ABIDE_fs-6.0.0/0051362/scripts/recon-all.log

Sat Oct  7 16:52:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051362 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_a/0051362/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051362
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-382 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:     264648728  256941216    7707512    1743000          0  252490564
-/+ buffers/cache:    4450652  260198076
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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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: 2017/10/07-14:52:35-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-382  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-6.0.0/0051362

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_a/0051362/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_a/0051362/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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_a/0051362/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-6.0.0/0051362/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 16:52:38 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 16:52:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-382 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 16:52:47 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.27153
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27153/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27153/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.27153/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 16:52:49 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.27153/nu0.mnc ./tmp.mri_nu_correct.mni.27153/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27153/0/ -iterations 1000 -distance 50
[ntraut@tars-382:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/] [2017-10-07 16:52:49] 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.27153/0/ ./tmp.mri_nu_correct.mni.27153/nu0.mnc ./tmp.mri_nu_correct.mni.27153/nu1.imp

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Number of iterations: 35 
CV of field change: 0.000960407
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.27153/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.27153/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.27153/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 16:53:52 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 16:53:52 CEST 2017
Ended   at Sat Oct  7 16:54:34 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 16:54:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7202, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach_avi.log 

TalAviQA: 0.97897
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 16:54:37 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-6.0.0/0051362/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-382 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 16:54:37 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.27866
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27866/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27866/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.27866/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 16:54:39 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.27866/nu0.mnc ./tmp.mri_nu_correct.mni.27866/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27866/0/
[ntraut@tars-382:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/] [2017-10-07 16:54:39] 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.27866/0/ ./tmp.mri_nu_correct.mni.27866/nu0.mnc ./tmp.mri_nu_correct.mni.27866/nu1.imp

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Number of iterations: 46 
CV of field change: 0.000997908
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 16:55:29 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.27866/nu1.mnc ./tmp.mri_nu_correct.mni.27866/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27866/1/
[ntraut@tars-382:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/] [2017-10-07 16:55:29] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27866/1/ ./tmp.mri_nu_correct.mni.27866/nu1.mnc ./tmp.mri_nu_correct.mni.27866/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 16 
CV of field change: 0.000999003
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27866/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-6.0.0/0051362/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27866/ones.mgz 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.27866/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.27866/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.27866/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/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.27866/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/input.mean.dat 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.27866/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.27866/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27866/ones.mgz --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/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.27866/ones.mgz --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/output.mean.dat 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.27866/ones.mgz
Loading ./tmp.mri_nu_correct.mni.27866/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.27866/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.27866/nu2.mnc ./tmp.mri_nu_correct.mni.27866/nu2.mnc mul 1.01814933025425786766
Saving result to './tmp.mri_nu_correct.mni.27866/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.27866/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.27866/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.27866/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 9 seconds.
mapping (13, 142) to ( 3, 110)
 
 
Sat Oct  7 16:56:40 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 16:56:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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
 1.07462   0.01554  -0.05627   0.84462;
 0.07216   1.01207   0.32031  -7.10692;
-0.00487  -0.35952   1.10685  -30.69774;
 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 = 19
Starting OpenSpline(): npoints = 19
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 66 (66), valley at 30 (30)
csf peak at 33, setting threshold to 55
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 64 (64), valley at 30 (30)
csf peak at 32, setting threshold to 53
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 13 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 16:58:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=6.0
skull bounding box = (45, 18, 17) --> (208, 168, 191)
using (99, 68, 104) as brain centroid...
mean wm in atlas = 108, using box (79,50,83) --> (119, 86,125) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 104 +- 7.6
after smoothing, mri peak at 105, scaling input intensities by 1.029
scaling channel 0 by 1.02857
initial log_p = -4.727
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.481188 @ (-9.091, 27.273, -9.091)
max log p =    -4.463854 @ (13.636, 4.545, 4.545)
max log p =    -4.383637 @ (-2.273, -6.818, -6.818)
max log p =    -4.374402 @ (-1.136, -3.409, 3.409)
max log p =    -4.367147 @ (0.568, 3.977, -1.705)
max log p =    -4.367147 @ (0.000, 0.000, 0.000)
Found translation: (1.7, 25.6, -9.7): log p = -4.367
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.058, old_max_log_p =-4.367 (thresh=-4.4)
 1.07500   0.00000   0.00000  -15.03327;
 0.00000   1.14759   0.45276  -38.73721;
 0.00000  -0.43171   0.98772   42.16184;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.041, old_max_log_p =-4.058 (thresh=-4.1)
 1.14574  -0.16103  -0.06353   1.14499;
 0.12979   1.05244   0.41522  -40.62932;
 0.00000  -0.43171   0.98772   42.16184;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.031, old_max_log_p =-4.041 (thresh=-4.0)
 1.06628  -0.01489  -0.02412  -9.39476;
-0.02362   1.19475   0.31027  -24.06453;
 0.01821  -0.31245   1.11098   11.98691;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.031, old_max_log_p =-4.031 (thresh=-4.0)
 1.06628  -0.01489  -0.02412  -9.39476;
-0.02362   1.19475   0.31027  -24.06453;
 0.01821  -0.31245   1.11098   11.98691;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.938, old_max_log_p =-4.031 (thresh=-4.0)
 1.12572  -0.04849   0.04787  -20.03093;
-0.02676   1.12839   0.36782  -21.21245;
-0.04728  -0.36655   1.02715   38.29771;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.928, old_max_log_p =-3.938 (thresh=-3.9)
 1.10488  -0.08378   0.03514  -11.99217;
 0.01028   1.14732   0.37611  -29.01690;
-0.04640  -0.35968   1.00789   39.65944;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.913, old_max_log_p =-3.928 (thresh=-3.9)
 1.10578  -0.07445   0.00141  -9.22585;
 0.01329   1.16839   0.30939  -25.86450;
-0.00927  -0.28109   1.01160   25.80788;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.908, old_max_log_p =-3.913 (thresh=-3.9)
 1.08505  -0.07305   0.00138  -6.71145;
 0.01298   1.15856   0.34232  -26.68442;
-0.00952  -0.31318   0.98217   32.84350;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 8 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.908, old_max_log_p =-3.908 (thresh=-3.9)
 1.08505  -0.07305   0.00138  -6.71145;
 0.01298   1.15856   0.34232  -26.68442;
-0.00952  -0.31318   0.98217   32.84350;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 9 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.887, old_max_log_p =-3.908 (thresh=-3.9)
 1.08597  -0.08705  -0.02005  -3.27618;
 0.03049   1.16840   0.30982  -27.65715;
 0.00899  -0.27695   0.99630   24.35400;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 10 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.877, old_max_log_p =-3.887 (thresh=-3.9)
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 11 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.877, old_max_log_p =-3.877 (thresh=-3.9)
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 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
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 014: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.877 (old=-4.727)
transform before final EM align:
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 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
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 016: -log(p) =    4.3  tol 0.000000
final transform:
 1.08724  -0.08715  -0.02007  -3.42635;
 0.03067   1.17020   0.31908  -28.95969;
 0.00877  -0.28750   0.99723   25.44662;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1966.520043
mri_em_register stimesec    2.616602
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   157604
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    285
mri_em_register ru_nivcsw   11258
registration took 16 minutes and 51 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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=126 y=82 z=109 r=68
      first estimation of the main basin volume: 1343203 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        16 found in the rest of the brain 
      global maximum in x=148, y=80, z=80, Imax=255
      CSF=17, 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=8640522601 voxels, voxel volume =1.000 
                     = 8640522601 mmm3 = 8640522.240 cm3
done.
PostAnalyze...Basin Prior
 209 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=127,y=93, z=105, r=9665 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 45406
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1037683078
  LEFT_CER     CSF_MIN=0, CSF_intensity=4, CSF_MAX=24 , nb = -1045574127
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = 1075535482
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=5, CSF_MAX=27 , nb = 1078867158
    OTHER      CSF_MIN=0, CSF_intensity=12, CSF_MAX=42 , nb = 1075114488
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    28,      29,        32,   63
  after  analyzing :    28,      31,        32,   39
   RIGHT_CER   
  before analyzing :    24,      41,        55,   71
  after  analyzing :    24,      50,        55,   55
   LEFT_CER    
  before analyzing :    24,      27,        32,   63
  after  analyzing :    24,      30,        32,   38
  RIGHT_BRAIN  
  before analyzing :    29,      30,        32,   63
  after  analyzing :    29,      31,        32,   39
  LEFT_BRAIN   
  before analyzing :    27,      29,        32,   60
  after  analyzing :    27,      31,        32,   38
     OTHER     
  before analyzing :    42,      74,        84,   93
  after  analyzing :    42,      80,        84,   83
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...68 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 67.135, std = 7.972

