ABIDE_fs-6.0.0/0050006/scripts/recon-all.log

Sat Oct  7 18:13:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050006 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050006
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-573 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:      65993848   59156296    6837552    1763032          0   54557664
-/+ buffers/cache:    4598632   61395216
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:09-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:09-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-16:13:10-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-573  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-6.0.0/0050006

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/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-6.0.0/0050006/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 18:13:14 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 18:13:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-573 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:13:25 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.10258
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10258/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10258/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.10258/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:13:28 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10258/nu0.mnc ./tmp.mri_nu_correct.mni.10258/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10258/0/ -iterations 1000 -distance 50
[ntraut@tars-573:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/] [2017-10-07 18:13:28] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.10258/0/ ./tmp.mri_nu_correct.mni.10258/nu0.mnc ./tmp.mri_nu_correct.mni.10258/nu1.imp

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Number of iterations: 61 
CV of field change: 0.000983766
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.10258/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.10258/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.10258/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 18:14:46 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 18:14:46 CEST 2017
Ended   at Sat Oct  7 18:15:26 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 18:15:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7494, pval=0.6675 >= 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-6.0.0/0050006/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach_avi.log 

TalAviQA: 0.97802
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 18:15:28 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-6.0.0/0050006/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-573 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 18:15:28 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.11283
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11283/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11283/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.11283/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:15:31 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.11283/nu0.mnc ./tmp.mri_nu_correct.mni.11283/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11283/0/
[ntraut@tars-573:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/] [2017-10-07 18:15:31] 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.11283/0/ ./tmp.mri_nu_correct.mni.11283/nu0.mnc ./tmp.mri_nu_correct.mni.11283/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00126908
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 18:16:25 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.11283/nu1.mnc ./tmp.mri_nu_correct.mni.11283/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11283/1/
[ntraut@tars-573:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/] [2017-10-07 18:16:25] 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.11283/1/ ./tmp.mri_nu_correct.mni.11283/nu1.mnc ./tmp.mri_nu_correct.mni.11283/nu2.imp

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Number of iterations: 50 
CV of field change: 0.00116069
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11283/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-6.0.0/0050006/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11283/ones.mgz 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.11283/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.11283/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.11283/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/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.11283/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/input.mean.dat 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.11283/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.11283/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11283/ones.mgz --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/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.11283/ones.mgz --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/output.mean.dat 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.11283/ones.mgz
Loading ./tmp.mri_nu_correct.mni.11283/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.11283/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.11283/nu2.mnc ./tmp.mri_nu_correct.mni.11283/nu2.mnc mul .78921812247572847802
Saving result to './tmp.mri_nu_correct.mni.11283/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.11283/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.11283/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.11283/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (10, 155) to ( 3, 110)
 
 
Sat Oct  7 18:17:55 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 18:17:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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
 1.03938  -0.02663  -0.11947  -2.32802;
 0.04816   0.97053   0.23096  -2.73907;
 0.08222  -0.18301   1.13977   30.61087;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 21
Starting OpenSpline(): npoints = 21
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 70 (70), valley at 50 (50)
csf peak at 35, setting threshold to 58
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 70 (70), valley at 49 (49)
csf peak at 35, setting threshold to 58
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 51 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 18:19:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=5.0
skull bounding box = (48, 47, 18) --> (208, 238, 223)
using (101, 111, 121) as brain centroid...
mean wm in atlas = 108, using box (81,87,96) --> (120, 134,146) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.8
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.253
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.238317 @ (-9.091, -9.091, -9.091)
max log p =    -4.197597 @ (4.545, 13.636, -4.545)
max log p =    -4.131002 @ (6.818, -6.818, 6.818)
max log p =    -4.098882 @ (-1.136, 1.136, -1.136)
max log p =    -4.088455 @ (-0.568, 0.568, -0.568)
max log p =    -4.074969 @ (0.284, 0.284, 0.284)
Found translation: (0.9, -0.3, -8.2): log p = -4.075
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.934, old_max_log_p =-4.075 (thresh=-4.1)
 1.06580  -0.15927  -0.02372   10.70670;
 0.14032   1.20979   0.18014  -69.03804;
 0.00000  -0.11161   0.99651   8.07736;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.934, old_max_log_p =-3.934 (thresh=-3.9)
 1.06580  -0.15927  -0.02372   10.70670;
 0.14032   1.20979   0.18014  -69.03804;
 0.00000  -0.11161   0.99651   8.07736;
 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=-3.833, old_max_log_p =-3.934 (thresh=-3.9)
 1.05132  -0.04320   0.06034  -8.04028;
 0.03416   1.23318   0.23959  -62.22223;
-0.07308  -0.18299   0.96223   29.65242;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.811, old_max_log_p =-3.833 (thresh=-3.8)
 1.03196  -0.07433   0.01864   1.85345;
 0.06734   1.24745   0.27801  -72.98422;
-0.04166  -0.22705   0.97279   28.69073;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.801, old_max_log_p =-3.811 (thresh=-3.8)
 1.03196  -0.07433   0.01864   1.85345;
 0.06734   1.24745   0.27801  -72.98422;
-0.04088  -0.22279   0.95455   30.23259;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.801, old_max_log_p =-3.801 (thresh=-3.8)
 1.03196  -0.07433   0.01864   1.85345;
 0.06734   1.24745   0.27801  -72.98422;
-0.04088  -0.22279   0.95455   30.23259;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.788, old_max_log_p =-3.801 (thresh=-3.8)
 1.03090  -0.05748   0.03876  -1.86785;
 0.05046   1.24855   0.27742  -70.92123;
-0.05789  -0.22206   0.95636   33.00936;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.787, old_max_log_p =-3.788 (thresh=-3.8)
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 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
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.787 (old=-4.253)
transform before final EM align:
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 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
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.3  tol 0.000000
final transform:
 1.03134  -0.05566   0.03093  -1.69494;
 0.05040   1.24709   0.27709  -70.67151;
-0.04940  -0.22226   0.95552   32.06758;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1395.444860
mri_em_register stimesec    1.555763
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   157614
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    171
mri_em_register ru_nivcsw   2884
registration took 12 minutes and 2 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=116 z=119 r=74
      first estimation of the main basin volume: 1713102 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=147, y=105, z=84, Imax=255
      CSF=14, 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=9517038391 voxels, voxel volume =1.000 
                     = 9517038391 mmm3 = 9517038.592 cm3
done.
PostAnalyze...Basin Prior
 63 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=123, z=111, r=10060 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=14, CSF_MAX=52 , nb = 42362
  RIGHT_CER    CSF_MIN=0, CSF_intensity=11, CSF_MAX=53 , nb = -1029149068
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=71 , nb = -1048385534
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=23, CSF_MAX=48 , nb = 1058576794
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=14, CSF_MAX=49 , nb = 1077599602
    OTHER      CSF_MIN=3, CSF_intensity=30, CSF_MAX=35 , nb = 1069764614
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    52,      51,        51,   67
  after  analyzing :    41,      51,        51,   55
   RIGHT_CER   
  before analyzing :    53,      49,        48,   69
  after  analyzing :    39,      49,        49,   54
   LEFT_CER    
  before analyzing :    71,      51,        45,   66
  after  analyzing :    38,      51,        51,   54
  RIGHT_BRAIN  
  before analyzing :    48,      49,        51,   67
  after  analyzing :    48,      50,        51,   54
  LEFT_BRAIN   
  before analyzing :    49,      50,        51,   67
  after  analyzing :    49,      50,        51,   54
     OTHER     
  before analyzing :    35,      33,        31,   40
  after  analyzing :    32,      33,        33,   34
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...68 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 70.136, std = 8.454

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.77, sigma = 2.84
      after  rotation: sse = 1.77, sigma = 2.84
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  1.83, its var is  2.36   
      before Erosion-Dilatation  0.01% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...43 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1704380 voxels, voxel volume = 1.000 mm3
           = 1704380 mmm3 = 1704.380 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    29.383533
mri_watershed stimesec    0.523920
mri_watershed ru_maxrss   831296
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   215158
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  8808
mri_watershed ru_oublock  2680
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    2145
mri_watershed ru_nivcsw   113
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:32:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=29.9
skull bounding box = (61, 63, 30) --> (195, 183, 206)
using (106, 103, 118) as brain centroid...
mean wm in atlas = 107, using box (90,88,96) --> (122, 117,139) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 3.7
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -3.839
************************************************
First Search limited to translation only.
************************************************
max log p =    -3.838664 @ (0.000, 0.000, 0.000)
max log p =    -3.806117 @ (-4.545, -4.545, -4.545)
max log p =    -3.624559 @ (2.273, 2.273, -2.273)
max log p =    -3.600117 @ (1.136, 1.136, -1.136)
max log p =    -3.600117 @ (0.000, 0.000, 0.000)
max log p =    -3.587332 @ (0.852, -0.852, -0.284)
Found translation: (-0.3, -2.0, -8.2): log p = -3.587
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.485, old_max_log_p =-3.587 (thresh=-3.6)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.06580   0.14032  -25.92068;
 0.00000  -0.13053   0.99144   8.56398;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.477, old_max_log_p =-3.485 (thresh=-3.5)
 1.07500   0.00000   0.00000  -9.81069;
 0.00000   1.14574   0.15084  -36.81149;
 0.00000  -0.12074   0.91709   15.83001;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.477, old_max_log_p =-3.477 (thresh=-3.5)
 1.07500   0.00000   0.00000  -9.81069;
 0.00000   1.14574   0.15084  -36.81149;
 0.00000  -0.12074   0.91709   15.83001;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.331, old_max_log_p =-3.477 (thresh=-3.5)
 1.03026  -0.08375   0.04361   1.07080;
 0.06884   1.11089   0.20991  -48.04515;
-0.07294  -0.20231   0.93719   36.45243;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.331, old_max_log_p =-3.331 (thresh=-3.3)
 1.03026  -0.08375   0.04361   1.07080;
 0.06884   1.11089   0.20991  -48.04515;
-0.07294  -0.20231   0.93719   36.45243;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.294, old_max_log_p =-3.331 (thresh=-3.3)
 1.03130  -0.08073   0.02826   1.78981;
 0.07019   1.11665   0.19507  -47.28871;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.292, old_max_log_p =-3.294 (thresh=-3.3)
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 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
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.292 (old=-3.839)
transform before final EM align:
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 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
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.8  tol 0.000000
final transform:
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1091.679039
mri_em_register stimesec    1.400787
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   158957
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    85
mri_em_register ru_nivcsw   1811
registration took 9 minutes and 22 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:41:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=29.9
skull bounding box = (61, 63, 30) --> (195, 183, 206)
using (106, 103, 118) as brain centroid...
mean wm in atlas = 107, using box (90,88,96) --> (122, 117,139) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 3.7
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 1.02888  -0.08054   0.02819   2.08266;
 0.07035   1.11927   0.19553  -47.67913;
-0.05470  -0.18472   0.93780   31.91876;
 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 (127, 62, 30) --> (193, 163, 204)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 4958 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 65, 27) --> (128, 167, 203)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 4947 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 143, 59) --> (180, 179, 115)
Left_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0
0 of 9 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 144, 54) --> (131, 182, 115)
Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0
0 of 17 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 131, 95) --> (148, 194, 127)
Brain_Stem: limiting intensities to 91.0 --> 132.0
0 of 45 (0.0%) samples deleted
using 9976 total control points for intensity normalization...
bias field = 0.971 +- 0.037
51 of 9976 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (127, 62, 30) --> (193, 163, 204)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
0 of 5587 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 65, 27) --> (128, 167, 203)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 5623 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 143, 59) --> (180, 179, 115)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
18 of 62 (29.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 144, 54) --> (131, 182, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
8 of 59 (13.6%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 131, 95) --> (148, 194, 127)
Brain_Stem: limiting intensities to 88.0 --> 132.0
11 of 132 (8.3%) samples deleted
using 11463 total control points for intensity normalization...
bias field = 1.039 +- 0.041
89 of 11316 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (127, 62, 30) --> (193, 163, 204)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
2 of 5644 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 65, 27) --> (128, 167, 203)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
5 of 5557 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 143, 59) --> (180, 179, 115)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
33 of 103 (32.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 144, 54) --> (131, 182, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
5 of 78 (6.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 131, 95) --> (148, 194, 127)
Brain_Stem: limiting intensities to 88.0 --> 132.0
43 of 188 (22.9%) samples deleted
using 11570 total control points for intensity normalization...
bias field = 1.036 +- 0.039
89 of 11328 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 38 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:43:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 

