=0
055/300: dt: 0.9000, rms radial error=168.369, avgs=0
060/300: dt: 0.9000, rms radial error=167.427, avgs=0
065/300: dt: 0.9000, rms radial error=166.487, avgs=0
070/300: dt: 0.9000, rms radial error=165.551, avgs=0
075/300: dt: 0.9000, rms radial error=164.619, avgs=0
080/300: dt: 0.9000, rms radial error=163.693, avgs=0
085/300: dt: 0.9000, rms radial error=162.773, avgs=0
090/300: dt: 0.9000, rms radial error=161.858, avgs=0
095/300: dt: 0.9000, rms radial error=160.947, avgs=0
100/300: dt: 0.9000, rms radial error=160.042, avgs=0
105/300: dt: 0.9000, rms radial error=159.144, avgs=0
110/300: dt: 0.9000, rms radial error=158.250, avgs=0
115/300: dt: 0.9000, rms radial error=157.361, avgs=0
120/300: dt: 0.9000, rms radial error=156.476, avgs=0
125/300: dt: 0.9000, rms radial error=155.597, avgs=0
130/300: dt: 0.9000, rms radial error=154.722, avgs=0
135/300: dt: 0.9000, rms radial error=153.852, avgs=0
140/300: dt: 0.9000, rms radial error=152.987, avgs=0
145/300: dt: 0.9000, rms radial error=152.126, avgs=0
150/300: dt: 0.9000, rms radial error=151.270, avgs=0
155/300: dt: 0.9000, rms radial error=150.420, avgs=0
160/300: dt: 0.9000, rms radial error=149.574, avgs=0
165/300: dt: 0.9000, rms radial error=148.733, avgs=0
170/300: dt: 0.9000, rms radial error=147.896, avgs=0
175/300: dt: 0.9000, rms radial error=147.064, avgs=0
180/300: dt: 0.9000, rms radial error=146.236, avgs=0
185/300: dt: 0.9000, rms radial error=145.413, avgs=0
190/300: dt: 0.9000, rms radial error=144.595, avgs=0
195/300: dt: 0.9000, rms radial error=143.781, avgs=0
200/300: dt: 0.9000, rms radial error=142.971, avgs=0
205/300: dt: 0.9000, rms radial error=142.166, avgs=0
210/300: dt: 0.9000, rms radial error=141.365, avgs=0
215/300: dt: 0.9000, rms radial error=140.569, avgs=0
220/300: dt: 0.9000, rms radial error=139.777, avgs=0
225/300: dt: 0.9000, rms radial error=138.989, avgs=0
230/300: dt: 0.9000, rms radial error=138.206, avgs=0
235/300: dt: 0.9000, rms radial error=137.427, avgs=0
240/300: dt: 0.9000, rms radial error=136.653, avgs=0
245/300: dt: 0.9000, rms radial error=135.883, avgs=0
250/300: dt: 0.9000, rms radial error=135.118, avgs=0
255/300: dt: 0.9000, rms radial error=134.357, avgs=0
260/300: dt: 0.9000, rms radial error=133.600, avgs=0
265/300: dt: 0.9000, rms radial error=132.848, avgs=0
270/300: dt: 0.9000, rms radial error=132.100, avgs=0
275/300: dt: 0.9000, rms radial error=131.357, avgs=0
280/300: dt: 0.9000, rms radial error=130.617, avgs=0
285/300: dt: 0.9000, rms radial error=129.882, avgs=0
290/300: dt: 0.9000, rms radial error=129.151, avgs=0
295/300: dt: 0.9000, rms radial error=128.423, avgs=0
300/300: dt: 0.9000, rms radial error=127.700, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19177.71
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 3502.03
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
epoch 3 (K=160.0), pass 1, starting sse = 465.95
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00298
epoch 4 (K=640.0), pass 1, starting sse = 58.39
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00527
final distance error %30.63
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    285.245636
mris_sphere stimesec    0.257960
mris_sphere ru_maxrss   234084
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33928
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11184
mris_sphere ru_oublock  11224
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8273
mris_sphere ru_nivcsw   20221
FSRUNTIME@ mris_sphere  0.0789 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 0.92 +- 0.58 (0.00-->8.27) (max @ vno 50224 --> 50233)
face area 0.02 +- 0.03 (-0.15-->0.64)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.296...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.101, avgs=0
005/300: dt: 0.9000, rms radial error=176.843, avgs=0
010/300: dt: 0.9000, rms radial error=176.290, avgs=0
015/300: dt: 0.9000, rms radial error=175.562, avgs=0
020/300: dt: 0.9000, rms radial error=174.730, avgs=0
025/300: dt: 0.9000, rms radial error=173.840, avgs=0
030/300: dt: 0.9000, rms radial error=172.918, avgs=0
035/300: dt: 0.9000, rms radial error=171.980, avgs=0
040/300: dt: 0.9000, rms radial error=171.033, avgs=0
045/300: dt: 0.9000, rms radial error=170.084, avgs=0
050/300: dt: 0.9000, rms radial error=169.135, avgs=0
055/300: dt: 0.9000, rms radial error=168.188, avgs=0
060/300: dt: 0.9000, rms radial error=167.249, avgs=0
065/300: dt: 0.9000, rms radial error=166.315, avgs=0
070/300: dt: 0.9000, rms radial error=165.385, avgs=0
075/300: dt: 0.9000, rms radial error=164.459, avgs=0
080/300: dt: 0.9000, rms radial error=163.539, avgs=0
085/300: dt: 0.9000, rms radial error=162.624, avgs=0
090/300: dt: 0.9000, rms radial error=161.714, avgs=0
095/300: dt: 0.9000, rms radial error=160.809, avgs=0
100/300: dt: 0.9000, rms radial error=159.908, avgs=0
105/300: dt: 0.9000, rms radial error=159.013, avgs=0
110/300: dt: 0.9000, rms radial error=158.122, avgs=0
115/300: dt: 0.9000, rms radial error=157.236, avgs=0
120/300: dt: 0.9000, rms radial error=156.355, avgs=0
125/300: dt: 0.9000, rms radial error=155.478, avgs=0
130/300: dt: 0.9000, rms radial error=154.606, avgs=0
135/300: dt: 0.9000, rms radial error=153.739, avgs=0
140/300: dt: 0.9000, rms radial error=152.877, avgs=0
145/300: dt: 0.9000, rms radial error=152.019, avgs=0
150/300: dt: 0.9000, rms radial error=151.166, avgs=0
155/300: dt: 0.9000, rms radial error=150.317, avgs=0
160/300: dt: 0.9000, rms radial error=149.473, avgs=0
165/300: dt: 0.9000, rms radial error=148.634, avgs=0
170/300: dt: 0.9000, rms radial error=147.798, avgs=0
175/300: dt: 0.9000, rms radial error=146.968, avgs=0
180/300: dt: 0.9000, rms radial error=146.142, avgs=0
185/300: dt: 0.9000, rms radial error=145.320, avgs=0
190/300: dt: 0.9000, rms radial error=144.503, avgs=0
195/300: dt: 0.9000, rms radial error=143.691, avgs=0
200/300: dt: 0.9000, rms radial error=142.882, avgs=0
205/300: dt: 0.9000, rms radial error=142.079, avgs=0
210/300: dt: 0.9000, rms radial error=141.280, avgs=0
215/300: dt: 0.9000, rms radial error=140.485, avgs=0
220/300: dt: 0.9000, rms radial error=139.694, avgs=0
225/300: dt: 0.9000, rms radial error=138.908, avgs=0
230/300: dt: 0.9000, rms radial error=138.127, avgs=0
235/300: dt: 0.9000, rms radial error=137.349, avgs=0
240/300: dt: 0.9000, rms radial error=136.576, avgs=0
245/300: dt: 0.9000, rms radial error=135.807, avgs=0
250/300: dt: 0.9000, rms radial error=135.043, avgs=0
255/300: dt: 0.9000, rms radial error=134.283, avgs=0
260/300: dt: 0.9000, rms radial error=133.526, avgs=0
265/300: dt: 0.9000, rms radial error=132.775, avgs=0
270/300: dt: 0.9000, rms radial error=132.027, avgs=0
275/300: dt: 0.9000, rms radial error=131.283, avgs=0
280/300: dt: 0.9000, rms radial error=130.544, avgs=0
285/300: dt: 0.9000, rms radial error=129.809, avgs=0
290/300: dt: 0.9000, rms radial error=129.078, avgs=0
295/300: dt: 0.9000, rms radial error=128.351, avgs=0
300/300: dt: 0.9000, rms radial error=127.628, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18474.20
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 2 (K=40.0), pass 1, starting sse = 3281.54
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 3 (K=160.0), pass 1, starting sse = 410.60
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00396
epoch 4 (K=640.0), pass 1, starting sse = 44.98
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/12 = 0.00633
final distance error %28.42
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    280.674331
mris_sphere stimesec    0.157975
mris_sphere ru_maxrss   226836
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   32626
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10888
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8395
mris_sphere ru_nivcsw   19808
FSRUNTIME@ mris_sphere  0.0780 hours 1 threads
PIDs (28866 28870) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 21:18:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 21:18:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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


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

#@# Fix Topology lh Sat Oct  7 21:18:33 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 lh 

#@# Fix Topology rh Sat Oct  7 21:18:33 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 rh 

Waiting for PID 29128 of (29128 29131) to complete...
Waiting for PID 29131 of (29128 29131) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 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=-344 (nv=158764, nf=318216, ne=477324, g=173)
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...
28132 ambiguous faces found in tessellation
segmenting defects...
126 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 55 into 47
      -merging segment 69 into 64
      -merging segment 70 into 65
      -merging segment 79 into 76
      -merging segment 83 into 82
      -merging segment 104 into 111
120 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4356  (-4.7178)
      -vertex     loglikelihood: -6.2727  (-3.1363)
      -normal dot loglikelihood: -3.5893  (-3.5893)
      -quad curv  loglikelihood: -6.1361  (-3.0681)
      Total Loglikelihood : -25.4338

CORRECTING DEFECT 0 (vertices=183, convex hull=140, v0=280)
After retessellation of defect 0 (v0=280), euler #=-114 (142578,422848,280156) : difference with theory (-117) = -3 

CORRECTING DEFECT 1 (vertices=13, convex hull=21, v0=2532)
After retessellation of defect 1 (v0=2532), euler #=-113 (142579,422860,280168) : difference with theory (-116) = -3 

CORRECTING DEFECT 2 (vertices=31, convex hull=63, v0=4193)
After retessellation of defect 2 (v0=4193), euler #=-112 (142594,422930,280224) : difference with theory (-115) = -3 

CORRECTING DEFECT 3 (vertices=33, convex hull=62, v0=14515)
After retessellation of defect 3 (v0=14515), euler #=-111 (142615,423021,280295) : difference with theory (-114) = -3 

CORRECTING DEFECT 4 (vertices=37, convex hull=82, v0=14552)
After retessellation of defect 4 (v0=14552), euler #=-110 (142633,423110,280367) : difference with theory (-113) = -3 

CORRECTING DEFECT 5 (vertices=4678, convex hull=1805, v0=15315)
XL defect detected...
After retessellation of defect 5 (v0=15315), euler #=-110 (143285,426027,282632) : difference with theory (-112) = -2 

CORRECTING DEFECT 6 (vertices=41, convex hull=68, v0=16122)
After retessellation of defect 6 (v0=16122), euler #=-109 (143294,426080,282677) : difference with theory (-111) = -2 

CORRECTING DEFECT 7 (vertices=23, convex hull=31, v0=16738)
After retessellation of defect 7 (v0=16738), euler #=-108 (143297,426096,282691) : difference with theory (-110) = -2 

CORRECTING DEFECT 8 (vertices=54, convex hull=31, v0=16906)
After retessellation of defect 8 (v0=16906), euler #=-107 (143300,426113,282706) : difference with theory (-109) = -2 

CORRECTING DEFECT 9 (vertices=54, convex hull=42, v0=18343)
After retessellation of defect 9 (v0=18343), euler #=-106 (143306,426147,282735) : difference with theory (-108) = -2 

CORRECTING DEFECT 10 (vertices=24, convex hull=51, v0=22129)
After retessellation of defect 10 (v0=22129), euler #=-105 (143316,426193,282772) : difference with theory (-107) = -2 

CORRECTING DEFECT 11 (vertices=58, convex hull=55, v0=22488)
After retessellation of defect 11 (v0=22488), euler #=-104 (143331,426264,282829) : difference with theory (-106) = -2 

CORRECTING DEFECT 12 (vertices=20, convex hull=56, v0=22608)
After retessellation of defect 12 (v0=22608), euler #=-103 (143342,426316,282871) : difference with theory (-105) = -2 

CORRECTING DEFECT 13 (vertices=64, convex hull=90, v0=23346)
After retessellation of defect 13 (v0=23346), euler #=-102 (143383,426480,282995) : difference with theory (-104) = -2 

CORRECTING DEFECT 14 (vertices=48, convex hull=72, v0=28181)
After retessellation of defect 14 (v0=28181), euler #=-101 (143404,426572,283067) : difference with theory (-103) = -2 

CORRECTING DEFECT 15 (vertices=84, convex hull=119, v0=30544)
After retessellation of defect 15 (v0=30544), euler #=-100 (143451,426765,283214) : difference with theory (-102) = -2 

CORRECTING DEFECT 16 (vertices=10, convex hull=13, v0=32493)
After retessellation of defect 16 (v0=32493), euler #=-99 (143453,426773,283221) : difference with theory (-101) = -2 

CORRECTING DEFECT 17 (vertices=60, convex hull=100, v0=33251)
After retessellation of defect 17 (v0=33251), euler #=-98 (143484,426906,283324) : difference with theory (-100) = -2 

CORRECTING DEFECT 18 (vertices=42, convex hull=73, v0=36702)
After retessellation of defect 18 (v0=36702), euler #=-97 (143498,426979,283384) : difference with theory (-99) = -2 

CORRECTING DEFECT 19 (vertices=17, convex hull=18, v0=40244)
After retessellation of defect 19 (v0=40244), euler #=-96 (143500,426990,283394) : difference with theory (-98) = -2 

CORRECTING DEFECT 20 (vertices=6, convex hull=20, v0=40606)
After retessellation of defect 20 (v0=40606), euler #=-95 (143501,426999,283403) : difference with theory (-97) = -2 

CORRECTING DEFECT 21 (vertices=51, convex hull=85, v0=42209)
After retessellation of defect 21 (v0=42209), euler #=-94 (143510,427064,283460) : difference with theory (-96) = -2 

CORRECTING DEFECT 22 (vertices=41, convex hull=68, v0=43148)
After retessellation of defect 22 (v0=43148), euler #=-93 (143530,427149,283526) : difference with theory (-95) = -2 

CORRECTING DEFECT 23 (vertices=11, convex hull=21, v0=43808)
After retessellation of defect 23 (v0=43808), euler #=-92 (143531,427158,283535) : difference with theory (-94) = -2 

CORRECTING DEFECT 24 (vertices=72, convex hull=109, v0=43819)
After retessellation of defect 24 (v0=43819), euler #=-91 (143540,427233,283602) : difference with theory (-93) = -2 

CORRECTING DEFECT 25 (vertices=35, convex hull=46, v0=46369)
After retessellation of defect 25 (v0=46369), euler #=-90 (143546,427270,283634) : difference with theory (-92) = -2 

CORRECTING DEFECT 26 (vertices=63, convex hull=31, v0=46734)
After retessellation of defect 26 (v0=46734), euler #=-89 (143553,427302,283660) : difference with theory (-91) = -2 

CORRECTING DEFECT 27 (vertices=122, convex hull=193, v0=50700)
After retessellation of defect 27 (v0=50700), euler #=-88 (143565,427429,283776) : difference with theory (-90) = -2 

CORRECTING DEFECT 28 (vertices=156, convex hull=132, v0=50981)
After retessellation of defect 28 (v0=50981), euler #=-87 (143627,427667,283953) : difference with theory (-89) = -2 

CORRECTING DEFECT 29 (vertices=5, convex hull=21, v0=51623)
After retessellation of defect 29 (v0=51623), euler #=-86 (143628,427676,283962) : difference with theory (-88) = -2 

CORRECTING DEFECT 30 (vertices=86, convex hull=60, v0=54980)
After retessellation of defect 30 (v0=54980), euler #=-85 (143651,427771,284035) : difference with theory (-87) = -2 

CORRECTING DEFECT 31 (vertices=87, convex hull=84, v0=57266)
After retessellation of defect 31 (v0=57266), euler #=-84 (143670,427863,284109) : difference with theory (-86) = -2 

CORRECTING DEFECT 32 (vertices=35, convex hull=53, v0=58363)
After retessellation of defect 32 (v0=58363), euler #=-83 (143685,427929,284161) : difference with theory (-85) = -2 

CORRECTING DEFECT 33 (vertices=23, convex hull=54, v0=58941)
After retessellation of defect 33 (v0=58941), euler #=-82 (143697,427987,284208) : difference with theory (-84) = -2 

CORRECTING DEFECT 34 (vertices=154, convex hull=31, v0=59136)
After retessellation of defect 34 (v0=59136), euler #=-81 (143704,428017,284232) : difference with theory (-83) = -2 

CORRECTING DEFECT 35 (vertices=19, convex hull=34, v0=60479)
After retessellation of defect 35 (v0=60479), euler #=-80 (143708,428040,284252) : difference with theory (-82) = -2 

CORRECTING DEFECT 36 (vertices=30, convex hull=85, v0=61693)
After retessellation of defect 36 (v0=61693), euler #=-79 (143725,428122,284318) : difference with theory (-81) = -2 

CORRECTING DEFECT 37 (vertices=23, convex hull=49, v0=63274)
After retessellation of defect 37 (v0=63274), euler #=-78 (143734,428168,284356) : difference with theory (-80) = -2 

CORRECTING DEFECT 38 (vertices=35, convex hull=43, v0=68767)
After retessellation of defect 38 (v0=68767), euler #=-77 (143741,428203,284385) : difference with theory (-79) = -2 

CORRECTING DEFECT 39 (vertices=51, convex hull=54, v0=68969)
After retessellation of defect 39 (v0=68969), euler #=-76 (143752,428257,284429) : difference with theory (-78) = -2 

CORRECTING DEFECT 40 (vertices=132, convex hull=85, v0=69230)
After retessellation of defect 40 (v0=69230), euler #=-75 (143789,428405,284541) : difference with theory (-77) = -2 

CORRECTING DEFECT 41 (vertices=53, convex hull=82, v0=69774)
After retessellation of defect 41 (v0=69774), euler #=-74 (143816,428521,284631) : difference with theory (-76) = -2 

CORRECTING DEFECT 42 (vertices=123, convex hull=120, v0=72986)
After retessellation of defect 42 (v0=72986), euler #=-73 (143862,428729,284794) : difference with theory (-75) = -2 

CORRECTING DEFECT 43 (vertices=17, convex hull=49, v0=73944)
After retessellation of defect 43 (v0=73944), euler #=-72 (143871,428775,284832) : difference with theory (-74) = -2 

CORRECTING DEFECT 44 (vertices=78, convex hull=135, v0=74123)
After retessellation of defect 44 (v0=74123), euler #=-71 (143889,428891,284931) : difference with theory (-73) = -2 

CORRECTING DEFECT 45 (vertices=43, convex hull=33, v0=76075)
After retessellation of defect 45 (v0=76075), euler #=-70 (143895,428921,284956) : difference with theory (-72) = -2 

CORRECTING DEFECT 46 (vertices=27, convex hull=64, v0=76758)
After retessellation of defect 46 (v0=76758), euler #=-69 (143907,428978,285002) : difference with theory (-71) = -2 

CORRECTING DEFECT 47 (vertices=617, convex hull=231, v0=77766)
After retessellation of defect 47 (v0=77766), euler #=-68 (144014,429412,285330) : difference with theory (-70) = -2 

CORRECTING DEFECT 48 (vertices=29, convex hull=48, v0=80186)
After retessellation of defect 48 (v0=80186), euler #=-67 (144022,429455,285366) : difference with theory (-69) = -2 

CORRECTING DEFECT 49 (vertices=46, convex hull=42, v0=81787)
After retessellation of defect 49 (v0=81787), euler #=-66 (144028,429487,285393) : difference with theory (-68) = -2 

CORRECTING DEFECT 50 (vertices=20, convex hull=58, v0=82150)
After retessellation of defect 50 (v0=82150), euler #=-65 (144041,429545,285439) : difference with theory (-67) = -2 

CORRECTING DEFECT 51 (vertices=233, convex hull=148, v0=85097)
After retessellation of defect 51 (v0=85097), euler #=-64 (144071,429712,285577) : difference with theory (-66) = -2 

CORRECTING DEFECT 52 (vertices=61, convex hull=86, v0=86538)
After retessellation of defect 52 (v0=86538), euler #=-64 (144085,429792,285643) : difference with theory (-65) = -1 

CORRECTING DEFECT 53 (vertices=7, convex hull=19, v0=87374)
After retessellation of defect 53 (v0=87374), euler #=-63 (144086,429800,285651) : difference with theory (-64) = -1 

CORRECTING DEFECT 54 (vertices=9, convex hull=21, v0=89105)
After retessellation of defect 54 (v0=89105), euler #=-62 (144088,429814,285664) : difference with theory (-63) = -1 

CORRECTING DEFECT 55 (vertices=63, convex hull=75, v0=89394)
After retessellation of defect 55 (v0=89394), euler #=-61 (144103,429895,285731) : difference with theory (-62) = -1 

CORRECTING DEFECT 56 (vertices=31, convex hull=58, v0=90341)
After retessellation of defect 56 (v0=90341), euler #=-60 (144122,429973,285791) : difference with theory (-61) = -1 

CORRECTING DEFECT 57 (vertices=9, convex hull=27, v0=90516)
After retessellation of defect 57 (v0=90516), euler #=-59 (144124,429986,285803) : difference with theory (-60) = -1 

CORRECTING DEFECT 58 (vertices=39, convex hull=51, v0=90697)
After retessellation of defect 58 (v0=90697), euler #=-58 (144135,430039,285846) : difference with theory (-59) = -1 

CORRECTING DEFECT 59 (vertices=21, convex hull=53, v0=91464)
After retessellation of defect 59 (v0=91464), euler #=-57 (144144,430084,285883) : difference with theory (-58) = -1 

CORRECTING DEFECT 60 (vertices=56, convex hull=82, v0=92002)
After retessellation of defect 60 (v0=92002), euler #=-56 (144174,430210,285980) : difference with theory (-57) = -1 

CORRECTING DEFECT 61 (vertices=31, convex hull=31, v0=92552)
After retessellation of defect 61 (v0=92552), euler #=-55 (144177,430231,285999) : difference with theory (-56) = -1 

CORRECTING DEFECT 62 (vertices=15, convex hull=26, v0=94755)
After retessellation of defect 62 (v0=94755), euler #=-54 (144181,430249,286014) : difference with theory (-55) = -1 