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.13, sigma = 4.60
      after  rotation: sse = 3.13, sigma = 4.60
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  3.20, its var is  3.89   
      before Erosion-Dilatation  0.40% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...48 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1482468 voxels, voxel volume = 1.000 mm3
           = 1482468 mmm3 = 1482.468 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    25.756084
mri_watershed stimesec    0.574912
mri_watershed ru_maxrss   821576
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   212733
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2568
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1148
mri_watershed ru_nivcsw   1191
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 17:16:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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=21.0
skull bounding box = (61, 33, 34) --> (192, 167, 190)
using (105, 78, 112) as brain centroid...
mean wm in atlas = 107, using box (89,62,93) --> (121, 94,131) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 104 +- 7.6
after smoothing, mri peak at 105, scaling input intensities by 1.019
scaling channel 0 by 1.01905
initial log_p = -4.535
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.021096 @ (-9.091, 27.273, -9.091)
max log p =    -3.959297 @ (4.545, -4.545, 4.545)
max log p =    -3.893008 @ (6.818, 2.273, -2.273)
max log p =    -3.870114 @ (-3.409, -1.136, 5.682)
max log p =    -3.867781 @ (-0.568, 0.568, 1.705)
max log p =    -3.861741 @ (-0.284, -1.420, -0.852)
Found translation: (-2.0, 23.0, -0.3): log p = -3.862
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.634, old_max_log_p =-3.862 (thresh=-3.9)
 1.07500   0.00000   0.00000  -11.64308;
 0.00000   1.19413   0.31997  -29.50821;
 0.00000  -0.25882   0.96593   28.23727;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.634, old_max_log_p =-3.634 (thresh=-3.6)
 1.07500   0.00000   0.00000  -11.64308;
 0.00000   1.19413   0.31997  -29.50821;
 0.00000  -0.25882   0.96593   28.23727;
 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=-3.487, old_max_log_p =-3.634 (thresh=-3.6)
 1.05409   0.00000   0.00000  -8.95114;
 0.00000   1.12932   0.37285  -25.11861;
 0.00000  -0.34312   0.97986   36.51017;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.487, old_max_log_p =-3.487 (thresh=-3.5)
 1.05409   0.00000   0.00000  -8.95114;
 0.00000   1.12932   0.37285  -25.11861;
 0.00000  -0.34312   0.97986   36.51017;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.463, old_max_log_p =-3.487 (thresh=-3.5)
 1.05405  -0.00919  -0.00325  -7.75645;
 0.00857   1.12249   0.37949  -26.73352;
 0.00014  -0.35196   0.97562   37.75048;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.463 (thresh=-3.5)
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.456 (thresh=-3.5)
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 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
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.456 (old=-4.535)
transform before final EM align:
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 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
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.9  tol 0.000000
final transform:
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1026.881890
mri_em_register stimesec    1.394787
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   158955
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    139
mri_em_register ru_nivcsw   4252
registration took 8 minutes and 53 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 17:25:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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=21.0
skull bounding box = (61, 33, 34) --> (192, 167, 190)
using (105, 78, 112) as brain centroid...
mean wm in atlas = 107, using box (89,62,93) --> (121, 94,131) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 104 +- 7.6
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
 1.05525  -0.01208   0.00471  -8.93147;
 0.00855   1.11986   0.37860  -26.39127;
-0.00847  -0.35063   0.97219   39.08956;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 37, 32) --> (191, 143, 189)
Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0
2 of 19 (10.5%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (68, 37, 31) --> (130, 136, 189)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 14 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 119, 62) --> (176, 155, 114)
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 119, 59) --> (129, 154, 114)
Right_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0
4 of 10 (40.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 104, 95) --> (146, 163, 124)
Brain_Stem: limiting intensities to 113.0 --> 132.0
3 of 7 (42.9%) samples deleted
using 50 total control points for intensity normalization...
bias field = 0.914 +- 0.090
0 of 41 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 37, 32) --> (191, 143, 189)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 121 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (68, 37, 31) --> (130, 136, 189)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 98 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 119, 62) --> (176, 155, 114)
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 119, 59) --> (129, 154, 114)
Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0
3 of 10 (30.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 104, 95) --> (146, 163, 124)
Brain_Stem: limiting intensities to 90.0 --> 132.0
14 of 32 (43.8%) samples deleted
using 261 total control points for intensity normalization...
bias field = 1.023 +- 0.074
0 of 244 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 37, 32) --> (191, 143, 189)
Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0
55 of 202 (27.2%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (68, 37, 31) --> (130, 136, 189)
Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0
80 of 227 (35.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 119, 62) --> (176, 155, 114)
Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0
3 of 6 (50.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 119, 59) --> (129, 154, 114)
Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0
1 of 7 (14.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 104, 95) --> (146, 163, 124)
Brain_Stem: limiting intensities to 91.0 --> 132.0
33 of 59 (55.9%) samples deleted
using 501 total control points for intensity normalization...
bias field = 0.978 +- 0.054
1 of 329 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 53 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 17:26:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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) = 1.29 (predicted orig area = 6.2)
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=0.854, neg=0, invalid=762
0001: dt=210.138032, rms=0.750 (12.251%), neg=0, invalid=762
0002: dt=155.446894, rms=0.728 (2.929%), neg=0, invalid=762
0003: dt=221.952000, rms=0.716 (1.536%), neg=0, invalid=762
0004: dt=143.515152, rms=0.710 (0.897%), neg=0, invalid=762
0005: dt=369.920000, rms=0.703 (0.929%), neg=0, invalid=762
0006: dt=110.976000, rms=0.699 (0.622%), neg=0, invalid=762
0007: dt=1183.744000, rms=0.690 (1.250%), neg=0, invalid=762
0008: dt=92.480000, rms=0.685 (0.700%), neg=0, invalid=762
0009: dt=517.888000, rms=0.684 (0.266%), neg=0, invalid=762
0010: dt=129.472000, rms=0.682 (0.225%), neg=0, invalid=762
0011: dt=129.472000, rms=0.682 (0.080%), neg=0, invalid=762
0012: dt=129.472000, rms=0.681 (0.133%), neg=0, invalid=762
0013: dt=129.472000, rms=0.679 (0.210%), neg=0, invalid=762
0014: dt=129.472000, rms=0.678 (0.244%), neg=0, invalid=762
0015: dt=129.472000, rms=0.676 (0.248%), neg=0, invalid=762
0016: dt=129.472000, rms=0.674 (0.241%), neg=0, invalid=762
0017: dt=129.472000, rms=0.673 (0.222%), neg=0, invalid=762
0018: dt=129.472000, rms=0.671 (0.223%), neg=0, invalid=762
0019: dt=129.472000, rms=0.670 (0.221%), neg=0, invalid=762
0020: dt=129.472000, rms=0.668 (0.188%), neg=0, invalid=762
0021: dt=129.472000, rms=0.667 (0.168%), neg=0, invalid=762
0022: dt=129.472000, rms=0.666 (0.166%), neg=0, invalid=762
0023: dt=129.472000, rms=0.665 (0.175%), neg=0, invalid=762
0024: dt=129.472000, rms=0.664 (0.158%), neg=0, invalid=762
0025: dt=129.472000, rms=0.663 (0.134%), neg=0, invalid=762
0026: dt=129.472000, rms=0.662 (0.121%), neg=0, invalid=762
0027: dt=129.472000, rms=0.662 (0.111%), neg=0, invalid=762
0028: dt=1183.744000, rms=0.661 (0.094%), neg=0, invalid=762
0029: dt=1183.744000, rms=0.661 (-5.946%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.661, neg=0, invalid=762
0030: dt=129.472000, rms=0.660 (0.213%), neg=0, invalid=762
0031: dt=517.888000, rms=0.659 (0.208%), neg=0, invalid=762
0032: dt=517.888000, rms=0.659 (-0.066%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.664, neg=0, invalid=762
0033: dt=136.982456, rms=0.658 (0.879%), neg=0, invalid=762
0034: dt=168.646240, rms=0.649 (1.407%), neg=0, invalid=762
0035: dt=82.666667, rms=0.645 (0.549%), neg=0, invalid=762
0036: dt=140.635193, rms=0.641 (0.678%), neg=0, invalid=762
0037: dt=36.288000, rms=0.639 (0.354%), neg=0, invalid=762
0038: dt=145.152000, rms=0.636 (0.398%), neg=0, invalid=762
0039: dt=112.746114, rms=0.633 (0.427%), neg=0, invalid=762
0040: dt=66.370370, rms=0.632 (0.277%), neg=0, invalid=762
0041: dt=145.152000, rms=0.630 (0.295%), neg=0, invalid=762
0042: dt=73.945946, rms=0.628 (0.277%), neg=0, invalid=762
0043: dt=82.944000, rms=0.627 (0.142%), neg=0, invalid=762
0044: dt=82.944000, rms=0.626 (0.235%), neg=0, invalid=762
0045: dt=82.944000, rms=0.624 (0.306%), neg=0, invalid=762
0046: dt=82.944000, rms=0.621 (0.389%), neg=0, invalid=762
0047: dt=82.944000, rms=0.618 (0.542%), neg=0, invalid=762
0048: dt=82.944000, rms=0.615 (0.551%), neg=0, invalid=762
0049: dt=82.944000, rms=0.612 (0.497%), neg=0, invalid=762
0050: dt=82.944000, rms=0.609 (0.423%), neg=0, invalid=762
0051: dt=82.944000, rms=0.606 (0.469%), neg=0, invalid=762
0052: dt=82.944000, rms=0.604 (0.394%), neg=0, invalid=762
0053: dt=82.944000, rms=0.602 (0.305%), neg=0, invalid=762
0054: dt=82.944000, rms=0.600 (0.222%), neg=0, invalid=762
0055: dt=82.944000, rms=0.599 (0.314%), neg=0, invalid=762
0056: dt=82.944000, rms=0.597 (0.223%), neg=0, invalid=762
0057: dt=82.944000, rms=0.596 (0.162%), neg=0, invalid=762
0058: dt=82.944000, rms=0.595 (0.147%), neg=0, invalid=762
0059: dt=82.944000, rms=0.594 (0.157%), neg=0, invalid=762
0060: dt=82.944000, rms=0.594 (0.126%), neg=0, invalid=762
0061: dt=82.944000, rms=0.593 (0.073%), neg=0, invalid=762
0062: dt=82.944000, rms=0.592 (0.145%), neg=0, invalid=762
0063: dt=82.944000, rms=0.592 (0.098%), neg=0, invalid=762
0064: dt=82.944000, rms=0.591 (0.074%), neg=0, invalid=762
0065: dt=124.416000, rms=0.591 (0.020%), neg=0, invalid=762
0066: dt=124.416000, rms=0.591 (-0.029%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.592, neg=0, invalid=762
0067: dt=103.680000, rms=0.590 (0.328%), neg=0, invalid=762
0068: dt=62.208000, rms=0.590 (0.041%), neg=0, invalid=762
0069: dt=62.208000, rms=0.590 (0.026%), neg=0, invalid=762
0070: dt=62.208000, rms=0.589 (0.028%), neg=0, invalid=762
0071: dt=62.208000, rms=0.589 (0.016%), neg=0, invalid=762
0072: dt=62.208000, rms=0.589 (0.003%), neg=0, invalid=762
0073: dt=145.152000, rms=0.589 (0.040%), neg=0, invalid=762
0074: dt=36.288000, rms=0.589 (0.009%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0075: dt=0.000000, rms=0.612 (0.094%), neg=0, invalid=762
0076: dt=0.000000, rms=0.612 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0077: dt=0.000000, rms=0.612 (0.094%), neg=0, invalid=762
0078: dt=0.000000, rms=0.612 (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=0.683, neg=0, invalid=762
0079: dt=5.040816, rms=0.664 (2.895%), neg=0, invalid=762
0080: dt=2.000000, rms=0.663 (0.090%), neg=0, invalid=762
0081: dt=2.000000, rms=0.663 (-0.033%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.663, neg=0, invalid=762
0082: dt=0.015750, rms=0.663 (0.069%), neg=0, invalid=762
0083: dt=0.013500, rms=0.663 (0.000%), neg=0, invalid=762
0084: dt=0.013500, rms=0.663 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.733, neg=0, invalid=762
0085: dt=1.536000, rms=0.727 (0.835%), neg=0, invalid=762
0086: dt=1.809524, rms=0.722 (0.705%), neg=0, invalid=762
0087: dt=0.448000, rms=0.722 (0.052%), neg=0, invalid=762
0088: dt=0.448000, rms=0.721 (0.039%), neg=0, invalid=762
0089: dt=0.448000, rms=0.721 (0.031%), neg=0, invalid=762
0090: dt=0.448000, rms=0.721 (0.002%), neg=0, invalid=762
0091: dt=1.792000, rms=0.720 (0.146%), neg=0, invalid=762
0092: dt=0.192000, rms=0.720 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.721, neg=0, invalid=762
0093: dt=1.280000, rms=0.719 (0.174%), neg=0, invalid=762
0094: dt=0.448000, rms=0.719 (0.020%), neg=0, invalid=762
0095: dt=0.448000, rms=0.719 (0.010%), neg=0, invalid=762
0096: dt=0.448000, rms=0.719 (0.007%), neg=0, invalid=762
0097: dt=0.448000, rms=0.719 (-0.002%), 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=0.676, neg=0, invalid=762
0098: dt=0.906929, rms=0.655 (3.093%), neg=0, invalid=762
0099: dt=0.080000, rms=0.654 (0.162%), neg=0, invalid=762
0100: dt=0.080000, rms=0.654 (-0.083%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.654, neg=0, invalid=762
0101: dt=0.028000, rms=0.654 (0.084%), neg=0, invalid=762
0102: dt=0.016000, rms=0.654 (0.009%), neg=0, invalid=762
0103: dt=0.016000, rms=0.654 (-0.008%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.10309 (17)
Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1093 voxels, overlap=0.746)
Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1093 voxels, peak = 16), gca=16.3
gca peak = 0.15565 (16)
mri peak = 0.07792 (17)
Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (541 voxels, overlap=0.819)
Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (541 voxels, peak = 16), gca=15.6
gca peak = 0.26829 (96)
mri peak = 0.08821 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (486 voxels, overlap=1.004)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (486 voxels, peak = 96), gca=96.0
gca peak = 0.20183 (93)
mri peak = 0.10406 (94)
Left_Pallidum (13): linear fit = 1.03 x + 0.0 (392 voxels, overlap=1.009)
Left_Pallidum (13): linear fit = 1.03 x + 0.0 (392 voxels, peak = 96), gca=96.3
gca peak = 0.21683 (55)
mri peak = 0.08895 (63)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, overlap=0.992)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, peak = 57), gca=57.5
gca peak = 0.30730 (58)
mri peak = 0.08092 (66)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (315 voxels, overlap=0.996)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (315 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.08453 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (42748 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (42748 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.07521 (99)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (38468 voxels, overlap=0.914)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (38468 voxels, peak = 104), gca=103.5
gca peak = 0.14995 (59)
mri peak = 0.03507 (62)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (9456 voxels, overlap=0.944)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (9456 voxels, peak = 60), gca=60.5
gca peak = 0.15082 (58)
mri peak = 0.03608 (68)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (11623 voxels, overlap=0.862)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (11623 voxels, peak = 62), gca=62.4
gca peak = 0.14161 (67)
mri peak = 0.09308 (74)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (431 voxels, overlap=0.757)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (431 voxels, peak = 73), gca=73.4
gca peak = 0.15243 (71)
mri peak = 0.09483 (79)
Left_Caudate (11): linear fit = 1.08 x + 0.0 (580 voxels, overlap=0.805)
Left_Caudate (11): linear fit = 1.08 x + 0.0 (580 voxels, peak = 76), gca=76.3
gca peak = 0.13336 (57)
mri peak = 0.03681 (61)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (6437 voxels, overlap=0.711)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (6437 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.04315 (68)
Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (7439 voxels, overlap=0.182)
Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (7439 voxels, peak = 67), gca=67.5
gca peak = 0.18181 (84)
mri peak = 0.06479 (87)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (3222 voxels, overlap=0.784)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (3222 voxels, peak = 89), gca=89.5
gca peak = 0.20573 (83)
mri peak = 0.07157 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3527 voxels, overlap=0.750)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3527 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.09125 (63)
Left_Amygdala (18): linear fit = 1.08 x + 0.0 (126 voxels, overlap=0.838)
Left_Amygdala (18): linear fit = 1.08 x + 0.0 (126 voxels, peak = 61), gca=61.3
gca peak = 0.39313 (56)
mri peak = 0.09524 (64)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (314 voxels, overlap=0.565)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (314 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.06368 (87)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2776 voxels, overlap=0.980)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2776 voxels, peak = 85), gca=84.6
gca peak = 0.11978 (83)
mri peak = 0.07083 (85)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2471 voxels, overlap=0.885)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2471 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.06972 (85)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (1363 voxels, overlap=0.774)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (1363 voxels, peak = 87), gca=86.5
gca peak = 0.14159 (79)
mri peak = 0.05882 (82)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (1464 voxels, overlap=0.999)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (1464 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.09181 (84)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (5472 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (5472 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.08096 (92)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (658 voxels, overlap=0.619)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (658 voxels, peak = 94), gca=94.2
gca peak = 0.12801 (89)
mri peak = 0.07407 (89)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (804 voxels, overlap=0.686)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (804 voxels, peak = 97), gca=96.6
gca peak = 0.20494 (23)
mri peak = 0.13793 (17)
gca peak = 0.15061 (21)
mri peak = 0.13296 (19)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (209 voxels, overlap=0.861)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (209 voxels, peak = 18), gca=18.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.07 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.89 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=0.654, neg=0, invalid=762
0104: dt=110.976000, rms=0.646 (1.224%), neg=0, invalid=762
0105: dt=295.936000, rms=0.641 (0.735%), neg=0, invalid=762
0106: dt=129.472000, rms=0.639 (0.323%), neg=0, invalid=762
0107: dt=221.952000, rms=0.636 (0.379%), neg=0, invalid=762
0108: dt=92.480000, rms=0.636 (0.132%), neg=0, invalid=762
0109: dt=517.888000, rms=0.633 (0.353%), neg=0, invalid=762
0110: dt=92.480000, rms=0.633 (0.115%), neg=0, invalid=762
0111: dt=517.888000, rms=0.632 (0.165%), neg=0, invalid=762
0112: dt=92.480000, rms=0.631 (0.111%), neg=0, invalid=762
0113: dt=517.888000, rms=0.630 (0.146%), neg=0, invalid=762
0114: dt=92.480000, rms=0.630 (0.079%), neg=0, invalid=762
0115: dt=517.888000, rms=0.629 (0.102%), neg=0, invalid=762
0116: dt=110.976000, rms=0.628 (0.072%), neg=0, invalid=762
0117: dt=295.936000, rms=0.628 (0.059%), neg=0, invalid=762
0118: dt=110.976000, rms=0.628 (0.046%), neg=0, invalid=762
0119: dt=110.976000, rms=0.628 (0.028%), neg=0, invalid=762
0120: dt=110.976000, rms=0.627 (0.049%), neg=0, invalid=762
0121: dt=110.976000, rms=0.627 (0.068%), neg=0, invalid=762
0122: dt=110.976000, rms=0.626 (0.068%), neg=0, invalid=762
0123: dt=110.976000, rms=0.626 (0.079%), neg=0, invalid=762
0124: dt=110.976000, rms=0.625 (0.079%), neg=0, invalid=762
0125: dt=110.976000, rms=0.625 (0.074%), neg=0, invalid=762
0126: dt=110.976000, rms=0.625 (0.073%), neg=0, invalid=762
0127: dt=110.976000, rms=0.624 (0.068%), neg=0, invalid=762
0128: dt=110.976000, rms=0.624 (0.072%), neg=0, invalid=762
0129: dt=110.976000, rms=0.623 (0.069%), neg=0, invalid=762
0130: dt=110.976000, rms=0.623 (0.062%), neg=0, invalid=762
0131: dt=110.976000, rms=0.622 (0.061%), neg=0, invalid=762
0132: dt=110.976000, rms=0.622 (0.056%), neg=0, invalid=762
0133: dt=110.976000, rms=0.622 (0.056%), neg=0, invalid=762
0134: dt=110.976000, rms=0.621 (0.050%), neg=0, invalid=762
0135: dt=110.976000, rms=0.621 (0.053%), neg=0, invalid=762
0136: dt=110.976000, rms=0.621 (0.049%), neg=0, invalid=762
0137: dt=110.976000, rms=0.620 (0.048%), neg=0, invalid=762
0138: dt=110.976000, rms=0.620 (0.047%), neg=0, invalid=762
0139: dt=110.976000, rms=0.620 (0.043%), neg=0, invalid=762
0140: dt=110.976000, rms=0.620 (0.043%), neg=0, invalid=762
0141: dt=110.976000, rms=0.619 (0.043%), neg=0, invalid=762
0142: dt=110.976000, rms=0.619 (0.046%), neg=0, invalid=762
0143: dt=110.976000, rms=0.619 (0.045%), neg=0, invalid=762
0144: dt=110.976000, rms=0.619 (0.043%), neg=0, invalid=762
0145: dt=110.976000, rms=0.618 (0.045%), neg=0, invalid=762
0146: dt=110.976000, rms=0.618 (0.044%), neg=0, invalid=762
0147: dt=110.976000, rms=0.618 (0.041%), neg=0, invalid=762
0148: dt=110.976000, rms=0.618 (0.035%), neg=0, invalid=762
0149: dt=110.976000, rms=0.617 (0.037%), neg=0, invalid=762
0150: dt=110.976000, rms=0.617 (0.036%), neg=0, invalid=762
0151: dt=110.976000, rms=0.617 (0.042%), neg=0, invalid=762
0152: dt=110.976000, rms=0.617 (0.043%), neg=0, invalid=762
0153: dt=110.976000, rms=0.616 (0.043%), neg=0, invalid=762
0154: dt=110.976000, rms=0.616 (0.037%), neg=0, invalid=762
0155: dt=110.976000, rms=0.616 (0.036%), neg=0, invalid=762
0156: dt=110.976000, rms=0.616 (0.032%), neg=0, invalid=762
0157: dt=110.976000, rms=0.615 (0.032%), neg=0, invalid=762
0158: dt=110.976000, rms=0.615 (0.029%), neg=0, invalid=762
0159: dt=110.976000, rms=0.615 (0.034%), neg=0, invalid=762
0160: dt=110.976000, rms=0.615 (0.034%), neg=0, invalid=762
0161: dt=110.976000, rms=0.615 (0.035%), neg=0, invalid=762
0162: dt=110.976000, rms=0.614 (0.033%), neg=0, invalid=762
0163: dt=110.976000, rms=0.614 (0.028%), neg=0, invalid=762
0164: dt=110.976000, rms=0.614 (0.022%), neg=0, invalid=762
0165: dt=110.976000, rms=0.614 (0.026%), neg=0, invalid=762
0166: dt=110.976000, rms=0.614 (0.022%), neg=0, invalid=762
0167: dt=110.976000, rms=0.614 (0.024%), neg=0, invalid=762
0168: dt=110.976000, rms=0.614 (0.030%), neg=0, invalid=762
0169: dt=110.976000, rms=0.613 (0.030%), neg=0, invalid=762
0170: dt=110.976000, rms=0.613 (0.025%), neg=0, invalid=762
0171: dt=110.976000, rms=0.613 (0.023%), neg=0, invalid=762
0172: dt=887.808000, rms=0.613 (0.016%), neg=0, invalid=762
0173: dt=887.808000, rms=0.613 (-0.640%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0174: dt=221.952000, rms=0.612 (0.226%), neg=0, invalid=762
0175: dt=129.472000, rms=0.612 (0.066%), neg=0, invalid=762
0176: dt=295.936000, rms=0.611 (0.023%), neg=0, invalid=762
0177: dt=295.936000, rms=0.611 (-0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.613, neg=0, invalid=762
0178: dt=111.157895, rms=0.610 (0.539%), neg=0, invalid=762
0179: dt=123.914894, rms=0.605 (0.709%), neg=0, invalid=762
0180: dt=67.918367, rms=0.602 (0.448%), neg=0, invalid=762
0181: dt=74.982249, rms=0.600 (0.392%), neg=0, invalid=762
0182: dt=70.846512, rms=0.598 (0.339%), neg=0, invalid=762
0183: dt=87.843137, rms=0.596 (0.296%), neg=0, invalid=762
0184: dt=62.208000, rms=0.595 (0.306%), neg=0, invalid=762
0185: dt=103.680000, rms=0.593 (0.280%), neg=0, invalid=762
0186: dt=36.288000, rms=0.591 (0.229%), neg=0, invalid=762
0187: dt=580.608000, rms=0.582 (1.529%), neg=0, invalid=762
0188: dt=82.944000, rms=0.581 (0.172%), neg=0, invalid=762
0189: dt=64.000000, rms=0.581 (0.142%), neg=0, invalid=762
0190: dt=82.944000, rms=0.580 (0.113%), neg=0, invalid=762
0191: dt=62.208000, rms=0.579 (0.141%), neg=0, invalid=762
0192: dt=82.944000, rms=0.579 (0.100%), neg=0, invalid=762
0193: dt=62.208000, rms=0.578 (0.127%), neg=0, invalid=762
0194: dt=82.944000, rms=0.577 (0.089%), neg=0, invalid=762
0195: dt=62.208000, rms=0.577 (0.122%), neg=0, invalid=762
0196: dt=82.944000, rms=0.576 (0.090%), neg=0, invalid=762
0197: dt=36.288000, rms=0.576 (0.096%), neg=0, invalid=762
0198: dt=580.608000, rms=0.571 (0.757%), neg=0, invalid=762
0199: dt=145.152000, rms=0.570 (0.163%), neg=0, invalid=762
0200: dt=36.288000, rms=0.570 (0.065%), neg=0, invalid=762
0201: dt=580.608000, rms=0.568 (0.405%), neg=0, invalid=762
0202: dt=81.351111, rms=0.566 (0.255%), neg=0, invalid=762
0203: dt=124.416000, rms=0.566 (0.082%), neg=0, invalid=762
0204: dt=82.944000, rms=0.565 (0.086%), neg=0, invalid=762
0205: dt=124.416000, rms=0.565 (0.069%), neg=0, invalid=762
0206: dt=82.944000, rms=0.564 (0.080%), neg=0, invalid=762
0207: dt=103.680000, rms=0.564 (0.074%), neg=0, invalid=762
0208: dt=62.208000, rms=0.564 (0.053%), neg=0, invalid=762
0209: dt=36.288000, rms=0.563 (0.031%), neg=0, invalid=762
0210: dt=36.288000, rms=0.563 (0.024%), neg=0, invalid=762
0211: dt=9.072000, rms=0.563 (0.009%), neg=0, invalid=762
0212: dt=1.134000, rms=0.563 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.564, neg=0, invalid=762
0213: dt=2.268000, rms=0.563 (0.105%), neg=0, invalid=762
0214: dt=2.268000, rms=0.563 (0.012%), neg=0, invalid=762
0215: dt=1.134000, rms=0.563 (0.005%), neg=0, invalid=762
0216: dt=0.070875, rms=0.563 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.569, neg=0, invalid=762
0217: dt=0.002734, rms=0.569 (0.088%), neg=0, invalid=762
0218: dt=0.001750, rms=0.569 (0.000%), neg=0, invalid=762
0219: dt=0.000109, rms=0.569 (0.000%), neg=0, invalid=762
0220: dt=0.000055, rms=0.569 (0.000%), neg=0, invalid=762
0221: dt=0.000014, rms=0.569 (0.000%), neg=0, invalid=762
0222: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.569, neg=0, invalid=762
0223: dt=0.000000, rms=0.569 (0.087%), neg=0, invalid=762
0224: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=762
0225: dt=0.000015, rms=0.569 (0.000%), neg=0, invalid=762
0226: dt=0.000008, rms=0.569 (0.000%), neg=0, invalid=762
0227: dt=0.000004, rms=0.569 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.588, neg=0, invalid=762
0228: dt=11.520000, rms=0.558 (5.156%), neg=0, invalid=762
0229: dt=4.032000, rms=0.553 (0.745%), neg=0, invalid=762
0230: dt=4.032000, rms=0.550 (0.601%), neg=0, invalid=762
0231: dt=0.180000, rms=0.550 (0.025%), neg=0, invalid=762
0232: dt=0.011250, rms=0.550 (0.001%), neg=0, invalid=762
0233: dt=0.005625, rms=0.550 (0.001%), neg=0, invalid=762
0234: dt=0.000703, rms=0.550 (0.000%), neg=0, invalid=762
0235: dt=0.000540, rms=0.550 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.550, neg=0, invalid=762
0236: dt=16.128000, rms=0.540 (1.819%), neg=0, invalid=762
0237: dt=11.520000, rms=0.538 (0.527%), neg=0, invalid=762
0238: dt=11.520000, rms=0.536 (0.335%), neg=0, invalid=762
0239: dt=2.880000, rms=0.535 (0.073%), neg=0, invalid=762
0240: dt=0.252000, rms=0.535 (0.004%), neg=0, invalid=762
0241: dt=0.252000, rms=0.535 (0.008%), neg=0, invalid=762
0242: dt=0.031500, rms=0.535 (0.003%), neg=0, invalid=762
0243: dt=0.007875, rms=0.535 (-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=0.560, neg=0, invalid=762
0244: dt=0.000000, rms=0.559 (0.095%), neg=0, invalid=762
0245: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=762
0246: dt=0.100000, rms=0.559 (-0.066%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.560, neg=0, invalid=762
0247: dt=0.000000, rms=0.559 (0.095%), neg=0, invalid=762
0248: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=762
0249: dt=0.100000, rms=0.559 (-0.044%), 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=0.519, neg=0, invalid=762
0250: dt=0.448000, rms=0.505 (2.848%), neg=0, invalid=762
0251: dt=0.448000, rms=0.501 (0.603%), neg=0, invalid=762
0252: dt=0.384000, rms=0.500 (0.308%), neg=0, invalid=762
0253: dt=0.384000, rms=0.499 (0.217%), neg=0, invalid=762
0254: dt=0.384000, rms=0.498 (0.164%), neg=0, invalid=762
0255: dt=0.384000, rms=0.497 (0.126%), neg=0, invalid=762
0256: dt=0.384000, rms=0.497 (0.101%), neg=0, invalid=762
0257: dt=0.384000, rms=0.496 (0.086%), neg=0, invalid=762
0258: dt=0.384000, rms=0.496 (0.073%), neg=0, invalid=762
0259: dt=0.384000, rms=0.496 (0.059%), neg=0, invalid=762
0260: dt=0.384000, rms=0.496 (0.057%), neg=0, invalid=762
0261: dt=0.384000, rms=0.495 (0.044%), neg=0, invalid=762
0262: dt=0.384000, rms=0.495 (0.044%), neg=0, invalid=762
0263: dt=0.384000, rms=0.495 (0.070%), neg=0, invalid=762
0264: dt=0.384000, rms=0.495 (0.034%), neg=0, invalid=762
0265: dt=0.384000, rms=0.494 (0.049%), neg=0, invalid=762
0266: dt=0.384000, rms=0.494 (0.065%), neg=0, invalid=762
0267: dt=0.384000, rms=0.494 (0.016%), neg=0, invalid=762
0268: dt=0.384000, rms=0.494 (0.015%), neg=0, invalid=762
0269: dt=0.448000, rms=0.494 (0.012%), neg=0, invalid=762
0270: dt=0.448000, rms=0.494 (0.011%), neg=0, invalid=762
0271: dt=0.448000, rms=0.494 (0.030%), neg=0, invalid=762
0272: dt=0.448000, rms=0.494 (0.008%), neg=0, invalid=762
0273: dt=0.448000, rms=0.493 (0.024%), neg=0, invalid=762
0274: dt=0.448000, rms=0.493 (0.009%), neg=0, invalid=762
0275: dt=0.384000, rms=0.493 (0.005%), neg=0, invalid=762
0276: dt=0.384000, rms=0.493 (0.010%), neg=0, invalid=762
0277: dt=0.384000, rms=0.493 (0.008%), neg=0, invalid=762
0278: dt=0.384000, rms=0.493 (0.018%), neg=0, invalid=762
0279: dt=0.384000, rms=0.493 (0.020%), neg=0, invalid=762
0280: dt=0.384000, rms=0.493 (0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.494, neg=0, invalid=762
0281: dt=0.384000, rms=0.488 (1.160%), neg=0, invalid=762
0282: dt=0.448000, rms=0.487 (0.262%), neg=0, invalid=762
0283: dt=0.448000, rms=0.487 (0.034%), neg=0, invalid=762
0284: dt=0.448000, rms=0.486 (0.007%), neg=0, invalid=762
0285: dt=0.448000, rms=0.486 (0.001%), neg=0, invalid=762
0286: dt=0.448000, rms=0.486 (-0.011%), 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=0.485, neg=0, invalid=762
0287: dt=0.000000, rms=0.484 (0.126%), neg=0, invalid=762
0288: dt=0.000000, rms=0.484 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.485, neg=0, invalid=762
0289: dt=129.472000, rms=0.484 (0.176%), neg=0, invalid=762
0290: dt=129.472000, rms=0.484 (0.025%), neg=0, invalid=762
0291: dt=129.472000, rms=0.484 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.485, neg=0, invalid=762
0292: dt=36.288000, rms=0.484 (0.204%), neg=0, invalid=762
0293: dt=36.288000, rms=0.483 (0.037%), neg=0, invalid=762
0294: dt=36.288000, rms=0.483 (0.018%), neg=0, invalid=762
0295: dt=36.288000, rms=0.483 (-0.015%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
0296: dt=104.594286, rms=0.481 (0.533%), neg=0, invalid=762
0297: dt=36.288000, rms=0.481 (0.118%), neg=0, invalid=762
0298: dt=36.288000, rms=0.481 (0.051%), neg=0, invalid=762
0299: dt=36.288000, rms=0.480 (0.077%), neg=0, invalid=762
0300: dt=36.288000, rms=0.480 (0.106%), neg=0, invalid=762
0301: dt=36.288000, rms=0.479 (0.122%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0302: dt=36.288000, rms=0.478 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0303: dt=36.288000, rms=0.478 (0.108%), neg=0, invalid=762
0304: dt=145.152000, rms=0.478 (0.040%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
iter 0, gcam->neg = 8
after 2 iterations, nbhd size=0, neg = 0
0305: dt=38.400000, rms=0.475 (0.702%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0306: dt=38.400000, rms=0.474 (0.351%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0307: dt=25.600000, rms=0.472 (0.345%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0308: dt=25.600000, rms=0.471 (0.173%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 0 iterations, nbhd size=0, neg = 0
0309: dt=25.600000, rms=0.470 (0.169%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 9 iterations, nbhd size=1, neg = 0
0310: dt=25.600000, rms=0.469 (0.223%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 1 iterations, nbhd size=0, neg = 0
0311: dt=25.600000, rms=0.468 (0.234%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0312: dt=25.600000, rms=0.467 (0.201%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 9 iterations, nbhd size=1, neg = 0
0313: dt=25.600000, rms=0.466 (0.177%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 9 iterations, nbhd size=1, neg = 0
0314: dt=25.600000, rms=0.465 (0.208%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 8 iterations, nbhd size=1, neg = 0
0315: dt=25.600000, rms=0.465 (0.163%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 11 iterations, nbhd size=1, neg = 0
0316: dt=25.600000, rms=0.464 (0.164%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 5 iterations, nbhd size=0, neg = 0
0317: dt=25.600000, rms=0.463 (0.176%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 9 iterations, nbhd size=1, neg = 0
0318: dt=25.600000, rms=0.462 (0.170%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 9 iterations, nbhd size=1, neg = 0
0319: dt=25.600000, rms=0.462 (0.151%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 10 iterations, nbhd size=1, neg = 0
0320: dt=25.600000, rms=0.461 (0.101%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 2 iterations, nbhd size=0, neg = 0
0321: dt=25.600000, rms=0.461 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 16 iterations, nbhd size=1, neg = 0
0322: dt=25.600000, rms=0.460 (0.079%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0323: dt=25.600000, rms=0.460 (0.077%), neg=0, invalid=762
0324: dt=25.600000, rms=0.460 (0.028%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 8 iterations, nbhd size=1, neg = 0
0325: dt=25.600000, rms=0.459 (0.059%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0326: dt=25.600000, rms=0.459 (0.049%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0327: dt=25.600000, rms=0.459 (0.047%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0328: dt=72.220183, rms=0.455 (0.937%), neg=0, invalid=762
0329: dt=25.600000, rms=0.454 (0.301%), neg=0, invalid=762
0330: dt=44.800000, rms=0.453 (0.133%), neg=0, invalid=762
0331: dt=44.800000, rms=0.453 (0.016%), neg=0, invalid=762
0332: dt=44.800000, rms=0.452 (0.269%), neg=0, invalid=762
0333: dt=44.800000, rms=0.452 (0.077%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0334: dt=44.800000, rms=0.451 (0.096%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0335: dt=44.800000, rms=0.451 (-0.069%), neg=0, invalid=762
0336: dt=23.500000, rms=0.451 (0.138%), neg=0, invalid=762
0337: dt=19.200000, rms=0.450 (0.047%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0338: dt=0.252000, rms=0.457 (0.119%), neg=0, invalid=762
0339: dt=0.108000, rms=0.457 (0.001%), neg=0, invalid=762
0340: dt=0.108000, rms=0.457 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0341: dt=3.047619, rms=0.457 (0.159%), neg=0, invalid=762
0342: dt=1.008000, rms=0.457 (0.005%), neg=0, invalid=762
0343: dt=1.008000, rms=0.457 (0.008%), neg=0, invalid=762
0344: dt=1.008000, rms=0.457 (-0.010%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.468, neg=0, invalid=762
0345: dt=1.024000, rms=0.467 (0.241%), neg=0, invalid=762
0346: dt=0.112000, rms=0.467 (0.006%), neg=0, invalid=762
0347: dt=0.112000, rms=0.467 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.467, neg=0, invalid=762
0348: dt=1.792000, rms=0.465 (0.394%), neg=0, invalid=762
0349: dt=1.024000, rms=0.465 (0.043%), neg=0, invalid=762
0350: dt=1.024000, rms=0.465 (-0.002%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
iter 0, gcam->neg = 901
after 13 iterations, nbhd size=1, neg = 0
0351: dt=2.271322, rms=0.424 (7.224%), neg=0, invalid=762
0352: dt=0.080000, rms=0.424 (0.060%), neg=0, invalid=762
0353: dt=0.080000, rms=0.424 (-0.066%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.425, neg=0, invalid=762
0354: dt=0.096000, rms=0.424 (0.239%), neg=0, invalid=762
0355: dt=0.000000, rms=0.424 (0.005%), neg=0, invalid=762
0356: dt=0.050000, rms=0.424 (-0.023%), 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=0.409, neg=0, invalid=762
0357: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0358: dt=32.368000, rms=0.409 (0.003%), neg=0, invalid=762
0359: dt=23.120000, rms=0.409 (0.000%), neg=0, invalid=762
0360: dt=23.120000, rms=0.409 (-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=0.409, neg=0, invalid=762
0361: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0362: dt=62.208000, rms=0.409 (0.040%), neg=0, invalid=762
0363: dt=145.152000, rms=0.409 (0.057%), neg=0, invalid=762
0364: dt=36.288000, rms=0.409 (0.010%), neg=0, invalid=762
0365: dt=36.288000, rms=0.409 (0.010%), neg=0, invalid=762
0366: dt=36.288000, rms=0.409 (0.016%), neg=0, invalid=762
0367: dt=36.288000, rms=0.409 (0.020%), neg=0, invalid=762
0368: dt=36.288000, rms=0.409 (0.020%), neg=0, invalid=762
0369: dt=36.288000, rms=0.409 (0.017%), neg=0, invalid=762
0370: dt=36.288000, rms=0.409 (0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0371: dt=11.200000, rms=0.409 (0.060%), neg=0, invalid=762
0372: dt=8.000000, rms=0.409 (0.012%), neg=0, invalid=762
0373: dt=8.000000, rms=0.409 (0.001%), neg=0, invalid=762
0374: dt=8.000000, rms=0.409 (-0.036%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0375: dt=75.397260, rms=0.407 (0.605%), neg=0, invalid=762
0376: dt=25.600000, rms=0.405 (0.313%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0377: dt=44.800000, rms=0.405 (0.136%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0378: dt=44.800000, rms=0.404 (0.115%), neg=0, invalid=762
0379: dt=44.800000, rms=0.403 (0.235%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
0380: dt=44.800000, rms=0.402 (0.202%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 1 iterations, nbhd size=0, neg = 0
0381: dt=44.800000, rms=0.402 (0.236%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0382: dt=44.800000, rms=0.401 (0.186%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 2 iterations, nbhd size=0, neg = 0
0383: dt=44.800000, rms=0.400 (0.178%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0384: dt=44.800000, rms=0.399 (0.149%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0385: dt=44.800000, rms=0.399 (0.107%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=1, neg = 0
0386: dt=44.800000, rms=0.399 (0.097%), neg=0, invalid=762
0387: dt=32.000000, rms=0.399 (0.019%), neg=0, invalid=762
0388: dt=32.000000, rms=0.399 (0.009%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0389: dt=32.000000, rms=0.399 (0.008%), neg=0, invalid=762
0390: dt=32.000000, rms=0.398 (0.013%), neg=0, invalid=762
0391: dt=32.000000, rms=0.398 (0.005%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.403, neg=0, invalid=762
0392: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.403, neg=0, invalid=762
0393: dt=2.304000, rms=0.403 (0.013%), neg=0, invalid=762
0394: dt=1.008000, rms=0.403 (0.002%), neg=0, invalid=762
0395: dt=1.008000, rms=0.403 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.411, neg=0, invalid=762
0396: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.411, neg=0, invalid=762
0397: dt=0.000000, rms=0.411 (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=0.397, neg=0, invalid=762
iter 0, gcam->neg = 579
after 14 iterations, nbhd size=1, neg = 0
0398: dt=1.280000, rms=0.388 (2.352%), neg=0, invalid=762
0399: dt=0.000015, rms=0.388 (0.000%), neg=0, invalid=762
0400: dt=0.000015, rms=0.388 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.388, neg=0, invalid=762
0401: dt=0.112000, rms=0.387 (0.074%), neg=0, invalid=762
0402: dt=0.080000, rms=0.387 (0.019%), neg=0, invalid=762
0403: dt=0.080000, rms=0.387 (0.010%), neg=0, invalid=762
0404: dt=0.080000, rms=0.387 (-0.025%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 1 minutes and 51 seconds.
mri_ca_register utimesec    8244.543638
mri_ca_register stimesec    9.166606
mri_ca_register ru_maxrss   1338304
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4529199
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63472
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    4230
mri_ca_register ru_nivcsw   35293
FSRUNTIME@ mri_ca_register  2.0309 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 19:28:48 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-382
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-6.0.0/0051362/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 6.21
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 = 0.09804 (17)
Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1417 voxels, overlap=0.811)
Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1417 voxels, peak = 17), gca=17.3
gca peak = 0.17677 (13)
mri peak = 0.08616 (17)
Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1306 voxels, overlap=0.892)
Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1306 voxels, peak = 16), gca=15.5
gca peak = 0.28129 (95)
mri peak = 0.10183 (95)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (382 voxels, overlap=1.015)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (382 voxels, peak = 96), gca=96.4
gca peak = 0.16930 (96)
mri peak = 0.11983 (94)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (349 voxels, overlap=1.014)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (349 voxels, peak = 98), gca=98.4
gca peak = 0.24553 (55)
mri peak = 0.07905 (63)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (509 voxels, overlap=0.962)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (509 voxels, peak = 62), gca=62.4
gca peak = 0.30264 (59)
mri peak = 0.07713 (62)
Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (470 voxels, overlap=1.015)
Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (470 voxels, peak = 63), gca=63.4
gca peak = 0.07580 (103)
mri peak = 0.08934 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31460 voxels, overlap=0.784)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31460 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.07237 (99)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, overlap=0.835)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.04272 (64)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (10203 voxels, overlap=0.946)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (10203 voxels, peak = 61), gca=60.6
gca peak = 0.11620 (58)
mri peak = 0.04483 (63)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (10917 voxels, overlap=0.806)
Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (10917 voxels, peak = 64), gca=63.5
gca peak = 0.30970 (66)
mri peak = 0.07820 (79)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (844 voxels, overlap=0.377)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (844 voxels, peak = 76), gca=75.6
gca peak = 0.15280 (69)
mri peak = 0.08963 (79)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (904 voxels, overlap=1.004)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (904 voxels, peak = 73), gca=73.5
gca peak = 0.13902 (56)
mri peak = 0.05161 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (5123 voxels, overlap=0.864)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (5123 voxels, peak = 62), gca=62.4
gca peak = 0.14777 (55)
mri peak = 0.05681 (68)
Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (6423 voxels, overlap=0.227)
Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (6423 voxels, peak = 66), gca=65.7
gca peak = 0.16765 (84)
mri peak = 0.07499 (86)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (2421 voxels, overlap=0.865)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (2421 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.08716 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2944 voxels, overlap=0.743)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2944 voxels, peak = 89), gca=89.5
gca peak = 0.29869 (57)
mri peak = 0.10451 (67)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (266 voxels, overlap=0.817)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (266 voxels, peak = 64), gca=63.6
gca peak = 0.33601 (57)
mri peak = 0.08961 (65)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (243 voxels, overlap=1.005)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (243 voxels, peak = 64), gca=63.6
gca peak = 0.11131 (90)
mri peak = 0.06785 (86)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (2474 voxels, overlap=0.992)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (2474 voxels, peak = 88), gca=87.8
gca peak = 0.11793 (83)
mri peak = 0.07065 (85)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (2597 voxels, overlap=0.950)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (2597 voxels, peak = 87), gca=86.7
gca peak = 0.08324 (81)
mri peak = 0.06699 (81)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (1357 voxels, overlap=0.759)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (1357 voxels, peak = 86), gca=86.3
gca peak = 0.10360 (77)
mri peak = 0.06001 (82)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1309 voxels, overlap=0.883)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1309 voxels, peak = 81), gca=81.2
gca peak = 0.08424 (78)
mri peak = 0.09242 (84)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (5773 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (5773 voxels, peak = 83), gca=83.1
gca peak = 0.12631 (89)
mri peak = 0.07270 (92)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (678 voxels, overlap=0.760)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (678 voxels, peak = 95), gca=94.8
gca peak = 0.14500 (87)
mri peak = 0.07380 (96)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (714 voxels, overlap=0.813)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (714 voxels, peak = 94), gca=93.5
gca peak = 0.14975 (24)
mri peak = 0.10010 (15)
gca peak = 0.19357 (14)
mri peak = 0.13450 (20)
Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (225 voxels, overlap=0.887)
Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (225 voxels, peak = 18), gca=17.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.10 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 1.11 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.17218 (16)
mri peak = 0.09804 (17)
Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1417 voxels, overlap=0.921)
Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1417 voxels, peak = 16), gca=16.0
gca peak = 0.16342 (15)
mri peak = 0.08616 (17)
Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (1306 voxels, overlap=0.743)
Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (1306 voxels, peak = 16), gca=16.4
gca peak = 0.25981 (97)
mri peak = 0.10183 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (382 voxels, overlap=1.015)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (382 voxels, peak = 97), gca=96.5
gca peak = 0.16584 (97)
mri peak = 0.11983 (94)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (349 voxels, overlap=1.009)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (349 voxels, peak = 97), gca=97.5
gca peak = 0.26963 (63)
mri peak = 0.07905 (63)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (509 voxels, overlap=1.004)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (509 voxels, peak = 62), gca=62.1
gca peak = 0.24587 (64)
mri peak = 0.07713 (62)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (470 voxels, overlap=1.013)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (470 voxels, peak = 64), gca=64.0
gca peak = 0.07772 (104)
mri peak = 0.08934 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31460 voxels, overlap=0.833)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31460 voxels, peak = 103), gca=103.5
gca peak = 0.07714 (104)
mri peak = 0.07237 (99)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, overlap=0.835)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, peak = 104), gca=104.0
gca peak = 0.09252 (61)
mri peak = 0.04272 (64)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (10203 voxels, overlap=0.979)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (10203 voxels, peak = 63), gca=62.5
gca peak = 0.10558 (64)
mri peak = 0.04483 (63)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (10917 voxels, overlap=0.965)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (10917 voxels, peak = 66), gca=65.6
gca peak = 0.24443 (76)
mri peak = 0.07820 (79)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (844 voxels, overlap=1.000)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (844 voxels, peak = 75), gca=74.9
gca peak = 0.12679 (73)
mri peak = 0.08963 (79)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (904 voxels, overlap=1.005)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (904 voxels, peak = 72), gca=71.9
gca peak = 0.12455 (62)
mri peak = 0.05161 (63)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (5123 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (5123 voxels, peak = 61), gca=61.1
gca peak = 0.12176 (66)
mri peak = 0.05681 (68)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (6423 voxels, overlap=0.991)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (6423 voxels, peak = 66), gca=66.0
gca peak = 0.15873 (90)
mri peak = 0.07499 (86)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2421 voxels, overlap=0.985)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2421 voxels, peak = 90), gca=89.6
gca peak = 0.15153 (90)
mri peak = 0.08716 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2944 voxels, overlap=0.967)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2944 voxels, peak = 90), gca=89.6
gca peak = 0.24255 (65)
mri peak = 0.10451 (67)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (266 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (266 voxels, peak = 65), gca=65.0
gca peak = 0.30515 (64)
mri peak = 0.08961 (65)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (243 voxels, overlap=1.021)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (243 voxels, peak = 64), gca=64.0
gca peak = 0.11020 (86)
mri peak = 0.06785 (86)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2474 voxels, overlap=0.952)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2474 voxels, peak = 86), gca=85.6
gca peak = 0.09848 (90)
mri peak = 0.07065 (85)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2597 voxels, overlap=0.982)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2597 voxels, peak = 89), gca=88.7
gca peak = 0.08936 (88)
mri peak = 0.06699 (81)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1357 voxels, overlap=0.939)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1357 voxels, peak = 87), gca=86.7
gca peak = 0.08162 (81)
mri peak = 0.06001 (82)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1309 voxels, overlap=0.999)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1309 voxels, peak = 81), gca=80.6
gca peak = 0.07305 (83)
mri peak = 0.09242 (84)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (5773 voxels, overlap=0.727)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (5773 voxels, peak = 82), gca=81.8
gca peak = 0.11574 (95)
mri peak = 0.07270 (92)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (678 voxels, overlap=0.846)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (678 voxels, peak = 93), gca=92.6
gca peak = 0.16271 (92)
mri peak = 0.07380 (96)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (714 voxels, overlap=0.951)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (714 voxels, peak = 94), gca=94.3
gca peak = 0.17034 (28)
mri peak = 0.10010 (15)
gca peak = 0.16541 (20)
mri peak = 0.13450 (20)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (225 voxels, overlap=0.744)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (225 voxels, peak = 20), gca=20.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15020 (36)
gca peak Left_Thalamus = 0.64095 (101)
gca peak Third_Ventricle = 0.17034 (28)
gca peak CSF = 0.21662 (40)
gca peak Left_Accumbens_area = 0.64436 (66)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11917 (35)
gca peak Right_Inf_Lat_Vent = 0.21972 (26)
gca peak Right_Accumbens_area = 0.29834 (74)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65358 (35)
gca peak WM_hypointensities = 0.07609 (77)
gca peak non_WM_hypointensities = 0.10019 (77)
gca peak Optic_Chiasm = 0.70601 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.04 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
77226 voxels changed in iteration 0 of unlikely voxel relabeling
258 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
42922 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels)
477 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 74328 changed. image ll: -2.098, PF=0.500
pass 2: 19205 changed. image ll: -2.097, PF=0.500
pass 3: 4935 changed.
42630 voxels changed in iteration 0 of unlikely voxel relabeling
261 voxels changed in iteration 1 of unlikely voxel relabeling
18 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6819 voxels changed in iteration 0 of unlikely voxel relabeling
96 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5863 voxels changed in iteration 0 of unlikely voxel relabeling
54 voxels changed in iteration 1 of unlikely voxel relabeling
24 voxels changed in iteration 2 of unlikely voxel relabeling
1 voxels changed in iteration 3 of unlikely voxel relabeling
1 voxels changed in iteration 4 of unlikely voxel relabeling
4175 voxels changed in iteration 0 of unlikely voxel relabeling
15 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3342.971791
mri_ca_label stimesec    1.430782
mri_ca_label ru_maxrss   2096384
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   711771
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63464
mri_ca_label ru_oublock  464
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    315
mri_ca_label ru_nivcsw   4504
auto-labeling took 54 minutes and 58 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/cc_up.lta 0051362 