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

== Number of threads available to mri_ca_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.12 (predicted orig area = 7.1)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.767, neg=0, invalid=762
0001: dt=226.354978, rms=0.724 (5.666%), neg=0, invalid=762
0002: dt=161.113043, rms=0.712 (1.602%), neg=0, invalid=762
0003: dt=369.920000, rms=0.704 (1.164%), neg=0, invalid=762
0004: dt=136.533333, rms=0.700 (0.592%), neg=0, invalid=762
0005: dt=517.888000, rms=0.695 (0.623%), neg=0, invalid=762
0006: dt=129.472000, rms=0.693 (0.266%), neg=0, invalid=762
0007: dt=887.808000, rms=0.689 (0.553%), neg=0, invalid=762
0008: dt=110.976000, rms=0.688 (0.222%), neg=0, invalid=762
0009: dt=110.976000, rms=0.688 (0.054%), neg=0, invalid=762
0010: dt=110.976000, rms=0.687 (0.097%), neg=0, invalid=762
0011: dt=110.976000, rms=0.686 (0.136%), neg=0, invalid=762
0012: dt=110.976000, rms=0.685 (0.157%), neg=0, invalid=762
0013: dt=110.976000, rms=0.684 (0.181%), neg=0, invalid=762
0014: dt=110.976000, rms=0.682 (0.179%), neg=0, invalid=762
0015: dt=110.976000, rms=0.681 (0.169%), neg=0, invalid=762
0016: dt=110.976000, rms=0.680 (0.154%), neg=0, invalid=762
0017: dt=110.976000, rms=0.679 (0.139%), neg=0, invalid=762
0018: dt=110.976000, rms=0.679 (0.117%), neg=0, invalid=762
0019: dt=110.976000, rms=0.678 (0.112%), neg=0, invalid=762
0020: dt=2071.552000, rms=0.676 (0.235%), neg=0, invalid=762
0021: dt=110.976000, rms=0.676 (0.089%), neg=0, invalid=762
0022: dt=110.976000, rms=0.675 (0.017%), neg=0, invalid=762
0023: dt=110.976000, rms=0.675 (0.025%), neg=0, invalid=762
0024: dt=110.976000, rms=0.675 (0.035%), neg=0, invalid=762
0025: dt=110.976000, rms=0.675 (0.056%), neg=0, invalid=762
0026: dt=110.976000, rms=0.674 (0.050%), neg=0, invalid=762
0027: dt=110.976000, rms=0.674 (0.056%), neg=0, invalid=762
0028: dt=110.976000, rms=0.674 (0.053%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.674, neg=0, invalid=762
0029: dt=221.952000, rms=0.672 (0.304%), neg=0, invalid=762
0030: dt=443.904000, rms=0.671 (0.102%), neg=0, invalid=762
0031: dt=443.904000, rms=0.671 (0.043%), neg=0, invalid=762
0032: dt=443.904000, rms=0.670 (0.188%), neg=0, invalid=762
0033: dt=443.904000, rms=0.669 (0.092%), neg=0, invalid=762
0034: dt=443.904000, rms=0.668 (0.162%), neg=0, invalid=762
0035: dt=443.904000, rms=0.667 (0.138%), neg=0, invalid=762
0036: dt=443.904000, rms=0.666 (0.110%), neg=0, invalid=762
0037: dt=443.904000, rms=0.665 (0.159%), neg=0, invalid=762
0038: dt=443.904000, rms=0.664 (0.171%), neg=0, invalid=762
0039: dt=443.904000, rms=0.663 (0.123%), neg=0, invalid=762
0040: dt=443.904000, rms=0.662 (0.156%), neg=0, invalid=762
0041: dt=443.904000, rms=0.662 (0.129%), neg=0, invalid=762
0042: dt=443.904000, rms=0.661 (0.093%), neg=0, invalid=762
0043: dt=443.904000, rms=0.660 (0.142%), neg=0, invalid=762
0044: dt=443.904000, rms=0.659 (0.126%), neg=0, invalid=762
0045: dt=443.904000, rms=0.658 (0.110%), neg=0, invalid=762
0046: dt=443.904000, rms=0.658 (0.077%), neg=0, invalid=762
0047: dt=129.472000, rms=0.658 (0.042%), neg=0, invalid=762
0048: dt=129.472000, rms=0.658 (0.001%), neg=0, invalid=762
0049: dt=129.472000, rms=0.658 (0.004%), neg=0, invalid=762
0050: dt=129.472000, rms=0.658 (0.005%), neg=0, invalid=762
0051: dt=129.472000, rms=0.658 (0.009%), neg=0, invalid=762
0052: dt=129.472000, rms=0.657 (0.009%), neg=0, invalid=762
0053: dt=129.472000, rms=0.657 (0.013%), neg=0, invalid=762
0054: dt=129.472000, rms=0.657 (0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.663, neg=0, invalid=762
0055: dt=78.278215, rms=0.660 (0.416%), neg=0, invalid=762
0056: dt=331.776000, rms=0.652 (1.235%), neg=0, invalid=762
0057: dt=62.608696, rms=0.650 (0.327%), neg=0, invalid=762
0058: dt=331.776000, rms=0.643 (1.009%), neg=0, invalid=762
0059: dt=44.444444, rms=0.640 (0.540%), neg=0, invalid=762
0060: dt=82.944000, rms=0.639 (0.048%), neg=0, invalid=762
0061: dt=82.944000, rms=0.638 (0.186%), neg=0, invalid=762
0062: dt=82.944000, rms=0.637 (0.251%), neg=0, invalid=762
0063: dt=82.944000, rms=0.635 (0.329%), neg=0, invalid=762
0064: dt=82.944000, rms=0.632 (0.470%), neg=0, invalid=762
0065: dt=82.944000, rms=0.628 (0.526%), neg=0, invalid=762
0066: dt=82.944000, rms=0.625 (0.441%), neg=0, invalid=762
0067: dt=82.944000, rms=0.623 (0.351%), neg=0, invalid=762
0068: dt=82.944000, rms=0.621 (0.390%), neg=0, invalid=762
0069: dt=82.944000, rms=0.619 (0.335%), neg=0, invalid=762
0070: dt=82.944000, rms=0.617 (0.211%), neg=0, invalid=762
0071: dt=82.944000, rms=0.616 (0.211%), neg=0, invalid=762
0072: dt=82.944000, rms=0.615 (0.227%), neg=0, invalid=762
0073: dt=82.944000, rms=0.614 (0.155%), neg=0, invalid=762
0074: dt=82.944000, rms=0.613 (0.136%), neg=0, invalid=762
0075: dt=82.944000, rms=0.612 (0.141%), neg=0, invalid=762
0076: dt=82.944000, rms=0.611 (0.114%), neg=0, invalid=762
0077: dt=82.944000, rms=0.611 (0.093%), neg=0, invalid=762
0078: dt=145.152000, rms=0.610 (0.062%), neg=0, invalid=762
0079: dt=145.152000, rms=0.610 (-0.250%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.611, neg=0, invalid=762
0080: dt=64.226148, rms=0.609 (0.334%), neg=0, invalid=762
0081: dt=124.416000, rms=0.609 (0.109%), neg=0, invalid=762
0082: dt=124.416000, rms=0.608 (0.070%), neg=0, invalid=762
0083: dt=124.416000, rms=0.607 (0.116%), neg=0, invalid=762
0084: dt=124.416000, rms=0.607 (-0.075%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.633, neg=0, invalid=762
0085: dt=9.600000, rms=0.632 (0.230%), neg=0, invalid=762
0086: dt=2.800000, rms=0.631 (0.013%), neg=0, invalid=762
0087: dt=2.800000, rms=0.631 (0.006%), neg=0, invalid=762
0088: dt=2.800000, rms=0.631 (-0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.632, neg=0, invalid=762
0089: dt=1.600000, rms=0.631 (0.112%), neg=0, invalid=762
0090: dt=0.500000, rms=0.631 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.691, neg=0, invalid=762
0091: dt=5.864407, rms=0.671 (2.915%), neg=0, invalid=762
0092: dt=5.025641, rms=0.669 (0.279%), neg=0, invalid=762
0093: dt=2.304000, rms=0.669 (0.017%), neg=0, invalid=762
0094: dt=2.304000, rms=0.669 (0.002%), neg=0, invalid=762
0095: dt=2.304000, rms=0.669 (-0.044%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.670, neg=0, invalid=762
0096: dt=0.000000, rms=0.669 (0.084%), neg=0, invalid=762
0097: dt=0.000000, rms=0.669 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.708, neg=0, invalid=762
0098: dt=0.020000, rms=0.707 (0.076%), neg=0, invalid=762
0099: dt=0.007000, rms=0.707 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.708, neg=0, invalid=762
0100: dt=0.320000, rms=0.707 (0.108%), neg=0, invalid=762
0101: dt=0.256000, rms=0.707 (0.014%), neg=0, invalid=762
0102: dt=0.256000, rms=0.707 (0.009%), neg=0, invalid=762
0103: dt=0.256000, rms=0.707 (-0.018%), 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=0.653, neg=0, invalid=762
0104: dt=0.693878, rms=0.640 (2.037%), neg=0, invalid=762
0105: dt=0.064000, rms=0.639 (0.074%), neg=0, invalid=762
0106: dt=0.064000, rms=0.639 (-0.063%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.640, neg=0, invalid=762
0107: dt=0.028000, rms=0.639 (0.108%), neg=0, invalid=762
0108: dt=0.004000, rms=0.639 (0.001%), neg=0, invalid=762
0109: dt=0.004000, rms=0.639 (-0.002%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.09740 (22)
Left_Lateral_Ventricle (4): linear fit = 1.22 x + 0.0 (723 voxels, overlap=0.468)
Left_Lateral_Ventricle (4): linear fit = 1.22 x + 0.0 (723 voxels, peak = 24), gca=24.3
gca peak = 0.15565 (16)
mri peak = 0.08725 (22)
Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (983 voxels, overlap=0.414)
Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (983 voxels, peak = 21), gca=21.4
gca peak = 0.26829 (96)
mri peak = 0.09091 (91)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1016 voxels, overlap=1.003)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1016 voxels, peak = 92), gca=91.7
gca peak = 0.20183 (93)
mri peak = 0.07473 (94)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (909 voxels, overlap=1.014)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (909 voxels, peak = 91), gca=90.7
gca peak = 0.21683 (55)
mri peak = 0.10283 (64)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (903 voxels, overlap=0.223)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (903 voxels, peak = 62), gca=62.4
gca peak = 0.30730 (58)
mri peak = 0.09265 (66)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1017 voxels, overlap=0.588)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1017 voxels, peak = 65), gca=64.7
gca peak = 0.11430 (101)
mri peak = 0.12476 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68436 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68436 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.12561 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (69742 voxels, overlap=0.587)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (69742 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.04342 (66)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (35342 voxels, overlap=0.566)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (35342 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.04774 (67)
Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (36742 voxels, overlap=0.536)
Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (36742 voxels, peak = 65), gca=64.7
gca peak = 0.14161 (67)
mri peak = 0.10644 (75)
Right_Caudate (50): linear fit = 1.09 x + 0.0 (905 voxels, overlap=0.562)
Right_Caudate (50): linear fit = 1.09 x + 0.0 (905 voxels, peak = 73), gca=72.7
gca peak = 0.15243 (71)
mri peak = 0.12975 (79)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (1122 voxels, overlap=0.650)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (1122 voxels, peak = 76), gca=75.6
gca peak = 0.13336 (57)
mri peak = 0.04221 (61)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (36388 voxels, overlap=0.936)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (36388 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.04284 (59)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35269 voxels, overlap=0.944)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35269 voxels, peak = 60), gca=59.6
gca peak = 0.18181 (84)
mri peak = 0.03868 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9481 voxels, overlap=0.517)
Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9481 voxels, peak = 94), gca=93.7
gca peak = 0.20573 (83)
mri peak = 0.04901 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8017 voxels, overlap=0.458)
Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8017 voxels, peak = 93), gca=92.5
gca peak = 0.21969 (57)
mri peak = 0.09678 (67)
Left_Amygdala (18): linear fit = 1.13 x + 0.0 (486 voxels, overlap=0.288)
Left_Amygdala (18): linear fit = 1.13 x + 0.0 (486 voxels, peak = 65), gca=64.7
gca peak = 0.39313 (56)
mri peak = 0.08696 (67)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (574 voxels, overlap=0.152)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (574 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.06497 (87)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5916 voxels, overlap=0.960)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5916 voxels, peak = 86), gca=86.3
gca peak = 0.11978 (83)
mri peak = 0.06782 (84)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5139 voxels, overlap=0.929)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5139 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.07183 (82)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2685 voxels, overlap=0.865)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2685 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.08491 (81)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2744 voxels, overlap=0.912)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2744 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.07592 (93)
Brain_Stem (16): linear fit = 1.15 x + 0.0 (11293 voxels, overlap=0.108)
Brain_Stem (16): linear fit = 1.15 x + 0.0 (11293 voxels, peak = 92), gca=92.4
gca peak = 0.13281 (86)
mri peak = 0.06537 (91)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1349 voxels, overlap=0.631)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1349 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.07649 (91)
Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1636 voxels, overlap=0.752)
Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1636 voxels, peak = 93), gca=93.0
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.08814 (21)
Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (393 voxels, overlap=0.804)
Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (393 voxels, peak = 20), gca=20.3
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 1.13 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.17 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=0.633, neg=0, invalid=762
0110: dt=129.472000, rms=0.626 (1.057%), neg=0, invalid=762
0111: dt=221.952000, rms=0.624 (0.359%), neg=0, invalid=762
0112: dt=295.936000, rms=0.622 (0.314%), neg=0, invalid=762
0113: dt=129.472000, rms=0.621 (0.116%), neg=0, invalid=762
0114: dt=517.888000, rms=0.619 (0.254%), neg=0, invalid=762
0115: dt=73.984000, rms=0.619 (0.080%), neg=0, invalid=762
0116: dt=443.904000, rms=0.618 (0.095%), neg=0, invalid=762
0117: dt=129.472000, rms=0.618 (0.116%), neg=0, invalid=762
0118: dt=129.472000, rms=0.618 (0.021%), neg=0, invalid=762
0119: dt=129.472000, rms=0.617 (0.051%), neg=0, invalid=762
0120: dt=129.472000, rms=0.617 (0.068%), neg=0, invalid=762
0121: dt=129.472000, rms=0.616 (0.077%), neg=0, invalid=762
0122: dt=129.472000, rms=0.616 (0.103%), neg=0, invalid=762
0123: dt=129.472000, rms=0.615 (0.119%), neg=0, invalid=762
0124: dt=129.472000, rms=0.614 (0.115%), neg=0, invalid=762
0125: dt=129.472000, rms=0.614 (0.108%), neg=0, invalid=762
0126: dt=129.472000, rms=0.613 (0.108%), neg=0, invalid=762
0127: dt=129.472000, rms=0.612 (0.096%), neg=0, invalid=762
0128: dt=129.472000, rms=0.612 (0.096%), neg=0, invalid=762
0129: dt=129.472000, rms=0.611 (0.088%), neg=0, invalid=762
0130: dt=129.472000, rms=0.611 (0.079%), neg=0, invalid=762
0131: dt=129.472000, rms=0.610 (0.086%), neg=0, invalid=762
0132: dt=129.472000, rms=0.610 (0.087%), neg=0, invalid=762
0133: dt=129.472000, rms=0.609 (0.079%), neg=0, invalid=762
0134: dt=129.472000, rms=0.609 (0.050%), neg=0, invalid=762
0135: dt=129.472000, rms=0.609 (0.060%), neg=0, invalid=762
0136: dt=129.472000, rms=0.608 (0.072%), neg=0, invalid=762
0137: dt=129.472000, rms=0.608 (0.057%), neg=0, invalid=762
0138: dt=129.472000, rms=0.608 (0.034%), neg=0, invalid=762
0139: dt=129.472000, rms=0.607 (0.046%), neg=0, invalid=762
0140: dt=129.472000, rms=0.607 (0.058%), neg=0, invalid=762
0141: dt=129.472000, rms=0.607 (0.059%), neg=0, invalid=762
0142: dt=129.472000, rms=0.606 (0.042%), neg=0, invalid=762
0143: dt=129.472000, rms=0.606 (0.044%), neg=0, invalid=762
0144: dt=129.472000, rms=0.606 (0.048%), neg=0, invalid=762
0145: dt=129.472000, rms=0.605 (0.055%), neg=0, invalid=762
0146: dt=129.472000, rms=0.605 (0.051%), neg=0, invalid=762
0147: dt=129.472000, rms=0.605 (0.043%), neg=0, invalid=762
0148: dt=129.472000, rms=0.605 (0.041%), neg=0, invalid=762
0149: dt=129.472000, rms=0.604 (0.043%), neg=0, invalid=762
0150: dt=129.472000, rms=0.604 (0.035%), neg=0, invalid=762
0151: dt=129.472000, rms=0.604 (0.043%), neg=0, invalid=762
0152: dt=129.472000, rms=0.604 (0.028%), neg=0, invalid=762
0153: dt=129.472000, rms=0.603 (0.031%), neg=0, invalid=762
0154: dt=129.472000, rms=0.603 (0.039%), neg=0, invalid=762
0155: dt=129.472000, rms=0.603 (0.041%), neg=0, invalid=762
0156: dt=129.472000, rms=0.603 (0.029%), neg=0, invalid=762
0157: dt=129.472000, rms=0.603 (0.016%), neg=0, invalid=762
0158: dt=129.472000, rms=0.603 (0.029%), neg=0, invalid=762
0159: dt=129.472000, rms=0.602 (0.040%), neg=0, invalid=762
0160: dt=129.472000, rms=0.602 (0.038%), neg=0, invalid=762
0161: dt=129.472000, rms=0.602 (0.021%), neg=0, invalid=762
0162: dt=129.472000, rms=0.602 (0.017%), neg=0, invalid=762
0163: dt=1479.680000, rms=0.602 (0.053%), neg=0, invalid=762
0164: dt=8.092000, rms=0.602 (0.002%), neg=0, invalid=762
0165: dt=8.092000, rms=0.602 (0.000%), neg=0, invalid=762
0166: dt=8.092000, rms=0.602 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.602, neg=0, invalid=762
0167: dt=129.472000, rms=0.601 (0.173%), neg=0, invalid=762
0168: dt=443.904000, rms=0.600 (0.093%), neg=0, invalid=762
0169: dt=129.472000, rms=0.600 (0.029%), neg=0, invalid=762
0170: dt=129.472000, rms=0.600 (0.015%), neg=0, invalid=762
0171: dt=129.472000, rms=0.600 (0.027%), neg=0, invalid=762
0172: dt=129.472000, rms=0.600 (0.032%), neg=0, invalid=762
0173: dt=129.472000, rms=0.599 (0.034%), neg=0, invalid=762
0174: dt=129.472000, rms=0.599 (0.029%), neg=0, invalid=762
0175: dt=129.472000, rms=0.599 (0.030%), neg=0, invalid=762
0176: dt=129.472000, rms=0.599 (0.035%), neg=0, invalid=762
0177: dt=129.472000, rms=0.599 (0.029%), neg=0, invalid=762
0178: dt=129.472000, rms=0.599 (0.032%), neg=0, invalid=762
0179: dt=129.472000, rms=0.598 (0.026%), neg=0, invalid=762
0180: dt=129.472000, rms=0.598 (0.026%), neg=0, invalid=762
0181: dt=129.472000, rms=0.598 (0.027%), neg=0, invalid=762
0182: dt=129.472000, rms=0.598 (0.021%), neg=0, invalid=762
0183: dt=129.472000, rms=0.598 (0.022%), neg=0, invalid=762
0184: dt=129.472000, rms=0.598 (0.020%), neg=0, invalid=762