CORRECTING DEFECT 63 (vertices=106, convex hull=117, v0=95865)
After retessellation of defect 63 (v0=95865), euler #=-52 (144234,430464,286178) : difference with theory (-54) = -2 

CORRECTING DEFECT 64 (vertices=151, convex hull=233, v0=96121)
After retessellation of defect 64 (v0=96121), euler #=-50 (144272,430681,286359) : difference with theory (-53) = -3 

CORRECTING DEFECT 65 (vertices=125, convex hull=110, v0=96322)
After retessellation of defect 65 (v0=96322), euler #=-49 (144287,430780,286444) : difference with theory (-52) = -3 

CORRECTING DEFECT 66 (vertices=26, convex hull=61, v0=96715)
After retessellation of defect 66 (v0=96715), euler #=-48 (144296,430829,286485) : difference with theory (-51) = -3 

CORRECTING DEFECT 67 (vertices=242, convex hull=243, v0=97159)
After retessellation of defect 67 (v0=97159), euler #=-47 (144381,431203,286775) : difference with theory (-50) = -3 

CORRECTING DEFECT 68 (vertices=373, convex hull=55, v0=100083)
After retessellation of defect 68 (v0=100083), euler #=-46 (144398,431275,286831) : difference with theory (-49) = -3 

CORRECTING DEFECT 69 (vertices=24, convex hull=32, v0=100468)
After retessellation of defect 69 (v0=100468), euler #=-45 (144400,431294,286849) : difference with theory (-48) = -3 

CORRECTING DEFECT 70 (vertices=17, convex hull=65, v0=102841)
After retessellation of defect 70 (v0=102841), euler #=-44 (144411,431351,286896) : difference with theory (-47) = -3 

CORRECTING DEFECT 71 (vertices=43, convex hull=26, v0=102920)
After retessellation of defect 71 (v0=102920), euler #=-43 (144416,431374,286915) : difference with theory (-46) = -3 

CORRECTING DEFECT 72 (vertices=9, convex hull=18, v0=104250)
After retessellation of defect 72 (v0=104250), euler #=-42 (144417,431381,286922) : difference with theory (-45) = -3 

CORRECTING DEFECT 73 (vertices=145, convex hull=129, v0=107535)
After retessellation of defect 73 (v0=107535), euler #=-40 (144454,431563,287069) : difference with theory (-44) = -4 

CORRECTING DEFECT 74 (vertices=23, convex hull=60, v0=107824)
After retessellation of defect 74 (v0=107824), euler #=-39 (144469,431629,287121) : difference with theory (-43) = -4 

CORRECTING DEFECT 75 (vertices=32, convex hull=64, v0=108064)
After retessellation of defect 75 (v0=108064), euler #=-38 (144491,431718,287189) : difference with theory (-42) = -4 

CORRECTING DEFECT 76 (vertices=1750, convex hull=572, v0=108846)
XL defect detected...
After retessellation of defect 76 (v0=108846), euler #=-39 (144892,433230,288299) : difference with theory (-41) = -2 

CORRECTING DEFECT 77 (vertices=23, convex hull=44, v0=109051)
After retessellation of defect 77 (v0=109051), euler #=-38 (144894,433255,288323) : difference with theory (-40) = -2 

CORRECTING DEFECT 78 (vertices=163, convex hull=79, v0=111380)
After retessellation of defect 78 (v0=111380), euler #=-36 (144918,433363,288409) : difference with theory (-39) = -3 

CORRECTING DEFECT 79 (vertices=8, convex hull=23, v0=111649)
After retessellation of defect 79 (v0=111649), euler #=-35 (144919,433373,288419) : difference with theory (-38) = -3 

CORRECTING DEFECT 80 (vertices=61, convex hull=98, v0=113734)
After retessellation of defect 80 (v0=113734), euler #=-34 (144950,433510,288526) : difference with theory (-37) = -3 

CORRECTING DEFECT 81 (vertices=188, convex hull=105, v0=115170)
After retessellation of defect 81 (v0=115170), euler #=-33 (144963,433595,288599) : difference with theory (-36) = -3 

CORRECTING DEFECT 82 (vertices=571, convex hull=163, v0=116032)
After retessellation of defect 82 (v0=116032), euler #=-33 (145049,433935,288853) : difference with theory (-35) = -2 

CORRECTING DEFECT 83 (vertices=32, convex hull=41, v0=116655)
After retessellation of defect 83 (v0=116655), euler #=-32 (145056,433969,288881) : difference with theory (-34) = -2 

CORRECTING DEFECT 84 (vertices=20, convex hull=63, v0=116872)
After retessellation of defect 84 (v0=116872), euler #=-31 (145070,434029,288928) : difference with theory (-33) = -2 

CORRECTING DEFECT 85 (vertices=19, convex hull=49, v0=117148)
After retessellation of defect 85 (v0=117148), euler #=-30 (145080,434074,288964) : difference with theory (-32) = -2 

CORRECTING DEFECT 86 (vertices=14, convex hull=29, v0=118718)
After retessellation of defect 86 (v0=118718), euler #=-29 (145082,434085,288974) : difference with theory (-31) = -2 

CORRECTING DEFECT 87 (vertices=7, convex hull=21, v0=118732)
After retessellation of defect 87 (v0=118732), euler #=-28 (145083,434093,288982) : difference with theory (-30) = -2 

CORRECTING DEFECT 88 (vertices=23, convex hull=56, v0=119551)
After retessellation of defect 88 (v0=119551), euler #=-27 (145093,434142,289022) : difference with theory (-29) = -2 

CORRECTING DEFECT 89 (vertices=28, convex hull=70, v0=119858)
After retessellation of defect 89 (v0=119858), euler #=-26 (145102,434199,289071) : difference with theory (-28) = -2 

CORRECTING DEFECT 90 (vertices=7, convex hull=18, v0=120656)
After retessellation of defect 90 (v0=120656), euler #=-25 (145103,434207,289079) : difference with theory (-27) = -2 

CORRECTING DEFECT 91 (vertices=31, convex hull=24, v0=121984)
After retessellation of defect 91 (v0=121984), euler #=-24 (145104,434219,289091) : difference with theory (-26) = -2 

CORRECTING DEFECT 92 (vertices=40, convex hull=19, v0=122257)
After retessellation of defect 92 (v0=122257), euler #=-23 (145104,434228,289101) : difference with theory (-25) = -2 

CORRECTING DEFECT 93 (vertices=45, convex hull=76, v0=124358)
After retessellation of defect 93 (v0=124358), euler #=-22 (145113,434289,289154) : difference with theory (-24) = -2 

CORRECTING DEFECT 94 (vertices=43, convex hull=43, v0=126648)
After retessellation of defect 94 (v0=126648), euler #=-21 (145129,434353,289203) : difference with theory (-23) = -2 

CORRECTING DEFECT 95 (vertices=81, convex hull=22, v0=126882)
After retessellation of defect 95 (v0=126882), euler #=-20 (145131,434364,289213) : difference with theory (-22) = -2 

CORRECTING DEFECT 96 (vertices=142, convex hull=132, v0=131182)
After retessellation of defect 96 (v0=131182), euler #=-19 (145164,434522,289339) : difference with theory (-21) = -2 

CORRECTING DEFECT 97 (vertices=65, convex hull=36, v0=132358)
After retessellation of defect 97 (v0=132358), euler #=-19 (145169,434556,289368) : difference with theory (-20) = -1 

CORRECTING DEFECT 98 (vertices=59, convex hull=34, v0=134230)
After retessellation of defect 98 (v0=134230), euler #=-18 (145174,434584,289392) : difference with theory (-19) = -1 

CORRECTING DEFECT 99 (vertices=30, convex hull=81, v0=137988)
After retessellation of defect 99 (v0=137988), euler #=-17 (145189,434664,289458) : difference with theory (-18) = -1 

CORRECTING DEFECT 100 (vertices=77, convex hull=112, v0=139495)
After retessellation of defect 100 (v0=139495), euler #=-16 (145235,434854,289603) : difference with theory (-17) = -1 

CORRECTING DEFECT 101 (vertices=6, convex hull=35, v0=140961)
After retessellation of defect 101 (v0=140961), euler #=-15 (145236,434867,289616) : difference with theory (-16) = -1 

CORRECTING DEFECT 102 (vertices=62, convex hull=104, v0=142366)
After retessellation of defect 102 (v0=142366), euler #=-14 (145257,434978,289707) : difference with theory (-15) = -1 

CORRECTING DEFECT 103 (vertices=31, convex hull=68, v0=142836)
After retessellation of defect 103 (v0=142836), euler #=-13 (145267,435035,289755) : difference with theory (-14) = -1 

CORRECTING DEFECT 104 (vertices=31, convex hull=28, v0=145003)
After retessellation of defect 104 (v0=145003), euler #=-12 (145268,435051,289771) : difference with theory (-13) = -1 

CORRECTING DEFECT 105 (vertices=1213, convex hull=509, v0=145849)
L defect detected...
After retessellation of defect 105 (v0=145849), euler #=-12 (145559,436188,290617) : difference with theory (-12) = 0 

CORRECTING DEFECT 106 (vertices=59, convex hull=101, v0=147878)
After retessellation of defect 106 (v0=147878), euler #=-11 (145593,436334,290730) : difference with theory (-11) = 0 

CORRECTING DEFECT 107 (vertices=51, convex hull=79, v0=148682)
After retessellation of defect 107 (v0=148682), euler #=-10 (145615,436431,290806) : difference with theory (-10) = 0 

CORRECTING DEFECT 108 (vertices=121, convex hull=106, v0=149185)
After retessellation of defect 108 (v0=149185), euler #=-9 (145656,436595,290930) : difference with theory (-9) = 0 

CORRECTING DEFECT 109 (vertices=597, convex hull=136, v0=150154)
After retessellation of defect 109 (v0=150154), euler #=-8 (145722,436856,291126) : difference with theory (-8) = 0 

CORRECTING DEFECT 110 (vertices=109, convex hull=121, v0=150331)
After retessellation of defect 110 (v0=150331), euler #=-7 (145747,436986,291232) : difference with theory (-7) = 0 

CORRECTING DEFECT 111 (vertices=23, convex hull=30, v0=150759)
After retessellation of defect 111 (v0=150759), euler #=-6 (145748,437002,291248) : difference with theory (-6) = 0 

CORRECTING DEFECT 112 (vertices=188, convex hull=48, v0=152908)
After retessellation of defect 112 (v0=152908), euler #=-5 (145756,437045,291284) : difference with theory (-5) = 0 

CORRECTING DEFECT 113 (vertices=59, convex hull=109, v0=154521)
After retessellation of defect 113 (v0=154521), euler #=-4 (145774,437143,291365) : difference with theory (-4) = 0 

CORRECTING DEFECT 114 (vertices=30, convex hull=70, v0=155588)
After retessellation of defect 114 (v0=155588), euler #=-3 (145786,437207,291418) : difference with theory (-3) = 0 

CORRECTING DEFECT 115 (vertices=28, convex hull=70, v0=156064)
After retessellation of defect 115 (v0=156064), euler #=-2 (145795,437257,291460) : difference with theory (-2) = 0 

CORRECTING DEFECT 116 (vertices=146, convex hull=95, v0=156326)
After retessellation of defect 116 (v0=156326), euler #=-1 (145837,437423,291585) : difference with theory (-1) = 0 

CORRECTING DEFECT 117 (vertices=100, convex hull=115, v0=157744)
After retessellation of defect 117 (v0=157744), euler #=0 (145854,437523,291669) : difference with theory (0) = 0 

CORRECTING DEFECT 118 (vertices=43, convex hull=69, v0=158331)
After retessellation of defect 118 (v0=158331), euler #=1 (145873,437606,291734) : difference with theory (1) = 0 

CORRECTING DEFECT 119 (vertices=13, convex hull=19, v0=158749)
After retessellation of defect 119 (v0=158749), euler #=2 (145874,437616,291744) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.30 (0.04-->11.86) (max @ vno 44778 --> 56635)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.30 (0.04-->11.86) (max @ vno 44778 --> 56635)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
444 mutations (35.0%), 823 crossovers (65.0%), 1501 vertices were eliminated
building final representation...
12890 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=145874, nf=291744, ne=437616, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 184.1 minutes
0 defective edges
removing intersecting faces
000: 1288 intersecting
001: 113 intersecting
002: 31 intersecting
003: 9 intersecting
004: 6 intersecting
005: 3 intersecting
mris_fix_topology utimesec    11050.300099
mris_fix_topology stimesec    1.940704
mris_fix_topology ru_maxrss   640620
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   126325
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  33552
mris_fix_topology ru_oublock  14704
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    732
mris_fix_topology ru_nivcsw   20545
FSRUNTIME@ mris_fix_topology lh  3.0684 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 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=-294 (nv=154026, nf=308640, ne=462960, g=148)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
18613 ambiguous faces found in tessellation
segmenting defects...
147 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 4 into 3
      -merging segment 56 into 62
      -merging segment 74 into 66
      -merging segment 88 into 71
      -merging segment 77 into 76
      -merging segment 96 into 92
      -merging segment 134 into 133
      -merging segment 137 into 133
      -merging segment 142 into 141
      -merging segment 145 into 141
137 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3764  (-4.6882)
      -vertex     loglikelihood: -6.2514  (-3.1257)
      -normal dot loglikelihood: -3.5644  (-3.5644)
      -quad curv  loglikelihood: -6.0734  (-3.0367)
      Total Loglikelihood : -25.2656

CORRECTING DEFECT 0 (vertices=154, convex hull=46, v0=586)
After retessellation of defect 0 (v0=586), euler #=-140 (142688,423487,280659) : difference with theory (-134) = 6 

CORRECTING DEFECT 1 (vertices=29, convex hull=70, v0=1312)
After retessellation of defect 1 (v0=1312), euler #=-139 (142700,423547,280708) : difference with theory (-133) = 6 

CORRECTING DEFECT 2 (vertices=27, convex hull=62, v0=7191)
After retessellation of defect 2 (v0=7191), euler #=-138 (142710,423598,280750) : difference with theory (-132) = 6 

CORRECTING DEFECT 3 (vertices=41, convex hull=64, v0=8063)
After retessellation of defect 3 (v0=8063), euler #=-136 (142720,423656,280800) : difference with theory (-131) = 5 

CORRECTING DEFECT 4 (vertices=28, convex hull=51, v0=11207)
After retessellation of defect 4 (v0=11207), euler #=-135 (142736,423725,280854) : difference with theory (-130) = 5 

CORRECTING DEFECT 5 (vertices=63, convex hull=55, v0=16474)
After retessellation of defect 5 (v0=16474), euler #=-134 (142745,423773,280894) : difference with theory (-129) = 5 

CORRECTING DEFECT 6 (vertices=83, convex hull=74, v0=16739)
After retessellation of defect 6 (v0=16739), euler #=-133 (142776,423895,280986) : difference with theory (-128) = 5 

CORRECTING DEFECT 7 (vertices=72, convex hull=97, v0=16802)
After retessellation of defect 7 (v0=16802), euler #=-132 (142809,424037,281096) : difference with theory (-127) = 5 

CORRECTING DEFECT 8 (vertices=36, convex hull=45, v0=19250)
After retessellation of defect 8 (v0=19250), euler #=-131 (142822,424096,281143) : difference with theory (-126) = 5 

CORRECTING DEFECT 9 (vertices=48, convex hull=46, v0=19759)
After retessellation of defect 9 (v0=19759), euler #=-130 (142830,424135,281175) : difference with theory (-125) = 5 

CORRECTING DEFECT 10 (vertices=8, convex hull=26, v0=20111)
After retessellation of defect 10 (v0=20111), euler #=-129 (142830,424142,281183) : difference with theory (-124) = 5 

CORRECTING DEFECT 11 (vertices=59, convex hull=50, v0=24782)
After retessellation of defect 11 (v0=24782), euler #=-128 (142839,424190,281223) : difference with theory (-123) = 5 

CORRECTING DEFECT 12 (vertices=31, convex hull=19, v0=25066)
After retessellation of defect 12 (v0=25066), euler #=-127 (142845,424213,281241) : difference with theory (-122) = 5 

CORRECTING DEFECT 13 (vertices=46, convex hull=51, v0=27961)
After retessellation of defect 13 (v0=27961), euler #=-126 (142849,424244,281269) : difference with theory (-121) = 5 

CORRECTING DEFECT 14 (vertices=40, convex hull=81, v0=28025)
After retessellation of defect 14 (v0=28025), euler #=-125 (142877,424361,281359) : difference with theory (-120) = 5 

CORRECTING DEFECT 15 (vertices=72, convex hull=87, v0=29203)
After retessellation of defect 15 (v0=29203), euler #=-124 (142906,424487,281457) : difference with theory (-119) = 5 

CORRECTING DEFECT 16 (vertices=1289, convex hull=771, v0=30574)
XL defect detected...
After retessellation of defect 16 (v0=30574), euler #=-124 (143310,426145,282711) : difference with theory (-118) = 6 

CORRECTING DEFECT 17 (vertices=29, convex hull=25, v0=33155)
After retessellation of defect 17 (v0=33155), euler #=-123 (143314,426163,282726) : difference with theory (-117) = 6 

CORRECTING DEFECT 18 (vertices=25, convex hull=62, v0=35960)
After retessellation of defect 18 (v0=35960), euler #=-122 (143323,426215,282770) : difference with theory (-116) = 6 

CORRECTING DEFECT 19 (vertices=26, convex hull=54, v0=36109)
After retessellation of defect 19 (v0=36109), euler #=-121 (143340,426287,282826) : difference with theory (-115) = 6 

CORRECTING DEFECT 20 (vertices=46, convex hull=91, v0=38390)
After retessellation of defect 20 (v0=38390), euler #=-120 (143352,426357,282885) : difference with theory (-114) = 6 

CORRECTING DEFECT 21 (vertices=31, convex hull=78, v0=39139)
After retessellation of defect 21 (v0=39139), euler #=-119 (143361,426415,282935) : difference with theory (-113) = 6 

CORRECTING DEFECT 22 (vertices=32, convex hull=59, v0=42109)
After retessellation of defect 22 (v0=42109), euler #=-118 (143378,426486,282990) : difference with theory (-112) = 6 

CORRECTING DEFECT 23 (vertices=37, convex hull=96, v0=43262)
After retessellation of defect 23 (v0=43262), euler #=-117 (143399,426589,283073) : difference with theory (-111) = 6 

CORRECTING DEFECT 24 (vertices=29, convex hull=77, v0=44238)
After retessellation of defect 24 (v0=44238), euler #=-116 (143417,426674,283141) : difference with theory (-110) = 6 

CORRECTING DEFECT 25 (vertices=12, convex hull=23, v0=44389)
After retessellation of defect 25 (v0=44389), euler #=-115 (143418,426685,283152) : difference with theory (-109) = 6 

CORRECTING DEFECT 26 (vertices=113, convex hull=137, v0=45118)
After retessellation of defect 26 (v0=45118), euler #=-114 (143453,426851,283284) : difference with theory (-108) = 6 

CORRECTING DEFECT 27 (vertices=87, convex hull=127, v0=47018)
After retessellation of defect 27 (v0=47018), euler #=-113 (143495,427033,283425) : difference with theory (-107) = 6 

CORRECTING DEFECT 28 (vertices=25, convex hull=26, v0=47579)
After retessellation of defect 28 (v0=47579), euler #=-112 (143501,427057,283444) : difference with theory (-106) = 6 

CORRECTING DEFECT 29 (vertices=293, convex hull=214, v0=49064)
After retessellation of defect 29 (v0=49064), euler #=-111 (143544,427284,283629) : difference with theory (-105) = 6 

CORRECTING DEFECT 30 (vertices=30, convex hull=67, v0=50715)
After retessellation of defect 30 (v0=50715), euler #=-110 (143566,427377,283701) : difference with theory (-104) = 6 

CORRECTING DEFECT 31 (vertices=20, convex hull=31, v0=52966)
After retessellation of defect 31 (v0=52966), euler #=-109 (143567,427391,283715) : difference with theory (-103) = 6 

CORRECTING DEFECT 32 (vertices=37, convex hull=104, v0=53534)
After retessellation of defect 32 (v0=53534), euler #=-108 (143581,427474,283785) : difference with theory (-102) = 6 

CORRECTING DEFECT 33 (vertices=35, convex hull=23, v0=54178)
After retessellation of defect 33 (v0=54178), euler #=-107 (143584,427491,283800) : difference with theory (-101) = 6 

CORRECTING DEFECT 34 (vertices=44, convex hull=34, v0=58407)
After retessellation of defect 34 (v0=58407), euler #=-106 (143592,427525,283827) : difference with theory (-100) = 6 

CORRECTING DEFECT 35 (vertices=23, convex hull=18, v0=62220)
After retessellation of defect 35 (v0=62220), euler #=-105 (143596,427541,283840) : difference with theory (-99) = 6 

CORRECTING DEFECT 36 (vertices=139, convex hull=93, v0=63142)
After retessellation of defect 36 (v0=63142), euler #=-104 (143635,427694,283955) : difference with theory (-98) = 6 

CORRECTING DEFECT 37 (vertices=49, convex hull=68, v0=64450)
After retessellation of defect 37 (v0=64450), euler #=-103 (143670,427826,284053) : difference with theory (-97) = 6 

CORRECTING DEFECT 38 (vertices=6, convex hull=17, v0=67531)
After retessellation of defect 38 (v0=67531), euler #=-102 (143670,427830,284058) : difference with theory (-96) = 6 

CORRECTING DEFECT 39 (vertices=29, convex hull=24, v0=67634)
After retessellation of defect 39 (v0=67634), euler #=-101 (143675,427851,284075) : difference with theory (-95) = 6 

CORRECTING DEFECT 40 (vertices=57, convex hull=58, v0=67801)
After retessellation of defect 40 (v0=67801), euler #=-100 (143694,427932,284138) : difference with theory (-94) = 6 

CORRECTING DEFECT 41 (vertices=46, convex hull=71, v0=68776)
After retessellation of defect 41 (v0=68776), euler #=-99 (143707,428003,284197) : difference with theory (-93) = 6 

CORRECTING DEFECT 42 (vertices=138, convex hull=44, v0=71332)
After retessellation of defect 42 (v0=71332), euler #=-98 (143718,428050,284234) : difference with theory (-92) = 6 

CORRECTING DEFECT 43 (vertices=47, convex hull=29, v0=72996)
After retessellation of defect 43 (v0=72996), euler #=-97 (143723,428076,284256) : difference with theory (-91) = 6 

CORRECTING DEFECT 44 (vertices=29, convex hull=58, v0=73159)
After retessellation of defect 44 (v0=73159), euler #=-96 (143734,428129,284299) : difference with theory (-90) = 6 