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-6.0.0/0051362/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/norm.mgz
33968 voxels in left wm, 36272 in right wm, xrange [123, 132]
searching rotation angles z=[-3 11], y=[-7  7]

searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.0  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.5  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 6.0  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.5  
searching scale 1 Z rot 6.7  
searching scale 1 Z rot 7.0  
searching scale 1 Z rot 7.2  
searching scale 1 Z rot 7.5  
searching scale 1 Z rot 7.7  
searching scale 1 Z rot 8.0  
searching scale 1 Z rot 8.2  
searching scale 1 Z rot 8.5  
searching scale 1 Z rot 8.7  
searching scale 1 Z rot 9.0  
searching scale 1 Z rot 9.2  
searching scale 1 Z rot 9.5  
searching scale 1 Z rot 9.7  
searching scale 1 Z rot 10.0  
searching scale 1 Z rot 10.2  
searching scale 1 Z rot 10.5  global minimum found at slice 127.3, rotations (-0.25, 3.72)
final transformation (x=127.3, yr=-0.254, zr=3.722):
 0.99788  -0.06492  -0.00443   6.58695;
 0.06492   0.99789  -0.00029   40.93382;
 0.00444  -0.00000   0.99999   24.43588;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 79 103
eigenvectors:
 0.00036   0.00494   0.99999;
-0.20476  -0.97880   0.00491;
 0.97881  -0.20476   0.00066;
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.8 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 20:24:31 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 20:24:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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...
931 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 103
gm peak at 69 (69), valley at 29 (29)
csf peak at 10, setting threshold to 49
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 109
gm peak at 69 (69), valley at 25 (25)
csf peak at 10, setting threshold to 49
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 27 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 20:27:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1436288 voxels in mask (pct=  8.56)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 20:28:01 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 (105.0): 106.1 +- 5.5 [79.0 --> 125.0]
GM (69.0) : 67.3 +- 9.7 [30.0 --> 95.0]
setting bottom of white matter range to 77.0
setting top of gray matter range to 86.7
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
16029 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4230 filled
2011 bright non-wm voxels segmented.
8181 diagonally connected voxels added...
white matter segmentation took 1.6 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 0.50 minutes
reading wm segmentation from wm.seg.mgz...
62 voxels added to wm to prevent paths from MTL structures to cortex
2599 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 49350 voxels turned on, 37268 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  27 found -  27 modified     |    TOTAL:  27
pass   2 (xy+):   0 found -  27 modified     |    TOTAL:  27
pass   1 (xy-):  28 found -  28 modified     |    TOTAL:  55
pass   2 (xy-):   0 found -  28 modified     |    TOTAL:  55
pass   1 (yz+):  35 found -  35 modified     |    TOTAL:  90
pass   2 (yz+):   0 found -  35 modified     |    TOTAL:  90
pass   1 (yz-):  20 found -  20 modified     |    TOTAL: 110
pass   2 (yz-):   0 found -  20 modified     |    TOTAL: 110
pass   1 (xz+):  22 found -  22 modified     |    TOTAL: 132
pass   2 (xz+):   0 found -  22 modified     |    TOTAL: 132
pass   1 (xz-):  24 found -  24 modified     |    TOTAL: 156
pass   2 (xz-):   0 found -  24 modified     |    TOTAL: 156
Iteration Number : 1
pass   1 (+++):  32 found -  32 modified     |    TOTAL:  32
pass   2 (+++):   0 found -  32 modified     |    TOTAL:  32
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  44
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  44
pass   1 (+++):  17 found -  17 modified     |    TOTAL:  61
pass   2 (+++):   0 found -  17 modified     |    TOTAL:  61
pass   1 (+++):  25 found -  25 modified     |    TOTAL:  86
pass   2 (+++):   0 found -  25 modified     |    TOTAL:  86
Iteration Number : 1
pass   1 (++): 186 found - 186 modified     |    TOTAL: 186
pass   2 (++):   0 found - 186 modified     |    TOTAL: 186
pass   1 (+-): 161 found - 161 modified     |    TOTAL: 347
pass   2 (+-):   0 found - 161 modified     |    TOTAL: 347
pass   1 (--): 146 found - 146 modified     |    TOTAL: 493
pass   2 (--):   0 found - 146 modified     |    TOTAL: 493
pass   1 (-+): 148 found - 148 modified     |    TOTAL: 641
pass   2 (-+):   0 found - 148 modified     |    TOTAL: 641
Iteration Number : 2
pass   1 (xy+):   6 found -   6 modified     |    TOTAL:   6
pass   2 (xy+):   0 found -   6 modified     |    TOTAL:   6
pass   1 (xy-):  10 found -  10 modified     |    TOTAL:  16
pass   2 (xy-):   0 found -  10 modified     |    TOTAL:  16
pass   1 (yz+):   9 found -   9 modified     |    TOTAL:  25
pass   2 (yz+):   0 found -   9 modified     |    TOTAL:  25
pass   1 (yz-):  14 found -  14 modified     |    TOTAL:  39
pass   2 (yz-):   0 found -  14 modified     |    TOTAL:  39
pass   1 (xz+):  11 found -  11 modified     |    TOTAL:  50
pass   2 (xz+):   0 found -  11 modified     |    TOTAL:  50
pass   1 (xz-):   8 found -   8 modified     |    TOTAL:  58
pass   2 (xz-):   0 found -   8 modified     |    TOTAL:  58
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   3 found -   3 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   3 modified     |    TOTAL:   7
Iteration Number : 2
pass   1 (++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+-):   8 found -   8 modified     |    TOTAL:  13
pass   2 (+-):   0 found -   8 modified     |    TOTAL:  13
pass   1 (--):   5 found -   5 modified     |    TOTAL:  18
pass   2 (--):   0 found -   5 modified     |    TOTAL:  18
pass   1 (-+):   3 found -   3 modified     |    TOTAL:  21
pass   2 (-+):   0 found -   3 modified     |    TOTAL:  21
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 972 (out of 550200: 0.176663)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 20:30:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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
 1.05525  -0.01208   0.00471  -8.93146;
 0.00855   1.11986   0.37860  -26.39128;
-0.00847  -0.35063   0.97219   39.08955;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.05525  -0.01208   0.00471  -8.93146;
 0.00855   1.11986   0.37860  -26.39128;
-0.00847  -0.35063   0.97219   39.08955;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1479 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75)
need search nearby
using seed (125, 120, 154), TAL = (3.0, 26.0, 8.0)
talairach voxel to voxel transform
 0.94752   0.00782  -0.00764   8.96793;
-0.00894   0.79585  -0.30988   33.03664;
 0.00503   0.28710   0.91677  -28.21438;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (125,  120,  154) --> (3.0, 26.0, 8.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (3.00, 26.00, 8.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, 26.00, 8.00) SRC: (110.11, 79.86, 147.96)
search lh wm seed point around talairach space (-15.00, 26.00, 8.00), SRC: (144.22, 79.54, 148.14)
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 20:31:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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


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

Total Number of Modified Voxels = 6 (out of 262326: 0.002287)
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: 986 vertices, 1093 faces
slice 50: 6772 vertices, 7029 faces
slice 60: 16201 vertices, 16598 faces
slice 70: 27815 vertices, 28233 faces
slice 80: 39674 vertices, 40149 faces
slice 90: 51788 vertices, 52210 faces
slice 100: 63920 vertices, 64361 faces
slice 110: 75793 vertices, 76244 faces
slice 120: 87301 vertices, 87756 faces
slice 130: 98558 vertices, 98983 faces
slice 140: 108849 vertices, 109274 faces
slice 150: 117696 vertices, 118067 faces
slice 160: 125736 vertices, 126037 faces
slice 170: 131774 vertices, 132052 faces
slice 180: 136714 vertices, 136940 faces
slice 190: 139470 vertices, 139584 faces
slice 200: 139540 vertices, 139630 faces
slice 210: 139540 vertices, 139630 faces
slice 220: 139540 vertices, 139630 faces
slice 230: 139540 vertices, 139630 faces
slice 240: 139540 vertices, 139630 faces
slice 250: 139540 vertices, 139630 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...
   139540 voxel in cpt #1: X=-90 [v=139540,e=418890,f=279260] located at (-26.377993, -22.056107, 41.319027)
For the whole surface: X=-90 [v=139540,e=418890,f=279260]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 20:31:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   7
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   7
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   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 : 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 = 8 (out of 271031: 0.002952)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 2086 vertices, 2272 faces
slice 50: 10639 vertices, 11008 faces
slice 60: 22283 vertices, 22706 faces
slice 70: 34252 vertices, 34680 faces
slice 80: 46088 vertices, 46527 faces
slice 90: 58181 vertices, 58626 faces
slice 100: 70753 vertices, 71195 faces
slice 110: 82778 vertices, 83214 faces
slice 120: 94244 vertices, 94716 faces
slice 130: 105086 vertices, 105505 faces
slice 140: 115466 vertices, 115848 faces
slice 150: 123939 vertices, 124300 faces
slice 160: 131098 vertices, 131382 faces
slice 170: 136552 vertices, 136815 faces
slice 180: 140723 vertices, 140934 faces
slice 190: 142742 vertices, 142838 faces
slice 200: 142742 vertices, 142838 faces
slice 210: 142742 vertices, 142838 faces
slice 220: 142742 vertices, 142838 faces
slice 230: 142742 vertices, 142838 faces
slice 240: 142742 vertices, 142838 faces
slice 250: 142742 vertices, 142838 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...
   142742 voxel in cpt #1: X=-96 [v=142742,e=428514,f=285676] located at (27.824986, -26.274376, 39.041965)
For the whole surface: X=-96 [v=142742,e=428514,f=285676]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 20:31:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 20:31:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

Waiting for PID 9697 of (9697 9700) to complete...
Waiting for PID 9700 of (9697 9700) 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 (9697 9700) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 20:31:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 20:31:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

Waiting for PID 9744 of (9744 9747) to complete...
Waiting for PID 9747 of (9744 9747) 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 = 45.9 mm, total surface area = 70309 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.7 minutes

step 000: RMS=0.163 (target=0.015)   
step 005: RMS=0.122 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.053 (target=0.015)   
step 035: RMS=0.048 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.042 (target=0.015)   
step 050: RMS=0.041 (target=0.015)   
step 055: RMS=0.039 (target=0.015)   
step 060: RMS=0.039 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    42.089601
mris_inflate stimesec    0.093985
mris_inflate ru_maxrss   206844
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29675
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  9840
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1977
mris_inflate ru_nivcsw   3253

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 46.5 mm, total surface area = 72131 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.7 minutes

step 000: RMS=0.160 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.089 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.052 (target=0.015)   
step 035: RMS=0.047 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.042 (target=0.015)   
step 050: RMS=0.041 (target=0.015)   
step 055: RMS=0.040 (target=0.015)   
step 060: RMS=0.039 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    43.002462
mris_inflate stimesec    0.097985
mris_inflate ru_maxrss   209472
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30331
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10064
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2299
mris_inflate ru_nivcsw   3284
PIDs (9744 9747) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 20:32:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 20:32:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

Waiting for PID 9811 of (9811 9814) to complete...
Waiting for PID 9814 of (9811 9814) 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 0.98 +- 0.57 (0.00-->6.39) (max @ vno 56216 --> 57424)
face area 0.03 +- 0.03 (-0.10-->0.68)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.325...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.043, avgs=0
005/300: dt: 0.9000, rms radial error=175.784, avgs=0
010/300: dt: 0.9000, rms radial error=175.228, avgs=0
015/300: dt: 0.9000, rms radial error=174.498, avgs=0
020/300: dt: 0.9000, rms radial error=173.666, avgs=0
025/300: dt: 0.9000, rms radial error=172.776, avgs=0
030/300: dt: 0.9000, rms radial error=171.852, avgs=0
035/300: dt: 0.9000, rms radial error=170.912, avgs=0
040/300: dt: 0.9000, rms radial error=169.967, avgs=0
045/300: dt: 0.9000, rms radial error=169.024, avgs=0
050/300: dt: 0.9000, rms radial error=168.082, avgs=0
055/300: dt: 0.9000, rms radial error=167.143, avgs=0
060/300: dt: 0.9000, rms radial error=166.207, avgs=0
065/300: dt: 0.9000, rms radial error=165.275, avgs=0
070/300: dt: 0.9000, rms radial error=164.348, avgs=0
075/300: dt: 0.9000, rms radial error=163.425, avgs=0
080/300: dt: 0.9000, rms radial error=162.506, avgs=0
085/300: dt: 0.9000, rms radial error=161.593, avgs=0
090/300: dt: 0.9000, rms radial error=160.684, avgs=0
095/300: dt: 0.9000, rms radial error=159.780, avgs=0
100/300: dt: 0.9000, rms radial error=158.881, avgs=0
105/300: dt: 0.9000, rms radial error=157.986, avgs=0
110/300: dt: 0.9000, rms radial error=157.096, avgs=0
115/300: dt: 0.9000, rms radial error=156.211, avgs=0
120/300: dt: 0.9000, rms radial error=155.331, avgs=0
125/300: dt: 0.9000, rms radial error=154.456, avgs=0
130/300: dt: 0.9000, rms radial error=153.585, avgs=0
135/300: dt: 0.9000, rms radial error=152.720, avgs=0
140/300: dt: 0.9000, rms radial error=151.860, avgs=0
145/300: dt: 0.9000, rms radial error=151.004, avgs=0
150/300: dt: 0.9000, rms radial error=150.153, avgs=0
155/300: dt: 0.9000, rms radial error=149.307, avgs=0
160/300: dt: 0.9000, rms radial error=148.465, avgs=0
165/300: dt: 0.9000, rms radial error=147.627, avgs=0
170/300: dt: 0.9000, rms radial error=146.795, avgs=0
175/300: dt: 0.9000, rms radial error=145.967, avgs=0
180/300: dt: 0.9000, rms radial error=145.143, avgs=0
185/300: dt: 0.9000, rms radial error=144.324, avgs=0
190/300: dt: 0.9000, rms radial error=143.509, avgs=0
195/300: dt: 0.9000, rms radial error=142.699, avgs=0
200/300: dt: 0.9000, rms radial error=141.893, avgs=0
205/300: dt: 0.9000, rms radial error=141.092, avgs=0
210/300: dt: 0.9000, rms radial error=140.295, avgs=0
215/300: dt: 0.9000, rms radial error=139.503, avgs=0
220/300: dt: 0.9000, rms radial error=138.714, avgs=0
225/300: dt: 0.9000, rms radial error=137.931, avgs=0
230/300: dt: 0.9000, rms radial error=137.152, avgs=0
235/300: dt: 0.9000, rms radial error=136.377, avgs=0
240/300: dt: 0.9000, rms radial error=135.606, avgs=0
245/300: dt: 0.9000, rms radial error=134.840, avgs=0
250/300: dt: 0.9000, rms radial error=134.078, avgs=0
255/300: dt: 0.9000, rms radial error=133.320, avgs=0
260/300: dt: 0.9000, rms radial error=132.567, avgs=0
265/300: dt: 0.9000, rms radial error=131.817, avgs=0
270/300: dt: 0.9000, rms radial error=131.072, avgs=0
275/300: dt: 0.9000, rms radial error=130.332, avgs=0
280/300: dt: 0.9000, rms radial error=129.595, avgs=0
285/300: dt: 0.9000, rms radial error=128.862, avgs=0
290/300: dt: 0.9000, rms radial error=128.134, avgs=0
295/300: dt: 0.9000, rms radial error=127.409, avgs=0
300/300: dt: 0.9000, rms radial error=126.689, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16231.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 2 (K=40.0), pass 1, starting sse = 2691.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
epoch 3 (K=160.0), pass 1, starting sse = 277.13
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00625
epoch 4 (K=640.0), pass 1, starting sse = 19.46
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/13 = 0.00584
final distance error %26.05
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    250.569907
mris_sphere stimesec    0.179972
mris_sphere ru_maxrss   205012
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   29731
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9864
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    11404
mris_sphere ru_nivcsw   20389
FSRUNTIME@ mris_sphere  0.0697 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 0.96 +- 0.56 (0.00-->8.10) (max @ vno 109163 --> 109164)
face area 0.03 +- 0.03 (-0.22-->0.71)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.323...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.717, avgs=0
005/300: dt: 0.9000, rms radial error=175.458, avgs=0
010/300: dt: 0.9000, rms radial error=174.902, avgs=0
015/300: dt: 0.9000, rms radial error=174.171, avgs=0
020/300: dt: 0.9000, rms radial error=173.340, avgs=0
025/300: dt: 0.9000, rms radial error=172.452, avgs=0
030/300: dt: 0.9000, rms radial error=171.535, avgs=0
035/300: dt: 0.9000, rms radial error=170.600, avgs=0
040/300: dt: 0.9000, rms radial error=169.658, avgs=0
045/300: dt: 0.9000, rms radial error=168.713, avgs=0
050/300: dt: 0.9000, rms radial error=167.769, avgs=0
055/300: dt: 0.9000, rms radial error=166.827, avgs=0
060/300: dt: 0.9000, rms radial error=165.889, avgs=0
065/300: dt: 0.9000, rms radial error=164.956, avgs=0
070/300: dt: 0.9000, rms radial error=164.026, avgs=0
075/300: dt: 0.9000, rms radial error=163.102, avgs=0
080/300: dt: 0.9000, rms radial error=162.182, avgs=0
085/300: dt: 0.9000, rms radial error=161.267, avgs=0
090/300: dt: 0.9000, rms radial error=160.357, avgs=0
095/300: dt: 0.9000, rms radial error=159.452, avgs=0
100/300: dt: 0.9000, rms radial error=158.553, avgs=0
105/300: dt: 0.9000, rms radial error=157.658, avgs=0
110/300: dt: 0.9000, rms radial error=156.768, avgs=0
115/300: dt: 0.9000, rms radial error=155.883, avgs=0
120/300: dt: 0.9000, rms radial error=155.004, avgs=0
125/300: dt: 0.9000, rms radial error=154.132, avgs=0
130/300: dt: 0.9000, rms radial error=153.264, avgs=0
135/300: dt: 0.9000, rms radial error=152.401, avgs=0
140/300: dt: 0.9000, rms radial error=151.543, avgs=0
145/300: dt: 0.9000, rms radial error=150.690, avgs=0
150/300: dt: 0.9000, rms radial error=149.842, avgs=0
155/300: dt: 0.9000, rms radial error=148.998, avgs=0
160/300: dt: 0.9000, rms radial error=148.159, avgs=0
165/300: dt: 0.9000, rms radial error=147.324, avgs=0
170/300: dt: 0.9000, rms radial error=146.494, avgs=0
175/300: dt: 0.9000, rms radial error=145.669, avgs=0
180/300: dt: 0.9000, rms radial error=144.848, avgs=0
185/300: dt: 0.9000, rms radial error=144.032, avgs=0
190/300: dt: 0.9000, rms radial error=143.220, avgs=0
195/300: dt: 0.9000, rms radial error=142.413, avgs=0
200/300: dt: 0.9000, rms radial error=141.610, avgs=0
205/300: dt: 0.9000, rms radial error=140.812, avgs=0
210/300: dt: 0.9000, rms radial error=140.018, avgs=0
215/300: dt: 0.9000, rms radial error=139.228, avgs=0
220/300: dt: 0.9000, rms radial error=138.443, avgs=0
225/300: dt: 0.9000, rms radial error=137.662, avgs=0
230/300: dt: 0.9000, rms radial error=136.885, avgs=0
235/300: dt: 0.9000, rms radial error=136.113, avgs=0
240/300: dt: 0.9000, rms radial error=135.346, avgs=0
245/300: dt: 0.9000, rms radial error=134.583, avgs=0
250/300: dt: 0.9000, rms radial error=133.824, avgs=0
255/300: dt: 0.9000, rms radial error=133.070, avgs=0
260/300: dt: 0.9000, rms radial error=132.320, avgs=0
265/300: dt: 0.9000, rms radial error=131.575, avgs=0
270/300: dt: 0.9000, rms radial error=130.834, avgs=0
275/300: dt: 0.9000, rms radial error=130.097, avgs=0
280/300: dt: 0.9000, rms radial error=129.364, avgs=0
285/300: dt: 0.9000, rms radial error=128.635, avgs=0
290/300: dt: 0.9000, rms radial error=127.910, avgs=0
295/300: dt: 0.9000, rms radial error=127.189, avgs=0
300/300: dt: 0.9000, rms radial error=126.472, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16617.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 2 (K=40.0), pass 1, starting sse = 2743.07
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 = 277.88
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00735
epoch 4 (K=640.0), pass 1, starting sse = 17.79
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/13 = 0.00721
final distance error %25.80
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    255.821109
mris_sphere stimesec    0.194970
mris_sphere ru_maxrss   209680
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   30386
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10048
mris_sphere ru_oublock  10088
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    11510
mris_sphere ru_nivcsw   20663
FSRUNTIME@ mris_sphere  0.0706 hours 1 threads
PIDs (9811 9814) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 20:36:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 20:36:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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


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

#@# Fix Topology lh Sat Oct  7 20:36:16 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 lh 

#@# Fix Topology rh Sat Oct  7 20:36:16 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 rh 

Waiting for PID 10068 of (10068 10071) to complete...
Waiting for PID 10071 of (10068 10071) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 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=-90 (nv=139540, nf=279260, ne=418890, g=46)
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...
4961 ambiguous faces found in tessellation
segmenting defects...
53 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 8 into 10
      -merging segment 26 into 25
      -merging segment 33 into 31
      -merging segment 43 into 40
49 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7351  (-4.8676)
      -vertex     loglikelihood: -6.6003  (-3.3002)
      -normal dot loglikelihood: -3.5944  (-3.5944)
      -quad curv  loglikelihood: -6.6237  (-3.3118)
      Total Loglikelihood : -26.5536

CORRECTING DEFECT 0 (vertices=151, convex hull=184, v0=317)
After retessellation of defect 0 (v0=317), euler #=-48 (136430,407816,271338) : difference with theory (-46) = 2 

CORRECTING DEFECT 1 (vertices=22, convex hull=63, v0=2270)
After retessellation of defect 1 (v0=2270), euler #=-47 (136439,407868,271382) : difference with theory (-45) = 2 

CORRECTING DEFECT 2 (vertices=24, convex hull=61, v0=9370)
After retessellation of defect 2 (v0=9370), euler #=-46 (136454,407940,271440) : difference with theory (-44) = 2 

CORRECTING DEFECT 3 (vertices=29, convex hull=44, v0=10793)
After retessellation of defect 3 (v0=10793), euler #=-45 (136463,407983,271475) : difference with theory (-43) = 2 

CORRECTING DEFECT 4 (vertices=99, convex hull=84, v0=14776)
After retessellation of defect 4 (v0=14776), euler #=-44 (136480,408064,271540) : difference with theory (-42) = 2 

CORRECTING DEFECT 5 (vertices=22, convex hull=43, v0=15817)
After retessellation of defect 5 (v0=15817), euler #=-43 (136484,408090,271563) : difference with theory (-41) = 2 

CORRECTING DEFECT 6 (vertices=6, convex hull=21, v0=19198)
After retessellation of defect 6 (v0=19198), euler #=-42 (136484,408096,271570) : difference with theory (-40) = 2 

CORRECTING DEFECT 7 (vertices=100, convex hull=125, v0=19356)
After retessellation of defect 7 (v0=19356), euler #=-41 (136528,408285,271716) : difference with theory (-39) = 2 

CORRECTING DEFECT 8 (vertices=12, convex hull=26, v0=26227)
After retessellation of defect 8 (v0=26227), euler #=-40 (136529,408294,271725) : difference with theory (-38) = 2 

CORRECTING DEFECT 9 (vertices=579, convex hull=457, v0=28697)
After retessellation of defect 9 (v0=28697), euler #=-38 (136756,409203,272409) : difference with theory (-37) = 1 

CORRECTING DEFECT 10 (vertices=24, convex hull=60, v0=30580)
After retessellation of defect 10 (v0=30580), euler #=-37 (136770,409270,272463) : difference with theory (-36) = 1 

CORRECTING DEFECT 11 (vertices=35, convex hull=48, v0=34972)
After retessellation of defect 11 (v0=34972), euler #=-36 (136792,409354,272526) : difference with theory (-35) = 1 

CORRECTING DEFECT 12 (vertices=36, convex hull=55, v0=37108)
After retessellation of defect 12 (v0=37108), euler #=-35 (136804,409411,272572) : difference with theory (-34) = 1 

CORRECTING DEFECT 13 (vertices=72, convex hull=109, v0=44035)
After retessellation of defect 13 (v0=44035), euler #=-34 (136839,409559,272686) : difference with theory (-33) = 1 

CORRECTING DEFECT 14 (vertices=5, convex hull=22, v0=51377)
After retessellation of defect 14 (v0=51377), euler #=-33 (136841,409572,272698) : difference with theory (-32) = 1 

CORRECTING DEFECT 15 (vertices=25, convex hull=55, v0=52421)
After retessellation of defect 15 (v0=52421), euler #=-32 (136852,409627,272743) : difference with theory (-31) = 1 

CORRECTING DEFECT 16 (vertices=31, convex hull=33, v0=58546)
After retessellation of defect 16 (v0=58546), euler #=-31 (136861,409665,272773) : difference with theory (-30) = 1 

CORRECTING DEFECT 17 (vertices=40, convex hull=46, v0=70995)
After retessellation of defect 17 (v0=70995), euler #=-30 (136874,409722,272818) : difference with theory (-29) = 1 

CORRECTING DEFECT 18 (vertices=520, convex hull=175, v0=71918)
After retessellation of defect 18 (v0=71918), euler #=-30 (136935,409997,273032) : difference with theory (-28) = 2 

CORRECTING DEFECT 19 (vertices=17, convex hull=30, v0=79301)
After retessellation of defect 19 (v0=79301), euler #=-29 (136936,410009,273044) : difference with theory (-27) = 2 

CORRECTING DEFECT 20 (vertices=31, convex hull=51, v0=80095)
After retessellation of defect 20 (v0=80095), euler #=-28 (136947,410058,273083) : difference with theory (-26) = 2 

CORRECTING DEFECT 21 (vertices=28, convex hull=62, v0=86157)
After retessellation of defect 21 (v0=86157), euler #=-27 (136959,410117,273131) : difference with theory (-25) = 2 

CORRECTING DEFECT 22 (vertices=9, convex hull=14, v0=89379)
After retessellation of defect 22 (v0=89379), euler #=-26 (136960,410122,273136) : difference with theory (-24) = 2 

CORRECTING DEFECT 23 (vertices=14, convex hull=23, v0=91068)
After retessellation of defect 23 (v0=91068), euler #=-25 (136963,410137,273149) : difference with theory (-23) = 2 

CORRECTING DEFECT 24 (vertices=38, convex hull=73, v0=93619)
After retessellation of defect 24 (v0=93619), euler #=-24 (136978,410224,273222) : difference with theory (-22) = 2 

CORRECTING DEFECT 25 (vertices=14, convex hull=21, v0=95774)
After retessellation of defect 25 (v0=95774), euler #=-23 (136981,410238,273234) : difference with theory (-21) = 2 

CORRECTING DEFECT 26 (vertices=6, convex hull=14, v0=98166)
After retessellation of defect 26 (v0=98166), euler #=-22 (136981,410242,273239) : difference with theory (-20) = 2 

CORRECTING DEFECT 27 (vertices=10, convex hull=20, v0=98358)
After retessellation of defect 27 (v0=98358), euler #=-21 (136982,410253,273250) : difference with theory (-19) = 2 

CORRECTING DEFECT 28 (vertices=34, convex hull=49, v0=100153)
After retessellation of defect 28 (v0=100153), euler #=-20 (136991,410298,273287) : difference with theory (-18) = 2 

CORRECTING DEFECT 29 (vertices=50, convex hull=76, v0=100269)
After retessellation of defect 29 (v0=100269), euler #=-18 (137024,410433,273391) : difference with theory (-17) = 1 

CORRECTING DEFECT 30 (vertices=51, convex hull=33, v0=102089)
After retessellation of defect 30 (v0=102089), euler #=-17 (137029,410455,273409) : difference with theory (-16) = 1 

CORRECTING DEFECT 31 (vertices=66, convex hull=101, v0=102406)
After retessellation of defect 31 (v0=102406), euler #=-16 (137038,410522,273468) : difference with theory (-15) = 1 

CORRECTING DEFECT 32 (vertices=6, convex hull=43, v0=103153)
After retessellation of defect 32 (v0=103153), euler #=-15 (137041,410542,273486) : difference with theory (-14) = 1 

CORRECTING DEFECT 33 (vertices=137, convex hull=137, v0=103184)
After retessellation of defect 33 (v0=103184), euler #=-14 (137065,410676,273597) : difference with theory (-13) = 1 

CORRECTING DEFECT 34 (vertices=60, convex hull=66, v0=104221)
After retessellation of defect 34 (v0=104221), euler #=-13 (137067,410711,273631) : difference with theory (-12) = 1 

CORRECTING DEFECT 35 (vertices=6, convex hull=27, v0=104323)
After retessellation of defect 35 (v0=104323), euler #=-12 (137068,410720,273640) : difference with theory (-11) = 1 

CORRECTING DEFECT 36 (vertices=19, convex hull=22, v0=107310)
After retessellation of defect 36 (v0=107310), euler #=-11 (137072,410740,273657) : difference with theory (-10) = 1 

CORRECTING DEFECT 37 (vertices=218, convex hull=243, v0=108766)
After retessellation of defect 37 (v0=108766), euler #=-9 (137184,411203,274010) : difference with theory (-9) = 0 

CORRECTING DEFECT 38 (vertices=24, convex hull=38, v0=112299)
After retessellation of defect 38 (v0=112299), euler #=-8 (137186,411223,274029) : difference with theory (-8) = 0 

CORRECTING DEFECT 39 (vertices=54, convex hull=98, v0=113157)
After retessellation of defect 39 (v0=113157), euler #=-7 (137209,411331,274115) : difference with theory (-7) = 0 

CORRECTING DEFECT 40 (vertices=24, convex hull=55, v0=113403)
After retessellation of defect 40 (v0=113403), euler #=-6 (137222,411391,274163) : difference with theory (-6) = 0 

CORRECTING DEFECT 41 (vertices=22, convex hull=49, v0=115546)
After retessellation of defect 41 (v0=115546), euler #=-5 (137231,411432,274196) : difference with theory (-5) = 0 

CORRECTING DEFECT 42 (vertices=40, convex hull=78, v0=115699)
After retessellation of defect 42 (v0=115699), euler #=-4 (137257,411543,274282) : difference with theory (-4) = 0 

CORRECTING DEFECT 43 (vertices=33, convex hull=50, v0=118325)
After retessellation of defect 43 (v0=118325), euler #=-3 (137266,411588,274319) : difference with theory (-3) = 0 

CORRECTING DEFECT 44 (vertices=173, convex hull=193, v0=118397)
After retessellation of defect 44 (v0=118397), euler #=-2 (137362,411971,274607) : difference with theory (-2) = 0 

CORRECTING DEFECT 45 (vertices=58, convex hull=115, v0=126950)
After retessellation of defect 45 (v0=126950), euler #=-1 (137404,412141,274736) : difference with theory (-1) = 0 

CORRECTING DEFECT 46 (vertices=23, convex hull=58, v0=131740)
After retessellation of defect 46 (v0=131740), euler #=0 (137412,412184,274772) : difference with theory (0) = 0 

CORRECTING DEFECT 47 (vertices=28, convex hull=71, v0=134411)
After retessellation of defect 47 (v0=134411), euler #=1 (137421,412237,274817) : difference with theory (1) = 0 

CORRECTING DEFECT 48 (vertices=30, convex hull=50, v0=134887)
After retessellation of defect 48 (v0=134887), euler #=2 (137434,412296,274864) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.87 +- 0.24 (0.08-->9.94) (max @ vno 31249 --> 33498)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.87 +- 0.24 (0.08-->9.94) (max @ vno 31249 --> 33498)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
190 mutations (36.3%), 334 crossovers (63.7%), 157 vertices were eliminated
building final representation...
2106 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=137434, nf=274864, ne=412296, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 28.6 minutes
0 defective edges
removing intersecting faces
000: 369 intersecting
001: 13 intersecting
mris_fix_topology utimesec    1713.312536
mris_fix_topology stimesec    0.224965
mris_fix_topology ru_maxrss   436676
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56235
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  9824
mris_fix_topology ru_oublock  13208
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    403
mris_fix_topology ru_nivcsw   4363
FSRUNTIME@ mris_fix_topology lh  0.4759 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 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=-96 (nv=142742, nf=285676, ne=428514, g=49)
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 6 iterations
marking ambiguous vertices...
5332 ambiguous faces found in tessellation
segmenting defects...
49 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
49 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.6576  (-4.8288)
      -vertex     loglikelihood: -6.5775  (-3.2887)
      -normal dot loglikelihood: -3.4957  (-3.4957)
      -quad curv  loglikelihood: -6.6309  (-3.3154)
      Total Loglikelihood : -26.3616

CORRECTING DEFECT 0 (vertices=17, convex hull=51, v0=278)
After retessellation of defect 0 (v0=278), euler #=-43 (139505,417196,277648) : difference with theory (-46) = -3 

CORRECTING DEFECT 1 (vertices=28, convex hull=73, v0=3964)
After retessellation of defect 1 (v0=3964), euler #=-42 (139514,417253,277697) : difference with theory (-45) = -3 

CORRECTING DEFECT 2 (vertices=33, convex hull=72, v0=4905)
After retessellation of defect 2 (v0=4905), euler #=-41 (139530,417332,277761) : difference with theory (-44) = -3 

CORRECTING DEFECT 3 (vertices=31, convex hull=68, v0=17019)
After retessellation of defect 3 (v0=17019), euler #=-40 (139549,417416,277827) : difference with theory (-43) = -3 

CORRECTING DEFECT 4 (vertices=27, convex hull=50, v0=30576)
After retessellation of defect 4 (v0=30576), euler #=-39 (139560,417468,277869) : difference with theory (-42) = -3 

CORRECTING DEFECT 5 (vertices=23, convex hull=66, v0=31763)
After retessellation of defect 5 (v0=31763), euler #=-38 (139569,417519,277912) : difference with theory (-41) = -3 