0185: dt=517.888000, rms=0.598 (0.013%), neg=0, invalid=762
0186: dt=517.888000, rms=0.598 (-0.116%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.599, neg=0, invalid=762
0187: dt=36.288000, rms=0.597 (0.284%), neg=0, invalid=762
0188: dt=145.152000, rms=0.595 (0.357%), neg=0, invalid=762
0189: dt=145.152000, rms=0.589 (0.950%), neg=0, invalid=762
0190: dt=36.288000, rms=0.589 (0.067%), neg=0, invalid=762
0191: dt=248.832000, rms=0.587 (0.303%), neg=0, invalid=762
0192: dt=111.659574, rms=0.583 (0.769%), neg=0, invalid=762
0193: dt=25.920000, rms=0.582 (0.072%), neg=0, invalid=762
0194: dt=25.920000, rms=0.582 (0.017%), neg=0, invalid=762
0195: dt=25.920000, rms=0.582 (0.031%), neg=0, invalid=762
0196: dt=25.920000, rms=0.582 (0.057%), neg=0, invalid=762
0197: dt=25.920000, rms=0.581 (0.107%), neg=0, invalid=762
0198: dt=25.920000, rms=0.580 (0.170%), neg=0, invalid=762
0199: dt=25.920000, rms=0.579 (0.228%), neg=0, invalid=762
0200: dt=25.920000, rms=0.577 (0.258%), neg=0, invalid=762
0201: dt=25.920000, rms=0.577 (0.038%), neg=0, invalid=762
0202: dt=25.920000, rms=0.577 (0.070%), neg=0, invalid=762
0203: dt=25.920000, rms=0.576 (0.100%), neg=0, invalid=762
0204: dt=25.920000, rms=0.576 (0.041%), neg=0, invalid=762
0205: dt=25.920000, rms=0.576 (0.041%), neg=0, invalid=762
0206: dt=0.810000, rms=0.576 (0.002%), neg=0, invalid=762
0207: dt=0.202500, rms=0.576 (0.000%), neg=0, invalid=762
0208: dt=0.035437, rms=0.576 (0.000%), neg=0, invalid=762
0209: dt=0.035437, rms=0.576 (0.000%), neg=0, invalid=762
0210: dt=0.004430, rms=0.576 (0.000%), neg=0, invalid=762
0211: dt=0.002215, rms=0.576 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.576, neg=0, invalid=762
0212: dt=0.007594, rms=0.576 (0.086%), neg=0, invalid=762
0213: dt=0.000000, rms=0.576 (0.000%), neg=0, invalid=762
0214: dt=0.000439, rms=0.576 (0.000%), neg=0, invalid=762
0215: dt=0.000220, rms=0.576 (0.000%), neg=0, invalid=762
0216: dt=0.000110, rms=0.576 (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=0.580, neg=0, invalid=762
0217: dt=0.000000, rms=0.580 (0.085%), neg=0, invalid=762
0218: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0219: dt=0.000002, rms=0.580 (0.000%), neg=0, invalid=762
0220: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
0221: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.580, neg=0, invalid=762
0222: dt=63.599284, rms=0.564 (2.775%), neg=0, invalid=762
0223: dt=25.600000, rms=0.555 (1.605%), neg=0, invalid=762
0224: dt=38.400000, rms=0.550 (0.831%), neg=0, invalid=762
0225: dt=25.253561, rms=0.547 (0.679%), neg=0, invalid=762
0226: dt=32.000000, rms=0.544 (0.544%), neg=0, invalid=762
0227: dt=25.600000, rms=0.541 (0.455%), neg=0, invalid=762
0228: dt=30.400000, rms=0.539 (0.420%), neg=0, invalid=762
0229: dt=25.500000, rms=0.537 (0.354%), neg=0, invalid=762
0230: dt=29.765079, rms=0.535 (0.344%), neg=0, invalid=762
0231: dt=25.339367, rms=0.534 (0.287%), neg=0, invalid=762
0232: dt=25.600000, rms=0.532 (0.286%), neg=0, invalid=762
0233: dt=32.000000, rms=0.531 (0.227%), neg=0, invalid=762
0234: dt=24.749245, rms=0.530 (0.255%), neg=0, invalid=762
0235: dt=25.600000, rms=0.529 (0.193%), neg=0, invalid=762
0236: dt=32.000000, rms=0.527 (0.203%), neg=0, invalid=762
0237: dt=24.236686, rms=0.527 (0.179%), neg=0, invalid=762
0238: dt=25.600000, rms=0.526 (0.167%), neg=0, invalid=762
0239: dt=32.000000, rms=0.525 (0.159%), neg=0, invalid=762
0240: dt=25.600000, rms=0.524 (0.148%), neg=0, invalid=762
0241: dt=25.600000, rms=0.523 (0.137%), neg=0, invalid=762
0242: dt=25.600000, rms=0.523 (0.121%), neg=0, invalid=762
0243: dt=38.400000, rms=0.522 (0.140%), neg=0, invalid=762
0244: dt=19.200000, rms=0.521 (0.124%), neg=0, invalid=762
0245: dt=44.800000, rms=0.520 (0.151%), neg=0, invalid=762
0246: dt=25.430464, rms=0.520 (0.107%), neg=0, invalid=762
0247: dt=25.600000, rms=0.519 (0.096%), neg=0, invalid=762
0248: dt=25.600000, rms=0.519 (0.091%), neg=0, invalid=762
0249: dt=32.000000, rms=0.518 (0.095%), neg=0, invalid=762
0250: dt=25.600000, rms=0.518 (0.084%), neg=0, invalid=762
0251: dt=32.000000, rms=0.518 (0.088%), neg=0, invalid=762
0252: dt=19.200000, rms=0.517 (0.078%), neg=0, invalid=762
0253: dt=44.800000, rms=0.517 (0.112%), neg=0, invalid=762
0254: dt=25.600000, rms=0.516 (0.069%), neg=0, invalid=762
0255: dt=32.000000, rms=0.516 (0.075%), neg=0, invalid=762
0256: dt=19.200000, rms=0.516 (0.068%), neg=0, invalid=762
0257: dt=44.800000, rms=0.515 (0.091%), neg=0, invalid=762
0258: dt=19.200000, rms=0.515 (0.058%), neg=0, invalid=762
0259: dt=44.800000, rms=0.514 (0.071%), neg=0, invalid=762
0260: dt=25.600000, rms=0.514 (0.067%), neg=0, invalid=762
0261: dt=32.000000, rms=0.514 (0.060%), neg=0, invalid=762
0262: dt=25.600000, rms=0.513 (0.052%), neg=0, invalid=762
0263: dt=32.000000, rms=0.513 (0.055%), neg=0, invalid=762
0264: dt=19.200000, rms=0.513 (0.053%), neg=0, invalid=762
0265: dt=44.800000, rms=0.513 (0.069%), neg=0, invalid=762
0266: dt=25.600000, rms=0.512 (0.047%), neg=0, invalid=762
0267: dt=25.600000, rms=0.512 (0.049%), neg=0, invalid=762
0268: dt=25.600000, rms=0.512 (0.077%), neg=0, invalid=762
0269: dt=25.600000, rms=0.511 (0.110%), neg=0, invalid=762
0270: dt=25.600000, rms=0.510 (0.130%), neg=0, invalid=762
0271: dt=25.600000, rms=0.510 (0.162%), neg=0, invalid=762
0272: dt=25.600000, rms=0.509 (0.159%), neg=0, invalid=762
0273: dt=25.600000, rms=0.508 (0.177%), neg=0, invalid=762
0274: dt=25.600000, rms=0.507 (0.172%), neg=0, invalid=762
0275: dt=25.600000, rms=0.506 (0.183%), neg=0, invalid=762
0276: dt=25.600000, rms=0.506 (0.015%), neg=0, invalid=762
0277: dt=25.600000, rms=0.506 (0.023%), neg=0, invalid=762
0278: dt=25.600000, rms=0.506 (0.051%), neg=0, invalid=762
0279: dt=25.600000, rms=0.505 (0.051%), neg=0, invalid=762
0280: dt=25.600000, rms=0.505 (0.006%), neg=0, invalid=762
0281: dt=25.600000, rms=0.505 (0.031%), neg=0, invalid=762
0282: dt=25.600000, rms=0.505 (0.052%), neg=0, invalid=762
0283: dt=25.600000, rms=0.505 (0.054%), neg=0, invalid=762
0284: dt=25.600000, rms=0.504 (0.058%), neg=0, invalid=762
0285: dt=25.600000, rms=0.504 (0.064%), neg=0, invalid=762
0286: dt=25.600000, rms=0.504 (0.083%), neg=0, invalid=762
0287: dt=6.400000, rms=0.504 (0.006%), neg=0, invalid=762
0288: dt=6.400000, rms=0.504 (0.004%), neg=0, invalid=762
0289: dt=11.200000, rms=0.504 (0.007%), neg=0, invalid=762
0290: dt=11.200000, rms=0.504 (0.002%), neg=0, invalid=762
0291: dt=11.200000, rms=0.504 (0.006%), neg=0, invalid=762
0292: dt=11.200000, rms=0.503 (0.010%), neg=0, invalid=762
0293: dt=11.200000, rms=0.503 (0.016%), neg=0, invalid=762
0294: dt=11.200000, rms=0.503 (0.016%), neg=0, invalid=762
0295: dt=11.200000, rms=0.503 (0.006%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0296: dt=0.000000, rms=0.520 (0.086%), neg=0, invalid=762
0297: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=762
0298: dt=0.150000, rms=0.520 (-0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.520, neg=0, invalid=762
0299: dt=0.000000, rms=0.520 (0.086%), neg=0, invalid=762
0300: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=762
0301: dt=0.150000, rms=0.520 (-0.011%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.553, neg=0, invalid=762
0302: dt=1.280000, rms=0.550 (0.564%), neg=0, invalid=762
0303: dt=0.448000, rms=0.550 (0.024%), neg=0, invalid=762
0304: dt=0.448000, rms=0.550 (-0.018%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.550, neg=0, invalid=762
0305: dt=1.024000, rms=0.549 (0.190%), neg=0, invalid=762
0306: dt=0.256000, rms=0.549 (0.005%), neg=0, invalid=762
0307: dt=0.256000, rms=0.549 (-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=0.515, neg=0, invalid=762
0308: dt=0.448000, rms=0.503 (2.313%), neg=0, invalid=762
0309: dt=0.448000, rms=0.500 (0.550%), neg=0, invalid=762
0310: dt=0.448000, rms=0.498 (0.305%), neg=0, invalid=762
0311: dt=0.448000, rms=0.498 (0.178%), neg=0, invalid=762
0312: dt=0.448000, rms=0.497 (0.129%), neg=0, invalid=762
0313: dt=0.448000, rms=0.496 (0.088%), neg=0, invalid=762
0314: dt=0.448000, rms=0.496 (0.076%), neg=0, invalid=762
0315: dt=0.448000, rms=0.496 (0.053%), neg=0, invalid=762
0316: dt=0.448000, rms=0.496 (0.047%), neg=0, invalid=762
0317: dt=0.448000, rms=0.495 (0.032%), neg=0, invalid=762
0318: dt=0.448000, rms=0.495 (0.059%), neg=0, invalid=762
0319: dt=0.448000, rms=0.495 (0.078%), neg=0, invalid=762
0320: dt=0.448000, rms=0.494 (0.070%), neg=0, invalid=762
0321: dt=0.448000, rms=0.494 (0.048%), neg=0, invalid=762
0322: dt=0.448000, rms=0.494 (0.037%), neg=0, invalid=762
0323: dt=0.448000, rms=0.494 (0.018%), neg=0, invalid=762
0324: dt=0.448000, rms=0.494 (-0.003%), neg=0, invalid=762
0325: dt=0.028000, rms=0.494 (0.000%), neg=0, invalid=762
0326: dt=0.000750, rms=0.494 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.494, neg=0, invalid=762
0327: dt=0.448000, rms=0.490 (0.957%), neg=0, invalid=762
0328: dt=0.448000, rms=0.489 (0.154%), neg=0, invalid=762
0329: dt=0.448000, rms=0.489 (0.043%), neg=0, invalid=762
0330: dt=0.448000, rms=0.489 (0.025%), neg=0, invalid=762
0331: dt=0.448000, rms=0.488 (0.015%), neg=0, invalid=762
0332: dt=0.224000, rms=0.488 (-0.001%), 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=0.487, neg=0, invalid=762
0333: dt=0.000000, rms=0.486 (0.103%), neg=0, invalid=762
0334: dt=0.000000, rms=0.486 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.487, neg=0, invalid=762
0335: dt=129.472000, rms=0.486 (0.140%), neg=0, invalid=762
0336: dt=110.976000, rms=0.486 (0.008%), neg=0, invalid=762
0337: dt=110.976000, rms=0.486 (0.020%), neg=0, invalid=762
0338: dt=110.976000, rms=0.486 (0.011%), neg=0, invalid=762
0339: dt=110.976000, rms=0.486 (0.007%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.486, neg=0, invalid=762
0340: dt=9.072000, rms=0.486 (0.111%), neg=0, invalid=762
0341: dt=1.620000, rms=0.486 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.486, neg=0, invalid=762
0342: dt=145.152000, rms=0.484 (0.386%), neg=0, invalid=762
0343: dt=31.104000, rms=0.484 (0.095%), neg=0, invalid=762
0344: dt=31.104000, rms=0.484 (0.039%), neg=0, invalid=762
0345: dt=31.104000, rms=0.483 (0.062%), neg=0, invalid=762
0346: dt=31.104000, rms=0.483 (0.079%), neg=0, invalid=762
0347: dt=31.104000, rms=0.483 (0.084%), neg=0, invalid=762
0348: dt=31.104000, rms=0.482 (0.087%), neg=0, invalid=762
0349: dt=31.104000, rms=0.482 (0.087%), neg=0, invalid=762
0350: dt=31.104000, rms=0.481 (0.074%), neg=0, invalid=762
0351: dt=248.832000, rms=0.481 (0.054%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0352: dt=11.200000, rms=0.481 (0.292%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 5 iterations, nbhd size=0, neg = 0
0353: dt=24.483221, rms=0.480 (0.126%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0354: dt=24.483221, rms=0.479 (0.167%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 3 iterations, nbhd size=0, neg = 0
0355: dt=24.483221, rms=0.478 (0.133%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 11 iterations, nbhd size=1, neg = 0
0356: dt=24.483221, rms=0.478 (0.024%), neg=0, invalid=762
iter 0, gcam->neg = 43
after 8 iterations, nbhd size=0, neg = 0
0357: dt=24.483221, rms=0.478 (0.040%), neg=0, invalid=762
iter 0, gcam->neg = 54
after 14 iterations, nbhd size=1, neg = 0
0358: dt=24.483221, rms=0.478 (0.114%), neg=0, invalid=762
iter 0, gcam->neg = 61
after 17 iterations, nbhd size=1, neg = 0
0359: dt=24.483221, rms=0.477 (0.170%), neg=0, invalid=762
iter 0, gcam->neg = 49
after 17 iterations, nbhd size=1, neg = 0
0360: dt=24.483221, rms=0.476 (0.224%), neg=0, invalid=762
iter 0, gcam->neg = 41
after 16 iterations, nbhd size=1, neg = 0
0361: dt=24.483221, rms=0.475 (0.213%), neg=0, invalid=762
iter 0, gcam->neg = 36
after 13 iterations, nbhd size=1, neg = 0
0362: dt=24.483221, rms=0.474 (0.237%), neg=0, invalid=762
iter 0, gcam->neg = 37
after 13 iterations, nbhd size=1, neg = 0
0363: dt=24.483221, rms=0.473 (0.189%), neg=0, invalid=762
iter 0, gcam->neg = 39
after 15 iterations, nbhd size=1, neg = 0
0364: dt=24.483221, rms=0.472 (0.148%), neg=0, invalid=762
iter 0, gcam->neg = 38
after 5 iterations, nbhd size=0, neg = 0
0365: dt=24.483221, rms=0.471 (0.150%), neg=0, invalid=762
iter 0, gcam->neg = 40
after 13 iterations, nbhd size=1, neg = 0
0366: dt=24.483221, rms=0.471 (0.109%), neg=0, invalid=762
iter 0, gcam->neg = 45
after 7 iterations, nbhd size=0, neg = 0
0367: dt=24.483221, rms=0.470 (0.068%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 1 iterations, nbhd size=0, neg = 0
0368: dt=44.800000, rms=0.470 (0.166%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 4 iterations, nbhd size=0, neg = 0
0369: dt=32.000000, rms=0.469 (0.061%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 11 iterations, nbhd size=1, neg = 0
0370: dt=32.000000, rms=0.469 (0.019%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0371: dt=32.000000, rms=0.469 (0.111%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 1 iterations, nbhd size=0, neg = 0
0372: dt=32.000000, rms=0.469 (0.059%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 1 iterations, nbhd size=0, neg = 0
0373: dt=32.000000, rms=0.468 (0.064%), neg=0, invalid=762
iter 0, gcam->neg = 19
after 8 iterations, nbhd size=0, neg = 0
0374: dt=32.000000, rms=0.468 (-0.021%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
0375: dt=38.400000, rms=0.465 (0.869%), neg=0, invalid=762
0376: dt=25.600000, rms=0.463 (0.285%), neg=0, invalid=762
0377: dt=32.000000, rms=0.462 (0.217%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0378: dt=32.000000, rms=0.462 (0.090%), neg=0, invalid=762
0379: dt=32.000000, rms=0.461 (0.262%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0380: dt=32.000000, rms=0.460 (0.150%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0381: dt=32.000000, rms=0.459 (0.170%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0382: dt=32.000000, rms=0.459 (0.016%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 1 iterations, nbhd size=0, neg = 0
0383: dt=32.000000, rms=0.459 (0.093%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0384: dt=32.000000, rms=0.459 (-0.018%), neg=0, invalid=762
0385: dt=38.400000, rms=0.458 (0.095%), neg=0, invalid=762
0386: dt=25.600000, rms=0.458 (0.063%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.465, neg=0, invalid=762
0387: dt=1.333333, rms=0.464 (0.109%), neg=0, invalid=762
0388: dt=0.576000, rms=0.464 (0.005%), neg=0, invalid=762
0389: dt=0.576000, rms=0.464 (0.001%), neg=0, invalid=762
0390: dt=0.576000, rms=0.464 (-0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.465, neg=0, invalid=762
0391: dt=5.066667, rms=0.464 (0.167%), neg=0, invalid=762
0392: dt=4.032000, rms=0.464 (0.027%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0393: dt=4.032000, rms=0.464 (0.017%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 4 iterations, nbhd size=0, neg = 0
0394: dt=4.032000, rms=0.464 (-0.026%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
0395: dt=0.000060, rms=0.472 (0.101%), neg=0, invalid=762
0396: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
0397: dt=1.280000, rms=0.471 (0.204%), neg=0, invalid=762
0398: dt=0.448000, rms=0.471 (0.016%), neg=0, invalid=762
0399: dt=0.448000, rms=0.471 (0.009%), neg=0, invalid=762
0400: dt=0.448000, rms=0.471 (-0.015%), 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=0.463, neg=0, invalid=762
iter 0, gcam->neg = 697
after 15 iterations, nbhd size=1, neg = 0
0401: dt=1.870968, rms=0.440 (4.885%), neg=0, invalid=762
0402: dt=0.007000, rms=0.440 (0.008%), neg=0, invalid=762
0403: dt=0.007000, rms=0.440 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.441, neg=0, invalid=762
0404: dt=0.096000, rms=0.440 (0.195%), neg=0, invalid=762
0405: dt=0.000438, rms=0.440 (0.007%), neg=0, invalid=762
0406: dt=0.000438, rms=0.440 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.429, neg=0, invalid=762
0407: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.429, neg=0, invalid=762
0408: dt=92.480000, rms=0.429 (0.014%), neg=0, invalid=762
0409: dt=129.472000, rms=0.429 (0.007%), neg=0, invalid=762
0410: dt=129.472000, rms=0.429 (0.002%), neg=0, invalid=762
0411: dt=129.472000, rms=0.429 (0.004%), neg=0, invalid=762
0412: dt=129.472000, rms=0.429 (0.002%), neg=0, invalid=762
0413: dt=129.472000, rms=0.429 (0.002%), neg=0, invalid=762
0414: dt=129.472000, rms=0.429 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.429, neg=0, invalid=762
0415: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.429, neg=0, invalid=762
0416: dt=145.152000, rms=0.429 (0.089%), neg=0, invalid=762
0417: dt=103.680000, rms=0.428 (0.042%), neg=0, invalid=762
0418: dt=103.680000, rms=0.428 (0.005%), neg=0, invalid=762
0419: dt=103.680000, rms=0.428 (0.074%), neg=0, invalid=762
0420: dt=103.680000, rms=0.428 (0.040%), neg=0, invalid=762
0421: dt=103.680000, rms=0.428 (0.020%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
0422: dt=6.400000, rms=0.428 (0.033%), neg=0, invalid=762
0423: dt=0.700000, rms=0.428 (0.001%), neg=0, invalid=762
0424: dt=0.700000, rms=0.428 (0.000%), neg=0, invalid=762
0425: dt=0.700000, rms=0.428 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0426: dt=93.288136, rms=0.425 (0.680%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0427: dt=22.235294, rms=0.424 (0.235%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0428: dt=22.235294, rms=0.424 (0.088%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0429: dt=22.235294, rms=0.424 (0.114%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0430: dt=22.235294, rms=0.423 (0.149%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 2 iterations, nbhd size=0, neg = 0