CORRECTING DEFECT 45 (vertices=45, convex hull=75, v0=74167)
After retessellation of defect 45 (v0=74167), euler #=-95 (143762,428244,284387) : difference with theory (-89) = 6 

CORRECTING DEFECT 46 (vertices=30, convex hull=63, v0=74483)
After retessellation of defect 46 (v0=74483), euler #=-94 (143771,428296,284431) : difference with theory (-88) = 6 

CORRECTING DEFECT 47 (vertices=27, convex hull=66, v0=74829)
After retessellation of defect 47 (v0=74829), euler #=-93 (143786,428366,284487) : difference with theory (-87) = 6 

CORRECTING DEFECT 48 (vertices=199, convex hull=130, v0=79933)
After retessellation of defect 48 (v0=79933), euler #=-92 (143796,428450,284562) : difference with theory (-86) = 6 

CORRECTING DEFECT 49 (vertices=66, convex hull=68, v0=79956)
After retessellation of defect 49 (v0=79956), euler #=-91 (143805,428504,284608) : difference with theory (-85) = 6 

CORRECTING DEFECT 50 (vertices=38, convex hull=48, v0=80972)
After retessellation of defect 50 (v0=80972), euler #=-90 (143826,428587,284671) : difference with theory (-84) = 6 

CORRECTING DEFECT 51 (vertices=36, convex hull=66, v0=83762)
After retessellation of defect 51 (v0=83762), euler #=-89 (143851,428687,284747) : difference with theory (-83) = 6 

CORRECTING DEFECT 52 (vertices=105, convex hull=64, v0=85254)
After retessellation of defect 52 (v0=85254), euler #=-88 (143860,428741,284793) : difference with theory (-82) = 6 

CORRECTING DEFECT 53 (vertices=63, convex hull=60, v0=86364)
After retessellation of defect 53 (v0=86364), euler #=-87 (143871,428797,284839) : difference with theory (-81) = 6 

CORRECTING DEFECT 54 (vertices=22, convex hull=34, v0=86689)
After retessellation of defect 54 (v0=86689), euler #=-86 (143875,428819,284858) : difference with theory (-80) = 6 

CORRECTING DEFECT 55 (vertices=44, convex hull=92, v0=88212)
After retessellation of defect 55 (v0=88212), euler #=-85 (143884,428886,284917) : difference with theory (-79) = 6 

CORRECTING DEFECT 56 (vertices=89, convex hull=138, v0=88578)
After retessellation of defect 56 (v0=88578), euler #=-84 (143929,429081,285068) : difference with theory (-78) = 6 

CORRECTING DEFECT 57 (vertices=32, convex hull=60, v0=88704)
After retessellation of defect 57 (v0=88704), euler #=-83 (143950,429168,285135) : difference with theory (-77) = 6 

CORRECTING DEFECT 58 (vertices=23, convex hull=60, v0=89385)
After retessellation of defect 58 (v0=89385), euler #=-82 (143962,429226,285182) : difference with theory (-76) = 6 

CORRECTING DEFECT 59 (vertices=39, convex hull=59, v0=89521)
After retessellation of defect 59 (v0=89521), euler #=-81 (143975,429287,285231) : difference with theory (-75) = 6 

CORRECTING DEFECT 60 (vertices=51, convex hull=63, v0=90368)
After retessellation of defect 60 (v0=90368), euler #=-79 (143984,429337,285274) : difference with theory (-74) = 5 

CORRECTING DEFECT 61 (vertices=42, convex hull=75, v0=91294)
After retessellation of defect 61 (v0=91294), euler #=-78 (144009,429446,285359) : difference with theory (-73) = 5 

CORRECTING DEFECT 62 (vertices=42, convex hull=20, v0=91925)
After retessellation of defect 62 (v0=91925), euler #=-77 (144016,429471,285378) : difference with theory (-72) = 5 

CORRECTING DEFECT 63 (vertices=11, convex hull=30, v0=91960)
After retessellation of defect 63 (v0=91960), euler #=-76 (144018,429486,285392) : difference with theory (-71) = 5 

CORRECTING DEFECT 64 (vertices=429, convex hull=284, v0=92053)
After retessellation of defect 64 (v0=92053), euler #=-74 (144123,429946,285749) : difference with theory (-70) = 4 

CORRECTING DEFECT 65 (vertices=25, convex hull=47, v0=92055)
After retessellation of defect 65 (v0=92055), euler #=-74 (144138,430010,285798) : difference with theory (-69) = 5 

CORRECTING DEFECT 66 (vertices=12, convex hull=27, v0=94792)
After retessellation of defect 66 (v0=94792), euler #=-73 (144141,430027,285813) : difference with theory (-68) = 5 

CORRECTING DEFECT 67 (vertices=30, convex hull=78, v0=95053)
After retessellation of defect 67 (v0=95053), euler #=-72 (144152,430093,285869) : difference with theory (-67) = 5 

CORRECTING DEFECT 68 (vertices=11, convex hull=13, v0=96319)
After retessellation of defect 68 (v0=96319), euler #=-71 (144154,430101,285876) : difference with theory (-66) = 5 

CORRECTING DEFECT 69 (vertices=518, convex hull=205, v0=96712)
After retessellation of defect 69 (v0=96712), euler #=-69 (144192,430312,286051) : difference with theory (-65) = 4 

CORRECTING DEFECT 70 (vertices=104, convex hull=57, v0=98239)
After retessellation of defect 70 (v0=98239), euler #=-68 (144215,430402,286119) : difference with theory (-64) = 4 

CORRECTING DEFECT 71 (vertices=62, convex hull=103, v0=98631)
After retessellation of defect 71 (v0=98631), euler #=-67 (144253,430559,286239) : difference with theory (-63) = 4 

CORRECTING DEFECT 72 (vertices=172, convex hull=140, v0=99979)
After retessellation of defect 72 (v0=99979), euler #=-66 (144304,430785,286415) : difference with theory (-62) = 4 

CORRECTING DEFECT 73 (vertices=84, convex hull=155, v0=100320)
After retessellation of defect 73 (v0=100320), euler #=-64 (144334,430947,286549) : difference with theory (-61) = 3 

CORRECTING DEFECT 74 (vertices=70, convex hull=111, v0=100489)
After retessellation of defect 74 (v0=100489), euler #=-63 (144371,431103,286669) : difference with theory (-60) = 3 

CORRECTING DEFECT 75 (vertices=54, convex hull=102, v0=100822)
After retessellation of defect 75 (v0=100822), euler #=-62 (144411,431266,286793) : difference with theory (-59) = 3 

CORRECTING DEFECT 76 (vertices=111, convex hull=52, v0=101004)
After retessellation of defect 76 (v0=101004), euler #=-61 (144420,431315,286834) : difference with theory (-58) = 3 

CORRECTING DEFECT 77 (vertices=28, convex hull=51, v0=102487)
After retessellation of defect 77 (v0=102487), euler #=-61 (144432,431372,286879) : difference with theory (-57) = 4 

CORRECTING DEFECT 78 (vertices=31, convex hull=24, v0=103509)
After retessellation of defect 78 (v0=103509), euler #=-60 (144438,431397,286899) : difference with theory (-56) = 4 

CORRECTING DEFECT 79 (vertices=61, convex hull=83, v0=104653)
After retessellation of defect 79 (v0=104653), euler #=-59 (144459,431495,286977) : difference with theory (-55) = 4 

CORRECTING DEFECT 80 (vertices=21, convex hull=52, v0=104745)
After retessellation of defect 80 (v0=104745), euler #=-58 (144469,431545,287018) : difference with theory (-54) = 4 

CORRECTING DEFECT 81 (vertices=31, convex hull=46, v0=104754)
After retessellation of defect 81 (v0=104754), euler #=-57 (144479,431591,287055) : difference with theory (-53) = 4 

CORRECTING DEFECT 82 (vertices=32, convex hull=70, v0=105306)
After retessellation of defect 82 (v0=105306), euler #=-56 (144491,431655,287108) : difference with theory (-52) = 4 

CORRECTING DEFECT 83 (vertices=22, convex hull=50, v0=106005)
After retessellation of defect 83 (v0=106005), euler #=-55 (144500,431703,287148) : difference with theory (-51) = 4 

CORRECTING DEFECT 84 (vertices=19, convex hull=24, v0=106928)
After retessellation of defect 84 (v0=106928), euler #=-54 (144504,431722,287164) : difference with theory (-50) = 4 

CORRECTING DEFECT 85 (vertices=86, convex hull=87, v0=108991)
After retessellation of defect 85 (v0=108991), euler #=-53 (144537,431855,287265) : difference with theory (-49) = 4 

CORRECTING DEFECT 86 (vertices=42, convex hull=61, v0=109890)
After retessellation of defect 86 (v0=109890), euler #=-52 (144546,431908,287310) : difference with theory (-48) = 4 

CORRECTING DEFECT 87 (vertices=85, convex hull=100, v0=109910)
After retessellation of defect 87 (v0=109910), euler #=-50 (144568,432018,287400) : difference with theory (-47) = 3 

CORRECTING DEFECT 88 (vertices=39, convex hull=39, v0=110684)
After retessellation of defect 88 (v0=110684), euler #=-49 (144575,432050,287426) : difference with theory (-46) = 3 

CORRECTING DEFECT 89 (vertices=67, convex hull=67, v0=110802)
After retessellation of defect 89 (v0=110802), euler #=-48 (144593,432131,287490) : difference with theory (-45) = 3 

CORRECTING DEFECT 90 (vertices=6, convex hull=24, v0=111002)
After retessellation of defect 90 (v0=111002), euler #=-47 (144593,432139,287499) : difference with theory (-44) = 3 

CORRECTING DEFECT 91 (vertices=110, convex hull=117, v0=111339)
After retessellation of defect 91 (v0=111339), euler #=-46 (144636,432320,287638) : difference with theory (-43) = 3 

CORRECTING DEFECT 92 (vertices=21, convex hull=27, v0=111848)
After retessellation of defect 92 (v0=111848), euler #=-45 (144641,432342,287656) : difference with theory (-42) = 3 

CORRECTING DEFECT 93 (vertices=28, convex hull=40, v0=112559)
After retessellation of defect 93 (v0=112559), euler #=-44 (144646,432371,287681) : difference with theory (-41) = 3 

CORRECTING DEFECT 94 (vertices=537, convex hull=225, v0=113084)
normal vector of length zero at vertex 150191 with 3 faces
normal vector of length zero at vertex 150191 with 3 faces
normal vector of length zero at vertex 150191 with 3 faces
normal vector of length zero at vertex 150191 with 3 faces
After retessellation of defect 94 (v0=113084), euler #=-43 (144757,432817,288017) : difference with theory (-40) = 3 

CORRECTING DEFECT 95 (vertices=73, convex hull=42, v0=114242)
After retessellation of defect 95 (v0=114242), euler #=-42 (144774,432886,288070) : difference with theory (-39) = 3 

CORRECTING DEFECT 96 (vertices=69, convex hull=133, v0=114895)
After retessellation of defect 96 (v0=114895), euler #=-41 (144794,433006,288171) : difference with theory (-38) = 3 

CORRECTING DEFECT 97 (vertices=73, convex hull=121, v0=116201)
After retessellation of defect 97 (v0=116201), euler #=-40 (144818,433134,288276) : difference with theory (-37) = 3 

CORRECTING DEFECT 98 (vertices=33, convex hull=60, v0=116405)
After retessellation of defect 98 (v0=116405), euler #=-39 (144836,433218,288343) : difference with theory (-36) = 3 

CORRECTING DEFECT 99 (vertices=226, convex hull=139, v0=116445)
After retessellation of defect 99 (v0=116445), euler #=-38 (144881,433424,288505) : difference with theory (-35) = 3 

CORRECTING DEFECT 100 (vertices=14, convex hull=23, v0=116480)
After retessellation of defect 100 (v0=116480), euler #=-37 (144882,433436,288517) : difference with theory (-34) = 3 

CORRECTING DEFECT 101 (vertices=137, convex hull=120, v0=118265)
After retessellation of defect 101 (v0=118265), euler #=-36 (144901,433561,288624) : difference with theory (-33) = 3 

CORRECTING DEFECT 102 (vertices=527, convex hull=179, v0=119213)
After retessellation of defect 102 (v0=119213), euler #=-36 (144978,433896,288882) : difference with theory (-32) = 4 

CORRECTING DEFECT 103 (vertices=17, convex hull=41, v0=122457)
After retessellation of defect 103 (v0=122457), euler #=-35 (144987,433934,288912) : difference with theory (-31) = 4 

CORRECTING DEFECT 104 (vertices=40, convex hull=25, v0=126513)
After retessellation of defect 104 (v0=126513), euler #=-34 (144994,433961,288933) : difference with theory (-30) = 4 

CORRECTING DEFECT 105 (vertices=113, convex hull=93, v0=126817)
After retessellation of defect 105 (v0=126817), euler #=-33 (145014,434060,289013) : difference with theory (-29) = 4 

CORRECTING DEFECT 106 (vertices=22, convex hull=30, v0=129456)
After retessellation of defect 106 (v0=129456), euler #=-32 (145017,434078,289029) : difference with theory (-28) = 4 

CORRECTING DEFECT 107 (vertices=108, convex hull=41, v0=132428)
After retessellation of defect 107 (v0=132428), euler #=-31 (145025,434121,289065) : difference with theory (-27) = 4 

CORRECTING DEFECT 108 (vertices=27, convex hull=30, v0=132484)
After retessellation of defect 108 (v0=132484), euler #=-30 (145028,434138,289080) : difference with theory (-26) = 4 

CORRECTING DEFECT 109 (vertices=52, convex hull=89, v0=134728)
After retessellation of defect 109 (v0=134728), euler #=-29 (145055,434256,289172) : difference with theory (-25) = 4 

CORRECTING DEFECT 110 (vertices=65, convex hull=87, v0=134872)
After retessellation of defect 110 (v0=134872), euler #=-28 (145081,434373,289264) : difference with theory (-24) = 4 

CORRECTING DEFECT 111 (vertices=61, convex hull=97, v0=136600)
After retessellation of defect 111 (v0=136600), euler #=-27 (145098,434463,289338) : difference with theory (-23) = 4 

CORRECTING DEFECT 112 (vertices=51, convex hull=66, v0=137839)
After retessellation of defect 112 (v0=137839), euler #=-26 (145126,434572,289420) : difference with theory (-22) = 4 

CORRECTING DEFECT 113 (vertices=19, convex hull=49, v0=139020)
After retessellation of defect 113 (v0=139020), euler #=-25 (145136,434622,289461) : difference with theory (-21) = 4 

CORRECTING DEFECT 114 (vertices=6, convex hull=29, v0=139209)
After retessellation of defect 114 (v0=139209), euler #=-24 (145137,434633,289472) : difference with theory (-20) = 4 

CORRECTING DEFECT 115 (vertices=59, convex hull=70, v0=139874)
After retessellation of defect 115 (v0=139874), euler #=-23 (145155,434717,289539) : difference with theory (-19) = 4 

CORRECTING DEFECT 116 (vertices=119, convex hull=53, v0=141308)
After retessellation of defect 116 (v0=141308), euler #=-22 (145164,434769,289583) : difference with theory (-18) = 4 

CORRECTING DEFECT 117 (vertices=125, convex hull=43, v0=142100)
After retessellation of defect 117 (v0=142100), euler #=-21 (145171,434808,289616) : difference with theory (-17) = 4 

CORRECTING DEFECT 118 (vertices=63, convex hull=36, v0=142143)
After retessellation of defect 118 (v0=142143), euler #=-20 (145175,434829,289634) : difference with theory (-16) = 4 

CORRECTING DEFECT 119 (vertices=41, convex hull=34, v0=142227)
After retessellation of defect 119 (v0=142227), euler #=-19 (145175,434840,289646) : difference with theory (-15) = 4 

CORRECTING DEFECT 120 (vertices=180, convex hull=84, v0=144328)
After retessellation of defect 120 (v0=144328), euler #=-18 (145207,434977,289752) : difference with theory (-14) = 4 

CORRECTING DEFECT 121 (vertices=56, convex hull=32, v0=145369)
After retessellation of defect 121 (v0=145369), euler #=-17 (145210,434997,289770) : difference with theory (-13) = 4 

CORRECTING DEFECT 122 (vertices=115, convex hull=74, v0=146482)
After retessellation of defect 122 (v0=146482), euler #=-16 (145219,435052,289817) : difference with theory (-12) = 4 

CORRECTING DEFECT 123 (vertices=29, convex hull=37, v0=146612)
After retessellation of defect 123 (v0=146612), euler #=-15 (145221,435074,289838) : difference with theory (-11) = 4 

CORRECTING DEFECT 124 (vertices=57, convex hull=84, v0=147091)
After retessellation of defect 124 (v0=147091), euler #=-14 (145244,435180,289922) : difference with theory (-10) = 4 

CORRECTING DEFECT 125 (vertices=6, convex hull=26, v0=147513)
After retessellation of defect 125 (v0=147513), euler #=-13 (145244,435188,289931) : difference with theory (-9) = 4 

CORRECTING DEFECT 126 (vertices=142, convex hull=98, v0=147692)
After retessellation of defect 126 (v0=147692), euler #=-12 (145274,435323,290037) : difference with theory (-8) = 4 

CORRECTING DEFECT 127 (vertices=214, convex hull=210, v0=147848)
After retessellation of defect 127 (v0=147848), euler #=-9 (145326,435579,290244) : difference with theory (-7) = 2 

CORRECTING DEFECT 128 (vertices=147, convex hull=117, v0=148708)
After retessellation of defect 128 (v0=148708), euler #=-8 (145359,435732,290365) : difference with theory (-6) = 2 

CORRECTING DEFECT 129 (vertices=163, convex hull=126, v0=149039)
After retessellation of defect 129 (v0=149039), euler #=-7 (145404,435925,290514) : difference with theory (-5) = 2 

CORRECTING DEFECT 130 (vertices=28, convex hull=64, v0=149523)
After retessellation of defect 130 (v0=149523), euler #=-6 (145413,435977,290558) : difference with theory (-4) = 2 

CORRECTING DEFECT 131 (vertices=8, convex hull=17, v0=150026)
After retessellation of defect 131 (v0=150026), euler #=-5 (145414,435986,290567) : difference with theory (-3) = 2 

CORRECTING DEFECT 132 (vertices=38, convex hull=88, v0=150190)
After retessellation of defect 132 (v0=150190), euler #=-4 (145432,436074,290638) : difference with theory (-2) = 2 

CORRECTING DEFECT 133 (vertices=286, convex hull=263, v0=151449)
After retessellation of defect 133 (v0=151449), euler #=-1 (145550,436569,291018) : difference with theory (-1) = 0 

CORRECTING DEFECT 134 (vertices=39, convex hull=54, v0=152043)
After retessellation of defect 134 (v0=152043), euler #=0 (145553,436600,291047) : difference with theory (0) = 0 

CORRECTING DEFECT 135 (vertices=67, convex hull=89, v0=152163)
After retessellation of defect 135 (v0=152163), euler #=1 (145576,436709,291134) : difference with theory (1) = 0 

CORRECTING DEFECT 136 (vertices=31, convex hull=40, v0=153056)
After retessellation of defect 136 (v0=153056), euler #=2 (145578,436728,291152) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.28 (0.02-->12.46) (max @ vno 74883 --> 87903)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.28 (0.02-->12.46) (max @ vno 74883 --> 87903)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
446 mutations (34.2%), 857 crossovers (65.8%), 669 vertices were eliminated
building final representation...
8448 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=145578, nf=291152, ne=436728, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 87.8 minutes
0 defective edges
removing intersecting faces
000: 1107 intersecting
001: 72 intersecting
002: 22 intersecting
003: 17 intersecting
004: 6 intersecting
mris_fix_topology utimesec    5268.424077
mris_fix_topology stimesec    0.213967
mris_fix_topology ru_maxrss   496532
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   59963
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  14584
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    746
mris_fix_topology ru_nivcsw   11799
FSRUNTIME@ mris_fix_topology rh  1.4628 hours 1 threads
PIDs (29128 29131) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 145874 - 437616 + 291744 = 2 --> 0 holes
      F =2V-4:          291744 = 291748-4 (0)
      2E=3F:            875232 = 875232 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 145578 - 436728 + 291152 = 2 --> 0 holes
      F =2V-4:          291152 = 291156-4 (0)
      2E=3F:            873456 = 873456 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 382 intersecting
001: 66 intersecting
002: 19 intersecting
003: 9 intersecting
004: 6 intersecting
005: 4 intersecting
006: 3 intersecting
expanding nbhd size to 2
007: 3 intersecting
expanding nbhd size to 3
008: 6 intersecting
009: 3 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 199 intersecting
001: 42 intersecting
002: 3 intersecting
expanding nbhd size to 2
003: 3 intersecting
004: 2 intersecting
expanding nbhd size to 3
005: 2 intersecting
expanding nbhd size to 4
006: 8 intersecting
007: 5 intersecting
expanding nbhd size to 5
008: 8 intersecting
009: 2 intersecting
expanding nbhd size to 6
010: 2 intersecting
expanding nbhd size to 7
011: 2 intersecting
expanding nbhd size to 8
012: 2 intersecting
expanding nbhd size to 9
013: 6 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:23:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:23:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 rh 