CORRECTING DEFECT 6 (vertices=23, convex hull=52, v0=52266)
After retessellation of defect 6 (v0=52266), euler #=-37 (139579,417568,277952) : difference with theory (-40) = -3 

CORRECTING DEFECT 7 (vertices=62, convex hull=62, v0=57596)
After retessellation of defect 7 (v0=57596), euler #=-36 (139588,417621,277997) : difference with theory (-39) = -3 

CORRECTING DEFECT 8 (vertices=25, convex hull=30, v0=57964)
After retessellation of defect 8 (v0=57964), euler #=-35 (139593,417651,278023) : difference with theory (-38) = -3 

CORRECTING DEFECT 9 (vertices=46, convex hull=58, v0=60159)
After retessellation of defect 9 (v0=60159), euler #=-34 (139616,417745,278095) : difference with theory (-37) = -3 

CORRECTING DEFECT 10 (vertices=25, convex hull=34, v0=60882)
After retessellation of defect 10 (v0=60882), euler #=-33 (139624,417781,278124) : difference with theory (-36) = -3 

CORRECTING DEFECT 11 (vertices=19, convex hull=22, v0=64261)
After retessellation of defect 11 (v0=64261), euler #=-32 (139628,417798,278138) : difference with theory (-35) = -3 

CORRECTING DEFECT 12 (vertices=24, convex hull=52, v0=65357)
After retessellation of defect 12 (v0=65357), euler #=-31 (139642,417858,278185) : difference with theory (-34) = -3 

CORRECTING DEFECT 13 (vertices=29, convex hull=44, v0=67242)
After retessellation of defect 13 (v0=67242), euler #=-30 (139655,417912,278227) : difference with theory (-33) = -3 

CORRECTING DEFECT 14 (vertices=17, convex hull=47, v0=70931)
After retessellation of defect 14 (v0=70931), euler #=-29 (139665,417960,278266) : difference with theory (-32) = -3 

CORRECTING DEFECT 15 (vertices=475, convex hull=203, v0=73007)
After retessellation of defect 15 (v0=73007), euler #=-28 (139676,418090,278386) : difference with theory (-31) = -3 

CORRECTING DEFECT 16 (vertices=35, convex hull=46, v0=75172)
After retessellation of defect 16 (v0=75172), euler #=-27 (139688,418143,278428) : difference with theory (-30) = -3 

CORRECTING DEFECT 17 (vertices=31, convex hull=59, v0=79717)
After retessellation of defect 17 (v0=79717), euler #=-26 (139706,418218,278486) : difference with theory (-29) = -3 

CORRECTING DEFECT 18 (vertices=33, convex hull=58, v0=84174)
After retessellation of defect 18 (v0=84174), euler #=-25 (139716,418269,278528) : difference with theory (-28) = -3 

CORRECTING DEFECT 19 (vertices=19, convex hull=30, v0=84669)
After retessellation of defect 19 (v0=84669), euler #=-24 (139721,418293,278548) : difference with theory (-27) = -3 

CORRECTING DEFECT 20 (vertices=29, convex hull=47, v0=89740)
After retessellation of defect 20 (v0=89740), euler #=-23 (139733,418351,278595) : difference with theory (-26) = -3 

CORRECTING DEFECT 21 (vertices=194, convex hull=192, v0=90782)
After retessellation of defect 21 (v0=90782), euler #=-22 (139807,418669,278840) : difference with theory (-25) = -3 

CORRECTING DEFECT 22 (vertices=30, convex hull=58, v0=92544)
After retessellation of defect 22 (v0=92544), euler #=-21 (139823,418741,278897) : difference with theory (-24) = -3 

CORRECTING DEFECT 23 (vertices=901, convex hull=252, v0=99871)
After retessellation of defect 23 (v0=99871), euler #=-21 (139964,419289,279304) : difference with theory (-23) = -2 

CORRECTING DEFECT 24 (vertices=22, convex hull=31, v0=102615)
After retessellation of defect 24 (v0=102615), euler #=-21 (139969,419319,279329) : difference with theory (-22) = -1 

CORRECTING DEFECT 25 (vertices=6, convex hull=33, v0=102730)
After retessellation of defect 25 (v0=102730), euler #=-20 (139972,419337,279345) : difference with theory (-21) = -1 

CORRECTING DEFECT 26 (vertices=235, convex hull=151, v0=104701)
After retessellation of defect 26 (v0=104701), euler #=-19 (140030,419585,279536) : difference with theory (-20) = -1 

CORRECTING DEFECT 27 (vertices=56, convex hull=100, v0=104938)
After retessellation of defect 27 (v0=104938), euler #=-18 (140064,419728,279646) : difference with theory (-19) = -1 

CORRECTING DEFECT 28 (vertices=27, convex hull=66, v0=108370)
After retessellation of defect 28 (v0=108370), euler #=-17 (140075,419786,279694) : difference with theory (-18) = -1 

CORRECTING DEFECT 29 (vertices=65, convex hull=72, v0=109020)
After retessellation of defect 29 (v0=109020), euler #=-16 (140112,419929,279801) : difference with theory (-17) = -1 

CORRECTING DEFECT 30 (vertices=24, convex hull=52, v0=111451)
After retessellation of defect 30 (v0=111451), euler #=-15 (140126,419990,279849) : difference with theory (-16) = -1 

CORRECTING DEFECT 31 (vertices=9, convex hull=19, v0=112632)
After retessellation of defect 31 (v0=112632), euler #=-14 (140128,420001,279859) : difference with theory (-15) = -1 

CORRECTING DEFECT 32 (vertices=10, convex hull=21, v0=113288)
After retessellation of defect 32 (v0=113288), euler #=-13 (140130,420011,279868) : difference with theory (-14) = -1 

CORRECTING DEFECT 33 (vertices=13, convex hull=22, v0=113314)
After retessellation of defect 33 (v0=113314), euler #=-12 (140134,420032,279886) : difference with theory (-13) = -1 

CORRECTING DEFECT 34 (vertices=13, convex hull=36, v0=113471)
After retessellation of defect 34 (v0=113471), euler #=-11 (140136,420050,279903) : difference with theory (-12) = -1 

CORRECTING DEFECT 35 (vertices=60, convex hull=82, v0=116269)
After retessellation of defect 35 (v0=116269), euler #=-10 (140163,420163,279990) : difference with theory (-11) = -1 

CORRECTING DEFECT 36 (vertices=67, convex hull=41, v0=118698)
After retessellation of defect 36 (v0=118698), euler #=-9 (140172,420206,280025) : difference with theory (-10) = -1 

CORRECTING DEFECT 37 (vertices=11, convex hull=29, v0=121145)
After retessellation of defect 37 (v0=121145), euler #=-8 (140174,420225,280043) : difference with theory (-9) = -1 

CORRECTING DEFECT 38 (vertices=86, convex hull=128, v0=121294)
After retessellation of defect 38 (v0=121294), euler #=-8 (140222,420427,280197) : difference with theory (-8) = 0 

CORRECTING DEFECT 39 (vertices=38, convex hull=65, v0=124465)
After retessellation of defect 39 (v0=124465), euler #=-7 (140243,420515,280265) : difference with theory (-7) = 0 

CORRECTING DEFECT 40 (vertices=57, convex hull=100, v0=126189)
After retessellation of defect 40 (v0=126189), euler #=-6 (140283,420677,280388) : difference with theory (-6) = 0 

CORRECTING DEFECT 41 (vertices=18, convex hull=55, v0=126471)
After retessellation of defect 41 (v0=126471), euler #=-5 (140293,420726,280428) : difference with theory (-5) = 0 

CORRECTING DEFECT 42 (vertices=17, convex hull=44, v0=128489)
After retessellation of defect 42 (v0=128489), euler #=-4 (140300,420762,280458) : difference with theory (-4) = 0 

CORRECTING DEFECT 43 (vertices=29, convex hull=35, v0=129786)
After retessellation of defect 43 (v0=129786), euler #=-3 (140309,420803,280491) : difference with theory (-3) = 0 

CORRECTING DEFECT 44 (vertices=43, convex hull=66, v0=131542)
After retessellation of defect 44 (v0=131542), euler #=-2 (140324,420870,280544) : difference with theory (-2) = 0 

CORRECTING DEFECT 45 (vertices=46, convex hull=65, v0=134176)
After retessellation of defect 45 (v0=134176), euler #=-1 (140347,420966,280618) : difference with theory (-1) = 0 

CORRECTING DEFECT 46 (vertices=62, convex hull=94, v0=139255)
After retessellation of defect 46 (v0=139255), euler #=0 (140371,421076,280705) : difference with theory (0) = 0 

CORRECTING DEFECT 47 (vertices=33, convex hull=55, v0=141021)
After retessellation of defect 47 (v0=141021), euler #=1 (140377,421119,280743) : difference with theory (1) = 0 

CORRECTING DEFECT 48 (vertices=18, convex hull=17, v0=142099)
After retessellation of defect 48 (v0=142099), euler #=2 (140379,421131,280754) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.87 +- 0.24 (0.05-->17.56) (max @ vno 112535 --> 140946)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.87 +- 0.24 (0.05-->17.56) (max @ vno 112535 --> 140946)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
168 mutations (36.4%), 293 crossovers (63.6%), 210 vertices were eliminated
building final representation...
2363 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=140379, nf=280754, ne=421131, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 31.9 minutes
0 defective edges
removing intersecting faces
000: 400 intersecting
001: 16 intersecting
mris_fix_topology utimesec    1911.850354
mris_fix_topology stimesec    0.165974
mris_fix_topology ru_maxrss   445440
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56784
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  10048
mris_fix_topology ru_oublock  13464
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    582
mris_fix_topology ru_nivcsw   2812
FSRUNTIME@ mris_fix_topology rh  0.5309 hours 1 threads
PIDs (10068 10071) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 137434 - 412296 + 274864 = 2 --> 0 holes
      F =2V-4:          274864 = 274868-4 (0)
      2E=3F:            824592 = 824592 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 140379 - 421131 + 280754 = 2 --> 0 holes
      F =2V-4:          280754 = 280758-4 (0)
      2E=3F:            842262 = 842262 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 27 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 96 intersecting
001: 3 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 21:08:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 21:08:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 rh 

Waiting for PID 11960 of (11960 11963) to complete...
Waiting for PID 11963 of (11960 11963) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
50338 bright wm thresholded.
2140 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.orig...
computing class statistics...
border white:    271136 voxels (1.62%)
border gray      285350 voxels (1.70%)
WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0]
GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70)
setting MAX_BORDER_WHITE to 110.1 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 43.7 (was 40)
setting MAX_GRAY to 91.9 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 54.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.6 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.80 +- 0.23 (0.01-->4.67) (max @ vno 31249 --> 33498)
face area 0.27 +- 0.13 (0.00-->4.60)
mean absolute distance = 0.75 +- 1.01
3335 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-8.7,    GM=66+-7.8
mean inside = 91.4, mean outside = 71.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=77.7, 66 (66) missing vertices, mean dist 0.1 [0.8 (%38.8)->0.7 (%61.2))]
%59 local maxima, %37 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 +- 0.26 (0.07-->4.56) (max @ vno 31249 --> 33498)
face area 0.27 +- 0.13 (0.00-->4.09)
mean absolute distance = 0.39 +- 0.68
4065 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3540618.0, rms=10.660
001: dt: 0.5000, sse=1974268.2, rms=7.457 (30.049%)
002: dt: 0.5000, sse=1323784.0, rms=5.562 (25.410%)
003: dt: 0.5000, sse=1051489.0, rms=4.531 (18.539%)
004: dt: 0.5000, sse=939244.1, rms=4.041 (10.804%)
005: dt: 0.5000, sse=901497.8, rms=3.862 (4.446%)
006: dt: 0.5000, sse=884533.2, rms=3.775 (2.247%)
rms = 3.75, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=880084.5, rms=3.747 (0.727%)
008: dt: 0.2500, sse=699975.3, rms=2.580 (31.144%)
009: dt: 0.2500, sse=652385.3, rms=2.196 (14.898%)
010: dt: 0.2500, sse=644630.6, rms=2.119 (3.518%)
011: dt: 0.2500, sse=638828.5, rms=2.056 (2.933%)
rms = 2.04, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=636563.9, rms=2.038 (0.909%)
013: dt: 0.1250, sse=626355.0, rms=1.928 (5.409%)
rms = 1.92, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=624691.9, rms=1.919 (0.438%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=80.9, 58 (12) missing vertices, mean dist -0.2 [0.5 (%68.5)->0.2 (%31.5))]
%71 local maxima, %24 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 +- 0.25 (0.09-->4.47) (max @ vno 31249 --> 33498)
face area 0.34 +- 0.16 (0.00-->5.15)
mean absolute distance = 0.29 +- 0.43
3983 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1225869.4, rms=4.651
015: dt: 0.5000, sse=952791.0, rms=3.309 (28.851%)
rms = 3.59, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=813511.2, rms=2.426 (26.691%)
017: dt: 0.2500, sse=761862.9, rms=1.973 (18.662%)
018: dt: 0.2500, sse=743503.1, rms=1.784 (9.597%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=738622.4, rms=1.734 (2.778%)
020: dt: 0.1250, sse=730369.2, rms=1.626 (6.219%)
rms = 1.62, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=728975.1, rms=1.618 (0.503%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
mean border=83.4, 60 (8) missing vertices, mean dist -0.2 [0.3 (%68.1)->0.2 (%31.9))]
%83 local maxima, %12 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 +- 0.25 (0.06-->4.38) (max @ vno 31249 --> 33498)
face area 0.33 +- 0.16 (0.00-->4.96)
mean absolute distance = 0.24 +- 0.35
3719 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=958960.1, rms=3.462
022: dt: 0.5000, sse=928767.7, rms=3.254 (6.005%)
rms = 3.54, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=777139.0, rms=2.213 (31.984%)
024: dt: 0.2500, sse=734648.7, rms=1.762 (20.376%)
025: dt: 0.2500, sse=719216.9, rms=1.625 (7.767%)
rms = 1.62, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=716656.9, rms=1.620 (0.338%)
027: dt: 0.1250, sse=704146.0, rms=1.482 (8.542%)
rms = 1.48, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=704427.9, rms=1.478 (0.240%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=84.3, 89 (7) missing vertices, mean dist -0.1 [0.3 (%55.2)->0.2 (%44.8))]
%87 local maxima, % 8 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-6.0.0/0051362/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=729573.2, rms=1.869
rms = 2.22, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=681402.6, rms=1.305 (30.188%)
030: dt: 0.2500, sse=669626.8, rms=1.073 (17.754%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
rms = 1.07, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=668227.1, rms=1.068 (0.499%)
positioning took 0.4 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7611 vertices
erasing segment 1 (vno[0] = 58612)
erasing segment 2 (vno[0] = 88117)
erasing segment 3 (vno[0] = 89101)
erasing segment 4 (vno[0] = 93875)
erasing segment 5 (vno[0] = 100044)
erasing segment 6 (vno[0] = 100985)
erasing segment 7 (vno[0] = 101104)
erasing segment 8 (vno[0] = 102956)
erasing segment 9 (vno[0] = 103883)
erasing segment 10 (vno[0] = 103989)
erasing segment 11 (vno[0] = 136981)
erasing segment 12 (vno[0] = 136984)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.area
vertex spacing 0.88 +- 0.26 (0.04-->4.36) (max @ vno 31249 --> 33498)
face area 0.32 +- 0.16 (0.00-->4.95)
refinement took 5.1 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
50338 bright wm thresholded.
2140 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.orig...
computing class statistics...
border white:    271136 voxels (1.62%)
border gray      285350 voxels (1.70%)
WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0]
GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 57.9 (was 70)
setting MAX_BORDER_WHITE to 109.1 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 46.7 (was 40)
setting MAX_GRAY to 90.9 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 57.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.80 +- 0.23 (0.02-->3.81) (max @ vno 76035 --> 81853)
face area 0.27 +- 0.13 (0.00-->2.73)
mean absolute distance = 0.77 +- 1.07
4154 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+-7.0,    GM=69+-7.8
mean inside = 91.4, mean outside = 72.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=79.9, 33 (33) missing vertices, mean dist 0.0 [0.9 (%42.7)->0.7 (%57.3))]
%54 local maxima, %41 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 +- 0.25 (0.06-->3.34) (max @ vno 121856 --> 124073)
face area 0.27 +- 0.13 (0.00-->2.19)
mean absolute distance = 0.43 +- 0.70
4655 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3318185.8, rms=10.113
001: dt: 0.5000, sse=1773009.0, rms=6.797 (32.789%)
002: dt: 0.5000, sse=1166424.5, rms=4.876 (28.267%)
003: dt: 0.5000, sse=958628.8, rms=4.016 (17.640%)
004: dt: 0.5000, sse=886030.7, rms=3.655 (8.985%)
005: dt: 0.5000, sse=862198.0, rms=3.534 (3.298%)
006: dt: 0.5000, sse=851194.4, rms=3.479 (1.562%)
rms = 3.47, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=852315.2, rms=3.468 (0.315%)
008: dt: 0.2500, sse=690643.2, rms=2.375 (31.534%)
009: dt: 0.2500, sse=655425.1, rms=2.041 (14.041%)
010: dt: 0.2500, sse=647600.1, rms=1.976 (3.187%)
rms = 1.93, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=641551.0, rms=1.930 (2.360%)
012: dt: 0.1250, sse=632027.6, rms=1.833 (4.996%)
rms = 1.82, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=631298.5, rms=1.824 (0.521%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
mean border=83.2, 44 (3) missing vertices, mean dist -0.3 [0.5 (%68.8)->0.2 (%31.2))]
%69 local maxima, %26 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 0.87 +- 0.25 (0.04-->3.23) (max @ vno 135724 --> 138129)
face area 0.33 +- 0.16 (0.00-->2.99)
mean absolute distance = 0.29 +- 0.43
3717 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1260292.9, rms=4.710
014: dt: 0.5000, sse=971364.9, rms=3.344 (28.994%)
rms = 3.39, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=845562.2, rms=2.587 (22.649%)
016: dt: 0.2500, sse=781193.5, rms=2.064 (20.225%)
017: dt: 0.2500, sse=762217.8, rms=1.819 (11.848%)
018: dt: 0.2500, sse=746678.6, rms=1.718 (5.570%)
019: dt: 0.2500, sse=741627.4, rms=1.655 (3.655%)
rms = 1.62, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=738555.7, rms=1.623 (1.917%)
021: dt: 0.1250, sse=733036.1, rms=1.546 (4.746%)
rms = 1.54, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=731436.4, rms=1.542 (0.282%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
mean border=85.5, 59 (1) missing vertices, mean dist -0.2 [0.3 (%68.0)->0.2 (%32.0))]
%82 local maxima, %14 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 0.87 +- 0.25 (0.07-->3.28) (max @ vno 96267 --> 139774)
face area 0.32 +- 0.16 (0.00-->3.06)
mean absolute distance = 0.24 +- 0.35
3979 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=947137.6, rms=3.330
023: dt: 0.5000, sse=897889.4, rms=2.902 (12.848%)
rms = 3.23, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=763824.3, rms=2.019 (30.430%)
025: dt: 0.2500, sse=727612.6, rms=1.614 (20.051%)
026: dt: 0.2500, sse=714116.2, rms=1.515 (6.126%)
rms = 1.50, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=711563.8, rms=1.502 (0.905%)
028: dt: 0.1250, sse=703371.6, rms=1.402 (6.601%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=703526.3, rms=1.401 (0.070%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=86.4, 77 (1) missing vertices, mean dist -0.1 [0.3 (%54.8)->0.2 (%45.2))]
%86 local maxima, %10 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-6.0.0/0051362/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=727127.6, rms=1.782
rms = 1.93, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=685293.9, rms=1.276 (28.403%)
031: dt: 0.2500, sse=671054.9, rms=1.028 (19.416%)
rms = 1.04, time step reduction 2 of 3 to 0.125...
rms = 1.02, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=671525.6, rms=1.024 (0.430%)
positioning took 0.4 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7527 vertices
erasing segment 1 (vno[0] = 59957)
erasing segment 2 (vno[0] = 101310)
erasing segment 3 (vno[0] = 101335)
erasing segment 4 (vno[0] = 102371)
erasing segment 5 (vno[0] = 103368)
erasing segment 6 (vno[0] = 103388)
erasing segment 7 (vno[0] = 105428)
erasing segment 8 (vno[0] = 108646)
erasing segment 9 (vno[0] = 110616)
erasing segment 10 (vno[0] = 110620)
erasing segment 11 (vno[0] = 110634)
erasing segment 12 (vno[0] = 115603)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.area
vertex spacing 0.87 +- 0.26 (0.04-->3.81) (max @ vno 76035 --> 81853)
face area 0.32 +- 0.16 (0.00-->3.08)
refinement took 5.3 minutes
PIDs (11960 11963) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 21:13:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 21:13:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

Waiting for PID 12501 of (12501 12504) to complete...
Waiting for PID 12504 of (12501 12504) 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 (12501 12504) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 21:13:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 21:13:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 12548 of (12548 12551) to complete...
Waiting for PID 12551 of (12548 12551) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 46.0 mm, total surface area = 79372 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.185 (target=0.015)   
step 005: RMS=0.128 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.064 (target=0.015)   
step 025: RMS=0.054 (target=0.015)   
step 030: RMS=0.046 (target=0.015)   
step 035: RMS=0.038 (target=0.015)   
step 040: RMS=0.033 (target=0.015)   
step 045: RMS=0.029 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    40.581830
mris_inflate stimesec    0.116982
mris_inflate ru_maxrss   201864
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   29579
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10768
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5392
mris_inflate ru_nivcsw   4806

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 46.7 mm, total surface area = 79872 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.180 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.053 (target=0.015)   
step 030: RMS=0.044 (target=0.015)   
step 035: RMS=0.037 (target=0.015)   
step 040: RMS=0.032 (target=0.015)   
step 045: RMS=0.028 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    41.607674
mris_inflate stimesec    0.104984
mris_inflate ru_maxrss   206156
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30140
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11000
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5434
mris_inflate ru_nivcsw   4897
PIDs (12548 12551) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 21:14:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sat Oct  7 21:14:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 12778 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12781 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12784 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12787 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12790 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12793 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12796 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12799 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12802 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12805 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12809 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...
Waiting for PID 12812 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = -7.994*4pi (-100.457) --> 9 handles
ICI = 204.3, FI = 1905.5, variation=31116.489
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
147 vertices thresholded to be in k1 ~ [-0.20 0.47], k2 ~ [-0.13 0.08]
total integrated curvature = 0.568*4pi (7.136) --> 0 handles
ICI = 1.5, FI = 8.7, variation=149.913
134 vertices thresholded to be in [-0.03 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
128 vertices thresholded to be in [-0.11 0.22]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = -7.224*4pi (-90.773) --> 8 handles
ICI = 193.9, FI = 1798.4, variation=29358.738
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
154 vertices thresholded to be in k1 ~ [-0.19 0.65], k2 ~ [-0.14 0.08]
total integrated curvature = 0.559*4pi (7.027) --> 0 handles
ICI = 1.5, FI = 9.1, variation=156.681
150 vertices thresholded to be in [-0.05 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
128 vertices thresholded to be in [-0.12 0.26]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023
done.
PIDs (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 21:15:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051362 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      [ 0051362/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                      [ 253 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.014552
WARN:    S explicit min:                          0.000000	vertex = 171

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 21:15:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051362 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      [ 0051362/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                      [ 254 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.727026
WARN:    S explicit min:                          0.000000	vertex = 1478