0431: dt=22.235294, rms=0.422 (0.158%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0432: dt=22.235294, rms=0.421 (0.182%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 8 iterations, nbhd size=1, neg = 0
0433: dt=22.235294, rms=0.421 (0.171%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 12 iterations, nbhd size=1, neg = 0
0434: dt=22.235294, rms=0.420 (0.122%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 3 iterations, nbhd size=0, neg = 0
0435: dt=22.235294, rms=0.420 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 2 iterations, nbhd size=0, neg = 0
0436: dt=38.400000, rms=0.420 (0.013%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 8 iterations, nbhd size=0, neg = 0
0437: dt=38.400000, rms=0.420 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 5 iterations, nbhd size=0, neg = 0
0438: dt=38.400000, rms=0.419 (0.035%), neg=0, invalid=762
iter 0, gcam->neg = 46
after 7 iterations, nbhd size=0, neg = 0
0439: dt=38.400000, rms=0.419 (0.028%), neg=0, invalid=762
iter 0, gcam->neg = 39
after 6 iterations, nbhd size=0, neg = 0
0440: dt=38.400000, rms=0.419 (0.038%), neg=0, invalid=762
iter 0, gcam->neg = 40
after 15 iterations, nbhd size=1, neg = 0
0441: dt=38.400000, rms=0.419 (0.036%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
0442: dt=0.000422, rms=0.422 (0.000%), neg=0, invalid=762
0443: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
iter 0, gcam->neg = 4
after 12 iterations, nbhd size=1, neg = 0
0444: dt=7.506173, rms=0.422 (0.038%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 3 iterations, nbhd size=0, neg = 0
0445: dt=14.352941, rms=0.422 (0.089%), neg=0, invalid=762
iter 0, gcam->neg = 77
after 18 iterations, nbhd size=1, neg = 0
0446: dt=34.813187, rms=0.421 (0.187%), neg=0, invalid=762
iter 0, gcam->neg = 95
after 15 iterations, nbhd size=1, neg = 0
0447: dt=29.052632, rms=0.420 (0.173%), neg=0, invalid=762
iter 0, gcam->neg = 210
after 25 iterations, nbhd size=1, neg = 0
0448: dt=29.052632, rms=0.420 (-0.568%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.426, neg=0, invalid=762
0449: dt=0.000050, rms=0.426 (0.000%), neg=0, invalid=762
0450: dt=0.000000, rms=0.426 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.426, neg=0, invalid=762
0451: dt=0.000000, rms=0.426 (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=0.417, neg=0, invalid=762
iter 0, gcam->neg = 508
after 14 iterations, nbhd size=1, neg = 0
0452: dt=1.068138, rms=0.409 (1.766%), neg=0, invalid=762
0453: dt=0.000027, rms=0.409 (0.000%), neg=0, invalid=762
0454: dt=0.000027, 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
0455: dt=0.192000, rms=0.409 (0.142%), neg=0, invalid=762
0456: dt=0.320000, rms=0.408 (0.126%), neg=0, invalid=762
0457: dt=0.320000, rms=0.408 (0.162%), neg=0, invalid=762
iter 0, gcam->neg = 59
after 9 iterations, nbhd size=1, neg = 0
0458: dt=0.320000, rms=0.407 (0.067%), neg=0, invalid=762
iter 0, gcam->neg = 52
after 16 iterations, nbhd size=1, neg = 0
0459: dt=0.320000, rms=0.407 (0.036%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0460: dt=0.320000, rms=0.407 (0.061%), neg=0, invalid=762
0461: dt=0.320000, rms=0.407 (0.048%), neg=0, invalid=762
0462: dt=0.320000, rms=0.407 (0.026%), neg=0, invalid=762
0463: dt=0.320000, rms=0.406 (0.050%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 0 iterations, nbhd size=0, neg = 0
0464: dt=0.320000, rms=0.406 (0.048%), neg=0, invalid=762
iter 0, gcam->neg = 15
after 3 iterations, nbhd size=0, neg = 0
0465: dt=0.320000, rms=0.406 (0.025%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 3 hours, 42 minutes and 28 seconds.
mri_ca_register utimesec    14246.964132
mri_ca_register stimesec    10.876346
mri_ca_register ru_maxrss   1340380
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   5262993
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  65112
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    4241
mri_ca_register ru_nivcsw   19184
FSRUNTIME@ mri_ca_register  3.7078 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 22:25:47 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-573
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-6.0.0/0050006/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.11
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 = 0.09072 (22)
Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (485 voxels, overlap=0.766)
Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (485 voxels, peak = 22), gca=21.9
gca peak = 0.17677 (13)
mri peak = 0.09707 (22)
Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (549 voxels, overlap=0.414)
Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (549 voxels, peak = 19), gca=19.0
gca peak = 0.28129 (95)
mri peak = 0.10693 (92)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (823 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (823 voxels, peak = 92), gca=91.7
gca peak = 0.16930 (96)
mri peak = 0.13614 (93)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (858 voxels, overlap=0.971)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (858 voxels, peak = 94), gca=93.6
gca peak = 0.24553 (55)
mri peak = 0.10943 (67)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1057 voxels, overlap=0.278)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1057 voxels, peak = 64), gca=63.5
gca peak = 0.30264 (59)
mri peak = 0.08655 (64)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (969 voxels, overlap=0.561)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (969 voxels, peak = 65), gca=64.6
gca peak = 0.07580 (103)
mri peak = 0.13466 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, overlap=0.595)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.13371 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.05172 (66)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (47831 voxels, overlap=0.795)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (47831 voxels, peak = 66), gca=65.8
gca peak = 0.11620 (58)
mri peak = 0.05170 (63)
Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (45145 voxels, overlap=0.739)
Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (45145 voxels, peak = 65), gca=64.7
gca peak = 0.30970 (66)
mri peak = 0.14346 (76)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1080 voxels, overlap=0.166)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1080 voxels, peak = 74), gca=74.2
gca peak = 0.15280 (69)
mri peak = 0.16741 (77)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1007 voxels, overlap=0.594)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1007 voxels, peak = 71), gca=70.7
gca peak = 0.13902 (56)
mri peak = 0.05015 (61)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (38897 voxels, overlap=0.914)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (38897 voxels, peak = 62), gca=62.4
gca peak = 0.14777 (55)
mri peak = 0.05034 (61)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35319 voxels, overlap=0.987)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35319 voxels, peak = 59), gca=58.6
gca peak = 0.16765 (84)
mri peak = 0.06262 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5000 voxels, overlap=0.623)
Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5000 voxels, peak = 93), gca=92.8
gca peak = 0.18739 (84)
mri peak = 0.06800 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5255 voxels, overlap=0.673)
Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5255 voxels, peak = 93), gca=92.8
gca peak = 0.29869 (57)
mri peak = 0.09751 (67)
Left_Amygdala (18): linear fit = 1.16 x + 0.0 (523 voxels, overlap=0.057)
Left_Amygdala (18): linear fit = 1.16 x + 0.0 (523 voxels, peak = 66), gca=66.4
gca peak = 0.33601 (57)
mri peak = 0.08288 (71)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (540 voxels, overlap=0.057)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (540 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.07651 (87)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5090 voxels, overlap=0.995)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5090 voxels, peak = 88), gca=87.8
gca peak = 0.11793 (83)
mri peak = 0.08171 (87)
Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (4738 voxels, overlap=0.950)
Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (4738 voxels, peak = 86), gca=85.9
gca peak = 0.08324 (81)
mri peak = 0.09787 (82)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (2062 voxels, overlap=0.705)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (2062 voxels, peak = 84), gca=83.8
gca peak = 0.10360 (77)
mri peak = 0.09535 (81)
Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, overlap=0.748)
Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, peak = 80), gca=79.7
gca peak = 0.08424 (78)
mri peak = 0.07595 (93)
Brain_Stem (16): linear fit = 1.13 x + 0.0 (10892 voxels, overlap=0.278)
Brain_Stem (16): linear fit = 1.13 x + 0.0 (10892 voxels, peak = 89), gca=88.5
gca peak = 0.12631 (89)
mri peak = 0.05955 (94)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1519 voxels, overlap=0.754)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1519 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.07319 (95)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1577 voxels, overlap=0.901)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1577 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.08855 (20)
gca peak = 0.19357 (14)
mri peak = 0.15054 (21)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (87 voxels, overlap=0.849)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (87 voxels, peak = 14), gca=14.5
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 1.14 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.20 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16968 (22)
mri peak = 0.09072 (22)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (485 voxels, overlap=0.799)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (485 voxels, peak = 23), gca=22.5
gca peak = 0.12269 (18)
mri peak = 0.09707 (22)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (549 voxels, overlap=0.684)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (549 voxels, peak = 18), gca=18.0
gca peak = 0.24779 (91)
mri peak = 0.10693 (92)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (823 voxels, overlap=1.002)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (823 voxels, peak = 91), gca=90.5
gca peak = 0.20154 (94)
mri peak = 0.13614 (93)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (858 voxels, overlap=1.004)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (858 voxels, peak = 94), gca=93.5
gca peak = 0.24791 (64)
mri peak = 0.10943 (67)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1057 voxels, overlap=1.002)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1057 voxels, peak = 63), gca=63.0
gca peak = 0.22572 (65)
mri peak = 0.08655 (64)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (969 voxels, overlap=1.006)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (969 voxels, peak = 65), gca=65.0
gca peak = 0.07581 (103)
mri peak = 0.13466 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, overlap=0.595)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.13371 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, peak = 104), gca=104.0
gca peak = 0.08621 (66)
mri peak = 0.05172 (66)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (47831 voxels, overlap=0.977)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (47831 voxels, peak = 65), gca=65.0
gca peak = 0.10555 (65)
mri peak = 0.05170 (63)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45145 voxels, overlap=0.965)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45145 voxels, peak = 65), gca=65.0
gca peak = 0.25483 (75)
mri peak = 0.14346 (76)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1080 voxels, overlap=1.000)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1080 voxels, peak = 75), gca=75.0
gca peak = 0.15167 (70)
mri peak = 0.16741 (77)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1007 voxels, overlap=0.715)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1007 voxels, peak = 70), gca=70.0
gca peak = 0.12891 (62)
mri peak = 0.05015 (61)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (38897 voxels, overlap=0.998)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (38897 voxels, peak = 61), gca=61.1
gca peak = 0.13819 (58)
mri peak = 0.05034 (61)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (35319 voxels, overlap=0.998)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (35319 voxels, peak = 59), gca=59.4
gca peak = 0.14189 (93)
mri peak = 0.06262 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5000 voxels, overlap=0.980)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5000 voxels, peak = 93), gca=92.5
gca peak = 0.16472 (93)
mri peak = 0.06800 (91)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5255 voxels, overlap=0.988)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5255 voxels, peak = 92), gca=91.6
gca peak = 0.30333 (68)
mri peak = 0.09751 (67)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (523 voxels, overlap=1.012)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (523 voxels, peak = 68), gca=68.0
gca peak = 0.29912 (68)
mri peak = 0.08288 (71)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (540 voxels, overlap=1.004)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (540 voxels, peak = 67), gca=67.0
gca peak = 0.11133 (86)
mri peak = 0.07651 (87)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5090 voxels, overlap=0.995)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5090 voxels, peak = 86), gca=85.6
gca peak = 0.10043 (86)
mri peak = 0.08171 (87)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4738 voxels, overlap=0.973)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4738 voxels, peak = 86), gca=86.0
gca peak = 0.08229 (84)
mri peak = 0.09787 (82)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (2062 voxels, overlap=0.835)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (2062 voxels, peak = 85), gca=85.3
gca peak = 0.10883 (78)
mri peak = 0.09535 (81)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2306 voxels, overlap=0.857)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2306 voxels, peak = 79), gca=79.2
gca peak = 0.07777 (89)
mri peak = 0.07595 (93)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (10892 voxels, overlap=0.816)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (10892 voxels, peak = 89), gca=89.4
gca peak = 0.11370 (96)
mri peak = 0.05955 (94)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1519 voxels, overlap=0.881)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1519 voxels, peak = 96), gca=95.5
gca peak = 0.16198 (91)
mri peak = 0.07319 (95)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1577 voxels, overlap=0.965)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1577 voxels, peak = 90), gca=89.6
gca peak = 0.16785 (31)
mri peak = 0.08855 (20)
gca peak = 0.18343 (17)
mri peak = 0.15054 (21)
Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (87 voxels, overlap=0.859)
Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (87 voxels, peak = 20), gca=19.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16329 (35)
gca peak Left_Thalamus = 0.64095 (101)
gca peak Third_Ventricle = 0.16785 (31)
gca peak CSF = 0.19138 (43)
gca peak Left_Accumbens_area = 0.88917 (64)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11914 (35)
gca peak Right_Inf_Lat_Vent = 0.18678 (27)
gca peak Right_Accumbens_area = 0.30005 (73)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14524 (37)
gca peak Fifth_Ventricle = 0.65271 (38)
gca peak WM_hypointensities = 0.07965 (76)
gca peak non_WM_hypointensities = 0.08569 (76)
gca peak Optic_Chiasm = 0.70851 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.06 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
64856 voxels changed in iteration 0 of unlikely voxel relabeling
432 voxels changed in iteration 1 of unlikely voxel relabeling
21 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
51500 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
530 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 68534 changed. image ll: -2.111, PF=0.500
pass 2: 17938 changed. image ll: -2.110, PF=0.500
pass 3: 5861 changed.
pass 4: 2219 changed.
43092 voxels changed in iteration 0 of unlikely voxel relabeling
330 voxels changed in iteration 1 of unlikely voxel relabeling
53 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8778 voxels changed in iteration 0 of unlikely voxel relabeling
171 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6596 voxels changed in iteration 0 of unlikely voxel relabeling
83 voxels changed in iteration 1 of unlikely voxel relabeling
45 voxels changed in iteration 2 of unlikely voxel relabeling
2 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
5887 voxels changed in iteration 0 of unlikely voxel relabeling
16 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3682.938108
mri_ca_label stimesec    1.682744
mri_ca_label ru_maxrss   2094028
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   698207
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  65104
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    270
mri_ca_label ru_nivcsw   4759
auto-labeling took 60 minutes and 37 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/cc_up.lta 0050006 