Waiting for PID 3867 of (3867 3870) to complete...
Waiting for PID 3870 of (3867 3870) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
34293 bright wm thresholded.
656 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.orig...
computing class statistics...
border white:    276628 voxels (1.65%)
border gray      335243 voxels (2.00%)
WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0]
GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70)
setting MAX_BORDER_WHITE to 110.7 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 51.7 (was 40)
setting MAX_GRAY to 93.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.25 (0.03-->5.62) (max @ vno 41855 --> 52144)
face area 0.27 +- 0.14 (0.00-->5.85)
mean absolute distance = 0.65 +- 0.81
3822 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-8.7,    GM=72+-6.1
mean inside = 93.0, mean outside = 76.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=81.6, 301 (301) missing vertices, mean dist 0.2 [0.6 (%37.9)->0.7 (%62.1))]
%72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.27 (0.03-->5.73) (max @ vno 41855 --> 52144)
face area 0.27 +- 0.14 (0.00-->5.29)
mean absolute distance = 0.37 +- 0.55
3910 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2594127.8, rms=8.379
001: dt: 0.5000, sse=1495255.6, rms=5.770 (31.143%)
002: dt: 0.5000, sse=1111286.5, rms=4.422 (23.361%)
003: dt: 0.5000, sse=965084.5, rms=3.804 (13.980%)
004: dt: 0.5000, sse=902894.1, rms=3.512 (7.663%)
005: dt: 0.5000, sse=878662.6, rms=3.378 (3.817%)
006: dt: 0.5000, sse=863832.9, rms=3.304 (2.192%)
rms = 3.27, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=863070.2, rms=3.274 (0.912%)
008: dt: 0.2500, sse=727426.4, rms=2.337 (28.629%)
009: dt: 0.2500, sse=698040.1, rms=2.095 (10.358%)
rms = 2.05, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=693159.5, rms=2.050 (2.119%)
011: dt: 0.1250, sse=686558.6, rms=1.996 (2.635%)
rms = 1.99, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=686173.8, rms=1.990 (0.318%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=84.9, 249 (95) missing vertices, mean dist -0.2 [0.4 (%75.1)->0.3 (%24.9))]
%83 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 0.88 +- 0.27 (0.09-->5.67) (max @ vno 41855 --> 52144)
face area 0.33 +- 0.17 (0.00-->6.78)
mean absolute distance = 0.26 +- 0.38
3868 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1253677.5, rms=4.461
013: dt: 0.5000, sse=948499.9, rms=2.868 (35.696%)
rms = 2.93, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=851385.1, rms=2.290 (20.148%)
015: dt: 0.2500, sse=806170.1, rms=1.914 (16.453%)
016: dt: 0.2500, sse=795726.5, rms=1.766 (7.696%)
rms = 1.72, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=788819.3, rms=1.719 (2.674%)
rms = 1.67, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=782337.2, rms=1.671 (2.790%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=86.6, 278 (64) missing vertices, mean dist -0.1 [0.3 (%65.3)->0.2 (%34.7))]
%88 local maxima, % 7 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 0.88 +- 0.27 (0.09-->5.58) (max @ vno 41855 --> 52144)
face area 0.32 +- 0.17 (0.00-->6.75)
mean absolute distance = 0.23 +- 0.33
3308 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=897526.2, rms=2.732
019: dt: 0.5000, sse=884461.6, rms=2.518 (7.810%)
rms = 2.79, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=794124.9, rms=1.881 (25.296%)
021: dt: 0.2500, sse=768843.8, rms=1.611 (14.349%)
022: dt: 0.2500, sse=774989.6, rms=1.558 (3.311%)
rms = 1.55, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=781992.4, rms=1.552 (0.352%)
rms = 1.51, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=757646.4, rms=1.510 (2.763%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=87.2, 357 (46) missing vertices, mean dist -0.0 [0.2 (%54.0)->0.2 (%46.0))]
%89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=768535.2, rms=1.694
025: dt: 0.5000, sse=770753.4, rms=1.642 (3.048%)
rms = 2.41, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=729075.9, rms=1.245 (24.195%)
rms = 1.25, time step reduction 2 of 3 to 0.125...
rms = 1.21, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=725656.4, rms=1.212 (2.615%)
positioning took 0.5 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 8271 vertices
erasing segment 1 (vno[0] = 55077)
erasing segment 2 (vno[0] = 80379)
erasing segment 3 (vno[0] = 91230)
erasing segment 4 (vno[0] = 95168)
erasing segment 5 (vno[0] = 97325)
erasing segment 6 (vno[0] = 99430)
erasing segment 7 (vno[0] = 100465)
erasing segment 8 (vno[0] = 102306)
erasing segment 9 (vno[0] = 103750)
erasing segment 10 (vno[0] = 105689)
erasing segment 11 (vno[0] = 109031)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.area
vertex spacing 0.88 +- 0.27 (0.04-->5.57) (max @ vno 41855 --> 52144)
face area 0.32 +- 0.17 (0.00-->6.58)
refinement took 5.2 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
34293 bright wm thresholded.
656 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.orig...
computing class statistics...
border white:    276628 voxels (1.65%)
border gray      335243 voxels (2.00%)
WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0]
GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70)
setting MAX_BORDER_WHITE to 108.7 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 52.7 (was 40)
setting MAX_GRAY to 91.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.6 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.80 +- 0.24 (0.02-->4.80) (max @ vno 74884 --> 86646)
face area 0.27 +- 0.14 (0.00-->3.84)
mean absolute distance = 0.65 +- 0.83
4031 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-7.8,    GM=73+-6.1
mean inside = 92.5, mean outside = 76.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=82.2, 202 (202) missing vertices, mean dist 0.2 [0.6 (%39.9)->0.7 (%60.1))]
%71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.26 (0.04-->5.98) (max @ vno 35333 --> 143154)
face area 0.27 +- 0.14 (0.00-->3.23)
mean absolute distance = 0.37 +- 0.56
4218 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2377997.2, rms=7.900
001: dt: 0.5000, sse=1386108.2, rms=5.430 (31.271%)
002: dt: 0.5000, sse=1047858.4, rms=4.199 (22.677%)
003: dt: 0.5000, sse=933180.9, rms=3.646 (13.165%)
004: dt: 0.5000, sse=882892.8, rms=3.403 (6.654%)
005: dt: 0.5000, sse=869807.1, rms=3.293 (3.237%)
006: dt: 0.5000, sse=853364.4, rms=3.237 (1.697%)
rms = 3.19, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=843710.1, rms=3.195 (1.313%)
008: dt: 0.2500, sse=714812.8, rms=2.291 (28.292%)
009: dt: 0.2500, sse=690878.7, rms=2.057 (10.189%)
rms = 2.02, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=702278.2, rms=2.016 (2.021%)
rms = 1.97, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=680809.0, rms=1.968 (2.364%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=85.2, 241 (46) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.3 (%26.6))]
%82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.26 (0.01-->6.23) (max @ vno 35333 --> 143154)
face area 0.33 +- 0.17 (0.00-->3.51)
mean absolute distance = 0.27 +- 0.40
3686 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1170159.5, rms=4.138
012: dt: 0.5000, sse=924853.6, rms=2.799 (32.345%)
rms = 2.84, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=837667.1, rms=2.256 (19.410%)
014: dt: 0.2500, sse=804004.9, rms=1.906 (15.518%)
015: dt: 0.2500, sse=786238.7, rms=1.779 (6.655%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=783844.8, rms=1.730 (2.753%)
rms = 1.68, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=782531.1, rms=1.684 (2.676%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=86.8, 238 (23) missing vertices, mean dist -0.1 [0.3 (%63.5)->0.2 (%36.5))]
%86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.26 (0.04-->6.25) (max @ vno 35333 --> 143154)
face area 0.32 +- 0.17 (0.00-->3.64)
mean absolute distance = 0.24 +- 0.35
3828 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=878056.4, rms=2.582
018: dt: 0.5000, sse=872984.1, rms=2.436 (5.660%)
rms = 2.65, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=794855.9, rms=1.869 (23.274%)
020: dt: 0.2500, sse=771151.7, rms=1.620 (13.316%)
rms = 1.57, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=762816.8, rms=1.575 (2.793%)
rms = 1.53, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=751332.1, rms=1.532 (2.714%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=87.4, 325 (18) missing vertices, mean dist -0.0 [0.3 (%53.3)->0.2 (%46.7))]
%88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=760450.4, rms=1.685
023: dt: 0.5000, sse=765409.2, rms=1.604 (4.785%)
rms = 2.31, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=728589.2, rms=1.253 (21.906%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
rms = 1.22, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=719645.2, rms=1.223 (2.342%)
positioning took 0.5 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7425 vertices
erasing segment 1 (vno[0] = 54668)
erasing segment 2 (vno[0] = 74790)
erasing segment 3 (vno[0] = 78775)
erasing segment 4 (vno[0] = 96968)
erasing segment 5 (vno[0] = 98092)
erasing segment 6 (vno[0] = 100203)
erasing segment 7 (vno[0] = 103185)
erasing segment 8 (vno[0] = 106167)
erasing segment 9 (vno[0] = 106209)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.area
vertex spacing 0.88 +- 0.27 (0.04-->6.49) (max @ vno 35333 --> 143154)
face area 0.32 +- 0.16 (0.00-->3.43)
refinement took 4.8 minutes
PIDs (3867 3870) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 00:28:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 00:28:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

Waiting for PID 4165 of (4165 4168) to complete...
Waiting for PID 4168 of (4165 4168) 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 (4165 4168) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 00:28:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 00:28:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 4209 of (4209 4212) to complete...
Waiting for PID 4212 of (4209 4212) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 47.3 mm, total surface area = 84438 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.188 (target=0.015)   
step 005: RMS=0.132 (target=0.015)   
step 010: RMS=0.103 (target=0.015)   
step 015: RMS=0.086 (target=0.015)   
step 020: RMS=0.074 (target=0.015)   
step 025: RMS=0.063 (target=0.015)   
step 030: RMS=0.054 (target=0.015)   
step 035: RMS=0.047 (target=0.015)   
step 040: RMS=0.041 (target=0.015)   
step 045: RMS=0.036 (target=0.015)   
step 050: RMS=0.033 (target=0.015)   
step 055: RMS=0.031 (target=0.015)   
step 060: RMS=0.029 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    47.679751
mris_inflate stimesec    0.120981
mris_inflate ru_maxrss   215248
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31393
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11424
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2066
mris_inflate ru_nivcsw   3590

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 46.3 mm, total surface area = 83700 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.188 (target=0.015)   
step 005: RMS=0.131 (target=0.015)   
step 010: RMS=0.103 (target=0.015)   
step 015: RMS=0.088 (target=0.015)   
step 020: RMS=0.077 (target=0.015)   
step 025: RMS=0.066 (target=0.015)   
step 030: RMS=0.056 (target=0.015)   
step 035: RMS=0.047 (target=0.015)   
step 040: RMS=0.042 (target=0.015)   
step 045: RMS=0.038 (target=0.015)   
step 050: RMS=0.035 (target=0.015)   
step 055: RMS=0.031 (target=0.015)   
step 060: RMS=0.029 (target=0.015)   
inflation complete.
inflation took 1.0 minutes
mris_inflate utimesec    63.951277
mris_inflate stimesec    0.106983
mris_inflate ru_maxrss   214468
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31197
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11408
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2125
mris_inflate ru_nivcsw   3649
PIDs (4209 4212) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 00:29:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 00:29:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 4311 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4314 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4317 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4320 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4323 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4326 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4329 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4332 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4335 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4338 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4341 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...
Waiting for PID 4345 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 31.185*4pi (391.885) --> -30 handles
ICI = 266.7, FI = 2345.5, variation=38079.671
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
168 vertices thresholded to be in k1 ~ [-0.52 0.37], k2 ~ [-0.15 0.10]
total integrated curvature = 0.381*4pi (4.787) --> 1 handles
ICI = 1.4, FI = 11.2, variation=181.055
158 vertices thresholded to be in [-0.03 0.03]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
126 vertices thresholded to be in [-0.21 0.11]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.024
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 23.705*4pi (297.882) --> -23 handles
ICI = 266.7, FI = 2247.7, variation=37002.831
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
179 vertices thresholded to be in k1 ~ [-0.38 0.27], k2 ~ [-0.18 0.10]
total integrated curvature = 0.294*4pi (3.693) --> 1 handles
ICI = 1.4, FI = 11.4, variation=187.106
160 vertices thresholded to be in [-0.02 0.03]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
127 vertices thresholded to be in [-0.18 0.12]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.025
done.
PIDs (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 00:31:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051348 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      [ 0051348/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                      [ 299 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.304746
WARN:    S explicit min:                          0.000000	vertex = 49

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 00:31:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051348 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      [ 0051348/rh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 290 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.113278
WARN:    S explicit min:                          0.000000	vertex = 55
#--------------------------------------------
#@# Sphere lh Sun Oct  8 00:31:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 00:31:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 4702 of (4702 4706) to complete...
Waiting for PID 4706 of (4702 4706) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0.276...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.87
pass 1: epoch 2 of 3 starting distance error %19.84
unfolding complete - removing small folds...
starting distance error %19.72
removing remaining folds...
final distance error %19.75
MRISunfold() return, current seed 1234
-01: dt=0.0000, 497 negative triangles
200: dt=0.9900, 497 negative triangles
201: dt=0.9900, 249 negative triangles
202: dt=0.9900, 150 negative triangles
203: dt=0.9900, 128 negative triangles
204: dt=0.9900, 105 negative triangles
205: dt=0.9900, 109 negative triangles
206: dt=0.9900, 94 negative triangles
207: dt=0.9900, 109 negative triangles
208: dt=0.9900, 98 negative triangles
209: dt=0.9900, 75 negative triangles
210: dt=0.9900, 77 negative triangles
211: dt=0.9900, 80 negative triangles
212: dt=0.9900, 65 negative triangles
213: dt=0.9900, 58 negative triangles
214: dt=0.9900, 49 negative triangles
215: dt=0.9900, 45 negative triangles
216: dt=0.9900, 36 negative triangles
217: dt=0.9900, 41 negative triangles
218: dt=0.9900, 37 negative triangles
219: dt=0.9900, 33 negative triangles
220: dt=0.9900, 31 negative triangles
221: dt=0.9900, 27 negative triangles
222: dt=0.9900, 24 negative triangles
223: dt=0.9900, 24 negative triangles
224: dt=0.9900, 23 negative triangles
225: dt=0.9900, 16 negative triangles
226: dt=0.9900, 16 negative triangles
227: dt=0.9900, 18 negative triangles
228: dt=0.9900, 19 negative triangles
229: dt=0.9900, 7 negative triangles
230: dt=0.9900, 9 negative triangles
231: dt=0.9900, 4 negative triangles
232: dt=0.9900, 4 negative triangles
233: dt=0.9900, 5 negative triangles
234: dt=0.9900, 3 negative triangles
235: dt=0.9900, 1 negative triangles
236: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.08 hours
mris_sphere utimesec    3874.372005
mris_sphere stimesec    1.644749
mris_sphere ru_maxrss   300416
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   52819
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10312
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    135768
mris_sphere ru_nivcsw   318891
FSRUNTIME@ mris_sphere  1.0760 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0.280...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.01
pass 1: epoch 2 of 3 starting distance error %19.95
unfolding complete - removing small folds...
starting distance error %19.81
removing remaining folds...
final distance error %19.85
MRISunfold() return, current seed 1234
-01: dt=0.0000, 288 negative triangles
293: dt=0.9900, 288 negative triangles
294: dt=0.9900, 111 negative triangles
295: dt=0.9900, 94 negative triangles
296: dt=0.9900, 80 negative triangles
297: dt=0.9900, 63 negative triangles
298: dt=0.9900, 68 negative triangles
299: dt=0.9900, 65 negative triangles
300: dt=0.9900, 64 negative triangles
301: dt=0.9900, 52 negative triangles
302: dt=0.9900, 59 negative triangles
303: dt=0.9900, 48 negative triangles
304: dt=0.9900, 54 negative triangles
305: dt=0.9900, 52 negative triangles
306: dt=0.9900, 46 negative triangles
307: dt=0.9900, 44 negative triangles
308: dt=0.9900, 42 negative triangles
309: dt=0.9900, 41 negative triangles
310: dt=0.9900, 38 negative triangles
311: dt=0.9900, 43 negative triangles
312: dt=0.9900, 39 negative triangles
313: dt=0.9900, 37 negative triangles
314: dt=0.9900, 38 negative triangles
315: dt=0.9900, 31 negative triangles
316: dt=0.9900, 35 negative triangles
317: dt=0.9900, 34 negative triangles
318: dt=0.9900, 26 negative triangles
319: dt=0.9900, 31 negative triangles
320: dt=0.9900, 26 negative triangles
321: dt=0.9900, 22 negative triangles
322: dt=0.9900, 22 negative triangles
323: dt=0.9900, 15 negative triangles
324: dt=0.9900, 17 negative triangles
325: dt=0.9900, 16 negative triangles
326: dt=0.9900, 19 negative triangles
327: dt=0.9900, 12 negative triangles
328: dt=0.9900, 18 negative triangles
329: dt=0.9900, 16 negative triangles
330: dt=0.9900, 16 negative triangles
331: dt=0.9900, 16 negative triangles
332: dt=0.9900, 17 negative triangles
333: dt=0.9900, 16 negative triangles
334: dt=0.9900, 10 negative triangles
335: dt=0.9900, 10 negative triangles
336: dt=0.9900, 11 negative triangles
337: dt=0.9900, 6 negative triangles
338: dt=0.9900, 8 negative triangles
339: dt=0.9900, 10 negative triangles
340: dt=0.9900, 8 negative triangles
341: dt=0.9900, 7 negative triangles
342: dt=0.9900, 9 negative triangles
343: dt=0.9900, 5 negative triangles
344: dt=0.9900, 5 negative triangles
345: dt=0.9900, 2 negative triangles
346: dt=0.9900, 4 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.15 hours
mris_sphere utimesec    4302.337945
mris_sphere stimesec    1.346795
mris_sphere ru_maxrss   299540
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   53112
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10288
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    150372
mris_sphere ru_nivcsw   314300
FSRUNTIME@ mris_sphere  1.1499 hours 1 threads
PIDs (4702 4706) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 01:40:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 01:40:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 10574 of (10574 10577) to complete...
Waiting for PID 10577 of (10574 10577) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 5.397
curvature mean = 0.042, std = 0.822
curvature mean = 0.024, std = 0.863
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 16.00) sse = 349481.3, tmin=1.1258
  d=32.00 min @ (-8.00, 0.00, 8.00) sse = 255635.6, tmin=2.2899
  d=16.00 min @ (4.00, 4.00, -4.00) sse = 230553.5, tmin=3.4594
  d=8.00 min @ (-2.00, 0.00, 2.00) sse = 214545.4, tmin=4.6626
  d=1.00 min @ (0.25, 0.25, -0.25) sse = 214239.8, tmin=8.2937
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 214222.4, tmin=9.4774
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.48 min
curvature mean = -0.003, std = 0.836
curvature mean = 0.008, std = 0.948
curvature mean = -0.009, std = 0.845
curvature mean = 0.003, std = 0.979
curvature mean = -0.010, std = 0.847
curvature mean = 0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.042, std = 0.410
curvature mean = 0.036, std = 0.249
curvature mean = 0.076, std = 0.244
curvature mean = 0.028, std = 0.307
curvature mean = 0.051, std = 0.378
curvature mean = 0.027, std = 0.334
curvature mean = 0.031, std = 0.494
curvature mean = 0.027, std = 0.345
curvature mean = 0.012, std = 0.605
MRISregister() return, current seed 0
-01: dt=0.0000, 162 negative triangles
114: dt=0.9900, 162 negative triangles
expanding nbhd size to 1
115: dt=0.9900, 222 negative triangles
116: dt=0.9900, 151 negative triangles
117: dt=0.9900, 139 negative triangles
118: dt=0.9900, 145 negative triangles
119: dt=0.9900, 142 negative triangles
120: dt=0.9900, 132 negative triangles
121: dt=0.9900, 114 negative triangles
122: dt=0.9900, 108 negative triangles
123: dt=0.9900, 89 negative triangles
124: dt=0.9900, 82 negative triangles
125: dt=0.9900, 75 negative triangles
126: dt=0.9900, 72 negative triangles
127: dt=0.9900, 65 negative triangles
128: dt=0.9900, 61 negative triangles
129: dt=0.9900, 55 negative triangles
130: dt=0.9900, 53 negative triangles
131: dt=0.9900, 47 negative triangles
132: dt=0.9900, 42 negative triangles
133: dt=0.9900, 35 negative triangles
134: dt=0.9900, 27 negative triangles
135: dt=0.9900, 29 negative triangles
136: dt=0.9900, 29 negative triangles
137: dt=0.9900, 28 negative triangles
138: dt=0.9900, 25 negative triangles
139: dt=0.9900, 18 negative triangles
140: dt=0.9900, 20 negative triangles
141: dt=0.9900, 21 negative triangles
142: dt=0.9900, 19 negative triangles
143: dt=0.9900, 17 negative triangles
144: dt=0.9900, 15 negative triangles
145: dt=0.9900, 18 negative triangles
146: dt=0.9900, 22 negative triangles
147: dt=0.9900, 16 negative triangles
148: dt=0.9900, 16 negative triangles
149: dt=0.9900, 15 negative triangles
150: dt=0.9900, 11 negative triangles
151: dt=0.9900, 9 negative triangles
152: dt=0.9900, 9 negative triangles
153: dt=0.9900, 7 negative triangles
154: dt=0.9900, 6 negative triangles
155: dt=0.9900, 8 negative triangles
156: dt=0.9900, 5 negative triangles
157: dt=0.9900, 5 negative triangles
158: dt=0.9900, 3 negative triangles
159: dt=0.9900, 3 negative triangles
160: dt=0.9900, 3 negative triangles
161: dt=0.9900, 2 negative triangles
162: dt=0.9900, 1 negative triangles
163: dt=0.9900, 1 negative triangles
164: dt=0.9900, 1 negative triangles
165: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.10 hours
mris_register utimesec    3959.446072
mris_register stimesec    2.863564
mris_register ru_maxrss   268916
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39473
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  10264
mris_register ru_oublock  10352
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    283323
mris_register ru_nivcsw   187665
FSRUNTIME@ mris_register  1.1001 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 5.530
curvature mean = 0.037, std = 0.806
curvature mean = 0.023, std = 0.865
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 32.00) sse = 330577.3, tmin=1.7733
  d=32.00 min @ (-8.00, -8.00, 0.00) sse = 325806.0, tmin=3.5554
  d=16.00 min @ (4.00, 4.00, -4.00) sse = 283991.1, tmin=5.2201
  d=8.00 min @ (0.00, 0.00, 2.00) sse = 283094.7, tmin=6.8810
  d=4.00 min @ (0.00, 0.00, -1.00) sse = 282233.6, tmin=8.5878
  d=2.00 min @ (-0.50, 0.00, 0.00) sse = 281958.2, tmin=10.2638
  d=1.00 min @ (0.25, 0.25, 0.00) sse = 281944.8, tmin=11.9313
  d=0.50 min @ (-0.12, -0.12, 0.12) sse = 281916.7, tmin=13.4244
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  13.42 min
curvature mean = 0.010, std = 0.830
curvature mean = 0.008, std = 0.950
curvature mean = 0.006, std = 0.841
curvature mean = 0.003, std = 0.979
curvature mean = 0.005, std = 0.843
curvature mean = 0.001, std = 0.992
2 Reading smoothwm
curvature mean = -0.041, std = 0.399
curvature mean = 0.034, std = 0.241
curvature mean = 0.075, std = 0.251
curvature mean = 0.027, std = 0.300
curvature mean = 0.050, std = 0.385
curvature mean = 0.026, std = 0.326
curvature mean = 0.030, std = 0.506
curvature mean = 0.026, std = 0.338
curvature mean = 0.010, std = 0.654
MRISregister() return, current seed 0
-01: dt=0.0000, 182 negative triangles
121: dt=0.9900, 182 negative triangles
expanding nbhd size to 1
122: dt=0.9900, 232 negative triangles
123: dt=0.9900, 166 negative triangles
124: dt=0.9900, 170 negative triangles
125: dt=0.9900, 164 negative triangles
126: dt=0.9900, 159 negative triangles
127: dt=0.9900, 156 negative triangles
128: dt=0.9900, 152 negative triangles
129: dt=0.9900, 144 negative triangles
130: dt=0.9900, 130 negative triangles
131: dt=0.9900, 126 negative triangles
132: dt=0.9900, 127 negative triangles
133: dt=0.9900, 133 negative triangles
134: dt=0.9900, 116 negative triangles
135: dt=0.9900, 110 negative triangles
136: dt=0.9900, 112 negative triangles
137: dt=0.9900, 98 negative triangles
138: dt=0.9900, 94 negative triangles
139: dt=0.9900, 97 negative triangles
140: dt=0.9900, 91 negative triangles
141: dt=0.9900, 90 negative triangles
142: dt=0.9900, 85 negative triangles
143: dt=0.9900, 87 negative triangles
144: dt=0.9900, 80 negative triangles
145: dt=0.9900, 75 negative triangles
146: dt=0.9900, 75 negative triangles
147: dt=0.9900, 68 negative triangles
148: dt=0.9900, 70 negative triangles
149: dt=0.9900, 67 negative triangles
150: dt=0.9900, 64 negative triangles
151: dt=0.9900, 61 negative triangles
152: dt=0.9900, 59 negative triangles
153: dt=0.9900, 65 negative triangles
154: dt=0.9900, 59 negative triangles
155: dt=0.9900, 59 negative triangles
156: dt=0.9900, 58 negative triangles
157: dt=0.9900, 53 negative triangles
158: dt=0.9900, 53 negative triangles
159: dt=0.9900, 51 negative triangles
160: dt=0.9900, 51 negative triangles
161: dt=0.9900, 47 negative triangles
162: dt=0.9900, 49 negative triangles
163: dt=0.9900, 41 negative triangles
164: dt=0.9900, 36 negative triangles
165: dt=0.9900, 43 negative triangles
166: dt=0.9900, 37 negative triangles
167: dt=0.9900, 30 negative triangles
168: dt=0.9900, 26 negative triangles
169: dt=0.9900, 28 negative triangles
170: dt=0.9900, 29 negative triangles
171: dt=0.9900, 23 negative triangles
172: dt=0.9900, 21 negative triangles
173: dt=0.9900, 21 negative triangles
174: dt=0.9900, 14 negative triangles
175: dt=0.9900, 11 negative triangles
176: dt=0.9900, 12 negative triangles
177: dt=0.9900, 14 negative triangles
178: dt=0.9900, 10 negative triangles
179: dt=0.9900, 8 negative triangles
180: dt=0.9900, 6 negative triangles
181: dt=0.9900, 9 negative triangles
182: dt=0.9900, 4 negative triangles
183: dt=0.9900, 5 negative triangles
184: dt=0.9900, 4 negative triangles
185: dt=0.9900, 4 negative triangles
186: dt=0.9900, 3 negative triangles
187: dt=0.9900, 6 negative triangles
188: dt=0.9900, 3 negative triangles
189: dt=0.9900, 4 negative triangles
190: dt=0.9900, 2 negative triangles
191: dt=0.9900, 4 negative triangles
192: dt=0.9900, 2 negative triangles
193: dt=0.9900, 1 negative triangles
194: dt=0.9900, 2 negative triangles
195: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.88 hours
mris_register utimesec    8524.866023
mris_register stimesec    3.690438
mris_register ru_maxrss   269536
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38253
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10352
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    260532
mris_register ru_nivcsw   239105
FSRUNTIME@ mris_register  1.8789 hours 1 threads
PIDs (10574 10577) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 03:33:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 03:33:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