WARN:    C lookup   max:                          229.934219
WARN:    C explicit max:                          74.243919	vertex = 112340
#--------------------------------------------
#@# Sphere lh Sat Oct  7 21:15:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 21:15:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 13159 of (13159 13163) to complete...
Waiting for PID 13163 of (13159 13163) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0.304...
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 %19.68
pass 1: epoch 2 of 3 starting distance error %19.45
unfolding complete - removing small folds...
starting distance error %19.35
removing remaining folds...
final distance error %19.37
MRISunfold() return, current seed 1234
-01: dt=0.0000, 159 negative triangles
276: dt=0.9900, 159 negative triangles
277: dt=0.9900, 72 negative triangles
278: dt=0.9900, 54 negative triangles
279: dt=0.9900, 50 negative triangles
280: dt=0.9900, 44 negative triangles
281: dt=0.9900, 46 negative triangles
282: dt=0.9900, 41 negative triangles
283: dt=0.9900, 43 negative triangles
284: dt=0.9900, 34 negative triangles
285: dt=0.9900, 32 negative triangles
286: dt=0.9900, 36 negative triangles
287: dt=0.9900, 30 negative triangles
288: dt=0.9900, 29 negative triangles
289: dt=0.9900, 28 negative triangles
290: dt=0.9900, 20 negative triangles
291: dt=0.9900, 27 negative triangles
292: dt=0.9900, 23 negative triangles
293: dt=0.9900, 27 negative triangles
294: dt=0.9900, 20 negative triangles
295: dt=0.9900, 25 negative triangles
296: dt=0.9900, 20 negative triangles
297: dt=0.9900, 25 negative triangles
298: dt=0.9900, 22 negative triangles
299: dt=0.9900, 24 negative triangles
300: dt=0.9900, 19 negative triangles
301: dt=0.9900, 22 negative triangles
302: dt=0.9900, 18 negative triangles
303: dt=0.9900, 24 negative triangles
304: dt=0.9900, 17 negative triangles
305: dt=0.9900, 23 negative triangles
306: dt=0.9900, 17 negative triangles
307: dt=0.9900, 23 negative triangles
308: dt=0.9900, 17 negative triangles
309: dt=0.9900, 22 negative triangles
310: dt=0.9900, 18 negative triangles
311: dt=0.9900, 23 negative triangles
312: dt=0.9900, 18 negative triangles
313: dt=0.9900, 23 negative triangles
314: dt=0.9405, 18 negative triangles
315: dt=0.9405, 23 negative triangles
316: dt=0.9405, 16 negative triangles
317: dt=0.9405, 19 negative triangles
318: dt=0.9405, 19 negative triangles
319: dt=0.9405, 19 negative triangles
320: dt=0.9405, 16 negative triangles
321: dt=0.9405, 21 negative triangles
322: dt=0.9405, 16 negative triangles
323: dt=0.9405, 19 negative triangles
324: dt=0.9405, 18 negative triangles
325: dt=0.9405, 20 negative triangles
326: dt=0.8935, 16 negative triangles
327: dt=0.8935, 22 negative triangles
328: dt=0.8935, 17 negative triangles
329: dt=0.8935, 17 negative triangles
330: dt=0.8935, 21 negative triangles
331: dt=0.8935, 18 negative triangles
332: dt=0.8935, 16 negative triangles
333: dt=0.8935, 23 negative triangles
334: dt=0.8935, 20 negative triangles
335: dt=0.8935, 15 negative triangles
336: dt=0.8935, 20 negative triangles
337: dt=0.8935, 16 negative triangles
338: dt=0.8935, 18 negative triangles
339: dt=0.8935, 18 negative triangles
340: dt=0.8935, 18 negative triangles
341: dt=0.8935, 15 negative triangles
342: dt=0.8935, 20 negative triangles
343: dt=0.8935, 15 negative triangles
344: dt=0.8935, 18 negative triangles
345: dt=0.8488, 17 negative triangles
346: dt=0.8488, 18 negative triangles
347: dt=0.8488, 16 negative triangles
348: dt=0.8488, 19 negative triangles
349: dt=0.8488, 15 negative triangles
350: dt=0.8488, 14 negative triangles
351: dt=0.8488, 19 negative triangles
352: dt=0.8488, 15 negative triangles
353: dt=0.8488, 15 negative triangles
354: dt=0.8488, 17 negative triangles
355: dt=0.8488, 12 negative triangles
356: dt=0.8488, 16 negative triangles
357: dt=0.8488, 13 negative triangles
358: dt=0.8488, 15 negative triangles
359: dt=0.8488, 10 negative triangles
360: dt=0.8488, 14 negative triangles
361: dt=0.8488, 10 negative triangles
362: dt=0.8488, 13 negative triangles
363: dt=0.8488, 10 negative triangles
364: dt=0.8488, 15 negative triangles
365: dt=0.8488, 9 negative triangles
366: dt=0.8488, 10 negative triangles
367: dt=0.8488, 8 negative triangles
368: dt=0.8488, 13 negative triangles
369: dt=0.8488, 8 negative triangles
370: dt=0.8488, 8 negative triangles
371: dt=0.8488, 8 negative triangles
372: dt=0.8488, 12 negative triangles
373: dt=0.8488, 7 negative triangles
374: dt=0.8488, 8 negative triangles
375: dt=0.8488, 6 negative triangles
376: dt=0.8488, 8 negative triangles
377: dt=0.8488, 5 negative triangles
378: dt=0.8488, 6 negative triangles
379: dt=0.8488, 6 negative triangles
380: dt=0.8488, 5 negative triangles
381: dt=0.8488, 4 negative triangles
382: dt=0.8488, 6 negative triangles
383: dt=0.8488, 4 negative triangles
384: dt=0.8488, 1 negative triangles
385: dt=0.8488, 1 negative triangles
386: dt=0.8488, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.12 hours
mris_sphere utimesec    4031.630099
mris_sphere stimesec    1.484774
mris_sphere ru_maxrss   282980
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   49988
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  9776
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    147514
mris_sphere ru_nivcsw   350615
FSRUNTIME@ mris_sphere  1.1207 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0.304...
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 %19.87
pass 1: epoch 2 of 3 starting distance error %19.77
unfolding complete - removing small folds...
starting distance error %19.68
removing remaining folds...
final distance error %19.69
MRISunfold() return, current seed 1234
-01: dt=0.0000, 240 negative triangles
176: dt=0.9900, 240 negative triangles
177: dt=0.9900, 147 negative triangles
178: dt=0.9900, 116 negative triangles
179: dt=0.9900, 116 negative triangles
180: dt=0.9900, 111 negative triangles
181: dt=0.9900, 105 negative triangles
182: dt=0.9900, 110 negative triangles
183: dt=0.9900, 106 negative triangles
184: dt=0.9900, 102 negative triangles
185: dt=0.9900, 99 negative triangles
186: dt=0.9900, 89 negative triangles
187: dt=0.9900, 93 negative triangles
188: dt=0.9900, 87 negative triangles
189: dt=0.9900, 83 negative triangles
190: dt=0.9900, 82 negative triangles
191: dt=0.9900, 76 negative triangles
192: dt=0.9900, 83 negative triangles
193: dt=0.9900, 73 negative triangles
194: dt=0.9900, 71 negative triangles
195: dt=0.9900, 66 negative triangles
196: dt=0.9900, 70 negative triangles
197: dt=0.9900, 62 negative triangles
198: dt=0.9900, 64 negative triangles
199: dt=0.9900, 60 negative triangles
200: dt=0.9900, 57 negative triangles
201: dt=0.9900, 55 negative triangles
202: dt=0.9900, 58 negative triangles
203: dt=0.9900, 54 negative triangles
204: dt=0.9900, 55 negative triangles
205: dt=0.9900, 49 negative triangles
206: dt=0.9900, 47 negative triangles
207: dt=0.9900, 43 negative triangles
208: dt=0.9900, 40 negative triangles
209: dt=0.9900, 40 negative triangles
210: dt=0.9900, 39 negative triangles
211: dt=0.9900, 42 negative triangles
212: dt=0.9900, 47 negative triangles
213: dt=0.9900, 41 negative triangles
214: dt=0.9900, 39 negative triangles
215: dt=0.9900, 46 negative triangles
216: dt=0.9900, 41 negative triangles
217: dt=0.9900, 43 negative triangles
218: dt=0.9900, 43 negative triangles
219: dt=0.9900, 42 negative triangles
220: dt=0.9405, 48 negative triangles
221: dt=0.9405, 45 negative triangles
222: dt=0.9405, 46 negative triangles
223: dt=0.9405, 50 negative triangles
224: dt=0.9405, 47 negative triangles
225: dt=0.9405, 45 negative triangles
226: dt=0.9405, 51 negative triangles
227: dt=0.9405, 48 negative triangles
228: dt=0.9405, 51 negative triangles
229: dt=0.9405, 51 negative triangles
230: dt=0.8935, 53 negative triangles
231: dt=0.8935, 55 negative triangles
232: dt=0.8935, 49 negative triangles
233: dt=0.8935, 54 negative triangles
234: dt=0.8935, 53 negative triangles
235: dt=0.8935, 53 negative triangles
236: dt=0.8935, 50 negative triangles
237: dt=0.8935, 62 negative triangles
238: dt=0.8935, 57 negative triangles
239: dt=0.8935, 54 negative triangles
240: dt=0.8488, 56 negative triangles
241: dt=0.8488, 56 negative triangles
242: dt=0.8488, 58 negative triangles
243: dt=0.8488, 56 negative triangles
244: dt=0.8488, 61 negative triangles
245: dt=0.8488, 63 negative triangles
246: dt=0.8488, 57 negative triangles
247: dt=0.8488, 57 negative triangles
248: dt=0.8488, 65 negative triangles
249: dt=0.8488, 60 negative triangles
250: dt=0.8064, 61 negative triangles
251: dt=0.8064, 66 negative triangles
252: dt=0.8064, 60 negative triangles
253: dt=0.8064, 66 negative triangles
254: dt=0.8064, 68 negative triangles
255: dt=0.8064, 63 negative triangles
256: dt=0.8064, 65 negative triangles
257: dt=0.8064, 59 negative triangles
258: dt=0.8064, 63 negative triangles
259: dt=0.8064, 67 negative triangles
260: dt=0.7660, 57 negative triangles
expanding nbhd size to 1
261: dt=0.9900, 62 negative triangles
262: dt=0.9900, 58 negative triangles
263: dt=0.9900, 56 negative triangles
264: dt=0.9900, 52 negative triangles
265: dt=0.9900, 51 negative triangles
266: dt=0.9900, 49 negative triangles
267: dt=0.9900, 52 negative triangles
268: dt=0.9900, 53 negative triangles
269: dt=0.9900, 50 negative triangles
270: dt=0.9405, 48 negative triangles
271: dt=0.9405, 45 negative triangles
272: dt=0.9405, 46 negative triangles
273: dt=0.9405, 47 negative triangles
274: dt=0.9405, 49 negative triangles
275: dt=0.9405, 49 negative triangles
276: dt=0.9405, 56 negative triangles
277: dt=0.9405, 54 negative triangles
278: dt=0.9405, 52 negative triangles
279: dt=0.9405, 51 negative triangles
280: dt=0.8935, 49 negative triangles
281: dt=0.8935, 48 negative triangles
282: dt=0.8935, 50 negative triangles
283: dt=0.8935, 51 negative triangles
284: dt=0.8935, 51 negative triangles
285: dt=0.8935, 49 negative triangles
286: dt=0.8935, 47 negative triangles
287: dt=0.8935, 46 negative triangles
288: dt=0.8935, 50 negative triangles
289: dt=0.8935, 50 negative triangles
290: dt=0.8488, 48 negative triangles
291: dt=0.8488, 50 negative triangles
292: dt=0.8488, 46 negative triangles
293: dt=0.8488, 45 negative triangles
294: dt=0.8488, 46 negative triangles
295: dt=0.8488, 46 negative triangles
296: dt=0.8488, 47 negative triangles
297: dt=0.8488, 49 negative triangles
298: dt=0.8488, 46 negative triangles
299: dt=0.8488, 46 negative triangles
300: dt=0.8064, 43 negative triangles
301: dt=0.8064, 43 negative triangles
302: dt=0.8064, 44 negative triangles
303: dt=0.8064, 48 negative triangles
304: dt=0.8064, 48 negative triangles
305: dt=0.8064, 47 negative triangles
306: dt=0.8064, 46 negative triangles
307: dt=0.8064, 44 negative triangles
308: dt=0.8064, 44 negative triangles
309: dt=0.8064, 43 negative triangles
310: dt=0.7660, 45 negative triangles
311: dt=0.7660, 48 negative triangles
312: dt=0.7660, 47 negative triangles
313: dt=0.7660, 46 negative triangles
314: dt=0.7660, 44 negative triangles
315: dt=0.7660, 43 negative triangles
316: dt=0.7660, 44 negative triangles
317: dt=0.7660, 43 negative triangles
318: dt=0.7660, 44 negative triangles
319: dt=0.7660, 42 negative triangles
320: dt=0.7277, 41 negative triangles
321: dt=0.7277, 41 negative triangles
322: dt=0.7277, 42 negative triangles
323: dt=0.7277, 42 negative triangles
324: dt=0.7277, 41 negative triangles
325: dt=0.7277, 39 negative triangles
326: dt=0.7277, 39 negative triangles
327: dt=0.7277, 39 negative triangles
328: dt=0.7277, 40 negative triangles
329: dt=0.7277, 42 negative triangles
330: dt=0.6914, 41 negative triangles
331: dt=0.6914, 41 negative triangles
332: dt=0.6914, 39 negative triangles
333: dt=0.6914, 38 negative triangles
334: dt=0.6914, 38 negative triangles
335: dt=0.6914, 41 negative triangles
336: dt=0.6914, 39 negative triangles
337: dt=0.6914, 37 negative triangles
338: dt=0.6914, 36 negative triangles
339: dt=0.6914, 35 negative triangles
340: dt=0.6914, 35 negative triangles
341: dt=0.6914, 37 negative triangles
342: dt=0.6914, 38 negative triangles
343: dt=0.6914, 38 negative triangles
344: dt=0.6914, 36 negative triangles
345: dt=0.6914, 35 negative triangles
346: dt=0.6914, 36 negative triangles
347: dt=0.6914, 36 negative triangles
348: dt=0.6914, 36 negative triangles
349: dt=0.6568, 36 negative triangles
350: dt=0.6568, 35 negative triangles
351: dt=0.6568, 32 negative triangles
352: dt=0.6568, 31 negative triangles
353: dt=0.6568, 30 negative triangles
354: dt=0.6568, 31 negative triangles
355: dt=0.6568, 30 negative triangles
356: dt=0.6568, 30 negative triangles
357: dt=0.6568, 29 negative triangles
358: dt=0.6568, 30 negative triangles
359: dt=0.6568, 29 negative triangles
360: dt=0.6568, 30 negative triangles
361: dt=0.6568, 31 negative triangles
362: dt=0.6568, 31 negative triangles
363: dt=0.6568, 29 negative triangles
364: dt=0.6568, 27 negative triangles
365: dt=0.6568, 29 negative triangles
366: dt=0.6568, 27 negative triangles
367: dt=0.6568, 28 negative triangles
368: dt=0.6568, 29 negative triangles
369: dt=0.6568, 27 negative triangles
370: dt=0.6568, 28 negative triangles
371: dt=0.6568, 26 negative triangles
372: dt=0.6568, 27 negative triangles
373: dt=0.6568, 28 negative triangles
374: dt=0.6568, 26 negative triangles
375: dt=0.6568, 26 negative triangles
376: dt=0.6568, 25 negative triangles
377: dt=0.6568, 26 negative triangles
378: dt=0.6568, 22 negative triangles
379: dt=0.6568, 24 negative triangles
380: dt=0.6568, 23 negative triangles
381: dt=0.6568, 24 negative triangles
382: dt=0.6568, 26 negative triangles
383: dt=0.6568, 23 negative triangles
384: dt=0.6568, 24 negative triangles
385: dt=0.6568, 21 negative triangles
386: dt=0.6568, 22 negative triangles
387: dt=0.6568, 20 negative triangles
388: dt=0.6568, 23 negative triangles
389: dt=0.6568, 24 negative triangles
390: dt=0.6568, 22 negative triangles
391: dt=0.6568, 21 negative triangles
392: dt=0.6568, 20 negative triangles
393: dt=0.6568, 20 negative triangles
394: dt=0.6568, 20 negative triangles
395: dt=0.6568, 20 negative triangles
396: dt=0.6568, 20 negative triangles
397: dt=0.6568, 18 negative triangles
398: dt=0.6568, 20 negative triangles
399: dt=0.6568, 19 negative triangles
400: dt=0.6568, 19 negative triangles
401: dt=0.6568, 18 negative triangles
402: dt=0.6568, 20 negative triangles
403: dt=0.6568, 18 negative triangles
404: dt=0.6568, 17 negative triangles
405: dt=0.6568, 15 negative triangles
406: dt=0.6568, 17 negative triangles
407: dt=0.6568, 16 negative triangles
408: dt=0.6568, 15 negative triangles
409: dt=0.6568, 13 negative triangles
410: dt=0.6568, 14 negative triangles
411: dt=0.6568, 13 negative triangles
412: dt=0.6568, 14 negative triangles
413: dt=0.6568, 13 negative triangles
414: dt=0.6568, 13 negative triangles
415: dt=0.6568, 13 negative triangles
416: dt=0.6568, 13 negative triangles
417: dt=0.6568, 13 negative triangles
418: dt=0.6568, 14 negative triangles
419: dt=0.6239, 14 negative triangles
420: dt=0.6239, 13 negative triangles
421: dt=0.6239, 14 negative triangles
422: dt=0.6239, 13 negative triangles
423: dt=0.6239, 12 negative triangles
424: dt=0.6239, 12 negative triangles
425: dt=0.6239, 14 negative triangles
426: dt=0.6239, 12 negative triangles
427: dt=0.6239, 14 negative triangles
428: dt=0.6239, 12 negative triangles
429: dt=0.6239, 13 negative triangles
430: dt=0.6239, 12 negative triangles
431: dt=0.6239, 12 negative triangles
432: dt=0.6239, 13 negative triangles
433: dt=0.6239, 11 negative triangles
434: dt=0.6239, 11 negative triangles
435: dt=0.6239, 9 negative triangles
436: dt=0.6239, 9 negative triangles
437: dt=0.6239, 9 negative triangles
438: dt=0.6239, 9 negative triangles
439: dt=0.6239, 8 negative triangles
440: dt=0.6239, 8 negative triangles
441: dt=0.6239, 8 negative triangles
442: dt=0.6239, 8 negative triangles
443: dt=0.6239, 8 negative triangles
444: dt=0.6239, 9 negative triangles
445: dt=0.6239, 8 negative triangles
446: dt=0.6239, 8 negative triangles
447: dt=0.6239, 8 negative triangles
448: dt=0.6239, 8 negative triangles
449: dt=0.5927, 8 negative triangles
450: dt=0.5927, 8 negative triangles
451: dt=0.5927, 8 negative triangles
452: dt=0.5927, 8 negative triangles
453: dt=0.5927, 9 negative triangles
454: dt=0.5927, 9 negative triangles
455: dt=0.5927, 10 negative triangles
456: dt=0.5927, 9 negative triangles
457: dt=0.5927, 9 negative triangles
458: dt=0.5927, 7 negative triangles
459: dt=0.5927, 7 negative triangles
460: dt=0.5927, 7 negative triangles
461: dt=0.5927, 5 negative triangles
462: dt=0.5927, 5 negative triangles
463: dt=0.5927, 5 negative triangles
464: dt=0.5927, 5 negative triangles
465: dt=0.5927, 5 negative triangles
466: dt=0.5927, 5 negative triangles
467: dt=0.5927, 5 negative triangles
468: dt=0.5927, 5 negative triangles
469: dt=0.5927, 5 negative triangles
470: dt=0.5927, 5 negative triangles
471: dt=0.5631, 5 negative triangles
472: dt=0.5631, 5 negative triangles
473: dt=0.5631, 5 negative triangles
474: dt=0.5631, 5 negative triangles
475: dt=0.5631, 5 negative triangles
476: dt=0.5631, 5 negative triangles
477: dt=0.5631, 4 negative triangles
478: dt=0.5631, 4 negative triangles
479: dt=0.5631, 4 negative triangles
480: dt=0.5631, 4 negative triangles
481: dt=0.5631, 4 negative triangles
482: dt=0.5631, 4 negative triangles
483: dt=0.5631, 4 negative triangles
484: dt=0.5631, 4 negative triangles
485: dt=0.5631, 3 negative triangles
486: dt=0.5631, 3 negative triangles
487: dt=0.5631, 2 negative triangles
488: dt=0.5631, 2 negative triangles
489: dt=0.5631, 2 negative triangles
490: dt=0.5631, 1 negative triangles
491: dt=0.5631, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.13 hours
mris_sphere utimesec    4066.987723
mris_sphere stimesec    1.503771
mris_sphere ru_maxrss   289064
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   50989
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10144
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    136147
mris_sphere ru_nivcsw   351069
FSRUNTIME@ mris_sphere  1.1254 hours 1 threads
PIDs (13159 13163) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sat Oct  7 22:23:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 Sat Oct  7 22:23:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 16948 of (16948 16951) to complete...
Waiting for PID 16951 of (16948 16951) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 5.239
curvature mean = 0.043, std = 0.822
curvature mean = 0.023, std = 0.854
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 371200.3, tmin=1.0119
  d=32.00 min @ (0.00, 8.00, -8.00) sse = 227945.4, tmin=2.0409
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 214262.2, tmin=3.0815
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 214118.2, tmin=4.1268
  d=4.00 min @ (1.00, 0.00, -1.00) sse = 211599.5, tmin=5.1804
  d=2.00 min @ (0.00, 0.00, 0.50) sse = 211414.9, tmin=6.2412
  d=1.00 min @ (-0.25, 0.25, -0.25) sse = 211170.0, tmin=7.3011
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 211164.3, tmin=8.3732
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   8.37 min
curvature mean = 0.005, std = 0.833
curvature mean = 0.008, std = 0.944
curvature mean = 0.001, std = 0.843
curvature mean = 0.003, std = 0.977
curvature mean = -0.002, std = 0.844
curvature mean = 0.001, std = 0.991
2 Reading smoothwm
curvature mean = -0.025, std = 0.306
curvature mean = 0.040, std = 0.250
curvature mean = 0.063, std = 0.324
curvature mean = 0.035, std = 0.308
curvature mean = 0.032, std = 0.510
curvature mean = 0.035, std = 0.336
curvature mean = 0.018, std = 0.651
curvature mean = 0.035, std = 0.347
curvature mean = 0.007, std = 0.762
MRISregister() return, current seed 0
-01: dt=0.0000, 167 negative triangles
113: dt=0.9900, 167 negative triangles
expanding nbhd size to 1
114: dt=0.9900, 204 negative triangles
115: dt=0.9900, 157 negative triangles
116: dt=0.9900, 148 negative triangles
117: dt=0.9900, 140 negative triangles
118: dt=0.9900, 132 negative triangles
119: dt=0.9900, 127 negative triangles
120: dt=0.9900, 116 negative triangles
121: dt=0.9900, 112 negative triangles
122: dt=0.9900, 101 negative triangles
123: dt=0.9900, 94 negative triangles
124: dt=0.9900, 87 negative triangles
125: dt=0.9900, 82 negative triangles
126: dt=0.9900, 80 negative triangles
127: dt=0.9900, 73 negative triangles
128: dt=0.9900, 74 negative triangles
129: dt=0.9900, 65 negative triangles
130: dt=0.9900, 62 negative triangles
131: dt=0.9900, 55 negative triangles
132: dt=0.9900, 48 negative triangles
133: dt=0.9900, 40 negative triangles
134: dt=0.9900, 33 negative triangles
135: dt=0.9900, 28 negative triangles
136: dt=0.9900, 27 negative triangles
137: dt=0.9900, 25 negative triangles
138: dt=0.9900, 27 negative triangles
139: dt=0.9900, 27 negative triangles
140: dt=0.9900, 25 negative triangles
141: dt=0.9900, 21 negative triangles
142: dt=0.9900, 20 negative triangles
143: dt=0.9900, 15 negative triangles
144: dt=0.9900, 17 negative triangles
145: dt=0.9900, 16 negative triangles
146: dt=0.9900, 15 negative triangles
147: dt=0.9900, 14 negative triangles
148: dt=0.9900, 15 negative triangles
149: dt=0.9900, 13 negative triangles
150: dt=0.9900, 14 negative triangles
151: dt=0.9900, 13 negative triangles
152: dt=0.9900, 14 negative triangles
153: dt=0.9900, 13 negative triangles
154: dt=0.9900, 12 negative triangles
155: dt=0.9900, 13 negative triangles
156: dt=0.9900, 12 negative triangles
157: dt=0.9900, 10 negative triangles
158: dt=0.9900, 10 negative triangles
159: dt=0.9900, 10 negative triangles
160: dt=0.9900, 10 negative triangles
161: dt=0.9900, 11 negative triangles
162: dt=0.9900, 9 negative triangles
163: dt=0.9900, 10 negative triangles
164: dt=0.9900, 8 negative triangles
165: dt=0.9900, 7 negative triangles
166: dt=0.9900, 7 negative triangles
167: dt=0.9900, 5 negative triangles
168: dt=0.9900, 4 negative triangles
169: dt=0.9900, 6 negative triangles
170: dt=0.9900, 3 negative triangles
171: dt=0.9900, 3 negative triangles
172: dt=0.9900, 3 negative triangles
173: dt=0.9900, 6 negative triangles
174: dt=0.9900, 2 negative triangles
175: dt=0.9900, 2 negative triangles
176: dt=0.9900, 2 negative triangles
177: dt=0.9900, 3 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.22 hours
mris_register utimesec    4379.367234
mris_register stimesec    3.831417
mris_register ru_maxrss   254388
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   36389
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  9776
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    394593
mris_register ru_nivcsw   241377
FSRUNTIME@ mris_register  1.2174 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 5.407
curvature mean = 0.012, std = 0.817
curvature mean = 0.028, std = 0.862
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 349887.2, tmin=1.0592
  d=32.00 min @ (-8.00, -8.00, -8.00) sse = 281110.0, tmin=2.1353
  d=16.00 min @ (0.00, 4.00, 4.00) sse = 235459.6, tmin=3.2279
  d=4.00 min @ (0.00, -1.00, 0.00) sse = 233899.3, tmin=5.4301
  d=2.00 min @ (0.50, 0.00, 0.00) sse = 233664.9, tmin=6.5381
  d=1.00 min @ (0.00, 0.25, 0.00) sse = 233574.2, tmin=7.6445
  d=0.50 min @ (-0.12, 0.00, 0.00) sse = 233554.8, tmin=8.7600
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   8.76 min
curvature mean = -0.001, std = 0.827
curvature mean = 0.010, std = 0.949
curvature mean = -0.003, std = 0.836
curvature mean = 0.004, std = 0.980
curvature mean = -0.004, std = 0.838
curvature mean = 0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.028, std = 0.316
curvature mean = 0.033, std = 0.244
curvature mean = 0.067, std = 0.318
curvature mean = 0.029, std = 0.301
curvature mean = 0.032, std = 0.495
curvature mean = 0.028, std = 0.328
curvature mean = 0.017, std = 0.629
curvature mean = 0.028, std = 0.339
curvature mean = 0.006, std = 0.733
MRISregister() return, current seed 0
-01: dt=0.0000, 112 negative triangles
112: dt=0.9900, 112 negative triangles
expanding nbhd size to 1
113: dt=0.9900, 131 negative triangles
114: dt=0.9900, 109 negative triangles
115: dt=0.9900, 107 negative triangles
116: dt=0.9900, 102 negative triangles
117: dt=0.9900, 101 negative triangles
118: dt=0.9900, 92 negative triangles
119: dt=0.9900, 89 negative triangles
120: dt=0.9900, 80 negative triangles
121: dt=0.9900, 70 negative triangles
122: dt=0.9900, 59 negative triangles
123: dt=0.9900, 59 negative triangles
124: dt=0.9900, 58 negative triangles
125: dt=0.9900, 56 negative triangles
126: dt=0.9900, 57 negative triangles
127: dt=0.9900, 56 negative triangles
128: dt=0.9900, 60 negative triangles
129: dt=0.9900, 60 negative triangles
130: dt=0.9900, 61 negative triangles
131: dt=0.9900, 60 negative triangles
132: dt=0.9900, 60 negative triangles
133: dt=0.9900, 60 negative triangles
134: dt=0.9900, 60 negative triangles
135: dt=0.9405, 62 negative triangles
136: dt=0.9405, 61 negative triangles
137: dt=0.9405, 61 negative triangles
138: dt=0.9405, 61 negative triangles
139: dt=0.9405, 60 negative triangles
140: dt=0.9405, 64 negative triangles
141: dt=0.9405, 62 negative triangles
142: dt=0.9405, 61 negative triangles
143: dt=0.9405, 62 negative triangles
144: dt=0.9405, 62 negative triangles
145: dt=0.8935, 67 negative triangles
146: dt=0.8935, 68 negative triangles
147: dt=0.8935, 67 negative triangles
148: dt=0.8935, 65 negative triangles
149: dt=0.8935, 65 negative triangles
150: dt=0.8935, 65 negative triangles
151: dt=0.8935, 66 negative triangles
152: dt=0.8935, 65 negative triangles
153: dt=0.8935, 64 negative triangles
154: dt=0.8935, 63 negative triangles
155: dt=0.8488, 64 negative triangles
156: dt=0.8488, 63 negative triangles
157: dt=0.8488, 62 negative triangles
158: dt=0.8488, 62 negative triangles
159: dt=0.8488, 64 negative triangles
160: dt=0.8488, 62 negative triangles
161: dt=0.8488, 62 negative triangles
162: dt=0.8488, 64 negative triangles
163: dt=0.8488, 63 negative triangles
164: dt=0.8488, 62 negative triangles
165: dt=0.8064, 62 negative triangles
166: dt=0.8064, 59 negative triangles
167: dt=0.8064, 59 negative triangles
168: dt=0.8064, 62 negative triangles
169: dt=0.8064, 63 negative triangles
170: dt=0.8064, 61 negative triangles
171: dt=0.8064, 59 negative triangles
172: dt=0.8064, 58 negative triangles
173: dt=0.8064, 59 negative triangles
174: dt=0.8064, 60 negative triangles
175: dt=0.7660, 59 negative triangles
176: dt=0.7660, 60 negative triangles
177: dt=0.7660, 60 negative triangles
178: dt=0.7660, 60 negative triangles
179: dt=0.7660, 58 negative triangles
180: dt=0.7660, 57 negative triangles
181: dt=0.7660, 66 negative triangles
182: dt=0.7660, 61 negative triangles
183: dt=0.7660, 60 negative triangles
184: dt=0.7660, 58 negative triangles
185: dt=0.7277, 58 negative triangles
186: dt=0.7277, 58 negative triangles
187: dt=0.7277, 59 negative triangles
188: dt=0.7277, 58 negative triangles
189: dt=0.7277, 56 negative triangles
190: dt=0.7277, 58 negative triangles
191: dt=0.7277, 56 negative triangles
192: dt=0.7277, 56 negative triangles
193: dt=0.7277, 54 negative triangles
194: dt=0.7277, 57 negative triangles
195: dt=0.7277, 54 negative triangles
196: dt=0.7277, 57 negative triangles
197: dt=0.7277, 54 negative triangles
198: dt=0.7277, 56 negative triangles
199: dt=0.7277, 55 negative triangles
200: dt=0.7277, 53 negative triangles
201: dt=0.7277, 53 negative triangles
202: dt=0.7277, 50 negative triangles
203: dt=0.7277, 50 negative triangles
204: dt=0.7277, 50 negative triangles
205: dt=0.7277, 50 negative triangles
206: dt=0.7277, 50 negative triangles
207: dt=0.7277, 48 negative triangles
208: dt=0.7277, 47 negative triangles
209: dt=0.7277, 53 negative triangles
210: dt=0.7277, 51 negative triangles
211: dt=0.7277, 47 negative triangles
212: dt=0.7277, 49 negative triangles
213: dt=0.7277, 47 negative triangles
214: dt=0.7277, 48 negative triangles
215: dt=0.7277, 47 negative triangles
216: dt=0.7277, 46 negative triangles
217: dt=0.7277, 45 negative triangles
218: dt=0.7277, 48 negative triangles
219: dt=0.7277, 46 negative triangles
220: dt=0.7277, 46 negative triangles
221: dt=0.7277, 45 negative triangles
222: dt=0.7277, 47 negative triangles
223: dt=0.7277, 44 negative triangles
224: dt=0.7277, 49 negative triangles
225: dt=0.7277, 47 negative triangles
226: dt=0.7277, 44 negative triangles
227: dt=0.7277, 46 negative triangles
228: dt=0.7277, 43 negative triangles
229: dt=0.7277, 45 negative triangles
230: dt=0.7277, 46 negative triangles
231: dt=0.7277, 46 negative triangles
232: dt=0.7277, 44 negative triangles
233: dt=0.7277, 45 negative triangles
234: dt=0.7277, 43 negative triangles
235: dt=0.7277, 45 negative triangles
236: dt=0.7277, 44 negative triangles
237: dt=0.7277, 44 negative triangles
238: dt=0.6914, 45 negative triangles
239: dt=0.6914, 44 negative triangles
240: dt=0.6914, 43 negative triangles
241: dt=0.6914, 42 negative triangles
242: dt=0.6914, 44 negative triangles
243: dt=0.6914, 43 negative triangles
244: dt=0.6914, 44 negative triangles
245: dt=0.6914, 41 negative triangles
246: dt=0.6914, 45 negative triangles
247: dt=0.6914, 46 negative triangles
248: dt=0.6914, 44 negative triangles
249: dt=0.6914, 42 negative triangles
250: dt=0.6914, 42 negative triangles
251: dt=0.6914, 43 negative triangles
252: dt=0.6914, 42 negative triangles
253: dt=0.6914, 43 negative triangles
254: dt=0.6914, 44 negative triangles
255: dt=0.6568, 45 negative triangles
256: dt=0.6568, 42 negative triangles
257: dt=0.6568, 43 negative triangles
258: dt=0.6568, 44 negative triangles
259: dt=0.6568, 41 negative triangles
260: dt=0.6568, 44 negative triangles
261: dt=0.6568, 45 negative triangles
262: dt=0.6568, 42 negative triangles
263: dt=0.6568, 42 negative triangles
264: dt=0.6568, 40 negative triangles
265: dt=0.6568, 42 negative triangles
266: dt=0.6568, 42 negative triangles
267: dt=0.6568, 40 negative triangles
268: dt=0.6568, 41 negative triangles
269: dt=0.6568, 42 negative triangles
270: dt=0.6568, 40 negative triangles
271: dt=0.6568, 42 negative triangles
272: dt=0.6568, 39 negative triangles
273: dt=0.6568, 39 negative triangles
274: dt=0.6568, 40 negative triangles
275: dt=0.6568, 39 negative triangles
276: dt=0.6568, 38 negative triangles
277: dt=0.6568, 41 negative triangles
278: dt=0.6568, 40 negative triangles
279: dt=0.6568, 38 negative triangles
280: dt=0.6568, 39 negative triangles
281: dt=0.6568, 39 negative triangles
282: dt=0.6568, 39 negative triangles
283: dt=0.6568, 39 negative triangles
284: dt=0.6568, 39 negative triangles
285: dt=0.6568, 39 negative triangles
286: dt=0.6239, 39 negative triangles
287: dt=0.6239, 36 negative triangles
288: dt=0.6239, 39 negative triangles
289: dt=0.6239, 37 negative triangles
290: dt=0.6239, 37 negative triangles
291: dt=0.6239, 35 negative triangles
292: dt=0.6239, 36 negative triangles
293: dt=0.6239, 33 negative triangles
294: dt=0.6239, 34 negative triangles
295: dt=0.6239, 32 negative triangles
296: dt=0.6239, 33 negative triangles
297: dt=0.6239, 32 negative triangles
298: dt=0.6239, 34 negative triangles
299: dt=0.6239, 33 negative triangles
300: dt=0.6239, 32 negative triangles
301: dt=0.6239, 31 negative triangles
302: dt=0.6239, 33 negative triangles
303: dt=0.6239, 30 negative triangles
304: dt=0.6239, 32 negative triangles
305: dt=0.6239, 33 negative triangles
306: dt=0.6239, 30 negative triangles
307: dt=0.6239, 31 negative triangles
308: dt=0.6239, 28 negative triangles
309: dt=0.6239, 30 negative triangles
310: dt=0.6239, 28 negative triangles
311: dt=0.6239, 29 negative triangles
312: dt=0.6239, 29 negative triangles
313: dt=0.6239, 29 negative triangles
314: dt=0.6239, 27 negative triangles
315: dt=0.6239, 28 negative triangles
316: dt=0.6239, 28 negative triangles
317: dt=0.6239, 27 negative triangles
318: dt=0.6239, 25 negative triangles
319: dt=0.6239, 27 negative triangles
320: dt=0.6239, 26 negative triangles
321: dt=0.6239, 25 negative triangles
322: dt=0.6239, 27 negative triangles
323: dt=0.6239, 25 negative triangles
324: dt=0.6239, 23 negative triangles
325: dt=0.6239, 23 negative triangles
326: dt=0.6239, 24 negative triangles
327: dt=0.6239, 24 negative triangles
328: dt=0.6239, 25 negative triangles
329: dt=0.6239, 24 negative triangles
330: dt=0.6239, 23 negative triangles
331: dt=0.6239, 22 negative triangles
332: dt=0.6239, 23 negative triangles
333: dt=0.6239, 23 negative triangles
334: dt=0.6239, 22 negative triangles
335: dt=0.6239, 23 negative triangles
336: dt=0.6239, 23 negative triangles
337: dt=0.6239, 23 negative triangles
338: dt=0.6239, 23 negative triangles
339: dt=0.6239, 25 negative triangles
340: dt=0.6239, 22 negative triangles
341: dt=0.5927, 23 negative triangles
342: dt=0.5927, 23 negative triangles
343: dt=0.5927, 23 negative triangles
344: dt=0.5927, 24 negative triangles
345: dt=0.5927, 22 negative triangles
346: dt=0.5927, 22 negative triangles
347: dt=0.5927, 22 negative triangles
348: dt=0.5927, 25 negative triangles
349: dt=0.5927, 22 negative triangles
350: dt=0.5927, 23 negative triangles
351: dt=0.5631, 23 negative triangles
352: dt=0.5631, 21 negative triangles
353: dt=0.5631, 21 negative triangles
354: dt=0.5631, 20 negative triangles
355: dt=0.5631, 19 negative triangles
356: dt=0.5631, 18 negative triangles
357: dt=0.5631, 19 negative triangles
358: dt=0.5631, 18 negative triangles
359: dt=0.5631, 15 negative triangles
360: dt=0.5631, 15 negative triangles
361: dt=0.5631, 17 negative triangles
362: dt=0.5631, 15 negative triangles
363: dt=0.5631, 14 negative triangles
364: dt=0.5631, 12 negative triangles
365: dt=0.5631, 14 negative triangles
366: dt=0.5631, 13 negative triangles
367: dt=0.5631, 12 negative triangles
368: dt=0.5631, 12 negative triangles
369: dt=0.5631, 13 negative triangles
370: dt=0.5631, 12 negative triangles
371: dt=0.5631, 12 negative triangles
372: dt=0.5631, 14 negative triangles
373: dt=0.5631, 15 negative triangles
374: dt=0.5350, 14 negative triangles
375: dt=0.5350, 13 negative triangles
376: dt=0.5350, 15 negative triangles
377: dt=0.5350, 15 negative triangles
378: dt=0.5350, 13 negative triangles
379: dt=0.5350, 13 negative triangles
380: dt=0.5350, 11 negative triangles
381: dt=0.5350, 14 negative triangles
382: dt=0.5350, 13 negative triangles
383: dt=0.5350, 10 negative triangles
384: dt=0.5350, 14 negative triangles
385: dt=0.5350, 11 negative triangles
386: dt=0.5350, 11 negative triangles
387: dt=0.5350, 13 negative triangles
388: dt=0.5350, 10 negative triangles
389: dt=0.5350, 14 negative triangles
390: dt=0.5350, 11 negative triangles
391: dt=0.5350, 13 negative triangles
392: dt=0.5350, 12 negative triangles
393: dt=0.5082, 11 negative triangles
394: dt=0.5082, 13 negative triangles
395: dt=0.5082, 11 negative triangles
396: dt=0.5082, 13 negative triangles
397: dt=0.5082, 10 negative triangles
398: dt=0.5082, 13 negative triangles
399: dt=0.5082, 10 negative triangles
400: dt=0.5082, 13 negative triangles
401: dt=0.5082, 12 negative triangles
402: dt=0.5082, 11 negative triangles
403: dt=0.4828, 10 negative triangles
404: dt=0.4828, 11 negative triangles
405: dt=0.4828, 10 negative triangles
406: dt=0.4828, 13 negative triangles
407: dt=0.4828, 11 negative triangles
408: dt=0.4828, 10 negative triangles
409: dt=0.4828, 11 negative triangles
410: dt=0.4828, 10 negative triangles
411: dt=0.4828, 11 negative triangles
412: dt=0.4828, 11 negative triangles
413: dt=0.4587, 11 negative triangles
414: dt=0.4587, 10 negative triangles
415: dt=0.4587, 11 negative triangles
416: dt=0.4587, 13 negative triangles
417: dt=0.4587, 10 negative triangles
418: dt=0.4587, 9 negative triangles
419: dt=0.4587, 9 negative triangles
420: dt=0.4587, 10 negative triangles
421: dt=0.4587, 9 negative triangles
422: dt=0.4587, 9 negative triangles
423: dt=0.4587, 11 negative triangles
424: dt=0.4587, 9 negative triangles
425: dt=0.4587, 9 negative triangles
426: dt=0.4587, 9 negative triangles
427: dt=0.4587, 9 negative triangles
428: dt=0.4587, 7 negative triangles
429: dt=0.4587, 7 negative triangles
430: dt=0.4587, 7 negative triangles
431: dt=0.4587, 7 negative triangles
432: dt=0.4587, 7 negative triangles
433: dt=0.4587, 7 negative triangles
434: dt=0.4587, 8 negative triangles
435: dt=0.4587, 7 negative triangles
436: dt=0.4587, 7 negative triangles
437: dt=0.4587, 7 negative triangles
438: dt=0.4357, 7 negative triangles
439: dt=0.4357, 7 negative triangles
440: dt=0.4357, 8 negative triangles
441: dt=0.4357, 8 negative triangles
442: dt=0.4357, 9 negative triangles
443: dt=0.4357, 7 negative triangles
444: dt=0.4357, 7 negative triangles
445: dt=0.4357, 7 negative triangles
446: dt=0.4357, 7 negative triangles
447: dt=0.4357, 7 negative triangles
448: dt=0.4139, 7 negative triangles
449: dt=0.4139, 7 negative triangles
450: dt=0.4139, 7 negative triangles
451: dt=0.4139, 8 negative triangles
452: dt=0.4139, 7 negative triangles
453: dt=0.4139, 7 negative triangles
454: dt=0.4139, 7 negative triangles
455: dt=0.4139, 7 negative triangles
456: dt=0.4139, 7 negative triangles
457: dt=0.4139, 8 negative triangles
458: dt=0.3932, 8 negative triangles
459: dt=0.3932, 7 negative triangles
460: dt=0.3932, 8 negative triangles
461: dt=0.3932, 8 negative triangles
462: dt=0.3932, 7 negative triangles
463: dt=0.3932, 7 negative triangles
464: dt=0.3932, 7 negative triangles
465: dt=0.3932, 7 negative triangles
466: dt=0.3932, 7 negative triangles
467: dt=0.3932, 6 negative triangles
468: dt=0.3932, 6 negative triangles
469: dt=0.3932, 6 negative triangles
470: dt=0.3932, 6 negative triangles
471: dt=0.3932, 6 negative triangles
472: dt=0.3932, 6 negative triangles
473: dt=0.3932, 6 negative triangles
474: dt=0.3932, 6 negative triangles
475: dt=0.3932, 7 negative triangles
476: dt=0.3932, 6 negative triangles
477: dt=0.3736, 6 negative triangles
478: dt=0.3736, 6 negative triangles
479: dt=0.3736, 6 negative triangles
480: dt=0.3736, 6 negative triangles
481: dt=0.3736, 5 negative triangles
482: dt=0.3736, 5 negative triangles
483: dt=0.3736, 5 negative triangles
484: dt=0.3736, 6 negative triangles
485: dt=0.3736, 5 negative triangles
486: dt=0.3736, 5 negative triangles
487: dt=0.3736, 5 negative triangles
488: dt=0.3736, 4 negative triangles
489: dt=0.3736, 4 negative triangles
490: dt=0.3736, 4 negative triangles
491: dt=0.3736, 4 negative triangles
492: dt=0.3736, 4 negative triangles
493: dt=0.3736, 4 negative triangles
494: dt=0.3736, 5 negative triangles
495: dt=0.3736, 4 negative triangles
496: dt=0.3736, 4 negative triangles
497: dt=0.3736, 4 negative triangles
498: dt=0.3549, 4 negative triangles
499: dt=0.3549, 4 negative triangles
500: dt=0.3549, 4 negative triangles
501: dt=0.3549, 5 negative triangles
502: dt=0.3549, 5 negative triangles
503: dt=0.3549, 6 negative triangles
504: dt=0.3549, 7 negative triangles
505: dt=0.3549, 5 negative triangles
506: dt=0.3549, 5 negative triangles
507: dt=0.3549, 6 negative triangles
508: dt=0.3372, 5 negative triangles
509: dt=0.3372, 4 negative triangles
510: dt=0.3372, 4 negative triangles
511: dt=0.3372, 4 negative triangles
512: dt=0.3372, 4 negative triangles
513: dt=0.3372, 4 negative triangles
514: dt=0.3372, 4 negative triangles
515: dt=0.3372, 4 negative triangles
516: dt=0.3372, 4 negative triangles
517: dt=0.3372, 4 negative triangles
518: dt=0.3203, 4 negative triangles
519: dt=0.3203, 4 negative triangles
520: dt=0.3203, 4 negative triangles
521: dt=0.3203, 4 negative triangles
522: dt=0.3203, 5 negative triangles
523: dt=0.3203, 4 negative triangles
524: dt=0.3203, 4 negative triangles
525: dt=0.3203, 4 negative triangles
526: dt=0.3203, 4 negative triangles
527: dt=0.3203, 4 negative triangles
528: dt=0.3043, 4 negative triangles
529: dt=0.3043, 4 negative triangles
530: dt=0.3043, 4 negative triangles
531: dt=0.3043, 4 negative triangles
532: dt=0.3043, 4 negative triangles
533: dt=0.3043, 4 negative triangles
534: dt=0.3043, 4 negative triangles
535: dt=0.3043, 4 negative triangles
536: dt=0.3043, 3 negative triangles
537: dt=0.3043, 3 negative triangles
538: dt=0.3043, 3 negative triangles
539: dt=0.3043, 4 negative triangles
540: dt=0.3043, 3 negative triangles
541: dt=0.3043, 3 negative triangles
542: dt=0.3043, 3 negative triangles
543: dt=0.3043, 3 negative triangles
544: dt=0.3043, 3 negative triangles
545: dt=0.3043, 3 negative triangles
546: dt=0.2891, 3 negative triangles
547: dt=0.2891, 3 negative triangles
548: dt=0.2891, 3 negative triangles
549: dt=0.2891, 3 negative triangles
550: dt=0.2891, 2 negative triangles
551: dt=0.2891, 2 negative triangles
552: dt=0.2891, 2 negative triangles
553: dt=0.2891, 2 negative triangles
554: dt=0.2891, 2 negative triangles
555: dt=0.2891, 2 negative triangles
556: dt=0.2891, 1 negative triangles
557: dt=0.2891, 1 negative triangles
558: dt=0.2891, 1 negative triangles
559: dt=0.2891, 1 negative triangles
560: dt=0.2891, 1 negative triangles
561: dt=0.2891, 1 negative triangles
562: dt=0.2891, 2 negative triangles
563: dt=0.2891, 1 negative triangles
564: dt=0.2891, 1 negative triangles
565: dt=0.2891, 1 negative triangles
566: dt=0.2746, 1 negative triangles
567: dt=0.2746, 1 negative triangles
568: dt=0.2746, 1 negative triangles
569: dt=0.2746, 1 negative triangles
570: dt=0.2746, 1 negative triangles
571: dt=0.2746, 1 negative triangles
572: dt=0.2746, 1 negative triangles
573: dt=0.2746, 1 negative triangles
574: dt=0.2746, 1 negative triangles
575: dt=0.2746, 1 negative triangles
576: dt=0.2609, 1 negative triangles
577: dt=0.2609, 1 negative triangles
578: dt=0.2609, 1 negative triangles
579: dt=0.2609, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.28 hours
mris_register utimesec    4781.612084
mris_register stimesec    4.023388
mris_register ru_maxrss   261864
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   37847
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10040
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    398217
mris_register ru_nivcsw   237851
FSRUNTIME@ mris_register  1.2827 hours 1 threads
PIDs (16948 16951) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sat Oct  7 23:40:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sat Oct  7 23:40:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