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-6.0.0/0050006/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/norm.mgz
78469 voxels in left wm, 70753 in right wm, xrange [119, 133]
searching rotation angles z=[-1 13], y=[-5  9]

searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.8  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.3  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.8  
searching scale 1 Z rot 9.1  
searching scale 1 Z rot 9.3  
searching scale 1 Z rot 9.6  
searching scale 1 Z rot 9.8  
searching scale 1 Z rot 10.1  
searching scale 1 Z rot 10.3  
searching scale 1 Z rot 10.6  
searching scale 1 Z rot 10.8  
searching scale 1 Z rot 11.1  
searching scale 1 Z rot 11.3  
searching scale 1 Z rot 11.6  
searching scale 1 Z rot 11.8  
searching scale 1 Z rot 12.1  
searching scale 1 Z rot 12.3  
searching scale 1 Z rot 12.6  
searching scale 1 Z rot 12.8  global minimum found at slice 125.0, rotations (1.81, 6.09)
final transformation (x=125.0, yr=1.805, zr=6.087):
 0.99387  -0.10604   0.03133   11.16102;
 0.10599   0.99436   0.00334   10.95006;
-0.03150  -0.00000   0.99950   15.99569;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 127
cc center is found at 127 104 116
eigenvectors:
 0.00099  -0.00060   1.00000;
-0.07342  -0.99730  -0.00053;
 0.99730  -0.07342  -0.00103;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.5 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 23:27:57 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 23:27:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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...
978 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 71 (71), valley at 23 (23)
csf peak at 36, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 71 (71), valley at 23 (23)
csf peak at 36, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 53 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 23:30:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1682152 voxels in mask (pct= 10.03)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 23:30:52 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (102.0): 102.3 +- 7.0 [79.0 --> 125.0]
GM (73.0) : 71.5 +- 8.9 [30.0 --> 95.0]
setting bottom of white matter range to 80.4
setting top of gray matter range to 89.3
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...
6846 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3552 filled
3106 bright non-wm voxels segmented.
2576 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 0.44 minutes
reading wm segmentation from wm.seg.mgz...
76 voxels added to wm to prevent paths from MTL structures to cortex
2541 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 31668 voxels turned on, 32540 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  20 found -  20 modified     |    TOTAL:  20
pass   2 (xy+):   0 found -  20 modified     |    TOTAL:  20
pass   1 (xy-):  23 found -  23 modified     |    TOTAL:  43
pass   2 (xy-):   0 found -  23 modified     |    TOTAL:  43
pass   1 (yz+):  30 found -  30 modified     |    TOTAL:  73
pass   2 (yz+):   0 found -  30 modified     |    TOTAL:  73
pass   1 (yz-):  27 found -  27 modified     |    TOTAL: 100
pass   2 (yz-):   0 found -  27 modified     |    TOTAL: 100
pass   1 (xz+):  12 found -  12 modified     |    TOTAL: 112
pass   2 (xz+):   0 found -  12 modified     |    TOTAL: 112
pass   1 (xz-):  23 found -  23 modified     |    TOTAL: 135
pass   2 (xz-):   0 found -  23 modified     |    TOTAL: 135
Iteration Number : 1
pass   1 (+++):  44 found -  44 modified     |    TOTAL:  44
pass   2 (+++):   0 found -  44 modified     |    TOTAL:  44
pass   1 (+++):  28 found -  28 modified     |    TOTAL:  72
pass   2 (+++):   0 found -  28 modified     |    TOTAL:  72
pass   1 (+++):  52 found -  52 modified     |    TOTAL: 124
pass   2 (+++):   0 found -  52 modified     |    TOTAL: 124
pass   1 (+++):  42 found -  42 modified     |    TOTAL: 166
pass   2 (+++):   0 found -  42 modified     |    TOTAL: 166
Iteration Number : 1
pass   1 (++): 104 found - 104 modified     |    TOTAL: 104
pass   2 (++):   0 found - 104 modified     |    TOTAL: 104
pass   1 (+-): 128 found - 128 modified     |    TOTAL: 232
pass   2 (+-):   0 found - 128 modified     |    TOTAL: 232
pass   1 (--): 105 found - 105 modified     |    TOTAL: 337
pass   2 (--):   0 found - 105 modified     |    TOTAL: 337
pass   1 (-+): 132 found - 132 modified     |    TOTAL: 469
pass   2 (-+):   0 found - 132 modified     |    TOTAL: 469
Iteration Number : 2
pass   1 (xy+):   9 found -   9 modified     |    TOTAL:   9
pass   2 (xy+):   0 found -   9 modified     |    TOTAL:   9
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  14
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  14
pass   1 (yz+):  13 found -  13 modified     |    TOTAL:  27
pass   2 (yz+):   0 found -  13 modified     |    TOTAL:  27
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  30
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  30
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  33
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  33
pass   1 (xz-):   8 found -   8 modified     |    TOTAL:  41
pass   2 (xz-):   0 found -   8 modified     |    TOTAL:  41
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   8
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  10
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  10
Iteration Number : 2
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   4 found -   4 modified     |    TOTAL:   7
pass   2 (+-):   0 found -   4 modified     |    TOTAL:   7
pass   1 (--):   2 found -   2 modified     |    TOTAL:   9
pass   2 (--):   0 found -   2 modified     |    TOTAL:   9
pass   1 (-+):   5 found -   5 modified     |    TOTAL:  14
pass   2 (-+):   0 found -   5 modified     |    TOTAL:  14
Iteration Number : 3
pass   1 (xy+):   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+):   3 found -   3 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   4
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 3
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
Iteration Number : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 850 (out of 580398: 0.146451)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 23:33:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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
 1.02888  -0.08054   0.02819   2.08265;
 0.07035   1.11927   0.19553  -47.67914;
-0.05470  -0.18472   0.93780   31.91875;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.02888  -0.08054   0.02819   2.08265;
 0.07035   1.11927   0.19553  -47.67914;
-0.05470  -0.18472   0.93780   31.91875;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2456 (min = 350, max = 1400), aspect = 1.34 (min = 0.10, max = 0.75)
need search nearby
using seed (125, 121, 151), TAL = (3.0, 23.0, 7.0)
talairach voxel to voxel transform
 0.96542   0.06253  -0.04206   2.31326;
-0.06817   0.85930  -0.17711   46.76616;
 0.04289   0.17290   1.02898  -24.68933;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (125,  121,  151) --> (3.0, 23.0, 7.0)
done.
writing output to filled.mgz...
filling took 0.6 minutes
talairach cc position changed to (3.00, 23.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, 23.00, 7.00) SRC: (106.83, 116.70, 156.20)
search lh wm seed point around talairach space (-15.00, 23.00, 7.00), SRC: (141.58, 114.25, 157.74)
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 23:33:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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