Waiting for PID 17075 of (17075 17078) to complete...
Waiting for PID 17078 of (17075 17078) 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 (17075 17078) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 03:33:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

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

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 03:33:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 17119 of (17119 17122) to complete...
Waiting for PID 17122 of (17119 17122) 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 (17119 17122) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 03:33:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 03:33:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 17165 of (17165 17168) to complete...
Waiting for PID 17168 of (17165 17168) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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...
2010 labels changed using aseg
relabeling using gibbs priors...
000:   3488 changed, 145874 examined...
001:    774 changed, 14441 examined...
002:    196 changed, 4263 examined...
003:     83 changed, 1167 examined...
004:     22 changed, 511 examined...
005:      6 changed, 142 examined...
006:      1 changed, 35 examined...
007:      1 changed, 7 examined...
008:      1 changed, 5 examined...
009:      0 changed, 8 examined...
302 labels changed using aseg
000: 158 total segments, 115 labels (487 vertices) changed
001: 41 total segments, 1 labels (3 vertices) changed
002: 40 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...
2035 vertices marked for relabeling...
2035 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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...
1297 labels changed using aseg
relabeling using gibbs priors...
000:   2958 changed, 145578 examined...
001:    712 changed, 12719 examined...
002:    205 changed, 4034 examined...
003:     72 changed, 1225 examined...
004:     32 changed, 429 examined...
005:     14 changed, 171 examined...
006:      6 changed, 77 examined...
007:      4 changed, 26 examined...
008:      2 changed, 21 examined...
009:      1 changed, 14 examined...
010:      1 changed, 9 examined...
011:      0 changed, 7 examined...
198 labels changed using aseg
000: 117 total segments, 80 labels (361 vertices) changed
001: 40 total segments, 3 labels (6 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 9 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1846 vertices marked for relabeling...
1846 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 16 seconds.
PIDs (17165 17168) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 03:33:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 03:33:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 rh 

Waiting for PID 17210 of (17210 17213) to complete...
Waiting for PID 17213 of (17210 17213) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
34293 bright wm thresholded.
656 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.orig...
computing class statistics...
border white:    276628 voxels (1.65%)
border gray      335243 voxels (2.00%)
WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0]
GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70)
setting MAX_BORDER_WHITE to 110.7 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 51.7 (was 40)
setting MAX_GRAY to 93.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=102+-8.7,    GM=72+-6.1
mean inside = 93.0, mean outside = 76.3
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.27 (0.04-->5.57) (max @ vno 41855 --> 52144)
face area 0.32 +- 0.17 (0.00-->6.60)
mean absolute distance = 0.61 +- 0.80
3617 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
deleting segment 4 with 336 points - only 0.00% unknown
deleting segment 5 with 47 points - only 0.00% unknown
deleting segment 6 with 119 points - only 3.36% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 77 points - only 0.00% unknown
deleting segment 9 with 70 points - only 0.00% unknown
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 11 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
mean border=81.4, 389 (389) missing vertices, mean dist 0.4 [0.9 (%12.3)->0.6 (%87.7))]
%71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.28 (0.04-->5.51) (max @ vno 144523 --> 99492)
face area 0.32 +- 0.17 (0.00-->6.09)
mean absolute distance = 0.36 +- 0.55
3645 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2198188.2, rms=7.356
001: dt: 0.5000, sse=1208734.9, rms=4.308 (41.429%)
002: dt: 0.5000, sse=992092.4, rms=3.339 (22.513%)
003: dt: 0.5000, sse=972265.1, rms=3.236 (3.073%)
004: dt: 0.5000, sse=945914.4, rms=3.096 (4.314%)
rms = 3.21, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=846407.2, rms=2.426 (21.663%)
006: dt: 0.2500, sse=812834.5, rms=2.121 (12.566%)
007: dt: 0.2500, sse=806034.5, rms=2.045 (3.584%)
rms = 2.02, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=804031.2, rms=2.022 (1.109%)
rms = 1.98, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=798708.2, rms=1.983 (1.957%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 135 points - only 0.00% unknown
deleting segment 3 with 37 points - only 0.00% unknown
deleting segment 5 with 8 points - only 0.00% unknown
deleting segment 6 with 80 points - only 1.25% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 88 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 26 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=84.8, 251 (90) missing vertices, mean dist -0.2 [0.4 (%76.1)->0.3 (%23.9))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.28 (0.06-->5.66) (max @ vno 41855 --> 52144)
face area 0.34 +- 0.18 (0.00-->6.99)
mean absolute distance = 0.26 +- 0.38
3620 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1244423.8, rms=4.359
010: dt: 0.5000, sse=934223.2, rms=2.776 (36.303%)
rms = 2.86, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=849653.2, rms=2.189 (21.152%)
012: dt: 0.2500, sse=812410.2, rms=1.812 (17.228%)
013: dt: 0.2500, sse=797293.2, rms=1.677 (7.441%)
rms = 1.64, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=799410.2, rms=1.641 (2.168%)
rms = 1.60, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=796795.0, rms=1.598 (2.616%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 173 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 53 points - only 0.00% unknown
deleting segment 4 with 11 points - only 0.00% unknown
deleting segment 5 with 99 points - only 1.01% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 98 points - only 0.00% unknown
deleting segment 8 with 68 points - only 0.00% unknown
deleting segment 9 with 16 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
mean border=86.5, 280 (62) missing vertices, mean dist -0.1 [0.3 (%65.6)->0.2 (%34.4))]
%88 local maxima, % 7 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 0.88 +- 0.28 (0.02-->6.17) (max @ vno 144523 --> 99492)
face area 0.33 +- 0.18 (0.00-->6.76)
mean absolute distance = 0.23 +- 0.33
3273 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=910425.6, rms=2.700
016: dt: 0.5000, sse=892113.8, rms=2.480 (8.124%)
rms = 2.74, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=801667.6, rms=1.839 (25.866%)
018: dt: 0.2500, sse=781060.2, rms=1.564 (14.946%)
rms = 1.52, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=772629.4, rms=1.515 (3.110%)
020: dt: 0.1250, sse=762512.5, rms=1.462 (3.550%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=761136.9, rms=1.465 (-0.215%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 8 points - only 0.00% unknown
deleting segment 1 with 224 points - only 0.00% unknown
deleting segment 2 with 51 points - only 0.00% unknown
deleting segment 3 with 13 points - only 0.00% unknown
deleting segment 4 with 109 points - only 3.67% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 92 points - only 0.00% unknown
deleting segment 7 with 85 points - only 0.00% unknown
deleting segment 8 with 16 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
mean border=87.2, 356 (51) missing vertices, mean dist -0.0 [0.2 (%54.1)->0.2 (%45.9))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=772832.8, rms=1.641
rms = 1.61, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=784003.3, rms=1.610 (1.883%)
023: dt: 0.2500, sse=750423.9, rms=1.412 (12.352%)
024: dt: 0.2500, sse=731587.2, rms=1.201 (14.948%)
rms = 1.28, time step reduction 2 of 3 to 0.125...
rms = 1.16, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=727564.8, rms=1.156 (3.733%)
positioning took 0.5 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 8258 vertices
erasing segment 0 (vno[0] = 21566)
erasing segment 2 (vno[0] = 55077)
erasing segment 3 (vno[0] = 80379)
erasing segment 4 (vno[0] = 85465)
erasing segment 5 (vno[0] = 88894)
erasing segment 6 (vno[0] = 91230)
erasing segment 7 (vno[0] = 100465)
erasing segment 8 (vno[0] = 102306)
erasing segment 9 (vno[0] = 103750)
erasing segment 10 (vno[0] = 105689)
erasing segment 11 (vno[0] = 109031)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.area
vertex spacing 0.88 +- 0.28 (0.02-->6.57) (max @ vno 99492 --> 144523)
face area 0.32 +- 0.17 (0.00-->6.56)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 0 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 9 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=60.3, 419 (419) missing vertices, mean dist 1.7 [0.3 (%0.0)->3.4 (%100.0))]
%13 local maxima, %36 large gradients and %46 min vals, 302 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=22132696.0, rms=27.788
001: dt: 0.0500, sse=19361198.0, rms=25.930 (6.686%)
002: dt: 0.0500, sse=17414760.0, rms=24.541 (5.356%)
003: dt: 0.0500, sse=15956048.0, rms=23.446 (4.462%)
004: dt: 0.0500, sse=14805253.0, rms=22.545 (3.845%)
005: dt: 0.0500, sse=13860292.0, rms=21.776 (3.408%)
006: dt: 0.0500, sse=13060360.0, rms=21.104 (3.087%)
007: dt: 0.0500, sse=12367739.0, rms=20.504 (2.843%)
008: dt: 0.0500, sse=11757229.0, rms=19.960 (2.652%)
009: dt: 0.0500, sse=11212186.0, rms=19.462 (2.497%)
010: dt: 0.0500, sse=10720632.0, rms=19.001 (2.367%)
positioning took 1.1 minutes
mean border=60.2, 350 (220) missing vertices, mean dist 1.5 [0.1 (%0.1)->2.9 (%99.9))]
%14 local maxima, %36 large gradients and %45 min vals, 277 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=11519686.0, rms=19.744
011: dt: 0.0500, sse=11068369.0, rms=19.328 (2.106%)
012: dt: 0.0500, sse=10655709.0, rms=18.940 (2.009%)
013: dt: 0.0500, sse=10276644.0, rms=18.576 (1.921%)
014: dt: 0.0500, sse=9927541.0, rms=18.234 (1.839%)
015: dt: 0.0500, sse=9605562.0, rms=17.913 (1.760%)
016: dt: 0.0500, sse=9307305.0, rms=17.611 (1.689%)
017: dt: 0.0500, sse=9030621.0, rms=17.325 (1.621%)
018: dt: 0.0500, sse=8773234.0, rms=17.055 (1.558%)
019: dt: 0.0500, sse=8533528.0, rms=16.800 (1.497%)
020: dt: 0.0500, sse=8310265.5, rms=16.559 (1.437%)
positioning took 1.1 minutes
mean border=60.1, 386 (167) missing vertices, mean dist 1.3 [0.1 (%0.7)->2.5 (%99.3))]
%14 local maxima, %36 large gradients and %45 min vals, 268 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=8431804.0, rms=16.696
021: dt: 0.0500, sse=8219282.0, rms=16.465 (1.385%)
022: dt: 0.0500, sse=8020377.5, rms=16.245 (1.333%)
023: dt: 0.0500, sse=7833301.0, rms=16.036 (1.287%)
024: dt: 0.0500, sse=7657397.0, rms=15.837 (1.242%)
025: dt: 0.0500, sse=7491480.5, rms=15.646 (1.202%)
026: dt: 0.0500, sse=7334121.5, rms=15.464 (1.168%)
027: dt: 0.0500, sse=7184450.5, rms=15.288 (1.138%)
028: dt: 0.0500, sse=7041449.5, rms=15.118 (1.113%)
029: dt: 0.0500, sse=6903952.5, rms=14.952 (1.094%)
030: dt: 0.0500, sse=6772098.0, rms=14.792 (1.073%)
positioning took 1.1 minutes
mean border=60.0, 415 (137) missing vertices, mean dist 1.2 [0.1 (%3.5)->2.3 (%96.5))]
%14 local maxima, %36 large gradients and %44 min vals, 249 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=6856944.0, rms=14.896
031: dt: 0.5000, sse=5888602.5, rms=13.670 (8.230%)
032: dt: 0.5000, sse=5177780.5, rms=12.688 (7.179%)
033: dt: 0.5000, sse=4613895.5, rms=11.851 (6.602%)
034: dt: 0.5000, sse=4146509.8, rms=11.105 (6.295%)
035: dt: 0.5000, sse=3736659.5, rms=10.408 (6.276%)
036: dt: 0.5000, sse=3362112.0, rms=9.726 (6.551%)
037: dt: 0.5000, sse=3013512.0, rms=9.048 (6.966%)
038: dt: 0.5000, sse=2707063.8, rms=8.407 (7.086%)
039: dt: 0.5000, sse=2454751.8, rms=7.841 (6.732%)
040: dt: 0.5000, sse=2248574.0, rms=7.346 (6.318%)
041: dt: 0.5000, sse=2090582.6, rms=6.942 (5.502%)
042: dt: 0.5000, sse=1968489.2, rms=6.612 (4.750%)
043: dt: 0.5000, sse=1877094.2, rms=6.355 (3.883%)
044: dt: 0.5000, sse=1806466.9, rms=6.148 (3.264%)
045: dt: 0.5000, sse=1758772.8, rms=6.004 (2.334%)
046: dt: 0.5000, sse=1723509.6, rms=5.894 (1.831%)
047: dt: 0.5000, sse=1699506.1, rms=5.819 (1.280%)
048: dt: 0.5000, sse=1681912.2, rms=5.761 (0.990%)
rms = 5.72, time step reduction 1 of 3 to 0.250...
049: dt: 0.5000, sse=1668087.0, rms=5.718 (0.754%)
050: dt: 0.2500, sse=1574821.5, rms=5.372 (6.055%)
051: dt: 0.2500, sse=1541478.8, rms=5.258 (2.109%)
rms = 5.27, time step reduction 2 of 3 to 0.125...
rms = 5.22, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1530856.6, rms=5.219 (0.754%)
positioning took 3.4 minutes
mean border=59.1, 3100 (54) missing vertices, mean dist 0.2 [0.2 (%43.3)->0.7 (%56.7))]
%28 local maxima, %26 large gradients and %40 min vals, 178 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=1787767.5, rms=5.295
053: dt: 0.5000, sse=1736785.1, rms=5.130 (3.119%)
054: dt: 0.5000, sse=1656761.4, rms=4.872 (5.031%)
rms = 5.02, time step reduction 1 of 3 to 0.250...
055: dt: 0.2500, sse=1558106.5, rms=4.447 (8.712%)
056: dt: 0.2500, sse=1538610.2, rms=4.350 (2.183%)
rms = 4.35, time step reduction 2 of 3 to 0.125...
057: dt: 0.2500, sse=1538449.4, rms=4.350 (0.006%)
058: dt: 0.1250, sse=1502240.5, rms=4.185 (3.779%)
rms = 4.16, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1495141.1, rms=4.156 (0.708%)
positioning took 1.4 minutes
mean border=58.6, 3362 (47) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.5 (%56.8))]
%38 local maxima, %16 large gradients and %39 min vals, 225 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1529577.9, rms=4.294
rms = 4.65, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1500595.4, rms=4.164 (3.005%)
rms = 4.14, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1493996.2, rms=4.142 (0.534%)
062: dt: 0.1250, sse=1481034.0, rms=4.080 (1.499%)
rms = 4.05, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1473755.0, rms=4.051 (0.709%)
positioning took 1.0 minutes
mean border=58.2, 7178 (42) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.4 (%56.0))]
%39 local maxima, %14 large gradients and %37 min vals, 226 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-6.0.0/0051348/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1489057.2, rms=4.112
rms = 4.33, time step reduction 1 of 3 to 0.250...
064: dt: 0.2500, sse=1468518.6, rms=4.022 (2.173%)
065: dt: 0.2500, sse=1448120.5, rms=3.954 (1.698%)
rms = 3.94, time step reduction 2 of 3 to 0.125...
066: dt: 0.2500, sse=1441680.8, rms=3.936 (0.441%)
067: dt: 0.1250, sse=1414598.0, rms=3.806 (3.311%)
rms = 3.77, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1406282.4, rms=3.772 (0.893%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.area.pial
vertex spacing 1.02 +- 0.49 (0.01-->7.42) (max @ vno 142655 --> 142771)
face area 0.41 +- 0.36 (0.00-->9.71)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 145874 vertices processed
25000 of 145874 vertices processed
50000 of 145874 vertices processed
75000 of 145874 vertices processed
100000 of 145874 vertices processed
125000 of 145874 vertices processed
0 of 145874 vertices processed
25000 of 145874 vertices processed
50000 of 145874 vertices processed
75000 of 145874 vertices processed
100000 of 145874 vertices processed
125000 of 145874 vertices processed
thickness calculation complete, 704:2293 truncations.
23080 vertices at 0 distance
78689 vertices at 1 distance
89152 vertices at 2 distance
52712 vertices at 3 distance
22098 vertices at 4 distance
7772 vertices at 5 distance
2744 vertices at 6 distance
1033 vertices at 7 distance
476 vertices at 8 distance
234 vertices at 9 distance
134 vertices at 10 distance
111 vertices at 11 distance
81 vertices at 12 distance
53 vertices at 13 distance
46 vertices at 14 distance
35 vertices at 15 distance
34 vertices at 16 distance
21 vertices at 17 distance
25 vertices at 18 distance
22 vertices at 19 distance
34 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.thickness
positioning took 17.9 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
34293 bright wm thresholded.
656 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.orig...
computing class statistics...
border white:    276628 voxels (1.65%)
border gray      335243 voxels (2.00%)
WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0]
GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70)
setting MAX_BORDER_WHITE to 108.7 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 52.7 (was 40)
setting MAX_GRAY to 91.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.6 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-7.8,    GM=73+-6.1
mean inside = 92.5, mean outside = 76.6
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 +- 0.27 (0.04-->6.49) (max @ vno 35333 --> 143154)
face area 0.32 +- 0.16 (0.00-->3.43)
mean absolute distance = 0.60 +- 0.80
3710 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 2 with 344 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 4 with 77 points - only 0.00% unknown
deleting segment 5 with 15 points - only 0.00% unknown
mean border=82.1, 401 (401) missing vertices, mean dist 0.4 [0.9 (%13.3)->0.5 (%86.7))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.89 +- 0.27 (0.06-->6.42) (max @ vno 35333 --> 143154)
face area 0.32 +- 0.17 (0.00-->3.97)
mean absolute distance = 0.36 +- 0.56
3815 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1928981.6, rms=6.702
001: dt: 0.5000, sse=1129069.0, rms=3.971 (40.750%)
002: dt: 0.5000, sse=966667.2, rms=3.173 (20.091%)
003: dt: 0.5000, sse=944354.2, rms=3.122 (1.605%)
004: dt: 0.5000, sse=924102.3, rms=3.002 (3.845%)
rms = 3.12, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=827519.1, rms=2.345 (21.886%)
006: dt: 0.2500, sse=796939.9, rms=2.046 (12.760%)
007: dt: 0.2500, sse=788934.7, rms=1.979 (3.255%)
rms = 1.96, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=819760.0, rms=1.964 (0.795%)
rms = 1.93, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=783494.0, rms=1.929 (1.776%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 1 with 174 points - only 0.00% unknown
deleting segment 2 with 69 points - only 0.00% unknown
deleting segment 3 with 22 points - only 0.00% unknown
mean border=85.2, 292 (106) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.88 +- 0.27 (0.03-->6.56) (max @ vno 35333 --> 143154)
face area 0.33 +- 0.18 (0.00-->4.07)
mean absolute distance = 0.27 +- 0.40
3623 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1150116.6, rms=4.014
010: dt: 0.5000, sse=937153.2, rms=2.704 (32.635%)
rms = 2.74, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=836995.9, rms=2.156 (20.248%)
012: dt: 0.2500, sse=805730.5, rms=1.803 (16.372%)
013: dt: 0.2500, sse=809552.6, rms=1.691 (6.238%)
rms = 1.66, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=782555.9, rms=1.656 (2.043%)
rms = 1.62, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=777586.9, rms=1.615 (2.479%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 230 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 71 points - only 0.00% unknown
deleting segment 3 with 69 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
mean border=86.7, 288 (63) missing vertices, mean dist -0.1 [0.3 (%63.7)->0.2 (%36.3))]
%86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.27 (0.03-->6.60) (max @ vno 35333 --> 143154)
face area 0.32 +- 0.17 (0.00-->3.98)
mean absolute distance = 0.24 +- 0.35
3724 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=868461.6, rms=2.531
016: dt: 0.5000, sse=880415.6, rms=2.401 (5.112%)
rms = 2.61, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=792988.7, rms=1.826 (23.958%)
018: dt: 0.2500, sse=793597.5, rms=1.574 (13.782%)
rms = 1.54, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=764112.3, rms=1.536 (2.445%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=757467.4, rms=1.490 (2.970%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 1 with 233 points - only 0.00% unknown
deleting segment 2 with 24 points - only 0.00% unknown
deleting segment 3 with 76 points - only 0.00% unknown
deleting segment 4 with 70 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 6 points - only 0.00% unknown
mean border=87.3, 328 (46) missing vertices, mean dist -0.0 [0.3 (%53.4)->0.2 (%46.6))]
%88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=765395.2, rms=1.639
021: dt: 0.5000, sse=770163.9, rms=1.575 (3.928%)
rms = 2.27, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=726946.9, rms=1.214 (22.908%)
rms = 1.22, time step reduction 2 of 3 to 0.125...
rms = 1.18, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=722509.5, rms=1.184 (2.513%)
positioning took 0.5 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7396 vertices
erasing segment 1 (vno[0] = 54668)
erasing segment 2 (vno[0] = 76066)
erasing segment 3 (vno[0] = 77481)
erasing segment 4 (vno[0] = 80021)
erasing segment 5 (vno[0] = 96968)
erasing segment 6 (vno[0] = 98092)
erasing segment 7 (vno[0] = 100203)
erasing segment 8 (vno[0] = 103185)
erasing segment 9 (vno[0] = 106167)
erasing segment 10 (vno[0] = 106209)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.area
vertex spacing 0.88 +- 0.27 (0.04-->6.76) (max @ vno 35333 --> 143154)
face area 0.32 +- 0.17 (0.00-->3.93)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=61.5, 416 (416) missing vertices, mean dist 1.7 [0.2 (%0.0)->3.4 (%100.0))]
%13 local maxima, %34 large gradients and %48 min vals, 418 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=20520196.0, rms=26.716
001: dt: 0.0500, sse=17991420.0, rms=24.956 (6.590%)
002: dt: 0.0500, sse=16206763.0, rms=23.634 (5.296%)
003: dt: 0.0500, sse=14864570.0, rms=22.589 (4.422%)
004: dt: 0.0500, sse=13801326.0, rms=21.725 (3.824%)
005: dt: 0.0500, sse=12924272.0, rms=20.986 (3.403%)
006: dt: 0.0500, sse=12178957.0, rms=20.337 (3.095%)
007: dt: 0.0500, sse=11531230.0, rms=19.755 (2.861%)
008: dt: 0.0500, sse=10959714.0, rms=19.227 (2.673%)
009: dt: 0.0500, sse=10449420.0, rms=18.743 (2.518%)
010: dt: 0.0500, sse=9989320.0, rms=18.295 (2.388%)
positioning took 1.1 minutes
mean border=61.3, 337 (206) missing vertices, mean dist 1.4 [0.1 (%0.1)->2.8 (%99.9))]
%14 local maxima, %34 large gradients and %47 min vals, 413 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=10784025.0, rms=19.061
011: dt: 0.0500, sse=10361136.0, rms=18.658 (2.116%)
012: dt: 0.0500, sse=9974506.0, rms=18.281 (2.018%)
013: dt: 0.0500, sse=9620483.0, rms=17.929 (1.924%)
014: dt: 0.0500, sse=9294502.0, rms=17.599 (1.842%)
015: dt: 0.0500, sse=8994681.0, rms=17.290 (1.758%)
016: dt: 0.0500, sse=8717550.0, rms=16.999 (1.683%)
017: dt: 0.0500, sse=8460822.0, rms=16.725 (1.613%)
018: dt: 0.0500, sse=8222816.0, rms=16.466 (1.544%)
019: dt: 0.0500, sse=8002075.5, rms=16.223 (1.477%)
020: dt: 0.0500, sse=7796357.0, rms=15.993 (1.419%)
positioning took 1.0 minutes
mean border=61.3, 358 (161) missing vertices, mean dist 1.3 [0.1 (%1.1)->2.5 (%98.9))]
%15 local maxima, %34 large gradients and %47 min vals, 425 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=7889266.5, rms=16.104
021: dt: 0.0500, sse=7693398.5, rms=15.883 (1.370%)
022: dt: 0.0500, sse=7510562.5, rms=15.674 (1.315%)
023: dt: 0.0500, sse=7338380.5, rms=15.475 (1.272%)
024: dt: 0.0500, sse=7176774.5, rms=15.285 (1.224%)
025: dt: 0.0500, sse=7024301.0, rms=15.104 (1.184%)
026: dt: 0.0500, sse=6880308.5, rms=14.931 (1.146%)
027: dt: 0.0500, sse=6743063.5, rms=14.764 (1.118%)
028: dt: 0.0500, sse=6611835.0, rms=14.603 (1.093%)
029: dt: 0.0500, sse=6485641.0, rms=14.446 (1.075%)
030: dt: 0.0500, sse=6363869.0, rms=14.293 (1.061%)
positioning took 1.1 minutes
mean border=61.2, 376 (132) missing vertices, mean dist 1.1 [0.1 (%4.8)->2.3 (%95.2))]
%15 local maxima, %34 large gradients and %46 min vals, 387 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=6422911.5, rms=14.367
031: dt: 0.5000, sse=5500829.0, rms=13.158 (8.416%)
032: dt: 0.5000, sse=4780914.5, rms=12.124 (7.861%)
033: dt: 0.5000, sse=4200959.0, rms=11.220 (7.458%)
034: dt: 0.5000, sse=3752715.8, rms=10.462 (6.751%)
035: dt: 0.5000, sse=3397909.8, rms=9.821 (6.126%)
036: dt: 0.5000, sse=3091365.5, rms=9.230 (6.024%)
037: dt: 0.5000, sse=2824522.0, rms=8.684 (5.911%)
038: dt: 0.5000, sse=2566864.5, rms=8.122 (6.467%)
039: dt: 0.5000, sse=2350258.0, rms=7.621 (6.179%)
040: dt: 0.5000, sse=2166930.8, rms=7.167 (5.949%)
041: dt: 0.5000, sse=2027087.6, rms=6.803 (5.089%)
042: dt: 0.5000, sse=1921119.4, rms=6.510 (4.296%)
043: dt: 0.5000, sse=1857344.2, rms=6.328 (2.793%)
044: dt: 0.5000, sse=1801126.2, rms=6.162 (2.625%)
045: dt: 0.5000, sse=1766811.2, rms=6.059 (1.683%)
046: dt: 0.5000, sse=1733037.4, rms=5.953 (1.740%)
047: dt: 0.5000, sse=1713136.8, rms=5.891 (1.053%)
048: dt: 0.5000, sse=1692935.1, rms=5.825 (1.104%)
rms = 5.78, time step reduction 1 of 3 to 0.250...
049: dt: 0.5000, sse=1679677.2, rms=5.784 (0.715%)
050: dt: 0.2500, sse=1593396.5, rms=5.468 (5.459%)
051: dt: 0.2500, sse=1564165.4, rms=5.370 (1.796%)
rms = 5.37, time step reduction 2 of 3 to 0.125...
052: dt: 0.2500, sse=1564888.5, rms=5.369 (0.008%)
053: dt: 0.1250, sse=1538145.8, rms=5.272 (1.815%)
rms = 5.25, time step reduction 3 of 3 to 0.062...
054: dt: 0.1250, sse=1531917.1, rms=5.250 (0.413%)
positioning took 3.7 minutes
mean border=60.3, 3448 (44) missing vertices, mean dist 0.2 [0.2 (%42.0)->0.8 (%58.0))]
%27 local maxima, %24 large gradients and %42 min vals, 228 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=1764203.1, rms=5.293
055: dt: 0.5000, sse=1726737.8, rms=5.180 (2.133%)
056: dt: 0.5000, sse=1627977.2, rms=4.847 (6.435%)
rms = 5.03, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1542813.8, rms=4.481 (7.535%)
058: dt: 0.2500, sse=1521949.6, rms=4.382 (2.209%)
rms = 4.39, time step reduction 2 of 3 to 0.125...
059: dt: 0.1250, sse=1510851.6, rms=4.332 (1.158%)
060: dt: 0.1250, sse=1495284.6, rms=4.260 (1.666%)
rms = 4.23, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1489195.0, rms=4.233 (0.630%)
positioning took 1.6 minutes
mean border=59.8, 3865 (34) missing vertices, mean dist 0.1 [0.2 (%40.8)->0.5 (%59.2))]
%36 local maxima, %16 large gradients and %41 min vals, 251 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=1527263.0, rms=4.365
rms = 4.65, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1501552.9, rms=4.253 (2.568%)
rms = 4.22, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1491370.2, rms=4.217 (0.858%)
064: dt: 0.1250, sse=1478646.5, rms=4.157 (1.425%)
rms = 4.13, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1470852.2, rms=4.126 (0.742%)
positioning took 1.0 minutes
mean border=59.4, 7625 (29) missing vertices, mean dist 0.1 [0.2 (%42.3)->0.4 (%57.7))]
%37 local maxima, %14 large gradients and %40 min vals, 251 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-6.0.0/0051348/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1483253.2, rms=4.159
rms = 4.31, time step reduction 1 of 3 to 0.250...
066: dt: 0.2500, sse=1464275.0, rms=4.077 (1.964%)
067: dt: 0.2500, sse=1441790.1, rms=3.999 (1.913%)
rms = 3.97, time step reduction 2 of 3 to 0.125...
068: dt: 0.2500, sse=1433126.2, rms=3.973 (0.653%)
069: dt: 0.1250, sse=1409773.8, rms=3.861 (2.829%)
rms = 3.82, time step reduction 3 of 3 to 0.062...
070: dt: 0.1250, sse=1400238.9, rms=3.821 (1.041%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.area.pial
vertex spacing 1.01 +- 0.49 (0.04-->8.53) (max @ vno 53052 --> 143015)
face area 0.40 +- 0.36 (0.00-->10.04)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 145578 vertices processed
25000 of 145578 vertices processed
50000 of 145578 vertices processed
75000 of 145578 vertices processed
100000 of 145578 vertices processed
125000 of 145578 vertices processed
0 of 145578 vertices processed
25000 of 145578 vertices processed
50000 of 145578 vertices processed
75000 of 145578 vertices processed
100000 of 145578 vertices processed
125000 of 145578 vertices processed
thickness calculation complete, 634:2599 truncations.
22912 vertices at 0 distance
78215 vertices at 1 distance
88903 vertices at 2 distance
52592 vertices at 3 distance
22570 vertices at 4 distance
8063 vertices at 5 distance
2950 vertices at 6 distance
1143 vertices at 7 distance
529 vertices at 8 distance
275 vertices at 9 distance
157 vertices at 10 distance
115 vertices at 11 distance
88 vertices at 12 distance
56 vertices at 13 distance
35 vertices at 14 distance
39 vertices at 15 distance
35 vertices at 16 distance
30 vertices at 17 distance
34 vertices at 18 distance
29 vertices at 19 distance
48 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.thickness
positioning took 18.1 minutes
PIDs (17210 17213) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 03:51:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label
Total face volume 298461
Total vertex volume 295075 (mask=0)
#@# 0051348 lh 295075
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 03:51:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label
Total face volume 295119
Total vertex volume 291788 (mask=0)
#@# 0051348 rh 291788
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 03:51:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 