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

Waiting for PID 20550 of (20550 20553) to complete...
Waiting for PID 20553 of (20550 20553) 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 (20550 20553) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sat Oct  7 23:40:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 Sat Oct  7 23:40:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 20595 of (20595 20598) to complete...
Waiting for PID 20598 of (20595 20598) 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 (20595 20598) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sat Oct  7 23:40:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 Sat Oct  7 23:40:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 20641 of (20641 20644) to complete...
Waiting for PID 20644 of (20641 20644) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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...
1025 labels changed using aseg
relabeling using gibbs priors...
000:   3102 changed, 137434 examined...
001:    723 changed, 12957 examined...
002:    192 changed, 4027 examined...
003:     66 changed, 1136 examined...
004:     25 changed, 378 examined...
005:     15 changed, 138 examined...
006:      7 changed, 78 examined...
007:      0 changed, 46 examined...
263 labels changed using aseg
000: 118 total segments, 74 labels (390 vertices) changed
001: 43 total segments, 2 labels (5 vertices) changed
002: 41 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1565 vertices marked for relabeling...
1565 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 15 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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...
954 labels changed using aseg
relabeling using gibbs priors...
000:   2782 changed, 140379 examined...
001:    630 changed, 11948 examined...
002:    136 changed, 3502 examined...
003:     27 changed, 844 examined...
004:     10 changed, 172 examined...
005:      2 changed, 61 examined...
006:      2 changed, 16 examined...
007:      2 changed, 11 examined...
008:      0 changed, 12 examined...
192 labels changed using aseg
000: 93 total segments, 56 labels (287 vertices) changed
001: 38 total segments, 1 labels (1 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1647 vertices marked for relabeling...
1647 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 15 seconds.
PIDs (20641 20644) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sat Oct  7 23:40:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sat Oct  7 23:40:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 rh 

Waiting for PID 20700 of (20700 20703) to complete...
Waiting for PID 20703 of (20700 20703) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
50338 bright wm thresholded.
2140 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.orig...
computing class statistics...
border white:    271136 voxels (1.62%)
border gray      285350 voxels (1.70%)
WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0]
GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70)
setting MAX_BORDER_WHITE to 110.1 (was 105)
setting MIN_BORDER_WHITE to 66.0 (was 85)
setting MAX_CSF to 43.7 (was 40)
setting MAX_GRAY to 91.9 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 54.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.6 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-8.7,    GM=66+-7.8
mean inside = 91.4, mean outside = 71.3
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 +- 0.26 (0.04-->4.36) (max @ vno 31249 --> 33498)
face area 0.32 +- 0.16 (0.00-->4.95)
mean absolute distance = 0.68 +- 0.95
3046 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 144 points - only 0.00% unknown
deleting segment 4 with 25 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
mean border=77.7, 99 (96) missing vertices, mean dist 0.3 [1.4 (%13.8)->0.6 (%86.2))]
%57 local maxima, %39 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 +- 0.26 (0.05-->4.36) (max @ vno 31249 --> 33498)
face area 0.32 +- 0.16 (0.00-->4.67)
mean absolute distance = 0.39 +- 0.67
3940 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2317248.0, rms=8.009
001: dt: 0.5000, sse=1207218.9, rms=4.673 (41.656%)
002: dt: 0.5000, sse=988920.8, rms=3.714 (20.508%)
rms = 3.74, time step reduction 1 of 3 to 0.250...
003: dt: 0.2500, sse=842465.0, rms=2.840 (23.550%)
004: dt: 0.2500, sse=783684.7, rms=2.387 (15.928%)
005: dt: 0.2500, sse=756921.8, rms=2.166 (9.252%)
006: dt: 0.2500, sse=746998.6, rms=2.079 (4.032%)
007: dt: 0.2500, sse=741460.3, rms=2.023 (2.716%)
rms = 1.98, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=738319.6, rms=1.985 (1.862%)
009: dt: 0.1250, sse=730242.0, rms=1.903 (4.132%)
rms = 1.89, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=731588.4, rms=1.893 (0.520%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 21 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 70 points - only 0.00% unknown
deleting segment 3 with 18 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 19 points - only 0.00% unknown
mean border=80.8, 65 (24) missing vertices, mean dist -0.2 [0.5 (%67.4)->0.2 (%32.6))]
%70 local maxima, %25 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 (0.05-->4.29) (max @ vno 31249 --> 33498)
face area 0.34 +- 0.17 (0.00-->4.97)
mean absolute distance = 0.29 +- 0.43
4006 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1181128.1, rms=4.435
011: dt: 0.5000, sse=934197.2, rms=3.209 (27.644%)
rms = 3.51, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=806668.9, rms=2.331 (27.349%)
013: dt: 0.2500, sse=756890.9, rms=1.867 (19.925%)
014: dt: 0.2500, sse=743499.5, rms=1.702 (8.831%)
rms = 1.66, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=738776.8, rms=1.660 (2.484%)
016: dt: 0.1250, sse=729700.2, rms=1.560 (5.978%)
rms = 1.56, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=729772.9, rms=1.559 (0.084%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 24 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
deleting segment 2 with 78 points - only 0.00% unknown
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 19 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 27 points - only 0.00% unknown
mean border=83.4, 67 (19) missing vertices, mean dist -0.2 [0.3 (%68.2)->0.2 (%31.8))]
%83 local maxima, %12 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-->4.29) (max @ vno 31249 --> 33498)
face area 0.33 +- 0.17 (0.00-->4.81)
mean absolute distance = 0.24 +- 0.35
3713 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=962354.9, rms=3.457
018: dt: 0.5000, sse=931446.5, rms=3.230 (6.586%)
rms = 3.50, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=778940.1, rms=2.188 (32.257%)
020: dt: 0.2500, sse=730164.4, rms=1.731 (20.869%)
021: dt: 0.2500, sse=719627.9, rms=1.600 (7.604%)
rms = 1.59, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=718016.0, rms=1.589 (0.689%)
023: dt: 0.1250, sse=706478.1, rms=1.453 (8.542%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=706194.9, rms=1.451 (0.137%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 27 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 97 points - only 0.00% unknown
deleting segment 3 with 15 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 23 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
deleting segment 7 with 27 points - only 0.00% unknown
mean border=84.3, 75 (12) missing vertices, mean dist -0.1 [0.3 (%55.6)->0.2 (%44.4))]
%87 local maxima, % 8 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-6.0.0/0051362/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=733117.8, rms=1.866
rms = 2.23, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=684842.8, rms=1.289 (30.930%)
026: dt: 0.2500, sse=671365.1, rms=1.053 (18.265%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
rms = 1.05, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=669013.6, rms=1.048 (0.539%)
positioning took 0.5 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 7623 vertices
erasing segment 1 (vno[0] = 53747)
erasing segment 2 (vno[0] = 87474)
erasing segment 3 (vno[0] = 88117)
erasing segment 4 (vno[0] = 89101)
erasing segment 5 (vno[0] = 100985)
erasing segment 6 (vno[0] = 101104)
erasing segment 7 (vno[0] = 102956)
erasing segment 8 (vno[0] = 103883)
erasing segment 9 (vno[0] = 103989)
erasing segment 10 (vno[0] = 136981)
erasing segment 11 (vno[0] = 136984)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.area
vertex spacing 0.88 +- 0.27 (0.04-->4.26) (max @ vno 31249 --> 33498)
face area 0.32 +- 0.17 (0.00-->4.80)
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=52.4, 121 (121) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.5 (%100.0))]
%15 local maxima, %52 large gradients and %28 min vals, 146 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=28055384.0, rms=32.374
001: dt: 0.0500, sse=24604220.0, rms=30.268 (6.505%)
002: dt: 0.0500, sse=22135340.0, rms=28.666 (5.292%)
003: dt: 0.0500, sse=20263342.0, rms=27.389 (4.455%)
004: dt: 0.0500, sse=18772902.0, rms=26.328 (3.874%)
005: dt: 0.0500, sse=17538790.0, rms=25.416 (3.464%)
006: dt: 0.0500, sse=16485822.0, rms=24.611 (3.167%)
007: dt: 0.0500, sse=15568580.0, rms=23.887 (2.939%)
008: dt: 0.0500, sse=14757121.0, rms=23.229 (2.758%)
009: dt: 0.0500, sse=14029563.0, rms=22.622 (2.613%)
010: dt: 0.0500, sse=13370368.0, rms=22.057 (2.495%)
positioning took 1.0 minutes
mean border=52.3, 101 (58) missing vertices, mean dist 1.4 [0.1 (%0.1)->1.9 (%99.9))]
%16 local maxima, %52 large gradients and %27 min vals, 139 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=14042560.0, rms=22.638
011: dt: 0.0500, sse=13435564.0, rms=22.119 (2.291%)
012: dt: 0.0500, sse=12877431.0, rms=21.631 (2.206%)
013: dt: 0.0500, sse=12361959.0, rms=21.170 (2.130%)
014: dt: 0.0500, sse=11884078.0, rms=20.734 (2.061%)
015: dt: 0.0500, sse=11439633.0, rms=20.320 (1.998%)
016: dt: 0.0500, sse=11025009.0, rms=19.926 (1.940%)
017: dt: 0.0500, sse=10636790.0, rms=19.549 (1.889%)
018: dt: 0.0500, sse=10272942.0, rms=19.190 (1.839%)
019: dt: 0.0500, sse=9930412.0, rms=18.845 (1.797%)
020: dt: 0.0500, sse=9606860.0, rms=18.513 (1.760%)
positioning took 1.0 minutes
mean border=52.2, 125 (45) missing vertices, mean dist 1.1 [0.1 (%1.0)->1.6 (%99.0))]
%16 local maxima, %52 large gradients and %27 min vals, 132 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=9686495.0, rms=18.602
021: dt: 0.0500, sse=9371891.0, rms=18.276 (1.756%)
022: dt: 0.0500, sse=9073899.0, rms=17.961 (1.723%)
023: dt: 0.0500, sse=8788424.0, rms=17.654 (1.710%)
024: dt: 0.0500, sse=8516461.0, rms=17.356 (1.686%)
025: dt: 0.0500, sse=8256819.0, rms=17.067 (1.665%)
026: dt: 0.0500, sse=8008072.0, rms=16.785 (1.650%)
027: dt: 0.0500, sse=7767634.0, rms=16.508 (1.649%)
028: dt: 0.0500, sse=7532790.5, rms=16.233 (1.666%)
029: dt: 0.0500, sse=7303655.5, rms=15.960 (1.681%)
030: dt: 0.0500, sse=7080246.0, rms=15.690 (1.696%)
positioning took 1.0 minutes
mean border=52.0, 194 (40) missing vertices, mean dist 0.9 [0.1 (%7.3)->1.4 (%92.7))]
%16 local maxima, %52 large gradients and %27 min vals, 101 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=7189676.0, rms=15.822
031: dt: 0.5000, sse=5544812.0, rms=13.688 (13.489%)
032: dt: 0.5000, sse=4331760.0, rms=11.864 (13.326%)
033: dt: 0.5000, sse=3425667.5, rms=10.299 (13.190%)
034: dt: 0.5000, sse=2761196.8, rms=8.969 (12.916%)
035: dt: 0.5000, sse=2311679.2, rms=7.950 (11.359%)
036: dt: 0.5000, sse=1984944.0, rms=7.109 (10.581%)
037: dt: 0.5000, sse=1772843.2, rms=6.512 (8.390%)
038: dt: 0.5000, sse=1630711.0, rms=6.071 (6.774%)
039: dt: 0.5000, sse=1552436.5, rms=5.820 (4.130%)
040: dt: 0.5000, sse=1497115.4, rms=5.627 (3.325%)
041: dt: 0.5000, sse=1468563.6, rms=5.531 (1.704%)
042: dt: 0.5000, sse=1441257.8, rms=5.428 (1.855%)
rms = 5.40, time step reduction 1 of 3 to 0.250...
043: dt: 0.5000, sse=1433032.0, rms=5.401 (0.503%)
044: dt: 0.2500, sse=1248631.9, rms=4.640 (14.085%)
045: dt: 0.2500, sse=1189336.5, rms=4.390 (5.397%)
rms = 4.40, time step reduction 2 of 3 to 0.125...
046: dt: 0.1250, sse=1170452.1, rms=4.302 (2.010%)
047: dt: 0.1250, sse=1146087.1, rms=4.183 (2.759%)
rms = 4.17, time step reduction 3 of 3 to 0.062...
048: dt: 0.1250, sse=1143226.6, rms=4.167 (0.392%)
positioning took 2.3 minutes
mean border=50.3, 1715 (21) missing vertices, mean dist 0.1 [0.2 (%45.8)->0.5 (%54.2))]
%29 local maxima, %41 large gradients and %24 min vals, 75 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=1475723.0, rms=4.932
049: dt: 0.5000, sse=1446556.1, rms=4.830 (2.063%)
050: dt: 0.5000, sse=1417588.8, rms=4.753 (1.584%)
rms = 4.89, time step reduction 1 of 3 to 0.250...
051: dt: 0.2500, sse=1212061.9, rms=3.775 (20.578%)
052: dt: 0.2500, sse=1160343.6, rms=3.478 (7.879%)
rms = 3.46, time step reduction 2 of 3 to 0.125...
053: dt: 0.2500, sse=1157887.4, rms=3.463 (0.437%)
054: dt: 0.1250, sse=1104117.4, rms=3.133 (9.516%)
055: dt: 0.1250, sse=1095801.1, rms=3.082 (1.641%)
rms = 3.08, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1095614.5, rms=3.080 (0.041%)
positioning took 1.2 minutes
mean border=49.2, 1764 (18) missing vertices, mean dist 0.1 [0.1 (%47.3)->0.3 (%52.7))]
%45 local maxima, %26 large gradients and %23 min vals, 54 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=1183838.0, rms=3.583
rms = 4.40, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1120580.6, rms=3.218 (10.182%)
058: dt: 0.2500, sse=1109509.1, rms=3.156 (1.930%)
rms = 3.18, time step reduction 2 of 3 to 0.125...
059: dt: 0.1250, sse=1100569.2, rms=3.098 (1.842%)
060: dt: 0.1250, sse=1087803.5, rms=3.018 (2.602%)
rms = 3.00, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1084016.1, rms=2.995 (0.740%)
positioning took 0.9 minutes
mean border=48.5, 3082 (17) missing vertices, mean dist 0.0 [0.2 (%49.4)->0.2 (%50.6))]
%49 local maxima, %21 large gradients and %23 min vals, 58 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-6.0.0/0051362/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1112475.9, rms=3.175
rms = 3.99, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1086285.2, rms=3.008 (5.247%)
rms = 2.97, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1077989.8, rms=2.974 (1.148%)
064: dt: 0.1250, sse=1064873.2, rms=2.881 (3.111%)
rms = 2.85, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1059108.0, rms=2.848 (1.148%)
positioning took 0.7 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.area.pial
vertex spacing 0.97 +- 0.42 (0.07-->5.63) (max @ vno 94052 --> 92948)
face area 0.38 +- 0.29 (0.00-->6.39)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 137434 vertices processed
25000 of 137434 vertices processed
50000 of 137434 vertices processed
75000 of 137434 vertices processed
100000 of 137434 vertices processed
125000 of 137434 vertices processed
0 of 137434 vertices processed
25000 of 137434 vertices processed
50000 of 137434 vertices processed
75000 of 137434 vertices processed
100000 of 137434 vertices processed
125000 of 137434 vertices processed
thickness calculation complete, 69:267 truncations.
32657 vertices at 0 distance
105432 vertices at 1 distance
83777 vertices at 2 distance
29332 vertices at 3 distance
7719 vertices at 4 distance
1971 vertices at 5 distance
587 vertices at 6 distance
210 vertices at 7 distance
71 vertices at 8 distance
39 vertices at 9 distance
26 vertices at 10 distance
11 vertices at 11 distance
11 vertices at 12 distance
8 vertices at 13 distance
5 vertices at 14 distance
1 vertices at 15 distance
4 vertices at 16 distance
0 vertices at 17 distance
0 vertices at 18 distance
3 vertices at 19 distance
6 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.thickness
positioning took 15.1 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
50338 bright wm thresholded.
2140 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.orig...
computing class statistics...
border white:    271136 voxels (1.62%)
border gray      285350 voxels (1.70%)
WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0]
GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 57.9 (was 70)
setting MAX_BORDER_WHITE to 109.1 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 46.7 (was 40)
setting MAX_GRAY to 90.9 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 57.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-7.0,    GM=69+-7.8
mean inside = 91.4, mean outside = 72.3
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 0.87 +- 0.26 (0.04-->3.81) (max @ vno 76035 --> 81853)
face area 0.32 +- 0.16 (0.00-->3.08)
mean absolute distance = 0.72 +- 0.98
3589 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 3 with 50 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 42 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
mean border=80.0, 97 (97) missing vertices, mean dist 0.3 [1.5 (%14.1)->0.6 (%85.9))]
%53 local maxima, %43 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 (0.08-->3.48) (max @ vno 125094 --> 125095)
face area 0.32 +- 0.16 (0.00-->3.28)
mean absolute distance = 0.41 +- 0.69
4196 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2257621.8, rms=7.757
001: dt: 0.5000, sse=1202501.1, rms=4.581 (40.942%)
002: dt: 0.5000, sse=959514.8, rms=3.489 (23.831%)
rms = 3.47, time step reduction 1 of 3 to 0.250...
003: dt: 0.5000, sse=962427.4, rms=3.465 (0.683%)
004: dt: 0.2500, sse=769587.2, rms=2.236 (35.485%)
005: dt: 0.2500, sse=748733.4, rms=1.948 (12.867%)
006: dt: 0.2500, sse=771115.4, rms=1.893 (2.828%)
007: dt: 0.2500, sse=726928.8, rms=1.835 (3.061%)
rms = 1.82, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=726530.8, rms=1.824 (0.598%)
009: dt: 0.1250, sse=720156.5, rms=1.749 (4.121%)
rms = 1.74, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=720314.9, rms=1.744 (0.252%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 1 with 39 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 5 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=83.1, 36 (15) missing vertices, mean dist -0.3 [0.5 (%67.9)->0.2 (%32.1))]
%69 local maxima, %26 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 0.87 +- 0.26 (0.08-->3.56) (max @ vno 90286 --> 91306)
face area 0.33 +- 0.17 (0.00-->3.62)
mean absolute distance = 0.29 +- 0.43
3720 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1206303.4, rms=4.476
011: dt: 0.5000, sse=940498.1, rms=3.184 (28.857%)
rms = 3.27, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=827395.2, rms=2.430 (23.698%)
013: dt: 0.2500, sse=764910.9, rms=1.887 (22.321%)
014: dt: 0.2500, sse=743948.0, rms=1.659 (12.088%)
015: dt: 0.2500, sse=737084.8, rms=1.578 (4.908%)
rms = 1.55, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=735605.4, rms=1.553 (1.597%)
017: dt: 0.1250, sse=728928.6, rms=1.472 (5.176%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=728401.2, rms=1.470 (0.140%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 41 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 8 points - only 0.00% unknown
mean border=85.5, 37 (6) missing vertices, mean dist -0.2 [0.3 (%68.0)->0.2 (%32.0))]
%82 local maxima, %14 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 0.87 +- 0.26 (0.05-->3.71) (max @ vno 90286 --> 91306)
face area 0.32 +- 0.16 (0.00-->3.66)
mean absolute distance = 0.24 +- 0.35
3960 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=947343.6, rms=3.323
019: dt: 0.5000, sse=885537.2, rms=2.876 (13.442%)
rms = 3.20, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=762906.6, rms=1.985 (30.981%)
021: dt: 0.2500, sse=726605.7, rms=1.571 (20.841%)
022: dt: 0.2500, sse=712995.9, rms=1.477 (5.977%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=710802.4, rms=1.465 (0.854%)
024: dt: 0.1250, sse=703615.1, rms=1.362 (7.002%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=704007.9, rms=1.362 (0.029%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 49 points - only 0.00% unknown
deleting segment 1 with 15 points - only 0.00% unknown
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
mean border=86.3, 60 (4) missing vertices, mean dist -0.1 [0.3 (%54.7)->0.2 (%45.3))]
%86 local maxima, %10 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-6.0.0/0051362/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=727711.0, rms=1.757
rms = 1.92, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=684951.9, rms=1.241 (29.346%)
027: dt: 0.2500, sse=678625.6, rms=1.000 (19.451%)
rms = 1.02, time step reduction 2 of 3 to 0.125...
rms = 0.99, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=672004.1, rms=0.995 (0.497%)
positioning took 0.5 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7520 vertices
erasing segment 1 (vno[0] = 92764)
erasing segment 2 (vno[0] = 101310)
erasing segment 3 (vno[0] = 101335)
erasing segment 4 (vno[0] = 102389)
erasing segment 5 (vno[0] = 105428)
erasing segment 6 (vno[0] = 108646)
erasing segment 7 (vno[0] = 110616)
erasing segment 8 (vno[0] = 110620)
erasing segment 9 (vno[0] = 110634)
erasing segment 10 (vno[0] = 115603)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.area
vertex spacing 0.87 +- 0.26 (0.04-->3.81) (max @ vno 76035 --> 81853)
face area 0.32 +- 0.16 (0.00-->3.64)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=55.1, 95 (95) missing vertices, mean dist 1.8 [0.9 (%0.0)->2.6 (%100.0))]
%19 local maxima, %50 large gradients and %27 min vals, 142 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=27662052.0, rms=31.772
001: dt: 0.0500, sse=24292656.0, rms=29.725 (6.441%)
002: dt: 0.0500, sse=21921022.0, rms=28.196 (5.146%)
003: dt: 0.0500, sse=20127574.0, rms=26.981 (4.307%)
004: dt: 0.0500, sse=18702730.0, rms=25.976 (3.726%)
005: dt: 0.0500, sse=17523722.0, rms=25.113 (3.320%)
006: dt: 0.0500, sse=16519805.0, rms=24.355 (3.020%)
007: dt: 0.0500, sse=15645714.0, rms=23.675 (2.793%)
008: dt: 0.0500, sse=14871352.0, rms=23.055 (2.616%)
009: dt: 0.0500, sse=14175755.0, rms=22.484 (2.476%)
010: dt: 0.0500, sse=13545235.0, rms=21.954 (2.359%)
positioning took 1.0 minutes
mean border=55.0, 46 (29) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.0 (%100.0))]
%20 local maxima, %50 large gradients and %26 min vals, 126 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=14265917.0, rms=22.562
011: dt: 0.0500, sse=13686088.0, rms=22.076 (2.151%)
012: dt: 0.0500, sse=13152846.0, rms=21.620 (2.066%)
013: dt: 0.0500, sse=12660011.0, rms=21.190 (1.990%)
014: dt: 0.0500, sse=12202967.0, rms=20.783 (1.921%)
015: dt: 0.0500, sse=11778816.0, rms=20.398 (1.853%)
016: dt: 0.0500, sse=11382946.0, rms=20.032 (1.795%)
017: dt: 0.0500, sse=11012960.0, rms=19.684 (1.739%)
018: dt: 0.0500, sse=10665669.0, rms=19.351 (1.690%)
019: dt: 0.0500, sse=10339025.0, rms=19.033 (1.645%)
020: dt: 0.0500, sse=10030674.0, rms=18.727 (1.605%)
positioning took 1.0 minutes
mean border=54.8, 57 (23) missing vertices, mean dist 1.2 [0.1 (%1.1)->1.6 (%98.9))]
%20 local maxima, %50 large gradients and %26 min vals, 131 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=10129137.0, rms=18.831
021: dt: 0.0500, sse=9828544.0, rms=18.530 (1.599%)
022: dt: 0.0500, sse=9543594.0, rms=18.240 (1.565%)
023: dt: 0.0500, sse=9270789.0, rms=17.958 (1.546%)
024: dt: 0.0500, sse=9010455.0, rms=17.684 (1.523%)
025: dt: 0.0500, sse=8761519.0, rms=17.419 (1.501%)
026: dt: 0.0500, sse=8521556.0, rms=17.159 (1.492%)
027: dt: 0.0500, sse=8288179.0, rms=16.902 (1.496%)
028: dt: 0.0500, sse=8059451.0, rms=16.647 (1.511%)
029: dt: 0.0500, sse=7834830.5, rms=16.392 (1.530%)
030: dt: 0.0500, sse=7613388.5, rms=16.137 (1.556%)
positioning took 1.0 minutes
mean border=54.7, 93 (18) missing vertices, mean dist 0.9 [0.1 (%7.5)->1.4 (%92.5))]
%20 local maxima, %50 large gradients and %25 min vals, 119 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=7719835.5, rms=16.259
031: dt: 0.5000, sse=6042261.5, rms=14.198 (12.673%)
032: dt: 0.5000, sse=4712188.5, rms=12.315 (13.262%)
033: dt: 0.5000, sse=3666560.2, rms=10.609 (13.857%)
034: dt: 0.5000, sse=2888434.2, rms=9.125 (13.985%)
035: dt: 0.5000, sse=2371557.2, rms=7.993 (12.402%)
036: dt: 0.5000, sse=2016408.0, rms=7.104 (11.125%)
037: dt: 0.5000, sse=1803989.9, rms=6.520 (8.223%)
038: dt: 0.5000, sse=1654930.1, rms=6.069 (6.916%)
039: dt: 0.5000, sse=1577672.4, rms=5.826 (4.006%)
040: dt: 0.5000, sse=1510126.4, rms=5.597 (3.923%)
041: dt: 0.5000, sse=1482742.4, rms=5.505 (1.650%)
042: dt: 0.5000, sse=1445740.5, rms=5.372 (2.415%)
rms = 5.37, time step reduction 1 of 3 to 0.250...
043: dt: 0.5000, sse=1443392.0, rms=5.365 (0.126%)
044: dt: 0.2500, sse=1239160.5, rms=4.535 (15.480%)
045: dt: 0.2500, sse=1181597.1, rms=4.291 (5.376%)
rms = 4.30, time step reduction 2 of 3 to 0.125...
046: dt: 0.1250, sse=1160428.4, rms=4.192 (2.303%)
047: dt: 0.1250, sse=1132128.1, rms=4.054 (3.287%)
rms = 4.03, time step reduction 3 of 3 to 0.062...
048: dt: 0.1250, sse=1127881.6, rms=4.032 (0.552%)
positioning took 2.3 minutes
mean border=52.9, 1453 (7) missing vertices, mean dist 0.1 [0.2 (%42.8)->0.4 (%57.2))]
%34 local maxima, %38 large gradients and %23 min vals, 66 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=1504454.8, rms=4.989
049: dt: 0.5000, sse=1478473.9, rms=4.903 (1.722%)
050: dt: 0.5000, sse=1422375.5, rms=4.719 (3.747%)
rms = 4.89, time step reduction 1 of 3 to 0.250...
051: dt: 0.2500, sse=1206137.0, rms=3.706 (21.479%)
052: dt: 0.2500, sse=1149790.5, rms=3.385 (8.646%)
rms = 3.36, time step reduction 2 of 3 to 0.125...
053: dt: 0.2500, sse=1145203.4, rms=3.359 (0.784%)
054: dt: 0.1250, sse=1087957.0, rms=3.004 (10.570%)
055: dt: 0.1250, sse=1078533.0, rms=2.944 (1.987%)
rms = 2.93, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1076756.9, rms=2.933 (0.370%)
positioning took 1.2 minutes
mean border=51.6, 1668 (7) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.3 (%55.5))]
%49 local maxima, %23 large gradients and %22 min vals, 50 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=1177186.4, rms=3.523
rms = 4.37, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1108495.4, rms=3.127 (11.240%)
058: dt: 0.2500, sse=1093491.8, rms=3.038 (2.841%)
rms = 3.05, time step reduction 2 of 3 to 0.125...
059: dt: 0.1250, sse=1084917.4, rms=2.981 (1.857%)
060: dt: 0.1250, sse=1072459.1, rms=2.902 (2.662%)
rms = 2.87, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1067705.2, rms=2.873 (1.000%)
positioning took 0.9 minutes
mean border=50.9, 2958 (7) missing vertices, mean dist 0.0 [0.2 (%47.6)->0.2 (%52.4))]
%53 local maxima, %19 large gradients and %22 min vals, 52 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-6.0.0/0051362/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1095686.0, rms=3.055
rms = 3.80, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1069292.0, rms=2.884 (5.605%)
rms = 2.84, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1059952.1, rms=2.840 (1.514%)
064: dt: 0.1250, sse=1047086.4, rms=2.748 (3.251%)
rms = 2.72, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1041974.0, rms=2.718 (1.106%)
positioning took 0.7 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.area.pial
vertex spacing 0.96 +- 0.40 (0.07-->5.59) (max @ vno 99312 --> 98230)
face area 0.37 +- 0.28 (0.00-->4.18)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 140379 vertices processed
25000 of 140379 vertices processed
50000 of 140379 vertices processed
75000 of 140379 vertices processed
100000 of 140379 vertices processed
125000 of 140379 vertices processed
0 of 140379 vertices processed
25000 of 140379 vertices processed
50000 of 140379 vertices processed
75000 of 140379 vertices processed
100000 of 140379 vertices processed
125000 of 140379 vertices processed
thickness calculation complete, 83:339 truncations.
33728 vertices at 0 distance
107234 vertices at 1 distance
84835 vertices at 2 distance
30392 vertices at 3 distance
8329 vertices at 4 distance
2269 vertices at 5 distance
688 vertices at 6 distance
205 vertices at 7 distance
74 vertices at 8 distance
40 vertices at 9 distance
16 vertices at 10 distance
20 vertices at 11 distance
18 vertices at 12 distance
15 vertices at 13 distance
9 vertices at 14 distance
4 vertices at 15 distance
6 vertices at 16 distance
8 vertices at 17 distance
1 vertices at 18 distance
1 vertices at 19 distance
0 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.thickness
positioning took 15.3 minutes
PIDs (20700 20703) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sat Oct  7 23:56:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label
Total face volume 217672
Total vertex volume 214840 (mask=0)
#@# 0051362 lh 214840
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sat Oct  7 23:56:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label
Total face volume 223356
Total vertex volume 220256 (mask=0)
#@# 0051362 rh 220256
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sat Oct  7 23:56:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 