Iteration Number : 1
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:  12
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:  12
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:  13
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:  13
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  16
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  16
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  18
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  18
pass   1 (xz-):   5 found -   5 modified     |    TOTAL:  23
pass   2 (xz-):   0 found -   5 modified     |    TOTAL:  23
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 (--):   3 found -   3 modified     |    TOTAL:   3
pass   2 (--):   0 found -   3 modified     |    TOTAL:   3
pass   1 (-+):   4 found -   4 modified     |    TOTAL:   7
pass   2 (-+):   0 found -   4 modified     |    TOTAL:   7
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 = 30 (out of 280687: 0.010688)
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: 2246 vertices, 2382 faces
slice 50: 9265 vertices, 9530 faces
slice 60: 17955 vertices, 18307 faces
slice 70: 29001 vertices, 29361 faces
slice 80: 39947 vertices, 40313 faces
slice 90: 52117 vertices, 52572 faces
slice 100: 65369 vertices, 65861 faces
slice 110: 78563 vertices, 79032 faces
slice 120: 91171 vertices, 91628 faces
slice 130: 103292 vertices, 103769 faces
slice 140: 115868 vertices, 116375 faces
slice 150: 126398 vertices, 126837 faces
slice 160: 135392 vertices, 135799 faces
slice 170: 143602 vertices, 143962 faces
slice 180: 150392 vertices, 150729 faces
slice 190: 156453 vertices, 156732 faces
slice 200: 160011 vertices, 160203 faces
slice 210: 160614 vertices, 160722 faces
slice 220: 160614 vertices, 160722 faces
slice 230: 160614 vertices, 160722 faces
slice 240: 160614 vertices, 160722 faces
slice 250: 160614 vertices, 160722 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...
   160614 voxel in cpt #1: X=-108 [v=160614,e=482166,f=321444] located at (-25.583124, -15.946038, 14.179648)
For the whole surface: X=-108 [v=160614,e=482166,f=321444]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 23:33:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:   9
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:   9
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  10
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  10
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  11
Iteration Number : 1
pass   1 (+++):   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 (--):   3 found -   3 modified     |    TOTAL:   3
pass   2 (--):   0 found -   3 modified     |    TOTAL:   3
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 15 (out of 277893: 0.005398)
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: 2642 vertices, 2824 faces
slice 50: 10235 vertices, 10544 faces
slice 60: 20000 vertices, 20380 faces
slice 70: 31129 vertices, 31551 faces
slice 80: 42855 vertices, 43229 faces
slice 90: 54815 vertices, 55243 faces
slice 100: 67830 vertices, 68286 faces
slice 110: 80377 vertices, 80814 faces
slice 120: 92596 vertices, 93064 faces
slice 130: 104464 vertices, 104884 faces
slice 140: 115812 vertices, 116329 faces
slice 150: 126283 vertices, 126717 faces
slice 160: 135533 vertices, 135910 faces
slice 170: 143299 vertices, 143608 faces
slice 180: 150104 vertices, 150398 faces
slice 190: 155440 vertices, 155685 faces
slice 200: 158605 vertices, 158745 faces
slice 210: 158914 vertices, 159006 faces
slice 220: 158914 vertices, 159006 faces
slice 230: 158914 vertices, 159006 faces
slice 240: 158914 vertices, 159006 faces
slice 250: 158914 vertices, 159006 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...
   158914 voxel in cpt #1: X=-92 [v=158914,e=477018,f=318012] located at (29.024014, -17.883068, 10.140586)
For the whole surface: X=-92 [v=158914,e=477018,f=318012]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 23:33:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 23:33:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

Waiting for PID 27981 of (27981 27984) to complete...
Waiting for PID 27984 of (27981 27984) 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 (27981 27984) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 23:33:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 23:33:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

Waiting for PID 28029 of (28029 28032) to complete...
Waiting for PID 28032 of (28029 28032) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 48.1 mm, total surface area = 83182 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.163 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.095 (target=0.015)   
step 015: RMS=0.082 (target=0.015)   
step 020: RMS=0.072 (target=0.015)   
step 025: RMS=0.067 (target=0.015)   
step 030: RMS=0.062 (target=0.015)   
step 035: RMS=0.059 (target=0.015)   
step 040: RMS=0.056 (target=0.015)   
step 045: RMS=0.055 (target=0.015)   
step 050: RMS=0.053 (target=0.015)   
step 055: RMS=0.054 (target=0.015)   
step 060: RMS=0.054 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    47.735743
mris_inflate stimesec    0.106983
mris_inflate ru_maxrss   234328
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33480
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11304
mris_inflate ru_oublock  11320
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2368
mris_inflate ru_nivcsw   3485

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.3 mm, total surface area = 82355 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.161 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.070 (target=0.015)   
step 025: RMS=0.061 (target=0.015)   
step 030: RMS=0.057 (target=0.015)   
step 035: RMS=0.052 (target=0.015)   
step 040: RMS=0.051 (target=0.015)   
step 045: RMS=0.049 (target=0.015)   
step 050: RMS=0.048 (target=0.015)   
step 055: RMS=0.047 (target=0.015)   
step 060: RMS=0.047 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    47.129835
mris_inflate stimesec    0.103984
mris_inflate ru_maxrss   232148
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33445
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11184
mris_inflate ru_oublock  11200
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2306
mris_inflate ru_nivcsw   3500
PIDs (28029 28032) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 23:34:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 23:34:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

Waiting for PID 28095 of (28095 28099) to complete...
Waiting for PID 28099 of (28095 28099) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.91 +- 0.56 (0.00-->7.11) (max @ vno 66493 --> 67872)
face area 0.02 +- 0.03 (-0.21-->0.77)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.283...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.523, avgs=0
005/300: dt: 0.9000, rms radial error=177.262, avgs=0
010/300: dt: 0.9000, rms radial error=176.703, avgs=0
015/300: dt: 0.9000, rms radial error=175.969, avgs=0
020/300: dt: 0.9000, rms radial error=175.137, avgs=0
025/300: dt: 0.9000, rms radial error=174.243, avgs=0
030/300: dt: 0.9000, rms radial error=173.316, avgs=0
035/300: dt: 0.9000, rms radial error=172.372, avgs=0
040/300: dt: 0.9000, rms radial error=171.419, avgs=0
045/300: dt: 0.9000, rms radial error=170.464, avgs=0
050/300: dt: 0.9000, rms radial error=169.509, avgs=0
055/300: dt: 0.9000, rms radial error=168.557, avgs=0
060/300: dt: 0.9000, rms radial error=167.607, avgs=0
065/300: dt: 0.9000, rms radial error=166.662, avgs=0
070/300: dt: 0.9000, rms radial error=165.722, avgs=0
075/300: dt: 0.9000, rms radial error=164.787, avgs=0
080/300: dt: 0.9000, rms radial error=163.857, avgs=0
085/300: dt: 0.9000, rms radial error=162.933, avgs=0
090/300: dt: 0.9000, rms radial error=162.014, avgs=0
095/300: dt: 0.9000, rms radial error=161.101, avgs=0
100/300: dt: 0.9000, rms radial error=160.193, avgs=0
105/300: dt: 0.9000, rms radial error=159.289, avgs=0
110/300: dt: 0.9000, rms radial error=158.391, avgs=0
115/300: dt: 0.9000, rms radial error=157.497, avgs=0
120/300: dt: 0.9000, rms radial error=156.609, avgs=0
125/300: dt: 0.9000, rms radial error=155.725, avgs=0
130/300: dt: 0.9000, rms radial error=154.846, avgs=0
135/300: dt: 0.9000, rms radial error=153.971, avgs=0
140/300: dt: 0.9000, rms radial error=153.101, avgs=0
145/300: dt: 0.9000, rms radial error=152.236, avgs=0
150/300: dt: 0.9000, rms radial error=151.376, avgs=0
155/300: dt: 0.9000, rms radial error=150.521, avgs=0
160/300: dt: 0.9000, rms radial error=149.670, avgs=0
165/300: dt: 0.9000, rms radial error=148.825, avgs=0
170/300: dt: 0.9000, rms radial error=147.984, avgs=0
175/300: dt: 0.9000, rms radial error=147.147, avgs=0
180/300: dt: 0.9000, rms radial error=146.315, avgs=0
185/300: dt: 0.9000, rms radial error=145.488, avgs=0
190/300: dt: 0.9000, rms radial error=144.665, avgs=0
195/300: dt: 0.9000, rms radial error=143.847, avgs=0
200/300: dt: 0.9000, rms radial error=143.034, avgs=0
205/300: dt: 0.9000, rms radial error=142.225, avgs=0
210/300: dt: 0.9000, rms radial error=141.420, avgs=0
215/300: dt: 0.9000, rms radial error=140.621, avgs=0
220/300: dt: 0.9000, rms radial error=139.825, avgs=0
225/300: dt: 0.9000, rms radial error=139.034, avgs=0
230/300: dt: 0.9000, rms radial error=138.247, avgs=0
235/300: dt: 0.9000, rms radial error=137.465, avgs=0
240/300: dt: 0.9000, rms radial error=136.689, avgs=0
245/300: dt: 0.9000, rms radial error=135.917, avgs=0
250/300: dt: 0.9000, rms radial error=135.149, avgs=0
255/300: dt: 0.9000, rms radial error=134.386, avgs=0
260/300: dt: 0.9000, rms radial error=133.627, avgs=0
265/300: dt: 0.9000, rms radial error=132.872, avgs=0
270/300: dt: 0.9000, rms radial error=132.122, avgs=0
275/300: dt: 0.9000, rms radial error=131.376, avgs=0
280/300: dt: 0.9000, rms radial error=130.634, avgs=0
285/300: dt: 0.9000, rms radial error=129.896, avgs=0
290/300: dt: 0.9000, rms radial error=129.162, avgs=0
295/300: dt: 0.9000, rms radial error=128.433, avgs=0
300/300: dt: 0.9000, rms radial error=127.708, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19409.92
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 2 (K=40.0), pass 1, starting sse = 3495.05
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 3 (K=160.0), pass 1, starting sse = 426.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00432
epoch 4 (K=640.0), pass 1, starting sse = 40.55
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/13 = 0.00780
final distance error %29.56
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    283.006976
mris_sphere stimesec    0.225965
mris_sphere ru_maxrss   234540
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33542
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11344
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8538
mris_sphere ru_nivcsw   19180
FSRUNTIME@ mris_sphere  0.0771 hours 1 threads

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.57 (0.00-->9.55) (max @ vno 95896 --> 97007)
face area 0.02 +- 0.03 (-0.42-->0.50)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.285...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.349, avgs=0
005/300: dt: 0.9000, rms radial error=177.090, avgs=0
010/300: dt: 0.9000, rms radial error=176.533, avgs=0
015/300: dt: 0.9000, rms radial error=175.802, avgs=0
020/300: dt: 0.9000, rms radial error=174.970, avgs=0
025/300: dt: 0.9000, rms radial error=174.080, avgs=0
030/300: dt: 0.9000, rms radial error=173.156, avgs=0
035/300: dt: 0.9000, rms radial error=172.215, avgs=0
040/300: dt: 0.9000, rms radial error=171.267, avgs=0
045/300: dt: 0.9000, rms radial error=170.316, avgs=0
050/300: dt: 0.9000, rms radial error=169.367, avgs=0
055/300: dt: 0.9000, rms radial error=168.421, avgs=0
060/300: dt: 0.9000, rms radial error=167.478, avgs=0
065/300: dt: 0.9000, rms radial error=166.539, avgs=0
070/300: dt: 0.9000, rms radial error=165.605, avgs=0
075/300: dt: 0.9000, rms radial error=164.675, avgs=0
080/300: dt: 0.9000, rms radial error=163.751, avgs=0
085/300: dt: 0.9000, rms radial error=162.831, avgs=0
090/300: dt: 0.9000, rms radial error=161.916, avgs=0
095/300: dt: 0.9000, rms radial error=161.006, avgs=0
100/300: dt: 0.9000, rms radial error=160.101, avgs=0
105/300: dt: 0.9000, rms radial error=159.200, avgs=0
110/300: dt: 0.9000, rms radial error=158.305, avgs=0
115/300: dt: 0.9000, rms radial error=157.414, avgs=0
120/300: dt: 0.9000, rms radial error=156.529, avgs=0
125/300: dt: 0.9000, rms radial error=155.648, avgs=0
130/300: dt: 0.9000, rms radial error=154.772, avgs=0
135/300: dt: 0.9000, rms radial error=153.900, avgs=0
140/300: dt: 0.9000, rms radial error=153.034, avgs=0
145/300: dt: 0.9000, rms radial error=152.172, avgs=0
150/300: dt: 0.9000, rms radial error=151.314, avgs=0
155/300: dt: 0.9000, rms radial error=150.461, avgs=0
160/300: dt: 0.9000, rms radial error=149.613, avgs=0
165/300: dt: 0.9000, rms radial error=148.770, avgs=0
170/300: dt: 0.9000, rms radial error=147.934, avgs=0
175/300: dt: 0.9000, rms radial error=147.098, avgs=0
180/300: dt: 0.9000, rms radial error=146.268, avgs=0
185/300: dt: 0.9000, rms radial error=145.444, avgs=0
190/300: dt: 0.9000, rms radial error=144.623, avgs=0
195/300: dt: 0.9000, rms radial error=143.807, avgs=0
200/300: dt: 0.9000, rms radial error=142.996, avgs=0
205/300: dt: 0.9000, rms radial error=142.189, avgs=0
210/300: dt: 0.9000, rms radial error=141.386, avgs=0
215/300: dt: 0.9000, rms radial error=140.589, avgs=0
220/300: dt: 0.9000, rms radial error=139.797, avgs=0
225/300: dt: 0.9000, rms radial error=139.008, avgs=0
230/300: dt: 0.9000, rms radial error=138.224, avgs=0
235/300: dt: 0.9000, rms radial error=137.444, avgs=0
240/300: dt: 0.9000, rms radial error=136.669, avgs=0
245/300: dt: 0.9000, rms radial error=135.898, avgs=0
250/300: dt: 0.9000, rms radial error=135.132, avgs=0
255/300: dt: 0.9000, rms radial error=134.370, avgs=0
260/300: dt: 0.9000, rms radial error=133.610, avgs=0
265/300: dt: 0.9000, rms radial error=132.856, avgs=0
270/300: dt: 0.9000, rms radial error=132.106, avgs=0
275/300: dt: 0.9000, rms radial error=131.361, avgs=0
280/300: dt: 0.9000, rms radial error=130.620, avgs=0
285/300: dt: 0.9000, rms radial error=129.882, avgs=0
290/300: dt: 0.9000, rms radial error=129.150, avgs=0
295/300: dt: 0.9000, rms radial error=128.420, avgs=0
300/300: dt: 0.9000, rms radial error=127.696, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19143.10
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 2 (K=40.0), pass 1, starting sse = 3424.21
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 414.57
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00325
epoch 4 (K=640.0), pass 1, starting sse = 38.91
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/10 = 0.00622
final distance error %30.79
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    268.332207
mris_sphere stimesec    0.252961
mris_sphere ru_maxrss   232368
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33504
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11184
mris_sphere ru_oublock  11224
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8364
mris_sphere ru_nivcsw   19398
FSRUNTIME@ mris_sphere  0.0746 hours 1 threads
PIDs (28095 28099) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 23:39:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 23:39:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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