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 = 314
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/ribbon.mgz
mris_volmask took 22.04 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 04:13:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 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 0051348 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 04:13:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 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 0051348 rh pial 

Waiting for PID 20413 of (20413 20416 20419 20422) to complete...
Waiting for PID 20416 of (20413 20416 20419 20422) to complete...
Waiting for PID 20419 of (20413 20416 20419 20422) to complete...
Waiting for PID 20422 of (20413 20416 20419 20422) 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 0051348 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461
Total vertex volume 295075 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1295    862   2558  3.108 0.408     0.086     0.016        7     0.8  bankssts
 1291    817   2982  3.141 0.615     0.136     0.032       24     1.6  caudalanteriorcingulate
 3991   2586   8713  2.938 0.572     0.126     0.049       54     8.6  caudalmiddlefrontal
 2277   1358   3500  2.251 0.583     0.125     0.041       30     3.8  cuneus
  681    446   1833  3.198 0.915     0.139     0.048       11     1.4  entorhinal
 4359   3009  10659  3.085 0.609     0.143     0.042       80     7.8  fusiform
 8501   5613  17859  2.863 0.579     0.135     0.040      142    14.2  inferiorparietal
 5389   3549  13909  3.066 0.654     0.136     0.044       99     9.6  inferiortemporal
 1753   1129   3372  2.633 0.840     0.136     0.039       32     2.4  isthmuscingulate
 7896   4799  14201  2.567 0.601     0.131     0.035      110    11.4  lateraloccipital
 3675   2465   8793  3.177 0.743     0.135     0.044       56     6.5  lateralorbitofrontal
 4583   2974   8146  2.485 0.678     0.135     0.041       70     7.3  lingual
 2761   1781   5626  2.622 0.815     0.144     0.057       69     7.3  medialorbitofrontal
 4480   2939  12382  3.261 0.678     0.141     0.049       85     8.2  middletemporal
  911    581   2234  3.128 0.637     0.119     0.036       11     1.2  parahippocampal
 2427   1524   4560  2.691 0.633     0.115     0.038       25     4.0  paracentral
 2805   1817   6740  3.004 0.585     0.137     0.045       45     5.3  parsopercularis
  936    595   2932  3.448 0.682     0.153     0.065       24     2.6  parsorbitalis
 1695   1126   3827  2.904 0.591     0.121     0.036       22     2.6  parstriangularis
 1844   1291   2003  1.800 0.453     0.135     0.041       20     3.6  pericalcarine
 7271   4512  12205  2.373 0.660     0.130     0.047      130    14.6  postcentral
 1837   1202   3970  2.919 0.990     0.155     0.043       37     3.0  posteriorcingulate
 8785   5298  15921  2.749 0.608     0.125     0.050      129    17.9  precentral
 5797   3826  12456  2.992 0.611     0.121     0.032       82     7.3  precuneus
 1334    867   3645  3.523 0.761     0.147     0.054       35     2.8  rostralanteriorcingulate
 9136   6102  22006  2.891 0.692     0.138     0.043      153    16.8  rostralmiddlefrontal
10656   6984  25467  3.084 0.736     0.134     0.049      175    22.9  superiorfrontal
 9304   6148  17892  2.616 0.572     0.134     0.043      160    17.6  superiorparietal
 5849   3850  13683  3.055 0.668     0.128     0.045      106    11.4  superiortemporal
 7492   5011  17145  2.950 0.568     0.122     0.039      115    13.2  supramarginal
  406    263   1081  2.757 0.552     0.160     0.058       16     0.8  frontalpole
  857    550   2959  3.606 0.677     0.155     0.065       17     2.4  temporalpole
  835    478   1519  2.627 0.574     0.121     0.056       15     1.8  transversetemporal
 4054   2645   8208  3.080 0.775     0.134     0.056       59    10.5  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 0051348 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461
Total vertex volume 295075 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1295    801   2558  3.108 0.408     0.126     0.041       32     2.1  bankssts
 1291   1194   2982  3.141 0.615     0.191     0.056       33     3.2  caudalanteriorcingulate
 3991   3202   8713  2.938 0.572     0.145     0.041       61     7.2  caudalmiddlefrontal
 2277   1762   3500  2.251 0.583     0.135     0.033       28     3.4  cuneus
  681    700   1833  3.198 0.915     0.182     0.053       18     1.6  entorhinal
 4359   4008  10659  3.085 0.609     0.175     0.047       76     9.6  fusiform
 8501   6770  17859  2.863 0.579     0.149     0.044      172    16.8  inferiorparietal
 5389   5394  13909  3.066 0.654     0.187     0.050       98    12.8  inferiortemporal
 1753   1478   3372  2.633 0.840     0.186     0.054       50     4.1  isthmuscingulate
 7896   6253  14201  2.567 0.601     0.133     0.032      160    11.6  lateraloccipital
 3675   2995   8793  3.177 0.743     0.158     0.046       69     7.3  lateralorbitofrontal
 4583   3738   8146  2.485 0.678     0.150     0.042       66     8.6  lingual
 2761   2512   5626  2.622 0.815     0.200     0.071       83     9.9  medialorbitofrontal
 4480   4315  12382  3.261 0.678     0.177     0.044       73     9.5  middletemporal
  911    886   2234  3.128 0.637     0.180     0.044       14     1.7  parahippocampal
 2427   1872   4560  2.691 0.633     0.137     0.037       26     4.1  paracentral
 2805   2598   6740  3.004 0.585     0.167     0.043       39     5.5  parsopercularis
  936   1000   2932  3.448 0.682     0.190     0.043       12     1.9  parsorbitalis
 1695   1465   3827  2.904 0.591     0.162     0.042       26     3.4  parstriangularis
 1844    976   2003  1.800 0.453     0.101     0.029       25     2.1  pericalcarine
 7271   5601  12205  2.373 0.660     0.129     0.035      141    12.2  postcentral
 1837   1475   3970  2.919 0.990     0.167     0.047       45     3.4  posteriorcingulate
 8785   5971  15921  2.749 0.608     0.120     0.035      114    12.7  precentral
 5797   4566  12456  2.992 0.611     0.143     0.037       99     9.7  precuneus
 1334   1355   3645  3.523 0.761     0.206     0.064       36     4.6  rostralanteriorcingulate
 9136   8523  22006  2.891 0.692     0.184     0.050      166    21.7  rostralmiddlefrontal
10656   9133  25467  3.084 0.736     0.166     0.055      306    30.1  superiorfrontal
 9304   7343  17892  2.616 0.572     0.145     0.039      147    16.3  superiorparietal
 5849   4833  13683  3.055 0.668     0.156     0.042      120    11.1  superiortemporal
 7492   6392  17145  2.950 0.568     0.149     0.040      117    12.9  supramarginal
  406    521   1081  2.757 0.552     0.230     0.051        6     1.1  frontalpole
  857   1113   2959  3.606 0.677     0.216     0.049       12     2.2  temporalpole
  835    686   1519  2.627 0.574     0.146     0.038        8     1.4  transversetemporal
 4054   2460   8208  3.080 0.775     0.142     0.050      104     8.0  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 0051348 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119
Total vertex volume 291788 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1866   1249   3599  3.078 0.450     0.105     0.025       13     1.8  bankssts
  897    549   1619  2.749 0.707     0.136     0.036       17     1.3  caudalanteriorcingulate
 3651   2404   7992  2.985 0.560     0.126     0.043       59     6.4  caudalmiddlefrontal
 2550   1602   4312  2.345 0.593     0.150     0.041       43     4.1  cuneus
  392    264   1431  3.604 0.782     0.137     0.042        5     0.7  entorhinal
 3955   2686   9504  3.056 0.679     0.133     0.046       69     7.7  fusiform
 9552   6227  20799  2.987 0.600     0.131     0.041      152    15.9  inferiorparietal
 4186   2672  10144  3.007 0.753     0.137     0.053       75    10.1  inferiortemporal
 1477    940   2764  2.659 0.979     0.142     0.037       28     2.0  isthmuscingulate
 6844   4180  12169  2.614 0.578     0.127     0.035       95     9.6  lateraloccipital
 3524   2301   8421  3.114 0.801     0.135     0.051       63     6.9  lateralorbitofrontal
 5122   3210   8947  2.547 0.707     0.136     0.042       79     8.8  lingual
 2656   1840   6657  2.855 0.634     0.146     0.058       59     7.0  medialorbitofrontal
 5169   3326  14311  3.260 0.682     0.133     0.046       92     9.8  middletemporal
 1043    648   2374  3.015 0.683     0.122     0.063       22     3.1  parahippocampal
 2779   1779   5278  2.769 0.596     0.110     0.035       33     3.9  paracentral
 1886   1273   4602  2.972 0.635     0.127     0.040       24     3.4  parsopercularis
 1086    724   3828  3.483 0.711     0.141     0.048       17     2.1  parsorbitalis
 1858   1305   4629  3.074 0.609     0.126     0.038       23     2.8  parstriangularis
 2404   1542   2435  1.802 0.510     0.142     0.041       34     4.0  pericalcarine
 7413   4639  12470  2.384 0.673     0.129     0.049      125    16.1  postcentral
 1907   1271   3874  2.855 0.665     0.135     0.031       29     2.4  posteriorcingulate
 9842   5967  17557  2.643 0.634     0.135     0.055      176    22.4  precentral
 5879   3942  12145  2.862 0.626     0.127     0.035       89     8.5  precuneus
 1035    666   2673  3.490 0.578     0.133     0.048       20     2.2  rostralanteriorcingulate
 9282   6081  20269  2.661 0.667     0.140     0.049      191    19.5  rostralmiddlefrontal
 9683   6527  24690  3.103 0.710     0.134     0.050      158    21.1  superiorfrontal
10818   6723  18241  2.513 0.556     0.125     0.044      165    19.9  superiorparietal
 6521   4251  16193  3.138 0.677     0.117     0.040       94    11.2  superiortemporal
 6951   4431  14404  2.915 0.609     0.132     0.062      166    22.1  supramarginal
  411    281   1394  2.944 0.690     0.182     0.056       12     1.0  frontalpole
  642    415   2287  3.469 0.692     0.172     0.074       19     2.1  temporalpole
  705    441   1402  2.611 0.448     0.130     0.036       11     0.8  transversetemporal
 3890   2517   8317  3.141 1.073     0.124     0.052       55     7.8  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 0051348 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119
Total vertex volume 291788 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1866   1111   3599  3.078 0.450     0.133     0.042       32     3.4  bankssts
  897    670   1619  2.749 0.707     0.163     0.046       16     1.9  caudalanteriorcingulate
 3651   2838   7992  2.985 0.560     0.159     0.049       68     8.2  caudalmiddlefrontal
 2550   2137   4312  2.345 0.593     0.156     0.041       46     4.6  cuneus
  392    519   1431  3.604 0.782     0.237     0.060        9     1.3  entorhinal
 3955   3420   9504  3.056 0.679     0.165     0.045       71     8.3  fusiform
 9552   7578  20799  2.987 0.600     0.144     0.040      161    16.9  inferiorparietal
 4186   3870  10144  3.007 0.753     0.179     0.052       84     9.8  inferiortemporal
 1477   1134   2764  2.659 0.979     0.167     0.048       42     3.2  isthmuscingulate
 6844   5033  12169  2.614 0.578     0.124     0.030       98     9.4  lateraloccipital
 3524   2939   8421  3.114 0.801     0.172     0.052       73     8.3  lateralorbitofrontal
 5122   4001   8947  2.547 0.707     0.148     0.040       84     9.0  lingual
 2656   2804   6657  2.855 0.634     0.215     0.062       56     8.0  medialorbitofrontal
 5169   5215  14311  3.260 0.682     0.179     0.048       83    11.6  middletemporal
 1043    873   2374  3.015 0.683     0.153     0.046       16     2.6  parahippocampal
 2779   2056   5278  2.769 0.596     0.132     0.037       42     4.8  paracentral
 1886   1738   4602  2.972 0.635     0.175     0.045       26     4.0  parsopercularis
 1086   1391   3828  3.483 0.711     0.199     0.043       13     2.0  parsorbitalis
 1858   1655   4629  3.074 0.609     0.157     0.042       26     3.3  parstriangularis
 2404   1279   2435  1.802 0.510     0.107     0.032       39     3.2  pericalcarine
 7413   5677  12470  2.384 0.673     0.135     0.037       89    12.2  postcentral
 1907   1551   3874  2.855 0.665     0.172     0.051       51     4.6  posteriorcingulate
 9842   6886  17557  2.643 0.634     0.125     0.035      125    15.6  precentral
 5879   4572  12145  2.862 0.626     0.148     0.044      107    10.0  precuneus
 1035    897   2673  3.490 0.578     0.187     0.051       26     2.4  rostralanteriorcingulate
 9282   8783  20269  2.661 0.667     0.199     0.058      180    26.7  rostralmiddlefrontal
 9683   8987  24690  3.103 0.710     0.177     0.051      186    23.4  superiorfrontal
10818   7605  18241  2.513 0.556     0.133     0.039      167    18.9  superiorparietal
 6521   5872  16193  3.138 0.677     0.163     0.043      103    12.9  superiortemporal
 6951   5240  14404  2.915 0.609     0.148     0.045      131    13.7  supramarginal
  411    636   1394  2.944 0.690     0.262     0.061        5     1.3  frontalpole
  642    874   2287  3.469 0.692     0.221     0.055        8     1.7  temporalpole
  705    600   1402  2.611 0.448     0.151     0.037        9     1.1  transversetemporal
 3890   2472   8317  3.141 1.073     0.153     0.071      151     8.9  insula
PIDs (20413 20416 20419 20422) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 04:15:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 04:15:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 20595 of (20595 20598) to complete...
Waiting for PID 20598 of (20595 20598) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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...
34 labels changed using aseg
relabeling using gibbs priors...
000:   9676 changed, 145874 examined...
001:   2278 changed, 37039 examined...
002:    666 changed, 11859 examined...
003:    286 changed, 3878 examined...
004:    124 changed, 1571 examined...
005:     62 changed, 744 examined...
006:     26 changed, 354 examined...
007:      9 changed, 131 examined...
008:      6 changed, 55 examined...
009:      4 changed, 31 examined...
010:      4 changed, 24 examined...
011:      1 changed, 21 examined...
012:      0 changed, 6 examined...
9 labels changed using aseg
000: 272 total segments, 188 labels (2279 vertices) changed
001: 96 total segments, 12 labels (33 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 46 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1279 vertices marked for relabeling...
1279 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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:   9413 changed, 145578 examined...
001:   2147 changed, 36725 examined...
002:    631 changed, 11344 examined...
003:    254 changed, 3571 examined...
004:     99 changed, 1477 examined...
005:     59 changed, 576 examined...
006:     34 changed, 351 examined...
007:     16 changed, 177 examined...
008:     11 changed, 90 examined...
009:      3 changed, 61 examined...
010:      0 changed, 21 examined...
5 labels changed using aseg
000: 270 total segments, 187 labels (2925 vertices) changed
001: 98 total segments, 15 labels (63 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 27 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1337 vertices marked for relabeling...
1337 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.
PIDs (20595 20598) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 04:15:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 04:15:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh white 