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 = 115
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/ribbon.mgz
mris_volmask took 16.48 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 00:12:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 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 0051362 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 00:12:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 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 0051362 rh pial 

Waiting for PID 22425 of (22425 22428 22431 22434) to complete...
Waiting for PID 22428 of (22425 22428 22431 22434) to complete...
Waiting for PID 22431 of (22425 22428 22431 22434) to complete...
Waiting for PID 22434 of (22425 22428 22431 22434) 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 0051362 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672
Total vertex volume 214840 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1329    909   1932  2.260 0.341     0.112     0.024        9     1.4  bankssts
  845    552   1385  2.190 0.709     0.138     0.030       13     0.9  caudalanteriorcingulate
 3441   2299   5801  2.331 0.413     0.124     0.033       34     4.5  caudalmiddlefrontal
 3049   1853   3327  1.720 0.396     0.141     0.042       42     5.3  cuneus
  609    418   1722  2.991 1.000     0.127     0.032        5     0.9  entorhinal
 4121   2721   9034  2.747 0.604     0.133     0.046       65     7.2  fusiform
 6010   3919   9580  2.276 0.418     0.130     0.034       80     8.0  inferiorparietal
 5024   3324  10421  2.598 0.638     0.143     0.050       90    10.2  inferiortemporal
 1560    989   2536  2.315 0.807     0.142     0.045       31     2.4  isthmuscingulate
 7455   4645  10315  2.055 0.517     0.139     0.040      106    11.3  lateraloccipital
 3782   2457   6707  2.517 0.565     0.134     0.046       54     7.1  lateralorbitofrontal
 5548   3606   7261  1.961 0.625     0.147     0.048       89    10.4  lingual
 2980   1989   4783  2.235 0.661     0.130     0.037       51     4.3  medialorbitofrontal
 4603   3113  10047  2.725 0.568     0.128     0.034       61     6.5  middletemporal
  946    638   2103  2.792 0.646     0.106     0.025        7     0.9  parahippocampal
 2131   1282   3007  2.264 0.462     0.103     0.030       16     2.5  paracentral
 2383   1548   4046  2.367 0.391     0.119     0.031       29     2.7  parsopercularis
 1153    725   2239  2.418 0.472     0.154     0.044       23     1.8  parsorbitalis
 2106   1351   3277  2.198 0.410     0.128     0.031       30     2.6  parstriangularis
 2429   1639   2527  1.759 0.473     0.139     0.044       28     4.4  pericalcarine
 7172   4461   9543  1.954 0.501     0.119     0.034       87     9.6  postcentral
 1731   1127   2803  2.240 0.730     0.139     0.037       30     2.7  posteriorcingulate
 7505   4555  11238  2.311 0.417     0.114     0.045       90    12.2  precentral
 5924   3885   9405  2.279 0.507     0.132     0.037       81     8.9  precuneus
 1065    663   1909  2.783 0.625     0.122     0.032       16     1.2  rostralanteriorcingulate
 9757   6459  15940  2.228 0.422     0.143     0.038      153    15.0  rostralmiddlefrontal
10002   6650  18998  2.513 0.469     0.130     0.037      117    13.8  superiorfrontal
 8142   5192  11965  2.131 0.384     0.129     0.032      114    10.3  superiorparietal
 5856   3836  11907  2.691 0.563     0.113     0.031       60     6.9  superiortemporal
 5253   3453   9104  2.381 0.468     0.138     0.039       76     8.0  supramarginal
  393    261    901  2.550 0.325     0.146     0.042        7     0.5  frontalpole
  695    456   2120  3.424 0.696     0.165     0.068       14     2.1  temporalpole
  740    404    900  2.130 0.356     0.116     0.044       10     1.0  transversetemporal
 3535   2293   6058  2.604 0.718     0.138     0.060       91     9.7  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 0051362 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672
Total vertex volume 214840 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1329    837   1932  2.260 0.341     0.124     0.034       20     1.9  bankssts
  845    688   1385  2.190 0.709     0.154     0.038       18     1.3  caudalanteriorcingulate
 3441   2640   5801  2.331 0.413     0.126     0.029       40     4.3  caudalmiddlefrontal
 3049   2116   3327  1.720 0.396     0.129     0.034       47     4.7  cuneus
  609    669   1722  2.991 1.000     0.180     0.048        8     1.4  entorhinal
 4121   3711   9034  2.747 0.604     0.169     0.048       89     8.9  fusiform
 6010   4464   9580  2.276 0.418     0.139     0.033       94     9.0  inferiorparietal
 5024   4447  10421  2.598 0.638     0.169     0.045      101    10.1  inferiortemporal
 1560   1221   2536  2.315 0.807     0.156     0.049       36     2.7  isthmuscingulate
 7455   5456  10315  2.055 0.517     0.131     0.035      124    11.3  lateraloccipital
 3782   2754   6707  2.517 0.565     0.147     0.044       67     7.1  lateralorbitofrontal
 5548   4029   7261  1.961 0.625     0.138     0.041       97     9.9  lingual
 2980   2300   4783  2.235 0.661     0.142     0.036       44     4.7  medialorbitofrontal
 4603   4083  10047  2.725 0.568     0.146     0.033       54     7.0  middletemporal
  946    903   2103  2.792 0.646     0.150     0.034        8     1.7  parahippocampal
 2131   1408   3007  2.264 0.462     0.115     0.028       20     2.6  paracentral
 2383   1878   4046  2.367 0.391     0.148     0.032       30     3.5  parsopercularis
 1153   1074   2239  2.418 0.472     0.167     0.040       15     2.0  parsorbitalis
 2106   1586   3277  2.198 0.410     0.149     0.035       31     3.1  parstriangularis
 2429   1302   2527  1.759 0.473     0.101     0.029       32     2.5  pericalcarine
 7172   5282   9543  1.954 0.501     0.125     0.026       71     8.1  postcentral
 1731   1292   2803  2.240 0.730     0.144     0.043       30     2.9  posteriorcingulate
 7505   5081  11238  2.311 0.417     0.108     0.027       82     8.3  precentral
 5924   4240   9405  2.279 0.507     0.136     0.056       94    18.1  precuneus
 1065    824   1909  2.783 0.625     0.154     0.048       25     2.2  rostralanteriorcingulate
 9757   7684  15940  2.228 0.422     0.159     0.041      156    17.7  rostralmiddlefrontal
10002   8119  18998  2.513 0.469     0.144     0.037      127    15.6  superiorfrontal
 8142   5937  11965  2.131 0.384     0.134     0.030      110    10.6  superiorparietal
 5856   4745  11907  2.691 0.563     0.139     0.035       90     9.4  superiortemporal
 5253   4127   9104  2.381 0.468     0.154     0.040       89     9.3  supramarginal
  393    437    901  2.550 0.325     0.189     0.035        5     0.7  frontalpole
  695    787   2120  3.424 0.696     0.192     0.048       11     1.7  temporalpole
  740    462    900  2.130 0.356     0.104     0.023        8     0.7  transversetemporal
 3535   2297   6058  2.604 0.718     0.145     0.049       72     7.7  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 0051362 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356
Total vertex volume 220256 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1343    891   2226  2.584 0.303     0.119     0.025       11     1.4  bankssts
  818    545   1143  1.989 0.596     0.145     0.024       15     0.7  caudalanteriorcingulate
 3132   2064   5414  2.430 0.380     0.120     0.029       33     3.7  caudalmiddlefrontal
 2700   1547   3426  1.979 0.542     0.135     0.039       42     4.2  cuneus
  563    369   1685  3.282 0.765     0.152     0.058       10     1.3  entorhinal
 4392   2866   8859  2.769 0.582     0.137     0.044       66     7.7  fusiform
 8540   5562  14602  2.450 0.414     0.126     0.029      104     9.4  inferiorparietal
 4913   3166   9642  2.677 0.604     0.132     0.041       73     7.9  inferiortemporal
 1469    898   2363  2.355 0.711     0.124     0.041       20     1.8  isthmuscingulate
 7185   4411   9107  1.982 0.474     0.134     0.036       94     9.8  lateraloccipital
 3580   2348   6316  2.511 0.681     0.131     0.044       58     6.0  lateralorbitofrontal
 5781   3625   8394  2.079 0.662     0.142     0.049       91    10.7  lingual
 2904   1942   5014  2.263 0.552     0.130     0.036       54     3.9  medialorbitofrontal
 5759   3776  12612  2.912 0.524     0.122     0.032       75     7.2  middletemporal
  905    610   2062  2.866 0.759     0.113     0.029        8     1.0  parahippocampal
 2628   1531   3529  2.255 0.415     0.111     0.030       20     3.3  paracentral
 2099   1349   3726  2.602 0.382     0.113     0.029       20     2.4  parsopercularis
 1349    860   2774  2.508 0.534     0.152     0.049       25     2.7  parsorbitalis
 2944   1935   5122  2.357 0.386     0.133     0.036       38     4.3  parstriangularis
 2744   1780   2962  1.857 0.510     0.134     0.042       32     5.0  pericalcarine
 6237   3618   8188  2.067 0.526     0.112     0.030       63     7.7  postcentral
 1910   1243   3303  2.277 0.647     0.144     0.041       35     2.8  posteriorcingulate
 7754   4444  11626  2.502 0.436     0.106     0.032       75    10.7  precentral
 5678   3664   8865  2.293 0.460     0.125     0.033       70     7.3  precuneus
  660    393    998  2.429 0.542     0.137     0.039       13     0.9  rostralanteriorcingulate
 9454   6249  15610  2.240 0.468     0.135     0.040      142    14.9  rostralmiddlefrontal
 9588   6340  17916  2.430 0.494     0.130     0.036      122    13.9  superiorfrontal
 8443   5285  12218  2.146 0.353     0.127     0.030      108     9.7  superiorparietal
 6054   3731  11140  2.727 0.526     0.104     0.027       55     6.2  superiortemporal
 5226   3250   8743  2.459 0.425     0.120     0.029       59     5.7  supramarginal
  499    283    971  2.437 0.481     0.146     0.044       13     0.8  frontalpole
  758    478   2225  3.290 0.797     0.161     0.060       15     2.0  temporalpole
  677    295    864  2.432 0.376     0.084     0.027        5     0.7  transversetemporal
 3808   2404   6566  2.638 0.970     0.130     0.049       70     7.6  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051362 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356
Total vertex volume 220256 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1343    826   2226  2.584 0.303     0.124     0.037       21     2.4  bankssts
  818    622   1143  1.989 0.596     0.181     0.052       75     2.0  caudalanteriorcingulate
 3132   2374   5414  2.430 0.380     0.123     0.025       34     3.3  caudalmiddlefrontal
 2700   1967   3426  1.979 0.542     0.125     0.033       37     4.0  cuneus
  563    595   1685  3.282 0.765     0.173     0.054        9     1.2  entorhinal
 4392   3574   8859  2.769 0.582     0.153     0.044       83     9.1  fusiform
 8540   6235  14602  2.450 0.414     0.130     0.029      105    10.7  inferiorparietal
 4913   3949   9642  2.677 0.604     0.147     0.039       90     8.3  inferiortemporal
 1469   1036   2363  2.355 0.711     0.148     0.046       45     2.8  isthmuscingulate
 7185   4880   9107  1.982 0.474     0.126     0.032      140     9.8  lateraloccipital
 3580   2630   6316  2.511 0.681     0.145     0.052       62     6.3  lateralorbitofrontal
 5781   4393   8394  2.079 0.662     0.142     0.039       90    10.4  lingual
 2904   2501   5014  2.263 0.552     0.157     0.043       43     5.2  medialorbitofrontal
 5759   4917  12612  2.912 0.524     0.136     0.032       58     8.1  middletemporal
  905    809   2062  2.866 0.759     0.149     0.037       10     1.5  parahippocampal
 2628   1628   3529  2.255 0.415     0.109     0.026       31     3.0  paracentral
 2099   1560   3726  2.602 0.382     0.129     0.034       26     3.1  parsopercularis
 1349   1336   2774  2.508 0.534     0.178     0.039       16     2.5  parsorbitalis
 2944   2395   5122  2.357 0.386     0.150     0.035       39     4.5  parstriangularis
 2744   1465   2962  1.857 0.510     0.102     0.029       36     3.1  pericalcarine
 6237   4338   8188  2.067 0.526     0.112     0.023       53     6.1  postcentral
 1910   1540   3303  2.277 0.647     0.160     0.044       35     3.7  posteriorcingulate
 7754   4834  11626  2.502 0.436     0.094     0.030      194     6.6  precentral
 5678   4049   8865  2.293 0.460     0.131     0.033       72     8.0  precuneus
  660    465    998  2.429 0.542     0.158     0.046       12     1.3  rostralanteriorcingulate
 9454   7475  15610  2.240 0.468     0.154     0.037      150    14.9  rostralmiddlefrontal
 9588   8084  17916  2.430 0.494     0.150     0.037      120    15.2  superiorfrontal
 8443   6110  12218  2.146 0.353     0.131     0.029      118    10.2  superiorparietal
 6054   4416  11140  2.727 0.526     0.116     0.026       66     6.7  superiortemporal
 5226   3743   8743  2.459 0.425     0.130     0.032       63     7.0  supramarginal
  499    483    971  2.437 0.481     0.172     0.034        6     0.7  frontalpole
  758    821   2225  3.290 0.797     0.180     0.046       12     1.7  temporalpole
  677    404    864  2.432 0.376     0.086     0.018        3     0.5  transversetemporal
 3808   2291   6566  2.638 0.970     0.133     0.062      100    12.2  insula
PIDs (22425 22428 22431 22434) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 00:14:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 00:14:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 22522 of (22522 22525) to complete...
Waiting for PID 22525 of (22522 22525) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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...
52 labels changed using aseg
relabeling using gibbs priors...
000:   8888 changed, 137434 examined...
001:   2108 changed, 34819 examined...
002:    573 changed, 11187 examined...
003:    237 changed, 3285 examined...
004:    108 changed, 1365 examined...
005:     43 changed, 629 examined...
006:     25 changed, 247 examined...
007:     18 changed, 154 examined...
008:      9 changed, 106 examined...
009:      1 changed, 57 examined...
010:      1 changed, 5 examined...
011:      2 changed, 9 examined...
012:      2 changed, 9 examined...
013:      0 changed, 6 examined...
16 labels changed using aseg
000: 244 total segments, 161 labels (2458 vertices) changed
001: 96 total segments, 13 labels (43 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 17 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1024 vertices marked for relabeling...
1024 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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...
38 labels changed using aseg
relabeling using gibbs priors...
000:   9060 changed, 140379 examined...
001:   2066 changed, 35768 examined...
002:    614 changed, 10811 examined...
003:    236 changed, 3404 examined...
004:    113 changed, 1317 examined...
005:     65 changed, 679 examined...
006:     32 changed, 346 examined...
007:     19 changed, 189 examined...
008:     10 changed, 108 examined...
009:      5 changed, 58 examined...
010:      2 changed, 32 examined...
011:      0 changed, 11 examined...
12 labels changed using aseg
000: 267 total segments, 174 labels (2107 vertices) changed
001: 98 total segments, 8 labels (46 vertices) changed
002: 90 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 34 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1223 vertices marked for relabeling...
1223 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (22522 22525) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 00:14:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 00:14:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh white 

Waiting for PID 22579 of (22579 22582) to complete...
Waiting for PID 22582 of (22579 22582) 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 0051362 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672
Total vertex volume 214840 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1593   1048   2725  2.328 0.427     0.153     0.042       28     2.8  G&S_frontomargin
 1655   1060   2781  2.316 0.559     0.150     0.042       25     2.8  G&S_occipital_inf
 1709    981   2410  2.113 0.448     0.125     0.047       23     3.2  G&S_paracentral
 1481    948   2785  2.491 0.460     0.135     0.041       23     2.2  G&S_subcentral
  710    468   1448  2.407 0.411     0.146     0.036       11     1.0  G&S_transv_frontopol
 1874   1247   3436  2.655 0.519     0.120     0.030       21     2.1  G&S_cingul-Ant
 1120    774   1843  2.296 0.439     0.113     0.023        8     1.0  G&S_cingul-Mid-Ant
 1271    853   2146  2.437 0.395     0.118     0.028       12     1.4  G&S_cingul-Mid-Post
  664    412   1550  2.901 0.431     0.153     0.047       12     1.1  G_cingul-Post-dorsal
  344    192    714  2.750 0.732     0.137     0.039        6     0.4  G_cingul-Post-ventral
 2598   1619   2940  1.655 0.413     0.148     0.046       40     4.9  G_cuneus
 1322    815   2613  2.426 0.410     0.133     0.041       24     1.9  G_front_inf-Opercular
  438    259    943  2.566 0.426     0.137     0.041       10     0.6  G_front_inf-Orbital
 1192    748   2289  2.365 0.394     0.142     0.040       23     1.8  G_front_inf-Triangul
 5345   3485  10471  2.377 0.422     0.142     0.040       98     8.4  G_front_middle
 7358   4741  15222  2.617 0.475     0.139     0.042      108    11.6  G_front_sup
  722    485   1296  2.523 0.728     0.153     0.058       13     1.6  G_Ins_lg&S_cent_ins
  948    535   2128  2.911 0.985     0.153     0.104       62     5.1  G_insular_short
 2168   1327   4252  2.428 0.467     0.147     0.043       42     3.4  G_occipital_middle
 1873   1061   2410  1.928 0.524     0.131     0.038       36     2.9  G_occipital_sup
 1719   1084   4038  2.805 0.597     0.140     0.054       31     3.4  G_oc-temp_lat-fusifor
 3950   2460   5146  1.850 0.646     0.160     0.056       77     8.8  G_oc-temp_med-Lingual
 1229    801   3182  2.957 0.836     0.112     0.028        9     1.3  G_oc-temp_med-Parahip
 2378   1475   4889  2.534 0.598     0.138     0.053       44     4.7  G_orbital
 2165   1390   4413  2.432 0.445     0.148     0.043       44     3.7  G_pariet_inf-Angular
 2525   1644   5129  2.543 0.486     0.149     0.045       44     4.2  G_pariet_inf-Supramar
 3153   2029   5375  2.204 0.392     0.137     0.036       51     4.4  G_parietal_sup
 2815   1623   3875  1.971 0.450     0.123     0.041       45     4.3  G_postcentral
 2708   1513   4828  2.492 0.372     0.119     0.051       46     5.9  G_precentral
 2864   1881   5589  2.380 0.514     0.143     0.042       51     4.5  G_precuneus
  903    580   1746  2.297 0.555     0.144     0.049       23     1.7  G_rectus
  681    429    805  1.977 0.965     0.097     0.050        8     1.0  G_subcallosal
  495    262    698  2.124 0.376     0.114     0.050        7     0.7  G_temp_sup-G_T_transv
 2105   1325   5588  2.965 0.579     0.132     0.042       32     3.1  G_temp_sup-Lateral
  574    379   1487  3.312 0.626     0.104     0.030        4     0.8  G_temp_sup-Plan_polar
  938    606   1893  2.617 0.423     0.130     0.042       14     1.4  G_temp_sup-Plan_tempo
 2809   1771   6845  2.738 0.692     0.158     0.072       80     8.2  G_temporal_inf
 2229   1468   5832  2.857 0.598     0.135     0.039       38     3.3  G_temporal_middle
  274    185    314  1.875 0.310     0.104     0.019        2     0.2  Lat_Fis-ant-Horizont
  394    275    491  2.086 0.295     0.115     0.021        3     0.3  Lat_Fis-ant-Vertical
  921    607   1110  2.332 0.320     0.119     0.034        7     1.2  Lat_Fis-post
 2039   1233   2367  1.809 0.505     0.142     0.043       34     3.2  Pole_occipital
 1721   1151   5196  3.150 0.744     0.152     0.055       31     4.0  Pole_temporal
 3236   2185   3608  1.900 0.522     0.128     0.041       36     5.6  S_calcarine
 3559   2306   3920  1.916 0.481     0.110     0.042       27     4.4  S_central
 1008    685   1367  2.133 0.368     0.106     0.020        6     0.9  S_cingul-Marginalis
  388    264    586  2.702 0.495     0.118     0.033        2     0.6  S_circular_insula_ant
 1405    985   1979  2.416 0.451     0.100     0.024        7     1.7  S_circular_insula_inf
 1717   1146   2213  2.334 0.353     0.107     0.024        9     1.8  S_circular_insula_sup
  817    557   1361  2.393 0.547     0.120     0.030        7     0.9  S_collat_transv_ant
  533    347    542  2.139 0.414     0.157     0.048        7     1.0  S_collat_transv_post
 2635   1788   3670  2.124 0.365     0.132     0.030       27     3.4  S_front_inf
 1484    992   1863  2.132 0.389     0.139     0.035       17     2.1  S_front_middle
 3047   2049   4364  2.175 0.356     0.119     0.030       29     3.6  S_front_sup
  253    167    338  2.217 0.332     0.123     0.025        2     0.3  S_interm_prim-Jensen
 2470   1623   3161  2.129 0.362     0.119     0.028       24     2.8  S_intrapariet&P_trans
 1061    698   1175  2.040 0.340     0.137     0.038       10     1.7  S_oc_middle&Lunatus
 1431    945   1811  2.143 0.306     0.127     0.027       13     1.6  S_oc_sup&transversal
  744    510   1070  2.179 0.302     0.096     0.019        4     0.6  S_occipital_ant
  754    534   1344  2.617 0.435     0.129     0.028        7     1.0  S_oc-temp_lat
 1990   1415   3021  2.457 0.407     0.121     0.028       15     2.1  S_oc-temp_med&Lingual
  505    349    643  2.016 0.409     0.125     0.028        3     0.6  S_orbital_lateral
  679    480    924  2.233 0.549     0.120     0.030        5     0.9  S_orbital_med-olfact
 1556   1066   2637  2.459 0.476     0.140     0.037       19     2.5  S_orbital-H_Shaped
 2484   1596   3065  2.118 0.445     0.116     0.028       19     2.8  S_parieto_occipital
 1182    716    771  1.486 0.690     0.156     0.052       36     2.2  S_pericallosal
 3675   2404   4338  1.992 0.365     0.112     0.024       31     3.5  S_postcentral
 1699   1123   2327  2.298 0.370     0.106     0.023       10     1.6  S_precentral-inf-part
 1262    837   1554  2.122 0.355     0.105     0.027        7     1.3  S_precentral-sup-part
  631    454    871  2.245 0.578     0.132     0.022        5     0.6  S_suborbital
 1037    708   1362  2.272 0.377     0.133     0.030        9     1.4  S_subparietal
 1765   1250   2535  2.358 0.420     0.122     0.026       12     2.1  S_temporal_inf
 5932   4012   8739  2.347 0.431     0.112     0.025       47     6.4  S_temporal_sup
  347    242    440  2.147 0.293     0.125     0.033        3     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 0051362 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356
Total vertex volume 220256 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
  970    624   1572  2.189 0.494     0.131     0.040       15     1.5  G&S_frontomargin
 1363    865   2035  2.091 0.494     0.133     0.031       17     1.6  G&S_occipital_inf
 1656    867   2210  2.141 0.524     0.107     0.035       16     2.3  G&S_paracentral
 1369    879   2474  2.487 0.450     0.139     0.043       19     2.0  G&S_subcentral
 1248    794   2515  2.569 0.490     0.162     0.050       33     2.6  G&S_transv_frontopol
 3069   2041   5009  2.276 0.535     0.140     0.037       47     4.4  G&S_cingul-Ant
 1306    891   2203  2.302 0.540     0.136     0.030       16     1.6  G&S_cingul-Mid-Ant
 1443    943   2484  2.399 0.465     0.119     0.032       14     1.6  G&S_cingul-Mid-Post
  679    423   1429  2.693 0.418     0.161     0.052       16     1.1  G_cingul-Post-dorsal
  388    221    879  2.755 0.609     0.127     0.045        5     0.6  G_cingul-Post-ventral
 2543   1439   3397  1.990 0.581     0.140     0.044       46     4.6  G_cuneus
 1507    932   3102  2.613 0.396     0.124     0.035       21     2.0  G_front_inf-Opercular
  485    290   1130  2.648 0.358     0.144     0.043       10     0.8  G_front_inf-Orbital
 1322    854   2711  2.445 0.363     0.148     0.048       25     2.3  G_front_inf-Triangul
 4406   2812   9175  2.457 0.417     0.147     0.049       95     8.1  G_front_middle
 6282   3960  12592  2.523 0.476     0.137     0.042      100    10.4  G_front_sup
  673    426   1229  2.730 0.710     0.149     0.070       17     2.1  G_Ins_lg&S_cent_ins
 1231    745   2385  2.515 1.455     0.154     0.071       42     3.5  G_insular_short
 2373   1447   4616  2.398 0.428     0.130     0.033       37     2.9  G_occipital_middle
 1815    991   2245  1.965 0.383     0.128     0.037       26     2.4  G_occipital_sup
 1932   1203   4390  2.794 0.651     0.153     0.060       44     4.6  G_oc-temp_lat-fusifor
 3872   2299   5903  2.101 0.724     0.146     0.055       69     7.8  G_oc-temp_med-Lingual
 1187    738   3330  3.262 0.743     0.136     0.049       17     2.2  G_oc-temp_med-Parahip
 2657   1677   5866  2.602 0.669     0.144     0.057       61     5.9  G_orbital
 3228   2015   6789  2.611 0.435     0.139     0.035       55     4.4  G_pariet_inf-Angular
 2584   1518   5068  2.652 0.445     0.126     0.032       38     3.0  G_pariet_inf-Supramar
 2174   1381   4018  2.303 0.332     0.135     0.033       33     2.7  G_parietal_sup
 2497   1186   3398  2.212 0.513     0.105     0.032       27     3.2  G_postcentral
 3142   1453   5268  2.698 0.388     0.097     0.039       42     5.4  G_precentral
 2694   1667   4822  2.362 0.459     0.140     0.043       53     4.2  G_precuneus
  818    554   1711  2.257 0.512     0.128     0.040       20     1.0  G_rectus
  341    188    589  2.800 0.664     0.086     0.028        2     0.3  G_subcallosal
  565    262    801  2.411 0.359     0.081     0.027        4     0.5  G_temp_sup-G_T_transv
 2157   1211   4625  2.835 0.511     0.113     0.036       29     2.8  G_temp_sup-Lateral
  873    547   1646  2.817 0.668     0.105     0.033        7     1.2  G_temp_sup-Plan_polar
  992    574   1536  2.513 0.383     0.103     0.027        8     1.0  G_temp_sup-Plan_tempo
 2668   1636   5754  2.708 0.651     0.138     0.050       52     5.1  G_temporal_inf
 3402   2106   8398  3.000 0.517     0.125     0.034       54     4.3  G_temporal_middle
  559    382    705  2.190 0.306     0.128     0.030        4     0.8  Lat_Fis-ant-Horizont
  357    233    569  2.564 0.345     0.130     0.033        4     0.4  Lat_Fis-ant-Vertical
 1422    891   1816  2.421 0.386     0.112     0.025        9     1.5  Lat_Fis-post
 3407   2000   3601  1.698 0.442     0.135     0.044       50     5.8  Pole_occipital
 1799   1182   5250  3.291 0.672     0.155     0.053       32     4.0  Pole_temporal
 2848   1938   3261  1.993 0.500     0.133     0.036       28     4.5  S_calcarine
 3133   2147   3614  1.980 0.483     0.112     0.024       19     3.6  S_central
 1394    946   1906  2.200 0.362     0.111     0.025       10     1.4  S_cingul-Marginalis
  545    360    843  2.716 0.553     0.111     0.029        3     0.6  S_circular_insula_ant
 1180    811   1692  2.444 0.485     0.087     0.018        5     0.9  S_circular_insula_inf
 1355    912   1918  2.482 0.429     0.113     0.027        8     1.6  S_circular_insula_sup
  916    655   1525  2.643 0.436     0.112     0.027        6     0.9  S_collat_transv_ant
  531    351    613  2.062 0.481     0.168     0.049        8     1.1  S_collat_transv_post
 2253   1500   2960  2.190 0.379     0.114     0.027       15     2.4  S_front_inf
 2322   1612   3231  2.069 0.398     0.117     0.025       16     2.7  S_front_middle
 2467   1679   3365  2.173 0.350     0.107     0.024       15     2.4  S_front_sup
  262    181    382  2.120 0.290     0.071     0.010        0     0.1  S_interm_prim-Jensen
 3668   2433   4852  2.183 0.351     0.119     0.024       34     3.4  S_intrapariet&P_trans
  826    554    848  1.935 0.405     0.147     0.035       11     1.1  S_oc_middle&Lunatus
 1813   1182   2196  2.077 0.337     0.125     0.027       18     1.9  S_oc_sup&transversal
  879    588   1211  2.346 0.313     0.106     0.019        6     0.7  S_occipital_ant
 1121    749   1865  2.626 0.430     0.109     0.025        9     1.1  S_oc-temp_lat
 1930   1389   3050  2.501 0.451     0.116     0.024       12     1.9  S_oc-temp_med&Lingual
  613    424    687  1.866 0.384     0.125     0.028        5     0.7  S_orbital_lateral
  912    631   1198  2.147 0.685     0.103     0.019        5     0.7  S_orbital_med-olfact
 1272    859   2143  2.484 0.560     0.129     0.034       14     1.8  S_orbital-H_Shaped
 2124   1377   2551  2.061 0.394     0.114     0.025       16     2.2  S_parieto_occipital
 1272    786    973  1.649 0.602     0.142     0.039       26     1.5  S_pericallosal
 2545   1658   3121  2.118 0.331     0.116     0.027       23     2.7  S_postcentral
 1727   1145   2379  2.490 0.344     0.103     0.020       10     1.5  S_precentral-inf-part
 1200    805   1638  2.390 0.375     0.096     0.018        5     1.0  S_precentral-sup-part
  312    213    478  2.310 0.320     0.143     0.029        3     0.4  S_suborbital
 1237    827   1821  2.343 0.413     0.126     0.027       12     1.5  S_subparietal
 1255    878   1945  2.658 0.554     0.122     0.027        9     1.6  S_temporal_inf
 6907   4670  10508  2.562 0.406     0.111     0.023       50     6.4  S_temporal_sup
  212    147    240  2.054 0.309     0.139     0.032        2     0.3  S_temporal_transverse
PIDs (22579 22582) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 00:15:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 00:15:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 22648 of (22648 22651) to complete...
Waiting for PID 22651 of (22648 22651) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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...
1380 labels changed using aseg
relabeling using gibbs priors...
000:   2007 changed, 137434 examined...
001:    500 changed, 9351 examined...
002:    144 changed, 2779 examined...
003:     64 changed, 855 examined...
004:     24 changed, 368 examined...
005:     11 changed, 147 examined...
006:      6 changed, 68 examined...
007:      5 changed, 34 examined...
008:      8 changed, 22 examined...
009:      3 changed, 35 examined...
010:      1 changed, 20 examined...
011:      0 changed, 6 examined...
211 labels changed using aseg
000: 60 total segments, 27 labels (172 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
530 vertices marked for relabeling...
530 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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...
1292 labels changed using aseg
relabeling using gibbs priors...
000:   1934 changed, 140379 examined...
001:    445 changed, 9245 examined...
002:    111 changed, 2507 examined...
003:     43 changed, 665 examined...
004:     19 changed, 256 examined...
005:     18 changed, 111 examined...
006:     14 changed, 98 examined...
007:     10 changed, 61 examined...
008:      7 changed, 50 examined...
009:     10 changed, 39 examined...
010:      7 changed, 40 examined...
011:      4 changed, 27 examined...
012:      3 changed, 18 examined...
013:      4 changed, 20 examined...
014:      3 changed, 20 examined...
015:      0 changed, 15 examined...
244 labels changed using aseg
000: 54 total segments, 21 labels (213 vertices) changed
001: 34 total segments, 1 labels (3 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
8 filter iterations complete (10 requested, 0 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
896 vertices marked for relabeling...
896 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (22648 22651) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 00:15:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 00:15:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh white 