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

#@# Fix Topology lh Sat Oct  7 23:39:22 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 lh 

#@# Fix Topology rh Sat Oct  7 23:39:22 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 rh 

Waiting for PID 28615 of (28615 28618) to complete...
Waiting for PID 28618 of (28615 28618) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 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=-108 (nv=160614, nf=321444, ne=482166, g=55)
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...
15866 ambiguous faces found in tessellation
segmenting defects...
56 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 21 into 14
      -merging segment 25 into 14
      -merging segment 36 into 38
53 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1987  (-4.5994)
      -vertex     loglikelihood: -5.8552  (-2.9276)
      -normal dot loglikelihood: -3.5753  (-3.5753)
      -quad curv  loglikelihood: -6.2378  (-3.1189)
      Total Loglikelihood : -24.8670

CORRECTING DEFECT 0 (vertices=60, convex hull=95, v0=3826)
After retessellation of defect 0 (v0=3826), euler #=-52 (151554,452337,300731) : difference with theory (-50) = 2 

CORRECTING DEFECT 1 (vertices=21, convex hull=50, v0=4325)
After retessellation of defect 1 (v0=4325), euler #=-51 (151562,452383,300770) : difference with theory (-49) = 2 

CORRECTING DEFECT 2 (vertices=270, convex hull=235, v0=10444)
After retessellation of defect 2 (v0=10444), euler #=-50 (151695,452892,301147) : difference with theory (-48) = 2 

CORRECTING DEFECT 3 (vertices=27, convex hull=62, v0=12555)
After retessellation of defect 3 (v0=12555), euler #=-49 (151704,452942,301189) : difference with theory (-47) = 2 

CORRECTING DEFECT 4 (vertices=21, convex hull=24, v0=13306)
After retessellation of defect 4 (v0=13306), euler #=-48 (151708,452958,301202) : difference with theory (-46) = 2 

CORRECTING DEFECT 5 (vertices=78, convex hull=91, v0=14968)
After retessellation of defect 5 (v0=14968), euler #=-47 (151722,453044,301275) : difference with theory (-45) = 2 

CORRECTING DEFECT 6 (vertices=22, convex hull=66, v0=21129)
After retessellation of defect 6 (v0=21129), euler #=-46 (151731,453095,301318) : difference with theory (-44) = 2 

CORRECTING DEFECT 7 (vertices=21, convex hull=59, v0=40671)
After retessellation of defect 7 (v0=40671), euler #=-45 (151741,453143,301357) : difference with theory (-43) = 2 

CORRECTING DEFECT 8 (vertices=107, convex hull=37, v0=41801)
After retessellation of defect 8 (v0=41801), euler #=-44 (151744,453167,301379) : difference with theory (-42) = 2 

CORRECTING DEFECT 9 (vertices=56, convex hull=44, v0=49317)
After retessellation of defect 9 (v0=49317), euler #=-43 (151748,453195,301404) : difference with theory (-41) = 2 

CORRECTING DEFECT 10 (vertices=766, convex hull=289, v0=49763)
After retessellation of defect 10 (v0=49763), euler #=-42 (151838,453607,301727) : difference with theory (-40) = 2 

CORRECTING DEFECT 11 (vertices=39, convex hull=69, v0=54593)
After retessellation of defect 11 (v0=54593), euler #=-41 (151865,453718,301812) : difference with theory (-39) = 2 

CORRECTING DEFECT 12 (vertices=381, convex hull=222, v0=58001)
After retessellation of defect 12 (v0=58001), euler #=-40 (151928,454020,302052) : difference with theory (-38) = 2 

CORRECTING DEFECT 13 (vertices=15, convex hull=27, v0=63491)
After retessellation of defect 13 (v0=63491), euler #=-39 (151935,454049,302075) : difference with theory (-37) = 2 

CORRECTING DEFECT 14 (vertices=1511, convex hull=717, v0=63848)
XL defect detected...
After retessellation of defect 14 (v0=63848), euler #=-36 (152399,455822,303387) : difference with theory (-36) = 0 

CORRECTING DEFECT 15 (vertices=22, convex hull=22, v0=74911)
After retessellation of defect 15 (v0=74911), euler #=-35 (152402,455838,303401) : difference with theory (-35) = 0 

CORRECTING DEFECT 16 (vertices=552, convex hull=155, v0=76707)
After retessellation of defect 16 (v0=76707), euler #=-34 (152474,456124,303616) : difference with theory (-34) = 0 

CORRECTING DEFECT 17 (vertices=10, convex hull=27, v0=79537)
After retessellation of defect 17 (v0=79537), euler #=-33 (152476,456138,303629) : difference with theory (-33) = 0 

CORRECTING DEFECT 18 (vertices=23, convex hull=47, v0=81151)
After retessellation of defect 18 (v0=81151), euler #=-32 (152480,456173,303661) : difference with theory (-32) = 0 

CORRECTING DEFECT 19 (vertices=10, convex hull=27, v0=81886)
After retessellation of defect 19 (v0=81886), euler #=-31 (152485,456194,303678) : difference with theory (-31) = 0 

CORRECTING DEFECT 20 (vertices=48, convex hull=27, v0=85509)
After retessellation of defect 20 (v0=85509), euler #=-30 (152492,456227,303705) : difference with theory (-30) = 0 

CORRECTING DEFECT 21 (vertices=42, convex hull=57, v0=88734)
After retessellation of defect 21 (v0=88734), euler #=-29 (152495,456259,303735) : difference with theory (-29) = 0 

CORRECTING DEFECT 22 (vertices=34, convex hull=21, v0=91490)
After retessellation of defect 22 (v0=91490), euler #=-28 (152500,456282,303754) : difference with theory (-28) = 0 

CORRECTING DEFECT 23 (vertices=829, convex hull=258, v0=94781)
After retessellation of defect 23 (v0=94781), euler #=-27 (152588,456672,304057) : difference with theory (-27) = 0 

CORRECTING DEFECT 24 (vertices=24, convex hull=41, v0=97771)
After retessellation of defect 24 (v0=97771), euler #=-26 (152603,456736,304107) : difference with theory (-26) = 0 

CORRECTING DEFECT 25 (vertices=950, convex hull=234, v0=97775)
After retessellation of defect 25 (v0=97775), euler #=-25 (152638,456946,304283) : difference with theory (-25) = 0 

CORRECTING DEFECT 26 (vertices=154, convex hull=79, v0=99562)
After retessellation of defect 26 (v0=99562), euler #=-24 (152648,457010,304338) : difference with theory (-24) = 0 

CORRECTING DEFECT 27 (vertices=21, convex hull=28, v0=100075)
After retessellation of defect 27 (v0=100075), euler #=-23 (152652,457032,304357) : difference with theory (-23) = 0 

CORRECTING DEFECT 28 (vertices=9, convex hull=29, v0=100543)
After retessellation of defect 28 (v0=100543), euler #=-22 (152654,457047,304371) : difference with theory (-22) = 0 

CORRECTING DEFECT 29 (vertices=27, convex hull=31, v0=101637)
After retessellation of defect 29 (v0=101637), euler #=-21 (152656,457065,304388) : difference with theory (-21) = 0 

CORRECTING DEFECT 30 (vertices=10, convex hull=26, v0=105322)
After retessellation of defect 30 (v0=105322), euler #=-20 (152658,457080,304402) : difference with theory (-20) = 0 

CORRECTING DEFECT 31 (vertices=32, convex hull=36, v0=105416)
After retessellation of defect 31 (v0=105416), euler #=-19 (152668,457121,304434) : difference with theory (-19) = 0 

CORRECTING DEFECT 32 (vertices=14, convex hull=29, v0=107803)
After retessellation of defect 32 (v0=107803), euler #=-18 (152671,457138,304449) : difference with theory (-18) = 0 

CORRECTING DEFECT 33 (vertices=135, convex hull=167, v0=109047)
After retessellation of defect 33 (v0=109047), euler #=-18 (152744,457442,304680) : difference with theory (-17) = 1 

CORRECTING DEFECT 34 (vertices=129, convex hull=106, v0=111588)
After retessellation of defect 34 (v0=111588), euler #=-17 (152783,457609,304809) : difference with theory (-16) = 1 

CORRECTING DEFECT 35 (vertices=1908, convex hull=685, v0=112772)
XL defect detected...
After retessellation of defect 35 (v0=112772), euler #=-15 (152851,458210,305344) : difference with theory (-15) = 0 

CORRECTING DEFECT 36 (vertices=23, convex hull=32, v0=115400)
After retessellation of defect 36 (v0=115400), euler #=-14 (152855,458232,305363) : difference with theory (-14) = 0 

CORRECTING DEFECT 37 (vertices=106, convex hull=52, v0=129063)
After retessellation of defect 37 (v0=129063), euler #=-13 (152871,458303,305419) : difference with theory (-13) = 0 

CORRECTING DEFECT 38 (vertices=5, convex hull=15, v0=130165)
After retessellation of defect 38 (v0=130165), euler #=-12 (152872,458309,305425) : difference with theory (-12) = 0 

CORRECTING DEFECT 39 (vertices=49, convex hull=71, v0=132039)
After retessellation of defect 39 (v0=132039), euler #=-11 (152899,458418,305508) : difference with theory (-11) = 0 

CORRECTING DEFECT 40 (vertices=21, convex hull=30, v0=133544)
After retessellation of defect 40 (v0=133544), euler #=-10 (152902,458436,305524) : difference with theory (-10) = 0 

CORRECTING DEFECT 41 (vertices=28, convex hull=60, v0=133632)
After retessellation of defect 41 (v0=133632), euler #=-9 (152911,458487,305567) : difference with theory (-9) = 0 

CORRECTING DEFECT 42 (vertices=46, convex hull=82, v0=136164)
After retessellation of defect 42 (v0=136164), euler #=-8 (152924,458561,305629) : difference with theory (-8) = 0 

CORRECTING DEFECT 43 (vertices=38, convex hull=64, v0=137730)
After retessellation of defect 43 (v0=137730), euler #=-7 (152942,458641,305692) : difference with theory (-7) = 0 

CORRECTING DEFECT 44 (vertices=122, convex hull=56, v0=139984)
After retessellation of defect 44 (v0=139984), euler #=-6 (152951,458697,305740) : difference with theory (-6) = 0 

CORRECTING DEFECT 45 (vertices=60, convex hull=25, v0=143095)
After retessellation of defect 45 (v0=143095), euler #=-5 (152957,458724,305762) : difference with theory (-5) = 0 

CORRECTING DEFECT 46 (vertices=20, convex hull=51, v0=146351)
After retessellation of defect 46 (v0=146351), euler #=-4 (152965,458767,305798) : difference with theory (-4) = 0 

CORRECTING DEFECT 47 (vertices=50, convex hull=74, v0=150371)
After retessellation of defect 47 (v0=150371), euler #=-3 (152977,458835,305855) : difference with theory (-3) = 0 

CORRECTING DEFECT 48 (vertices=34, convex hull=87, v0=151922)
After retessellation of defect 48 (v0=151922), euler #=-2 (152999,458936,305935) : difference with theory (-2) = 0 

CORRECTING DEFECT 49 (vertices=52, convex hull=74, v0=154557)
After retessellation of defect 49 (v0=154557), euler #=-1 (153019,459024,306004) : difference with theory (-1) = 0 

CORRECTING DEFECT 50 (vertices=11, convex hull=26, v0=156893)
After retessellation of defect 50 (v0=156893), euler #=0 (153021,459039,306018) : difference with theory (0) = 0 

CORRECTING DEFECT 51 (vertices=13, convex hull=26, v0=160355)
After retessellation of defect 51 (v0=160355), euler #=1 (153024,459056,306033) : difference with theory (1) = 0 

CORRECTING DEFECT 52 (vertices=11, convex hull=28, v0=160590)
After retessellation of defect 52 (v0=160590), euler #=2 (153025,459069,306046) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.26 (0.03-->11.36) (max @ vno 121583 --> 126997)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.26 (0.03-->11.36) (max @ vno 121583 --> 126997)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
198 mutations (32.9%), 404 crossovers (67.1%), 966 vertices were eliminated
building final representation...
7589 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=153025, nf=306046, ne=459069, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 70.5 minutes
0 defective edges
removing intersecting faces
000: 651 intersecting
001: 18 intersecting
002: 5 intersecting
mris_fix_topology utimesec    4230.759826
mris_fix_topology stimesec    0.305953
mris_fix_topology ru_maxrss   530052
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   63828
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22608
mris_fix_topology ru_oublock  14832
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    667
mris_fix_topology ru_nivcsw   9041
FSRUNTIME@ mris_fix_topology lh  1.1747 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 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=-92 (nv=158914, nf=318012, ne=477018, g=47)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 12 iterations
marking ambiguous vertices...
13495 ambiguous faces found in tessellation
segmenting defects...
32 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 6 into 4
      -merging segment 7 into 4
30 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1832  (-4.5916)
      -vertex     loglikelihood: -5.8634  (-2.9317)
      -normal dot loglikelihood: -3.6471  (-3.6471)
      -quad curv  loglikelihood: -6.1569  (-3.0785)
      Total Loglikelihood : -24.8507