Waiting for PID 20641 of (20641 20644) to complete...
Waiting for PID 20644 of (20641 20644) 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 0051348 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461
Total vertex volume 295075 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1420    977   3392  2.803 0.718     0.153     0.047       32     2.7  G&S_frontomargin
 1429    908   3098  2.762 0.493     0.130     0.030       19     1.7  G&S_occipital_inf
 2034   1160   3528  2.440 0.704     0.132     0.058       36     5.5  G&S_paracentral
 1747   1148   3837  2.971 0.571     0.145     0.046       31     2.9  G&S_subcentral
  740    508   2484  3.050 0.599     0.159     0.060       23     1.7  G&S_transv_frontopol
 2300   1549   5525  3.154 0.654     0.123     0.039       39     3.5  G&S_cingul-Ant
 1361    914   3113  3.010 0.563     0.116     0.028       18     1.5  G&S_cingul-Mid-Ant
 1306    888   3032  3.140 0.775     0.138     0.034       18     1.8  G&S_cingul-Mid-Post
  759    499   2363  3.375 0.834     0.172     0.060       22     1.9  G_cingul-Post-dorsal
  339    200    659  2.766 0.721     0.150     0.067        8     0.7  G_cingul-Post-ventral
 2159   1281   3523  2.195 0.699     0.138     0.051       42     4.8  G_cuneus
 1676   1088   4665  3.215 0.542     0.151     0.055       36     3.7  G_front_inf-Opercular
  387    251   1302  3.381 0.764     0.187     0.093       17     1.9  G_front_inf-Orbital
  885    564   2503  3.037 0.534     0.145     0.045       17     1.5  G_front_inf-Triangul
 5407   3431  15756  3.111 0.695     0.152     0.063      126    14.7  G_front_middle
 7236   4596  19000  3.151 0.807     0.154     0.064      164    20.7  G_front_sup
  998    612   2065  3.014 0.847     0.150     0.081       17     4.2  G_Ins_lg&S_cent_ins
  847    547   2557  3.434 0.901     0.151     0.075       22     2.8  G_insular_short
 2499   1447   6515  3.053 0.599     0.140     0.038       50     3.6  G_occipital_middle
 1754   1029   3506  2.673 0.558     0.135     0.041       31     2.9  G_occipital_sup
 1676   1136   4753  3.317 0.585     0.158     0.044       40     3.2  G_oc-temp_lat-fusifor
 3206   1983   5895  2.374 0.707     0.142     0.048       60     6.0  G_oc-temp_med-Lingual
 1426    893   3965  3.302 0.778     0.137     0.052       27     2.7  G_oc-temp_med-Parahip
 2306   1522   7400  3.384 0.746     0.144     0.056       53     5.0  G_orbital
 3399   2218   8590  2.850 0.697     0.157     0.062       91     9.1  G_pariet_inf-Angular
 3473   2247   8822  2.956 0.606     0.136     0.058       81     9.4  G_pariet_inf-Supramar
 3508   2220   7318  2.534 0.621     0.155     0.060       87     9.5  G_parietal_sup
 2822   1599   5064  2.396 0.659     0.146     0.069       81     8.5  G_postcentral
 3308   1773   6479  2.755 0.664     0.137     0.074       72     9.9  G_precentral
 2971   1921   8097  3.133 0.625     0.144     0.050       69     5.9  G_precuneus
  884    540   2246  2.730 0.594     0.163     0.060       26     2.3  G_rectus
  776    470   1361  2.547 1.157     0.151     0.093       34     3.6  G_subcallosal
  662    371   1283  2.551 0.571     0.124     0.053       13     1.3  G_temp_sup-G_T_transv
 2000   1290   6528  3.340 0.684     0.153     0.059       53     4.4  G_temp_sup-Lateral
  849    568   2264  3.510 0.615     0.097     0.044       22     2.1  G_temp_sup-Plan_polar
 1363    883   3259  3.007 0.543     0.129     0.049       22     2.7  G_temp_sup-Plan_tempo
 3098   2012   9172  3.117 0.684     0.151     0.055       81     6.8  G_temporal_inf
 2378   1519   7635  3.415 0.660     0.158     0.062       56     5.7  G_temporal_middle
  284    194    596  3.092 0.457     0.086     0.016        1     0.2  Lat_Fis-ant-Horizont
  308    205    521  2.724 0.440     0.089     0.023        1     0.3  Lat_Fis-ant-Vertical
 1301    869   1993  2.959 0.564     0.109     0.029        9     1.6  Lat_Fis-post
 2379   1372   3294  2.148 0.616     0.127     0.039       34     3.8  Pole_occipital
 1942   1294   6491  3.392 0.776     0.163     0.061       43     5.1  Pole_temporal
 2308   1581   2989  2.180 0.679     0.121     0.033       22     3.5  S_calcarine
 3734   2477   4942  2.269 0.588     0.111     0.029       27     4.8  S_central
 1163    792   1852  2.642 0.398     0.089     0.014        6     0.6  S_cingul-Marginalis
  520    347    889  3.163 0.509     0.105     0.033        3     0.7  S_circular_insula_ant
 1494   1003   2399  3.045 0.631     0.111     0.037       10     2.5  S_circular_insula_inf
 1868   1255   2855  2.706 0.527     0.106     0.028       12     2.2  S_circular_insula_sup
  839    586   1916  3.023 0.705     0.127     0.038       10     1.5  S_collat_transv_ant
  465    323    657  2.467 0.473     0.133     0.031        3     0.7  S_collat_transv_post
 2347   1559   3941  2.667 0.514     0.112     0.028       16     2.7  S_front_inf
 1685   1151   2532  2.649 0.515     0.122     0.030       12     2.1  S_front_middle
 3314   2224   6093  2.781 0.452     0.102     0.025       18     3.5  S_front_sup
  780    514   1182  2.834 0.431     0.100     0.020        4     0.7  S_interm_prim-Jensen
 3814   2710   6645  2.770 0.458     0.117     0.024       29     3.8  S_intrapariet&P_trans
  962    669   1464  2.610 0.383     0.108     0.018        5     0.7  S_oc_middle&Lunatus
 1920   1266   2999  2.673 0.368     0.100     0.018       10     1.5  S_oc_sup&transversal
  812    527   1657  2.986 0.467     0.125     0.026        9     0.8  S_occipital_ant
 1213    819   2146  2.906 0.419     0.101     0.022        7     1.0  S_oc-temp_lat
 2044   1474   3790  2.814 0.471     0.129     0.031       25     2.6  S_oc-temp_med&Lingual
  278    204    531  2.602 0.752     0.143     0.035        3     0.5  S_orbital_lateral
  625    437   1029  2.487 0.789     0.138     0.038        6     1.0  S_orbital_med-olfact
 1465    981   3103  3.245 0.756     0.131     0.036       16     2.3  S_orbital-H_Shaped
 2194   1492   3472  2.574 0.476     0.101     0.018       17     1.6  S_parieto_occipital
 1704   1060   2235  2.560 1.108     0.136     0.027       26     1.6  S_pericallosal
 3064   2125   4915  2.574 0.484     0.110     0.025       24     3.2  S_postcentral
 1828   1203   3257  2.820 0.544     0.104     0.026       12     2.0  S_precentral-inf-part
 1554   1040   2618  2.797 0.488     0.112     0.030       13     1.9  S_precentral-sup-part
  764    522   1417  2.875 0.669     0.122     0.027        6     0.9  S_suborbital
 1060    710   1899  3.105 0.607     0.115     0.024        6     1.1  S_subparietal
 1565   1057   2520  2.994 0.517     0.109     0.021        8     1.6  S_temporal_inf
 5708   3888  11041  2.909 0.497     0.116     0.027       55     5.9  S_temporal_sup
  473    313    642  2.546 0.292     0.100     0.018        2     0.4  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 0051348 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119
Total vertex volume 291788 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
  884    584   2105  2.701 0.642     0.147     0.037       15     1.6  G&S_frontomargin
  849    492   1916  2.885 0.565     0.130     0.039       15     1.1  G&S_occipital_inf
 2198   1257   3792  2.423 0.693     0.133     0.070       51     6.9  G&S_paracentral
 1828   1230   4223  2.992 0.595     0.134     0.038       24     2.8  G&S_subcentral
 1261    807   3302  2.724 0.662     0.164     0.077       46     4.2  G&S_transv_frontopol
 2964   2035   6939  3.124 0.671     0.132     0.043       48     5.5  G&S_cingul-Ant
 1338    888   2914  2.985 0.642     0.127     0.036       22     2.0  G&S_cingul-Mid-Ant
 1484    991   3134  3.063 0.603     0.125     0.031       17     1.9  G&S_cingul-Mid-Post
  656    396   1863  3.260 0.697     0.158     0.049       16     1.2  G_cingul-Post-dorsal
  312    207    736  2.839 0.704     0.166     0.046        7     0.6  G_cingul-Post-ventral
 2370   1494   3886  2.196 0.632     0.151     0.046       41     4.0  G_cuneus
 1432    968   4826  3.318 0.511     0.159     0.062       34     3.9  G_front_inf-Opercular
  366    250   1364  3.401 0.489     0.173     0.060        8     0.9  G_front_inf-Orbital
  608    418   2006  3.280 0.525     0.149     0.054       12     1.3  G_front_inf-Triangul
 4311   2730  12559  3.004 0.650     0.158     0.066      123    11.6  G_front_middle
 6077   3944  17799  3.235 0.735     0.148     0.063      130    16.6  G_front_sup
  699    454   1823  3.528 0.949     0.140     0.086       15     2.8  G_Ins_lg&S_cent_ins
  631    403   2463  3.830 0.900     0.147     0.057       10     1.3  G_insular_short
 2189   1332   5276  2.920 0.596     0.144     0.044       45     3.9  G_occipital_middle
 1878   1129   3615  2.567 0.533     0.131     0.041       32     3.0  G_occipital_sup
 1916   1225   5318  3.191 0.771     0.151     0.066       53     5.7  G_oc-temp_lat-fusifor
 3381   2022   6085  2.499 0.707     0.143     0.053       64     7.1  G_oc-temp_med-Lingual
 1223    765   3897  3.376 0.827     0.143     0.071       29     4.0  G_oc-temp_med-Parahip
 2516   1634   8589  3.470 0.806     0.152     0.061       65     6.1  G_orbital
 4148   2493  10209  3.014 0.742     0.153     0.068      117    11.6  G_pariet_inf-Angular
 2957   1832   7341  3.019 0.675     0.149     0.092      113    14.6  G_pariet_inf-Supramar
 3920   2290   6712  2.320 0.614     0.152     0.068       93    11.5  G_parietal_sup
 2593   1487   4520  2.331 0.658     0.151     0.069       72     8.3  G_postcentral
 3857   2096   7154  2.603 0.698     0.153     0.077      107    12.3  G_precentral
 2428   1608   5860  2.789 0.551     0.130     0.038       49     3.8  G_precuneus
  774    540   2651  3.151 0.586     0.190     0.076       27     2.6  G_rectus
  729    408    846  1.932 1.259     0.087     0.036       12     1.1  G_subcallosal
  516    316   1222  2.763 0.530     0.138     0.042       10     0.7  G_temp_sup-G_T_transv
 2586   1655   8106  3.394 0.630     0.146     0.068       66     7.7  G_temp_sup-Lateral
 1117    772   2601  3.161 0.818     0.127     0.043       11     1.9  G_temp_sup-Plan_polar
 1466    969   3319  3.045 0.520     0.132     0.040       18     2.7  G_temp_sup-Plan_tempo
 2422   1459   6799  3.166 0.783     0.141     0.066       53     7.3  G_temporal_inf
 3124   1987  10355  3.408 0.700     0.150     0.056       73     6.9  G_temporal_middle
  324    238    624  3.086 0.570     0.099     0.020        1     0.3  Lat_Fis-ant-Horizont
  198    139    353  2.837 0.633     0.115     0.024        1     0.2  Lat_Fis-ant-Vertical
 1707   1143   2799  3.017 0.478     0.113     0.029       14     2.0  Lat_Fis-post
 3458   2031   5331  2.329 0.684     0.133     0.038       52     5.6  Pole_occipital
 1503   1003   4615  3.202 0.815     0.165     0.067       43     4.2  Pole_temporal
 2469   1616   3088  2.253 0.799     0.126     0.031       23     3.2  S_calcarine
 3921   2543   4795  2.176 0.505     0.114     0.036       34     5.9  S_central
 1563   1070   2453  2.574 0.443     0.097     0.020        9     1.2  S_cingul-Marginalis
  537    367   1024  3.189 0.519     0.107     0.058       10     0.8  S_circular_insula_ant
 1228    801   1858  2.788 0.669     0.086     0.018        5     1.0  S_circular_insula_inf
 1461    976   2378  2.947 0.554     0.103     0.026        7     1.7  S_circular_insula_sup
  636    461   1404  2.945 0.474     0.122     0.031        5     0.9  S_collat_transv_ant
  517    361    914  2.913 0.644     0.138     0.033        5     0.7  S_collat_transv_post
 2110   1444   3659  2.650 0.563     0.112     0.035       33     3.3  S_front_inf
 2568   1719   4186  2.378 0.564     0.129     0.037       30     4.0  S_front_middle
 2987   2095   5167  2.609 0.501     0.107     0.026       16     3.4  S_front_sup
  670    421    974  2.759 0.417     0.110     0.027        4     0.8  S_interm_prim-Jensen
 4536   2992   7538  2.700 0.428     0.107     0.027       38     4.7  S_intrapariet&P_trans
  699    473    957  2.355 0.410     0.108     0.018        5     0.5  S_oc_middle&Lunatus
 1753   1193   2631  2.624 0.442     0.108     0.022       11     1.6  S_oc_sup&transversal
  574    382    930  2.808 0.549     0.108     0.024        4     0.5  S_occipital_ant
 1222    833   2005  2.721 0.469     0.120     0.024       10     1.3  S_oc-temp_lat
 1803   1287   3220  2.921 0.536     0.107     0.021       11     1.5  S_oc-temp_med&Lingual
  372    270    687  2.894 0.576     0.125     0.031        3     0.5  S_orbital_lateral
  530    356    937  2.606 0.724     0.124     0.036        4     0.7  S_orbital_med-olfact
 1304    853   2659  3.077 0.665     0.118     0.039       14     1.8  S_orbital-H_Shaped
 2413   1627   4113  2.783 0.562     0.126     0.030       31     3.0  S_parieto_occipital
 1490    932   1600  2.259 0.757     0.131     0.027       23     1.3  S_pericallosal
 3455   2260   5289  2.619 0.450     0.104     0.028       26     4.1  S_postcentral
 2127   1425   3593  2.898 0.542     0.103     0.023       11     2.2  S_precentral-inf-part
 1598   1069   2612  2.674 0.472     0.117     0.029       12     2.0  S_precentral-sup-part
  338    248    573  2.395 0.491     0.121     0.046        3     0.7  S_suborbital
 1150    800   2528  3.317 0.569     0.111     0.025        9     1.0  S_subparietal
  919    626   1696  2.954 0.609     0.111     0.028        5     1.1  S_temporal_inf
 7302   4970  13924  3.026 0.494     0.105     0.023       53     7.3  S_temporal_sup
  443    299    548  2.333 0.410     0.115     0.023        3     0.4  S_temporal_transverse
PIDs (20641 20644) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 04:16:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 04:16:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 20745 of (20745 20748) to complete...
Waiting for PID 20748 of (20745 20748) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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...
2041 labels changed using aseg
relabeling using gibbs priors...
000:   2159 changed, 145874 examined...
001:    511 changed, 10044 examined...
002:    143 changed, 2959 examined...
003:     60 changed, 806 examined...
004:     29 changed, 341 examined...
005:     22 changed, 172 examined...
006:     19 changed, 109 examined...
007:     11 changed, 88 examined...
008:     10 changed, 66 examined...
009:      7 changed, 61 examined...
010:      9 changed, 41 examined...
011:      4 changed, 43 examined...
012:      2 changed, 26 examined...
013:      1 changed, 12 examined...
014:      1 changed, 5 examined...
015:      1 changed, 7 examined...
016:      0 changed, 9 examined...
310 labels changed using aseg
000: 78 total segments, 45 labels (492 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
887 vertices marked for relabeling...
887 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 0051348 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...
1589 labels changed using aseg
relabeling using gibbs priors...
000:   2302 changed, 145578 examined...
001:    555 changed, 10437 examined...
002:    149 changed, 3148 examined...
003:     62 changed, 893 examined...
004:     38 changed, 342 examined...
005:     29 changed, 213 examined...
006:     25 changed, 158 examined...
007:     10 changed, 123 examined...
008:      9 changed, 62 examined...
009:      6 changed, 44 examined...
010:      3 changed, 28 examined...
011:      1 changed, 22 examined...
012:      2 changed, 7 examined...
013:      3 changed, 12 examined...
014:      4 changed, 15 examined...
015:      4 changed, 24 examined...
016:      4 changed, 20 examined...
017:      6 changed, 20 examined...
018:      4 changed, 25 examined...
019:      9 changed, 18 examined...
020:      3 changed, 31 examined...
021:      1 changed, 17 examined...
022:      2 changed, 7 examined...
023:      1 changed, 12 examined...
024:      1 changed, 7 examined...
025:      1 changed, 7 examined...
026:      0 changed, 7 examined...
334 labels changed using aseg
000: 63 total segments, 30 labels (661 vertices) changed
001: 36 total segments, 3 labels (3 vertices) changed
002: 33 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...
736 vertices marked for relabeling...
736 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 18 seconds.
PIDs (20745 20748) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 04:16:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 04:16:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh white 