Waiting for PID 22701 of (22701 22704) to complete...
Waiting for PID 22704 of (22701 22704) 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 0051362 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672
Total vertex volume 214840 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1556   1023   2624  2.331 0.652     0.132     0.030       21     1.7  caudalanteriorcingulate
 3703   2478   6167  2.323 0.407     0.124     0.034       36     4.9  caudalmiddlefrontal
 3857   2381   4406  1.764 0.399     0.133     0.038       47     6.1  cuneus
  575    387   1589  3.023 1.007     0.125     0.031        5     0.8  entorhinal
 3732   2479   7433  2.660 0.550     0.132     0.043       49     6.0  fusiform
 5946   3896   9649  2.284 0.422     0.133     0.035       83     8.1  inferiorparietal
 5067   3348  11409  2.677 0.686     0.145     0.054      102    11.3  inferiortemporal
 1531    965   2505  2.351 0.789     0.142     0.045       30     2.4  isthmuscingulate
 7668   4715  10682  2.063 0.528     0.138     0.039      117    11.5  lateraloccipital
 4456   2880   8108  2.495 0.575     0.141     0.052       74     9.3  lateralorbitofrontal
 5606   3645   7290  1.953 0.618     0.147     0.048       90    10.5  lingual
 2460   1634   4181  2.220 0.668     0.127     0.039       44     3.7  medialorbitofrontal
 6090   4116  12262  2.623 0.568     0.125     0.033       76     8.3  middletemporal
  996    670   2232  2.798 0.656     0.105     0.026        8     1.0  parahippocampal
 2466   1481   3583  2.285 0.456     0.103     0.030       19     2.9  paracentral
 2336   1500   3938  2.382 0.387     0.121     0.032       30     2.7  parsopercularis
  988    646   1608  2.293 0.474     0.135     0.036       15     1.4  parsorbitalis
 2457   1595   3853  2.216 0.393     0.128     0.031       33     3.0  parstriangularis
 2433   1645   2534  1.765 0.466     0.137     0.043       27     4.4  pericalcarine
 7964   4999  10583  1.967 0.488     0.120     0.034       95    10.6  postcentral
 1864   1209   2935  2.251 0.719     0.137     0.038       30     2.8  posteriorcingulate
 7444   4504  11161  2.321 0.416     0.114     0.045       90    12.0  precentral
 5713   3760   9249  2.298 0.501     0.137     0.039       82     8.9  precuneus
 1487    950   2573  2.742 0.599     0.126     0.031       20     1.7  rostralanteriorcingulate
 7182   4726  11925  2.213 0.433     0.144     0.038      117    11.1  rostralmiddlefrontal
11171   7449  20797  2.458 0.468     0.134     0.037      145    15.9  superiorfrontal
 6431   4122   9517  2.143 0.377     0.129     0.032       87     8.0  superiorparietal
 7507   4956  15552  2.705 0.618     0.119     0.034       82    10.0  superiortemporal
 4858   3182   8355  2.384 0.472     0.136     0.038       69     7.1  supramarginal
  737    401    896  2.125 0.354     0.115     0.044       10     1.0  transversetemporal
 2979   1919   5244  2.675 0.718     0.136     0.058       79     8.0  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0051362 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356
Total vertex volume 220256 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1065    708   1668  2.117 0.647     0.148     0.028       19     1.2  caudalanteriorcingulate
 3289   2159   5622  2.424 0.383     0.120     0.030       35     3.9  caudalmiddlefrontal
 3166   1815   4019  1.970 0.511     0.131     0.037       46     4.8  cuneus
  514    337   1541  3.270 0.786     0.150     0.055        8     1.1  entorhinal
 4024   2643   7826  2.718 0.550     0.136     0.045       60     7.1  fusiform
 8443   5493  14279  2.443 0.415     0.128     0.029      106     9.6  inferiorparietal
 5296   3408  10727  2.712 0.633     0.133     0.041       78     8.5  inferiortemporal
 1442    891   2290  2.356 0.690     0.124     0.041       19     1.7  isthmuscingulate
 7236   4434   9116  1.966 0.470     0.134     0.036       95     9.9  lateraloccipital
 4162   2739   7529  2.481 0.686     0.133     0.044       67     7.1  lateralorbitofrontal
 5688   3546   8246  2.080 0.657     0.141     0.049       88    10.5  lingual
 2400   1527   3889  2.093 0.827     0.121     0.039       57     3.7  medialorbitofrontal
 6884   4509  14449  2.860 0.515     0.120     0.031       84     8.4  middletemporal
  956    651   2225  2.901 0.753     0.118     0.029       10     1.1  parahippocampal
 2729   1588   3667  2.249 0.419     0.112     0.031       21     3.5  paracentral
 2679   1710   4651  2.562 0.383     0.117     0.032       28     3.3  parsopercularis
 1217    767   2397  2.492 0.514     0.147     0.051       23     2.4  parsorbitalis
 2710   1793   4521  2.309 0.408     0.135     0.038       36     4.0  parstriangularis
 2687   1740   2888  1.855 0.512     0.133     0.042       31     4.8  pericalcarine
 6889   4036   9150  2.087 0.517     0.114     0.031       72     8.3  postcentral
 1971   1284   3372  2.278 0.643     0.143     0.041       35     2.8  posteriorcingulate
 7487   4278  11344  2.511 0.435     0.105     0.032       72    10.4  precentral
 5816   3773   9134  2.292 0.464     0.127     0.033       74     7.5  precuneus
  854    520   1257  2.463 0.516     0.138     0.037       15     1.2  rostralanteriorcingulate
 6933   4598  11622  2.218 0.454     0.136     0.040      107    11.2  rostralmiddlefrontal
12494   8201  22495  2.393 0.499     0.132     0.037      174    18.4  superiorfrontal
 7068   4436  10377  2.161 0.353     0.127     0.030       92     8.1  superiorparietal
 7752   4833  14945  2.771 0.573     0.112     0.032       80     9.9  superiortemporal
 5015   3105   8443  2.467 0.439     0.117     0.028       55     5.2  supramarginal
  648    280    841  2.458 0.371     0.083     0.027        5     0.6  transversetemporal
 2972   1949   5728  2.864 0.744     0.129     0.042       42     4.9  insula
PIDs (22701 22704) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 00:16:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 pctsurfcon --s 0051362 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 00:16:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts

 pctsurfcon --s 0051362 --rh-only 

Waiting for PID 22766 of (22766 22776) to complete...
Waiting for PID 22776 of (22766 22776) to complete...

 pctsurfcon --s 0051362 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts/pctsurfcon.log
Sun Oct  8 00:16:05 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-6.0.0/0051362/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-382 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-6.0.0/0051362/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.wm.mgh --regheader 0051362 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 72496
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.wm.mgh
Dim: 137434 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.gm.mgh --projfrac 0.3 --regheader 0051362 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 89117
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.gm.mgh
Dim: 137434 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.w-g.pct.mgh --annot 0051362 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/lh.w-g.pct.mgh --annot 0051362 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/lh.w-g.pct.mgh
Vertex Area is 0.647128 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 0051362 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts/pctsurfcon.log
Sun Oct  8 00:16:05 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-6.0.0/0051362/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-382 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-6.0.0/0051362/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.wm.mgh --regheader 0051362 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 72873
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.wm.mgh
Dim: 140379 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.gm.mgh --projfrac 0.3 --regheader 0051362 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 89908
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.gm.mgh
Dim: 140379 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.w-g.pct.mgh --annot 0051362 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.w-g.pct.mgh --annot 0051362 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.w-g.pct.mgh
Vertex Area is 0.633852 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 (22766 22776) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 00:16:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1434 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1397 voxels changed to hypointensity...
2826 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 00:16:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362

 mri_aparc2aseg --s 0051362 --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 00:16:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362

 mri_aparc2aseg --s 0051362 --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 00:16:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362

 mri_aparc2aseg --s 0051362 --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 22994 of (22994 22997 23000) to complete...
Waiting for PID 22997 of (22994 22997 23000) to complete...
Waiting for PID 23000 of (22994 22997 23000) to complete...

 mri_aparc2aseg --s 0051362 --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 0051362
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/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 6.21
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 16
rescaling Left_Inf_Lat_Vent from 34 --> 36
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 61
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 97
rescaling Third_Ventricle from 25 --> 29
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 64
rescaling Left_Amygdala from 56 --> 65
rescaling CSF from 32 --> 42
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 94
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 66
rescaling Right_Lateral_Ventricle from 13 --> 16
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 36
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 77
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 430878
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 114 changed.
pass 2: 1 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051362 --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 0051362
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/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 6.21
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 16
rescaling Left_Inf_Lat_Vent from 34 --> 36
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 61
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 97
rescaling Third_Ventricle from 25 --> 29
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 64
rescaling Left_Amygdala from 56 --> 65
rescaling CSF from 32 --> 42
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 94
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 66
rescaling Right_Lateral_Ventricle from 13 --> 16
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 36
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 77
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 430873
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 114 changed.
pass 2: 1 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051362 --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 0051362
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/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 6.21
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 16
rescaling Left_Inf_Lat_Vent from 34 --> 36
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 61
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 72
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 97
rescaling Third_Ventricle from 25 --> 29
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 64
rescaling Left_Amygdala from 56 --> 65
rescaling CSF from 32 --> 42
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 94
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 66
rescaling Right_Lateral_Ventricle from 13 --> 16
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 64
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 36
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 77
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 430873
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 114 changed.
pass 2: 1 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (22994 22997 23000) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 00:24:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri

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

Sun Oct  8 00:24:40 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-6.0.0/0051362/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-382 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-6.0.0/0051362/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-382
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 00:24:40 CEST 2017 
Ended   at Sun Oct  8 00:24:47 CEST 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 00:24:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362

 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 0051362 


$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 0051362 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1467537 mm^3    (det: 1.327466 )
Computing euler number
orig.nofix lheno =  -90, rheno = -96
orig.nofix lhholes =   46, rhholes = 49
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
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 00:26:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362

 mri_aparc2aseg --s 0051362 --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 0051362
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-6.0.0/0051362/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8160 vertices from left hemi
Ripped 7885 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-6.0.0/0051362/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 868255
Used brute-force search on 224 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 1.000000
     1 k 1451.000000
     2 k 30.000000
     3 k 2.000000
     4 k 1.000000
     5 k 1.000000
Fixing Parahip RH WM
  Found 9 clusters
     0 k 2.000000
     1 k 1.000000
     2 k 1.000000
     3 k 5.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1339.000000
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 0051362 --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 0051362 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-382
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1467537 mm^3    (det: 1.327466 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
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-6.0.0/0051362/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 00:36:33 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 24489 of (24489 24495 24501 24506 24513) to complete...
Waiting for PID 24495 of (24489 24495 24501 24506 24513) to complete...
Waiting for PID 24501 of (24489 24495 24501 24506 24513) to complete...
Waiting for PID 24506 of (24489 24495 24501 24506 24513) to complete...
Waiting for PID 24513 of (24489 24495 24501 24506 24513) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 614
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4743
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 789
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8698
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 290
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4367
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 683
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6666
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 506
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6290
mri_label2label: Done

PIDs (24489 24495 24501 24506 24513) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 24565 of (24565 24571 24577 24582) to complete...
Waiting for PID 24571 of (24565 24571 24577 24582) to complete...
Waiting for PID 24577 of (24565 24571 24577 24582) to complete...
Waiting for PID 24582 of (24565 24571 24577 24582) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 419
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4489
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 944
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14533
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 332
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4513
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 842
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4264
mri_label2label: Done

PIDs (24565 24571 24577 24582) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 24645 of (24645 24652 24658 24663 24670) to complete...
Waiting for PID 24652 of (24645 24652 24658 24663 24670) to complete...
Waiting for PID 24658 of (24645 24652 24658 24663 24670) to complete...
Waiting for PID 24663 of (24645 24652 24658 24663 24670) to complete...
Waiting for PID 24670 of (24645 24652 24658 24663 24670) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 2033
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6674
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 4236
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 12350
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 230
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2248
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 98
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1388
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 67
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1266
mri_label2label: Done

PIDs (24645 24652 24658 24663 24670) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 24783 of (24783 24789 24795 24801 24807) to complete...
Waiting for PID 24789 of (24783 24789 24795 24801 24807) to complete...
Waiting for PID 24795 of (24783 24789 24795 24801 24807) to complete...
Waiting for PID 24801 of (24783 24789 24795 24801 24807) to complete...
Waiting for PID 24807 of (24783 24789 24795 24801 24807) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 156
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1170
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 232
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2324
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 73
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1577
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 349
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2345
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 269
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2588
mri_label2label: Done

PIDs (24783 24789 24795 24801 24807) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 24854 of (24854 24860 24866 24871) to complete...
Waiting for PID 24860 of (24854 24860 24866 24871) to complete...
Waiting for PID 24866 of (24854 24860 24866 24871) to complete...
Waiting for PID 24871 of (24854 24860 24866 24871) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 196
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1745
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 322
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7357
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 134
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2046
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 289
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1440
mri_label2label: Done

PIDs (24854 24860 24866 24871) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 24918 of (24918 24924 24930 24936 24940) to complete...
Waiting for PID 24924 of (24918 24924 24930 24936 24940) to complete...
Waiting for PID 24930 of (24918 24924 24930 24936 24940) to complete...
Waiting for PID 24936 of (24918 24924 24930 24936 24940) to complete...
Waiting for PID 24940 of (24918 24924 24930 24936 24940) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 1457
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4862
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 1960
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5294
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 58
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 571
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 36
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 506
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434
Number of reverse mapping hits = 16
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 466
mri_label2label: Done

PIDs (24918 24924 24930 24936 24940) completed and logs appended.

 mris_label2annot --s 0051362 --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-6.0.0/0051362/label
cmdline mris_label2annot --s 0051362 --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-382
machine  x86_64
user     ntraut

subject 0051362
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-6.0.0/0051362/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 93569 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051362 --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-6.0.0/0051362/label
cmdline mris_label2annot --s 0051362 --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-382
machine  x86_64
user     ntraut

subject 0051362
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-6.0.0/0051362/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 111381 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 217672
Total vertex volume 214840 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1325    754   1887  2.063 0.492     0.135     0.051       25     2.6  BA1_exvivo
 4548   2930   5954  2.026 0.402     0.115     0.025       45     4.5  BA2_exvivo
 1081    753   1034  1.756 0.379     0.132     0.040       13     1.5  BA3a_exvivo
 2775   1709   3637  1.876 0.546     0.116     0.037       31     3.9  BA3b_exvivo
 1767    976   2550  2.362 0.402     0.113     0.043       19     3.4  BA4a_exvivo
 1505    852   1907  2.377 0.365     0.100     0.070       19     3.5  BA4p_exvivo
 8379   5343  15087  2.423 0.448     0.123     0.039       95    11.6  BA6_exvivo
 2279   1458   3928  2.404 0.386     0.118     0.031       27     2.7  BA44_exvivo
 3261   2153   5259  2.197 0.394     0.138     0.035       49     4.5  BA45_exvivo
 4153   2732   4693  1.778 0.479     0.136     0.044       51     7.6  V1_exvivo
 9886   6077  11461  1.809 0.524     0.150     0.049      174    18.9  V2_exvivo
 1716   1137   3309  2.490 0.464     0.128     0.032       21     2.1  MT_exvivo
  615    393   1940  3.317 0.829     0.131     0.043        7     1.3  perirhinal_exvivo
  575    424   1106  2.563 0.723     0.126     0.031        4     0.8  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 0051362 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 217672
Total vertex volume 214840 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
  903    496   1213  2.009 0.477     0.141     0.057       19     1.9  BA1_exvivo
 1848   1163   2447  1.984 0.400     0.108     0.022       18     1.6  BA2_exvivo
  905    628    819  1.731 0.356     0.136     0.042       11     1.4  BA3a_exvivo
 1851   1152   2086  1.684 0.429     0.109     0.034       18     2.4  BA3b_exvivo
 1755    976   2496  2.383 0.389     0.109     0.040       16     3.3  BA4a_exvivo
 1245    711   1516  2.307 0.380     0.101     0.078       18     3.0  BA4p_exvivo
 4422   2751   7801  2.415 0.439     0.124     0.041       52     6.4  BA6_exvivo
 1443    918   2421  2.352 0.377     0.124     0.034       20     1.9  BA44_exvivo
 1251    818   2318  2.312 0.420     0.130     0.034       18     1.8  BA45_exvivo
 4362   2856   5023  1.799 0.484     0.133     0.043       52     7.7  V1_exvivo
 4990   3123   5165  1.619 0.464     0.155     0.050       91    10.0  V2_exvivo
  467    324    883  2.531 0.414     0.124     0.025        5     0.5  MT_exvivo
  304    193    994  3.284 0.763     0.107     0.023        2     0.3  perirhinal_exvivo
  307    222    542  2.351 0.477     0.109     0.022        1     0.3  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 00:39:41 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 25117 of (25117 25123 25129 25134 25139) to complete...
Waiting for PID 25123 of (25117 25123 25129 25134 25139) to complete...
Waiting for PID 25129 of (25117 25123 25129 25134 25139) to complete...
Waiting for PID 25134 of (25117 25123 25129 25134 25139) to complete...
Waiting for PID 25139 of (25117 25123 25129 25134 25139) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 343
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4305
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 414
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7101
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 162
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4142
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 290
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4812
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 636
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6383
mri_label2label: Done

PIDs (25117 25123 25129 25134 25139) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 25206 of (25206 25212 25218 25223) to complete...
Waiting for PID 25212 of (25206 25212 25218 25223) to complete...
Waiting for PID 25218 of (25206 25212 25218 25223) to complete...
Waiting for PID 25223 of (25206 25212 25218 25223) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 374
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4847
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 1059
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13315
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 1190
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8102
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 1560
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6915
mri_label2label: Done

PIDs (25206 25212 25218 25223) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 25272 of (25272 25278 25284 25289 25295) to complete...
Waiting for PID 25278 of (25272 25278 25284 25289 25295) to complete...
Waiting for PID 25284 of (25272 25278 25284 25289 25295) to complete...
Waiting for PID 25289 of (25272 25278 25284 25289 25295) to complete...
Waiting for PID 25295 of (25272 25278 25284 25289 25295) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 2239
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6966
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 3440
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11456
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 601
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2533
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 113
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1151
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 81
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 833
mri_label2label: Done

PIDs (25272 25278 25284 25289 25295) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 25352 of (25352 25358 25364 25369 25376) to complete...
Waiting for PID 25358 of (25352 25358 25364 25369 25376) to complete...
Waiting for PID 25364 of (25352 25358 25364 25369 25376) to complete...
Waiting for PID 25369 of (25352 25358 25364 25369 25376) to complete...
Waiting for PID 25376 of (25352 25358 25364 25369 25376) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 119
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 995
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 138
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2826
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 56
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1754
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2316
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 170
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1558
mri_label2label: Done

PIDs (25352 25358 25364 25369 25376) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 25424 of (25424 25430 25436 25442) to complete...
Waiting for PID 25430 of (25424 25430 25436 25442) to complete...
Waiting for PID 25436 of (25424 25430 25436 25442) to complete...
Waiting for PID 25442 of (25424 25430 25436 25442) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 128
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1617
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 559
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7518
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 142
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1154
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 415
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1593
mri_label2label: Done

PIDs (25424 25430 25436 25442) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 25489 of (25489 25495 25501 25506 25511) to complete...
Waiting for PID 25495 of (25489 25495 25501 25506 25511) to complete...
Waiting for PID 25501 of (25489 25495 25501 25506 25511) to complete...
Waiting for PID 25506 of (25489 25495 25501 25506 25511) to complete...
Waiting for PID 25511 of (25489 25495 25501 25506 25511) 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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 1544
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4776
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 1776
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5213
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 113
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 381
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 68
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 762
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 0051362 --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 = 0051362
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-6.0.0/0051362/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379
Number of reverse mapping hits = 42
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 333
mri_label2label: Done

PIDs (25489 25495 25501 25506 25511) completed and logs appended.

 mris_label2annot --s 0051362 --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-6.0.0/0051362/label
cmdline mris_label2annot --s 0051362 --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-382
machine  x86_64
user     ntraut

subject 0051362
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-6.0.0/0051362/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 96718 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051362 --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-6.0.0/0051362/label
cmdline mris_label2annot --s 0051362 --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-382
machine  x86_64
user     ntraut

subject 0051362
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-6.0.0/0051362/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 115481 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 223356
Total vertex volume 220256 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
 1048    442   1395  2.226 0.480     0.107     0.035       14     1.3  BA1_exvivo
 3160   1905   4198  2.202 0.408     0.112     0.029       29     3.6  BA2_exvivo
 1099    786   1108  1.804 0.373     0.141     0.033       10     1.6  BA3a_exvivo
 1991   1225   2381  1.786 0.494     0.107     0.026       16     2.4  BA3b_exvivo
 1780    908   2574  2.493 0.429     0.103     0.037       17     3.1  BA4a_exvivo
 1382    832   1929  2.417 0.436     0.097     0.025        8     1.5  BA4p_exvivo
 7618   4554  12980  2.501 0.427     0.111     0.034       80    10.4  BA6_exvivo
 3778   2404   6305  2.542 0.384     0.110     0.028       32     4.1  BA44_exvivo
 5188   3382   8915  2.342 0.449     0.138     0.041       75     8.4  BA45_exvivo
 4605   2869   5541  1.886 0.519     0.130     0.041       58     8.2  V1_exvivo
 8740   5230  10763  1.921 0.571     0.144     0.047      140    15.1  V2_exvivo
 2331   1492   3572  2.330 0.357     0.114     0.026       21     2.2  MT_exvivo
  555    363   1833  3.408 0.768     0.123     0.039        7     0.9  perirhinal_exvivo
  386    246    815  3.042 0.605     0.154     0.049        6     0.9  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 0051362 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 223356
Total vertex volume 220256 (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) = 1467537 mm^3    (det: 1.327466 )
lhCtxGM: 214036.958 213091.000  diff=  946.0  pctdiff= 0.442
rhCtxGM: 218949.061 217938.000  diff= 1011.1  pctdiff= 0.462
lhCtxWM: 219192.958 219856.000  diff= -663.0  pctdiff=-0.302
rhCtxWM: 219057.185 220134.000  diff=-1076.8  pctdiff=-0.492
SubCortGMVol  57435.000
SupraTentVol  948745.161 (946066.000) diff=2679.161 pctdiff=0.282
SupraTentVolNotVent  931192.161 (928513.000) diff=2679.161 pctdiff=0.288
BrainSegVol  1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299
BrainSegVolNotVent  1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002
BrainSegVolNotVent  1048570.000
CerebellumVol 119866.000
VentChorVol   17553.000
3rd4th5thCSF   4131.000
CSFVol   932.000, OptChiasmVol   191.000
MaskVol 1473252.000
  742    284    917  2.186 0.499     0.097     0.038        9     0.9  BA1_exvivo
 1868   1086   2586  2.217 0.436     0.101     0.024       14     1.9  BA2_exvivo
  979    713    923  1.772 0.332     0.142     0.031        9     1.4  BA3a_exvivo
 1575    998   1662  1.690 0.393     0.102     0.023        9     1.7  BA3b_exvivo
 1069    551   1538  2.468 0.445     0.109     0.046       13     2.4  BA4a_exvivo
 1146    714   1674  2.507 0.403     0.093     0.021        5     1.2  BA4p_exvivo
 4918   2842   8396  2.533 0.429     0.109     0.034       54     6.7  BA6_exvivo
  925    609   1862  2.680 0.331     0.116     0.032       10     1.2  BA44_exvivo
 1469    955   2919  2.504 0.388     0.145     0.043       25     2.4  BA45_exvivo
 4421   2768   5210  1.878 0.517     0.130     0.042       55     8.1  V1_exvivo
 4838   2849   5735  1.829 0.550     0.148     0.052       83     9.3  V2_exvivo
  359    209    635  2.391 0.350     0.138     0.038        6     0.6  MT_exvivo
  326    205   1104  3.505 0.662     0.113     0.032        3     0.3  perirhinal_exvivo
  263    177    547  3.012 0.691     0.152     0.043        3     0.6  entorhinal_exvivo

Started at Sat Oct 7 16:52:34 CEST 2017 
Ended   at Sun Oct 8 00:42:52 CEST 2017
#@#%# recon-all-run-time-hours 7.838
recon-all -s 0051362 finished without error at Sun Oct  8 00:42:52 CEST 2017