Waiting for PID 20791 of (20791 20794) to complete...
Waiting for PID 20794 of (20791 20794) 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 0051348 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461
Total vertex volume 295075 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1797   1159   3776  3.025 0.610     0.128     0.029       27     2.1  caudalanteriorcingulate
 4379   2832   9327  2.914 0.567     0.125     0.049       59     9.3  caudalmiddlefrontal
 3082   1882   5057  2.326 0.595     0.116     0.038       45     5.0  cuneus
  644    412   1746  3.182 0.931     0.138     0.047       11     1.4  entorhinal
 3932   2716   9414  3.069 0.599     0.140     0.039       71     6.6  fusiform
 8956   5901  19297  2.884 0.585     0.135     0.040      150    15.0  inferiorparietal
 5398   3576  13895  3.036 0.655     0.140     0.046      103    10.3  inferiortemporal
 1712   1114   3326  2.645 0.812     0.140     0.040       32     2.4  isthmuscingulate
 7886   4781  13977  2.568 0.584     0.129     0.035      110    11.1  lateraloccipital
 4255   2855  10522  3.174 0.802     0.141     0.047       71     8.3  lateralorbitofrontal
 4711   3048   8282  2.463 0.686     0.136     0.041       72     7.7  lingual
 2259   1455   4812  2.689 0.765     0.152     0.055       52     5.6  medialorbitofrontal
 5887   3855  15519  3.230 0.657     0.134     0.044       98     9.6  middletemporal
  945    605   2327  3.146 0.637     0.119     0.036       12     1.2  parahippocampal
 2715   1695   5195  2.744 0.658     0.117     0.043       30     5.1  paracentral
 2635   1713   6239  2.992 0.597     0.136     0.046       42     5.0  parsopercularis
  941    612   2335  3.159 0.528     0.133     0.052       17     2.1  parsorbitalis
 2116   1389   4572  2.859 0.605     0.123     0.036       26     3.2  parstriangularis
 1795   1256   1945  1.810 0.455     0.137     0.042       20     3.6  pericalcarine
 8118   5047  13540  2.383 0.661     0.131     0.049      144    17.2  postcentral
 2015   1335   4248  2.898 0.995     0.151     0.041       37     3.1  posteriorcingulate
 8627   5216  15680  2.754 0.603     0.126     0.049      126    17.3  precentral
 5808   3826  12786  3.000 0.610     0.125     0.034       90     7.8  precuneus
 1895   1213   4673  3.247 0.924     0.140     0.059       59     4.8  rostralanteriorcingulate
 6728   4425  17223  2.974 0.725     0.141     0.047      125    13.3  rostralmiddlefrontal
11854   7821  28643  3.032 0.736     0.135     0.049      201    24.9  superiorfrontal
 7452   4998  14265  2.616 0.558     0.134     0.039      116    13.0  superiorparietal
 7703   5081  18915  3.142 0.668     0.127     0.044      131    14.7  superiortemporal
 6790   4554  15089  2.929 0.557     0.123     0.041      108    12.6  supramarginal
  823    471   1504  2.621 0.578     0.123     0.057       15     1.8  transversetemporal
 3308   2158   6947  3.138 0.749     0.129     0.054       47     8.5  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 0051348 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119
Total vertex volume 291788 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
  951    591   1700  2.720 0.690     0.135     0.035       18     1.4  caudalanteriorcingulate
 3834   2532   8413  2.987 0.557     0.127     0.043       61     6.8  caudalmiddlefrontal
 3058   1929   5218  2.382 0.593     0.146     0.039       50     4.7  cuneus
  385    260   1417  3.581 0.778     0.137     0.039        4     0.6  entorhinal
 3770   2563   9083  3.057 0.674     0.134     0.046       68     7.5  fusiform
 9516   6184  20429  2.977 0.599     0.131     0.040      150    15.8  inferiorparietal
 4309   2785  10263  2.977 0.745     0.136     0.052       71    10.0  inferiortemporal
 1445    917   2701  2.649 0.969     0.143     0.037       28     2.0  isthmuscingulate
 6965   4265  12184  2.601 0.581     0.127     0.036       95     9.8  lateraloccipital
 4004   2616  10087  3.116 0.815     0.145     0.054       80     8.7  lateralorbitofrontal
 4952   3100   8697  2.548 0.710     0.136     0.042       77     8.5  lingual
 2283   1508   5300  2.605 0.990     0.141     0.054       50     5.4  medialorbitofrontal
 6450   4174  16984  3.209 0.660     0.128     0.042      105    11.1  middletemporal
 1106    694   2554  3.061 0.695     0.123     0.061       22     3.1  parahippocampal
 2882   1836   5467  2.768 0.621     0.112     0.039       38     4.6  paracentral
 2264   1523   5374  2.958 0.623     0.129     0.043       30     4.2  parsopercularis
  964    639   3099  3.394 0.641     0.138     0.046       15     1.8  parsorbitalis
 1735   1228   4102  3.013 0.642     0.120     0.033       18     2.3  parstriangularis
 2394   1526   2436  1.804 0.507     0.141     0.041       32     3.9  pericalcarine
 8287   5152  13878  2.419 0.684     0.129     0.051      142    18.6  postcentral
 1956   1300   3956  2.862 0.673     0.135     0.032       30     2.5  posteriorcingulate
 9656   5836  17233  2.641 0.633     0.135     0.055      174    22.2  precentral
 5995   4042  12579  2.871 0.621     0.125     0.034       90     8.0  precuneus
 1432    936   3429  3.302 0.672     0.126     0.043       25     2.6  rostralanteriorcingulate
 6949   4495  15683  2.693 0.718     0.140     0.050      144    15.2  rostralmiddlefrontal
12350   8358  30480  2.997 0.710     0.136     0.049      211    26.1  superiorfrontal
 9210   5718  15542  2.508 0.552     0.125     0.044      140    16.9  superiorparietal
 8389   5488  21034  3.185 0.662     0.121     0.042      125    15.0  superiortemporal
 6616   4226  13764  2.899 0.613     0.134     0.064      165    21.8  supramarginal
  686    426   1404  2.632 0.443     0.129     0.036       11     0.8  transversetemporal
 3100   2044   7297  3.376 0.793     0.123     0.054       43     6.4  insula
PIDs (20791 20794) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 04:17:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 pctsurfcon --s 0051348 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 04:17:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts

 pctsurfcon --s 0051348 --rh-only 

Waiting for PID 20861 of (20861 20872) to complete...
Waiting for PID 20872 of (20861 20872) to complete...

 pctsurfcon --s 0051348 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts/pctsurfcon.log
Sun Oct  8 04:17:37 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-6.0.0/0051348/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-553 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-6.0.0/0051348/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.wm.mgh --regheader 0051348 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 74697
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.wm.mgh
Dim: 145874 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.gm.mgh --projfrac 0.3 --regheader 0051348 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 93173
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.gm.mgh
Dim: 145874 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.w-g.pct.mgh --annot 0051348 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/lh.w-g.pct.mgh --annot 0051348 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/lh.w-g.pct.mgh
Vertex Area is 0.64788 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 0051348 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts/pctsurfcon.log
Sun Oct  8 04:17:37 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-6.0.0/0051348/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-553 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-6.0.0/0051348/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.wm.mgh --regheader 0051348 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 74420
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.wm.mgh
Dim: 145578 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.gm.mgh --projfrac 0.3 --regheader 0051348 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 92828
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.gm.mgh
Dim: 145578 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.w-g.pct.mgh --annot 0051348 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.w-g.pct.mgh --annot 0051348 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.w-g.pct.mgh
Vertex Area is 0.645438 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 (20861 20872) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 04:17:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1626 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1436 voxels changed to hypointensity...
3006 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 04:18:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348

 mri_aparc2aseg --s 0051348 --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 04:18:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348

 mri_aparc2aseg --s 0051348 --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 04:18:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348

 mri_aparc2aseg --s 0051348 --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 21038 of (21038 21041 21044) to complete...
Waiting for PID 21041 of (21038 21041 21044) to complete...
Waiting for PID 21044 of (21038 21041 21044) to complete...

 mri_aparc2aseg --s 0051348 --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 0051348
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.83
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 69
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 38
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 65
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 38
rescaling Fourth_Ventricle from 22 --> 25
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 66
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 53
rescaling Left_Accumbens_area from 62 --> 63
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 69
rescaling Right_Lateral_Ventricle from 13 --> 22
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 83
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 66
rescaling Right_Amygdala from 55 --> 66
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 84
rescaling Fifth_Ventricle from 40 --> 46
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  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 = 579829
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 212 changed.
pass 2: 13 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051348 --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 0051348
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.83
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 69
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 38
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 65
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 38
rescaling Fourth_Ventricle from 22 --> 25
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 66
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 53
rescaling Left_Accumbens_area from 62 --> 63
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 69
rescaling Right_Lateral_Ventricle from 13 --> 22
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 83
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 66
rescaling Right_Amygdala from 55 --> 66
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 84
rescaling Fifth_Ventricle from 40 --> 46
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  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 = 579907
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 212 changed.
pass 2: 13 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051348 --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 0051348
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.83
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 69
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 38
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 65
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 38
rescaling Fourth_Ventricle from 22 --> 25
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 66
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 53
rescaling Left_Accumbens_area from 62 --> 63
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 69
rescaling Right_Lateral_Ventricle from 13 --> 22
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 83
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 83
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 66
rescaling Right_Amygdala from 55 --> 66
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 84
rescaling Fifth_Ventricle from 40 --> 46
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  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 = 579907
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 212 changed.
pass 2: 13 changed.
pass 3: 3 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (21038 21041 21044) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 04:29:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri

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

Sun Oct  8 04:29:21 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-6.0.0/0051348/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-553 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-6.0.0/0051348/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-553
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 04:29:21 CEST 2017 
Ended   at Sun Oct  8 04:29:28 CEST 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 04:29:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348

 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 0051348 


$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 0051348 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1528850 mm^3    (det: 1.274229 )
Computing euler number
orig.nofix lheno = -344, rheno = -294
orig.nofix lhholes =  173, rhholes = 148
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
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 04:33:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348

 mri_aparc2aseg --s 0051348 --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 0051348
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-6.0.0/0051348/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8711 vertices from left hemi
Ripped 7702 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-6.0.0/0051348/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 963420
Used brute-force search on 30 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 976.000000
     3 k 1.000000
     4 k 1.000000
     5 k 4.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 5.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 4.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1166.000000
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 0051348 --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 0051348 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-553
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1528850 mm^3    (det: 1.274229 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
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-6.0.0/0051348/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 04:43:42 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22059 of (22059 22065 22071 22075 22082) to complete...
Waiting for PID 22065 of (22059 22065 22071 22075 22082) to complete...
Waiting for PID 22071 of (22059 22065 22071 22075 22082) to complete...
Waiting for PID 22075 of (22059 22065 22071 22075 22082) to complete...
Waiting for PID 22082 of (22059 22065 22071 22075 22082) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 554
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4683
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 772
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8681
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 262
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4339
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 519
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6502
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 986
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6770
mri_label2label: Done

PIDs (22059 22065 22071 22075 22082) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22144 of (22144 22150 22156 22161) to complete...
Waiting for PID 22150 of (22144 22150 22156 22161) to complete...
Waiting for PID 22156 of (22144 22150 22156 22161) to complete...
Waiting for PID 22161 of (22144 22150 22156 22161) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 482
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4552
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 2062
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15651
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 597
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4778
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 582
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4004
mri_label2label: Done

PIDs (22144 22150 22156 22161) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22201 of (22201 22207 22213 22219 22223) to complete...
Waiting for PID 22207 of (22201 22207 22213 22219 22223) to complete...
Waiting for PID 22213 of (22201 22207 22213 22219 22223) to complete...
Waiting for PID 22219 of (22201 22207 22213 22219 22223) to complete...
Waiting for PID 22223 of (22201 22207 22213 22219 22223) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 1287
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5928
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 3171
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11285
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 372
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2390
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 121
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1411
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 114
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1313
mri_label2label: Done

PIDs (22201 22207 22213 22219 22223) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 22313 of (22313 22319 22325 22331 22336) to complete...
Waiting for PID 22319 of (22313 22319 22325 22331 22336) to complete...
Waiting for PID 22325 of (22313 22319 22325 22331 22336) to complete...
Waiting for PID 22331 of (22313 22319 22325 22331 22336) to complete...
Waiting for PID 22336 of (22313 22319 22325 22331 22336) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 161
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1175
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 303
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2395
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 64
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1568
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 181
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2177
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 295
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2614
mri_label2label: Done

PIDs (22313 22319 22325 22331 22336) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 22379 of (22379 22385 22391 22397) to complete...
Waiting for PID 22385 of (22379 22385 22391 22397) to complete...
Waiting for PID 22391 of (22379 22385 22391 22397) to complete...
Waiting for PID 22397 of (22379 22385 22391 22397) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 204
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1753
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 1148
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8183
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 305
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2217
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 213
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1364
mri_label2label: Done

PIDs (22379 22385 22391 22397) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 22436 of (22436 22442 22448 22454 22460) to complete...
Waiting for PID 22442 of (22436 22442 22448 22454 22460) to complete...
Waiting for PID 22448 of (22436 22442 22448 22454 22460) to complete...
Waiting for PID 22454 of (22436 22442 22448 22454 22460) to complete...
Waiting for PID 22460 of (22436 22442 22448 22454 22460) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 886
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4291
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 1388
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4722
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 598
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 39
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 509
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874
Number of reverse mapping hits = 49
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 499
mri_label2label: Done

PIDs (22436 22442 22448 22454 22460) completed and logs appended.

 mris_label2annot --s 0051348 --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-6.0.0/0051348/label
cmdline mris_label2annot --s 0051348 --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-553
machine  x86_64
user     ntraut

subject 0051348
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-6.0.0/0051348/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 101874 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051348 --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-6.0.0/0051348/label
cmdline mris_label2annot --s 0051348 --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-553
machine  x86_64
user     ntraut

subject 0051348
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-6.0.0/0051348/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 119513 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 298461
Total vertex volume 295075 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1327    725   2278  2.407 0.682     0.164     0.088       47     5.2  BA1_exvivo
 4308   2826   7852  2.606 0.575     0.124     0.037       65     7.0  BA2_exvivo
 1181    798   1329  2.070 0.477     0.129     0.031       11     1.5  BA3a_exvivo
 2711   1737   4322  2.209 0.648     0.119     0.034       34     3.6  BA3b_exvivo
 1868   1101   3548  2.687 0.636     0.125     0.052       25     4.3  BA4a_exvivo
 1668    975   2569  2.697 0.507     0.111     0.047       19     3.5  BA4p_exvivo
10326   6396  22270  2.943 0.712     0.134     0.058      176    25.5  BA6_exvivo
 2657   1747   6169  3.008 0.588     0.139     0.046       44     5.1  BA44_exvivo
 2754   1827   6125  2.827 0.601     0.132     0.040       40     4.9  BA45_exvivo
 3379   2190   3866  1.774 0.491     0.132     0.043       40     6.5  V1_exvivo
 8629   5261  14332  2.428 0.583     0.132     0.042      138    14.4  V2_exvivo
 1936   1200   4361  2.945 0.501     0.129     0.031       28     2.5  MT_exvivo
  599    367   1676  3.249 0.737     0.126     0.048        8     1.2  perirhinal_exvivo
  657    437   1588  3.111 0.848     0.132     0.040        9     1.0  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 0051348 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 298461
Total vertex volume 295075 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
  837    449   1387  2.375 0.651     0.166     0.081       22     3.0  BA1_exvivo
 1831   1132   3208  2.521 0.562     0.118     0.042       33     3.1  BA2_exvivo
 1005    690   1070  2.046 0.477     0.136     0.032        9     1.3  BA3a_exvivo
 1634   1077   2235  1.954 0.433     0.105     0.025       13     1.7  BA3b_exvivo
 1865   1110   3451  2.764 0.579     0.122     0.048       22     4.1  BA4a_exvivo
 1302    791   2008  2.639 0.516     0.111     0.046       15     2.6  BA4p_exvivo
 5938   3541  11577  2.803 0.721     0.140     0.070      121    18.6  BA6_exvivo
 1722   1137   4391  3.040 0.603     0.149     0.055       36     3.9  BA44_exvivo
 1142    735   2894  2.962 0.505     0.132     0.037       17     1.7  BA45_exvivo
 3645   2333   4208  1.787 0.491     0.132     0.044       46     7.1  V1_exvivo
 4297   2578   6564  2.301 0.581     0.134     0.039       64     6.7  V2_exvivo
  485    302   1151  2.942 0.515     0.141     0.037        7     0.7  MT_exvivo
  300    183    819  3.253 0.616     0.111     0.031        2     0.4  perirhinal_exvivo
  358    242    947  3.391 0.941     0.140     0.039        4     0.7  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 04:47:44 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 22623 of (22623 22629 22635 22639 22647) to complete...
Waiting for PID 22629 of (22623 22629 22635 22639 22647) to complete...
Waiting for PID 22635 of (22623 22629 22635 22639 22647) to complete...
Waiting for PID 22639 of (22623 22629 22635 22639 22647) to complete...
Waiting for PID 22647 of (22623 22629 22635 22639 22647) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 667
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4629
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 920
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7607
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 319
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4299
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 502
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5024
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1170
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6917
mri_label2label: Done

PIDs (22623 22629 22635 22639 22647) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 22704 of (22704 22710 22716 22721) to complete...
Waiting for PID 22710 of (22704 22710 22716 22721) to complete...
Waiting for PID 22716 of (22704 22710 22716 22721) to complete...
Waiting for PID 22721 of (22704 22710 22716 22721) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 766
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5239
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1854
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14110
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1037
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7949
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 751
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6106
mri_label2label: Done

PIDs (22704 22710 22716 22721) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 22761 of (22761 22767 22773 22779 22784) to complete...
Waiting for PID 22767 of (22761 22767 22773 22779 22784) to complete...
Waiting for PID 22773 of (22761 22767 22773 22779 22784) to complete...
Waiting for PID 22779 of (22761 22767 22773 22779 22784) to complete...
Waiting for PID 22784 of (22761 22767 22773 22779 22784) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1848
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6575
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 3210
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11226
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 224
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2156
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1143
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 78
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 830
mri_label2label: Done

PIDs (22761 22767 22773 22779 22784) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 22845 of (22845 22851 22856 22861 22869) to complete...
Waiting for PID 22851 of (22845 22851 22856 22861 22869) to complete...
Waiting for PID 22856 of (22845 22851 22856 22861 22869) to complete...
Waiting for PID 22861 of (22845 22851 22856 22861 22869) to complete...
Waiting for PID 22869 of (22845 22851 22856 22861 22869) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 176
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1052
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 353
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3041
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 107
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1805
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 180
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2363
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 241
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1629
mri_label2label: Done

PIDs (22845 22851 22856 22861 22869) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 22916 of (22916 22922 22928 22934) to complete...
Waiting for PID 22922 of (22916 22922 22928 22934) to complete...
Waiting for PID 22928 of (22916 22922 22928 22934) to complete...
Waiting for PID 22934 of (22916 22922 22928 22934) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 249
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1738
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1068
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8027
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1145
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 118
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1296
mri_label2label: Done

PIDs (22916 22922 22928 22934) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 22973 of (22973 22979 22985 22990 22995) to complete...
Waiting for PID 22979 of (22973 22979 22985 22990 22995) to complete...
Waiting for PID 22985 of (22973 22979 22985 22990 22995) to complete...
Waiting for PID 22990 of (22973 22979 22985 22990 22995) to complete...
Waiting for PID 22995 of (22973 22979 22985 22990 22995) 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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1195
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4427
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 1594
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5031
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 19
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 287
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 50
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 744
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 0051348 --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 = 0051348
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-6.0.0/0051348/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578
Number of reverse mapping hits = 33
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 324
mri_label2label: Done

PIDs (22973 22979 22985 22990 22995) completed and logs appended.

 mris_label2annot --s 0051348 --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-6.0.0/0051348/label
cmdline mris_label2annot --s 0051348 --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-553
machine  x86_64
user     ntraut

subject 0051348
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-6.0.0/0051348/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 101178 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051348 --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-6.0.0/0051348/label
cmdline mris_label2annot --s 0051348 --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-553
machine  x86_64
user     ntraut

subject 0051348
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-6.0.0/0051348/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 120056 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 295119
Total vertex volume 291788 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
 1168    621   1987  2.306 0.629     0.156     0.083       38     4.7  BA1_exvivo
 4029   2522   6633  2.574 0.540     0.119     0.042       60     7.3  BA2_exvivo
 1309    863   1321  2.004 0.434     0.125     0.034       11     1.8  BA3a_exvivo
 2367   1548   3651  2.044 0.524     0.123     0.042       31     4.1  BA3b_exvivo
 2126   1212   3614  2.570 0.606     0.134     0.063       49     5.6  BA4a_exvivo
 1751   1053   2679  2.577 0.461     0.115     0.048       17     3.3  BA4p_exvivo
 8640   5364  18904  2.929 0.742     0.138     0.060      168    22.4  BA6_exvivo
 4060   2739   9087  2.966 0.610     0.121     0.034       45     5.6  BA44_exvivo
 3731   2538   9720  3.033 0.682     0.138     0.051       77     8.3  BA45_exvivo
 4212   2582   4966  1.854 0.558     0.145     0.044       65     7.9  V1_exvivo
 8513   5255  14687  2.552 0.597     0.135     0.041      129    13.7  V2_exvivo
 1646   1036   3494  2.945 0.547     0.126     0.036       25     2.2  MT_exvivo
  533    338   1747  3.607 0.657     0.148     0.050       10     1.2  perirhinal_exvivo
  315    216   1211  3.672 0.690     0.141     0.053        6     0.6  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 0051348 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 295119
Total vertex volume 291788 (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) = 1528850 mm^3    (det: 1.274229 )
lhCtxGM: 292852.920 292167.000  diff=  685.9  pctdiff= 0.234
rhCtxGM: 289186.484 288228.000  diff=  958.5  pctdiff= 0.331
lhCtxWM: 195089.304 195334.000  diff= -244.7  pctdiff=-0.125
rhCtxWM: 189816.852 191319.000  diff=-1502.1  pctdiff=-0.791
SubCortGMVol  61024.000
SupraTentVol  1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264
SupraTentVolNotVent  1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269
BrainSegVol  1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289
BrainSegVolNotVent  1198124.000 (1197916.560) diff=207.440 pctdiff=0.017
BrainSegVolNotVent  1198124.000
CerebellumVol 169931.000
VentChorVol   22650.000
3rd4th5thCSF   4898.000
CSFVol  1361.000, OptChiasmVol   105.000
MaskVol 1589178.000
  797    426   1209  2.141 0.585     0.166     0.065       30     2.4  BA1_exvivo
 2239   1374   3830  2.532 0.549     0.122     0.052       36     5.3  BA2_exvivo
 1221    800   1118  1.978 0.404     0.125     0.031       10     1.6  BA3a_exvivo
 1744   1176   2360  1.905 0.370     0.103     0.029       12     1.9  BA3b_exvivo
 1241    704   2213  2.643 0.670     0.137     0.065       29     3.3  BA4a_exvivo
 1405    841   2072  2.613 0.409     0.115     0.048       18     2.6  BA4p_exvivo
 5768   3556  12025  2.830 0.749     0.146     0.067      127    17.0  BA6_exvivo
  831    573   2362  3.187 0.605     0.130     0.040       12     1.3  BA44_exvivo
  900    634   2815  3.189 0.556     0.155     0.060       18     2.4  BA45_exvivo
 4000   2467   4587  1.846 0.558     0.143     0.043       60     7.4  V1_exvivo
 4616   2817   7474  2.419 0.609     0.139     0.043       73     7.4  V2_exvivo
  225    136    547  3.007 0.432     0.126     0.030        4     0.2  MT_exvivo
  316    203   1092  3.658 0.468     0.140     0.045        4     0.6  perirhinal_exvivo
  219    149    850  3.646 0.971     0.144     0.046        4     0.4  entorhinal_exvivo

Started at Sat Oct 7 17:01:48 CEST 2017 
Ended   at Sun Oct 8 04:51:17 CEST 2017
#@#%# recon-all-run-time-hours 11.825
recon-all -s 0051348 finished without error at Sun Oct  8 04:51:17 CEST 2017