CORRECTING DEFECT 0 (vertices=71, convex hull=92, v0=158)
After retessellation of defect 0 (v0=158), euler #=-25 (151242,451658,300391) : difference with theory (-27) = -2 

CORRECTING DEFECT 1 (vertices=26, convex hull=53, v0=19594)
After retessellation of defect 1 (v0=19594), euler #=-24 (151253,451713,300436) : difference with theory (-26) = -2 

CORRECTING DEFECT 2 (vertices=9, convex hull=21, v0=27143)
After retessellation of defect 2 (v0=27143), euler #=-23 (151253,451720,300444) : difference with theory (-25) = -2 

CORRECTING DEFECT 3 (vertices=1954, convex hull=617, v0=36596)
XL defect detected...
After retessellation of defect 3 (v0=36596), euler #=-22 (151449,452625,301154) : difference with theory (-24) = -2 

CORRECTING DEFECT 4 (vertices=1329, convex hull=670, v0=45991)
XL defect detected...
After retessellation of defect 4 (v0=45991), euler #=-20 (151789,454029,302220) : difference with theory (-23) = -3 

CORRECTING DEFECT 5 (vertices=50, convex hull=66, v0=56055)
After retessellation of defect 5 (v0=56055), euler #=-19 (151818,454145,302308) : difference with theory (-22) = -3 

CORRECTING DEFECT 6 (vertices=389, convex hull=327, v0=82549)
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 3 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 3 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 3 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 3 faces
normal vector of length zero at vertex 154914 with 3 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
normal vector of length zero at vertex 154914 with 4 faces
After retessellation of defect 6 (v0=82549), euler #=-18 (151965,454752,302769) : difference with theory (-21) = -3 

CORRECTING DEFECT 7 (vertices=188, convex hull=153, v0=86552)
After retessellation of defect 7 (v0=86552), euler #=-17 (152008,454951,302926) : difference with theory (-20) = -3 

CORRECTING DEFECT 8 (vertices=96, convex hull=125, v0=88132)
After retessellation of defect 8 (v0=88132), euler #=-16 (152021,455049,303012) : difference with theory (-19) = -3 

CORRECTING DEFECT 9 (vertices=27, convex hull=15, v0=99763)
After retessellation of defect 9 (v0=99763), euler #=-15 (152022,455057,303020) : difference with theory (-18) = -3 

CORRECTING DEFECT 10 (vertices=1102, convex hull=465, v0=108461)
L defect detected...
After retessellation of defect 10 (v0=108461), euler #=-16 (152279,456096,303801) : difference with theory (-17) = -1 

CORRECTING DEFECT 11 (vertices=44, convex hull=91, v0=108594)
After retessellation of defect 11 (v0=108594), euler #=-15 (152299,456199,303885) : difference with theory (-16) = -1 

CORRECTING DEFECT 12 (vertices=911, convex hull=254, v0=109473)
After retessellation of defect 12 (v0=109473), euler #=-14 (152382,456567,304171) : difference with theory (-15) = -1 

CORRECTING DEFECT 13 (vertices=191, convex hull=93, v0=112780)
After retessellation of defect 13 (v0=112780), euler #=-14 (152427,456743,304302) : difference with theory (-14) = 0 

CORRECTING DEFECT 14 (vertices=314, convex hull=145, v0=115593)
After retessellation of defect 14 (v0=115593), euler #=-13 (152460,456907,304434) : difference with theory (-13) = 0 

CORRECTING DEFECT 15 (vertices=31, convex hull=59, v0=116463)
After retessellation of defect 15 (v0=116463), euler #=-12 (152474,456974,304488) : difference with theory (-12) = 0 

CORRECTING DEFECT 16 (vertices=55, convex hull=88, v0=118352)
After retessellation of defect 16 (v0=118352), euler #=-11 (152504,457100,304585) : difference with theory (-11) = 0 

CORRECTING DEFECT 17 (vertices=58, convex hull=43, v0=125173)
After retessellation of defect 17 (v0=125173), euler #=-10 (152513,457145,304622) : difference with theory (-10) = 0 

CORRECTING DEFECT 18 (vertices=168, convex hull=70, v0=126569)
After retessellation of defect 18 (v0=126569), euler #=-9 (152526,457215,304680) : difference with theory (-9) = 0 

CORRECTING DEFECT 19 (vertices=49, convex hull=42, v0=129221)
After retessellation of defect 19 (v0=129221), euler #=-8 (152537,457264,304719) : difference with theory (-8) = 0 

CORRECTING DEFECT 20 (vertices=112, convex hull=35, v0=131139)
After retessellation of defect 20 (v0=131139), euler #=-7 (152538,457285,304740) : difference with theory (-7) = 0 

CORRECTING DEFECT 21 (vertices=26, convex hull=58, v0=136509)
After retessellation of defect 21 (v0=136509), euler #=-6 (152547,457334,304781) : difference with theory (-6) = 0 

CORRECTING DEFECT 22 (vertices=65, convex hull=78, v0=141888)
After retessellation of defect 22 (v0=141888), euler #=-5 (152563,457415,304847) : difference with theory (-5) = 0 

CORRECTING DEFECT 23 (vertices=30, convex hull=27, v0=141911)
After retessellation of defect 23 (v0=141911), euler #=-4 (152565,457428,304859) : difference with theory (-4) = 0 

CORRECTING DEFECT 24 (vertices=114, convex hull=103, v0=145450)
After retessellation of defect 24 (v0=145450), euler #=-3 (152586,457540,304951) : difference with theory (-3) = 0 

CORRECTING DEFECT 25 (vertices=37, convex hull=94, v0=146732)
After retessellation of defect 25 (v0=146732), euler #=-2 (152607,457641,305032) : difference with theory (-2) = 0 

CORRECTING DEFECT 26 (vertices=49, convex hull=86, v0=150850)
After retessellation of defect 26 (v0=150850), euler #=-1 (152635,457761,305125) : difference with theory (-1) = 0 

CORRECTING DEFECT 27 (vertices=112, convex hull=141, v0=153022)
After retessellation of defect 27 (v0=153022), euler #=0 (152681,457967,305286) : difference with theory (0) = 0 

CORRECTING DEFECT 28 (vertices=50, convex hull=88, v0=155124)
After retessellation of defect 28 (v0=155124), euler #=1 (152706,458079,305374) : difference with theory (1) = 0 

CORRECTING DEFECT 29 (vertices=38, convex hull=84, v0=157208)
After retessellation of defect 29 (v0=157208), euler #=2 (152724,458166,305444) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.24 (0.02-->11.72) (max @ vno 83717 --> 93593)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.24 (0.02-->11.72) (max @ vno 83717 --> 93593)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
82 mutations (31.1%), 182 crossovers (68.9%), 740 vertices were eliminated
building final representation...
6190 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=152724, nf=305444, ne=458166, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 44.0 minutes
0 defective edges
removing intersecting faces
000: 568 intersecting
001: 12 intersecting
mris_fix_topology utimesec    2640.701552
mris_fix_topology stimesec    0.981850
mris_fix_topology ru_maxrss   512368
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   59154
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  22368
mris_fix_topology ru_oublock  14712
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    407
mris_fix_topology ru_nivcsw   4466
FSRUNTIME@ mris_fix_topology rh  0.7335 hours 1 threads
PIDs (28615 28618) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 153025 - 459069 + 306046 = 2 --> 0 holes
      F =2V-4:          306046 = 306050-4 (0)
      2E=3F:            918138 = 918138 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 152724 - 458166 + 305444 = 2 --> 0 holes
      F =2V-4:          305444 = 305448-4 (0)
      2E=3F:            916332 = 916332 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 123 intersecting
001: 18 intersecting
002: 4 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 132 intersecting
001: 9 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:50:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:50:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 rh 

Waiting for PID 1320 of (1320 1323) to complete...
Waiting for PID 1323 of (1320 1323) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
19474 bright wm thresholded.
3500 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.orig...
computing class statistics...
border white:    288670 voxels (1.72%)
border gray      347901 voxels (2.07%)
WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0]
GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70)
setting MAX_BORDER_WHITE to 110.9 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 52.8 (was 40)
setting MAX_GRAY to 95.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.03-->7.04) (max @ vno 77459 --> 152075)
face area 0.28 +- 0.14 (0.00-->8.73)
mean absolute distance = 0.64 +- 0.80
5404 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-5.2,    GM=71+-6.1
mean inside = 94.2, mean outside = 78.2
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=83.3, 167 (167) missing vertices, mean dist 0.2 [0.5 (%42.0)->0.7 (%58.0))]
%83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.04-->7.15) (max @ vno 77459 --> 152075)
face area 0.28 +- 0.14 (0.00-->10.04)
mean absolute distance = 0.31 +- 0.51
3489 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2737872.2, rms=8.446
001: dt: 0.5000, sse=1601978.5, rms=5.807 (31.251%)
002: dt: 0.5000, sse=1160721.5, rms=4.345 (25.169%)
003: dt: 0.5000, sse=993428.0, rms=3.639 (16.258%)
004: dt: 0.5000, sse=917421.2, rms=3.263 (10.333%)
005: dt: 0.5000, sse=891752.8, rms=3.127 (4.161%)
006: dt: 0.5000, sse=871919.6, rms=3.012 (3.690%)
rms = 2.98, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=868484.8, rms=2.985 (0.896%)
008: dt: 0.2500, sse=741577.9, rms=2.012 (32.589%)
009: dt: 0.2500, sse=720294.9, rms=1.836 (8.727%)
rms = 1.80, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=715609.6, rms=1.797 (2.148%)
rms = 1.77, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=713068.8, rms=1.773 (1.334%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=85.9, 137 (60) missing vertices, mean dist -0.2 [0.3 (%75.4)->0.3 (%24.6))]
%89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.07-->7.16) (max @ vno 77459 --> 152075)
face area 0.35 +- 0.17 (0.00-->13.66)
mean absolute distance = 0.23 +- 0.38
3591 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1257121.0, rms=4.087
012: dt: 0.5000, sse=962587.1, rms=2.559 (37.377%)
013: dt: 0.5000, sse=941239.1, rms=2.448 (4.351%)
rms = 2.43, time step reduction 1 of 3 to 0.250...
014: dt: 0.5000, sse=937403.0, rms=2.429 (0.766%)
015: dt: 0.2500, sse=858673.9, rms=1.706 (29.761%)
016: dt: 0.2500, sse=839972.4, rms=1.557 (8.771%)
rms = 1.52, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=837607.2, rms=1.520 (2.364%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=832455.5, rms=1.492 (1.840%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=87.5, 157 (48) missing vertices, mean dist -0.1 [0.2 (%67.8)->0.2 (%32.2))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.07-->7.15) (max @ vno 77459 --> 152075)
face area 0.34 +- 0.17 (0.00-->13.94)
mean absolute distance = 0.21 +- 0.32
3258 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=931380.2, rms=2.522
019: dt: 0.5000, sse=883103.1, rms=2.029 (19.566%)
rms = 2.13, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=822568.7, rms=1.589 (21.685%)
021: dt: 0.2500, sse=820281.9, rms=1.383 (12.934%)
022: dt: 0.2500, sse=803458.6, rms=1.325 (4.240%)
rms = 1.32, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=802911.9, rms=1.321 (0.291%)
rms = 1.30, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=801105.9, rms=1.297 (1.781%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.0, 159 (33) missing vertices, mean dist -0.0 [0.2 (%54.9)->0.2 (%45.1))]
%93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=807180.8, rms=1.483
025: dt: 0.5000, sse=799083.2, rms=1.369 (7.704%)
rms = 1.70, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=776283.5, rms=1.158 (15.442%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=778308.6, rms=1.135 (2.006%)
rms = 1.10, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=770976.8, rms=1.105 (2.639%)
positioning took 0.6 minutes
generating cortex label...
20 non-cortical segments detected
only using segment with 7416 vertices
erasing segment 0 (vno[0] = 37102)
erasing segment 2 (vno[0] = 74662)
erasing segment 3 (vno[0] = 90456)
erasing segment 4 (vno[0] = 106432)
erasing segment 5 (vno[0] = 106538)
erasing segment 6 (vno[0] = 107647)
erasing segment 7 (vno[0] = 107694)
erasing segment 8 (vno[0] = 107698)
erasing segment 9 (vno[0] = 108911)
erasing segment 10 (vno[0] = 109987)
erasing segment 11 (vno[0] = 110897)
erasing segment 12 (vno[0] = 111828)
erasing segment 13 (vno[0] = 112774)
erasing segment 14 (vno[0] = 114550)
erasing segment 15 (vno[0] = 123498)
erasing segment 16 (vno[0] = 126692)
erasing segment 17 (vno[0] = 128472)
erasing segment 18 (vno[0] = 129161)
erasing segment 19 (vno[0] = 129217)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.03-->7.07) (max @ vno 77459 --> 152075)
face area 0.33 +- 0.17 (0.00-->13.83)
refinement took 5.9 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
19474 bright wm thresholded.
3500 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.orig...
computing class statistics...
border white:    288670 voxels (1.72%)
border gray      347901 voxels (2.07%)
WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0]
GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70)
setting MAX_BORDER_WHITE to 110.9 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 53.8 (was 40)
setting MAX_GRAY to 95.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.03-->6.45) (max @ vno 106323 --> 152152)
face area 0.28 +- 0.13 (0.00-->6.14)
mean absolute distance = 0.62 +- 0.76
5103 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-6.1,    GM=72+-5.2
mean inside = 94.0, mean outside = 78.1
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.4, 102 (102) missing vertices, mean dist 0.2 [0.5 (%43.2)->0.7 (%56.8))]
%81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.08-->6.68) (max @ vno 106323 --> 152152)
face area 0.28 +- 0.13 (0.00-->5.46)
mean absolute distance = 0.30 +- 0.48
3451 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2656823.5, rms=8.274
001: dt: 0.5000, sse=1536624.8, rms=5.592 (32.408%)
002: dt: 0.5000, sse=1104104.9, rms=4.113 (26.455%)
003: dt: 0.5000, sse=942800.1, rms=3.390 (17.578%)
004: dt: 0.5000, sse=870693.2, rms=3.008 (11.255%)
005: dt: 0.5000, sse=844174.9, rms=2.857 (5.046%)
006: dt: 0.5000, sse=830967.4, rms=2.764 (3.236%)
rms = 2.76, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=829254.0, rms=2.760 (0.134%)
008: dt: 0.2500, sse=701601.4, rms=1.678 (39.195%)
009: dt: 0.2500, sse=686544.6, rms=1.455 (13.285%)
rms = 1.41, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=678947.2, rms=1.410 (3.148%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=675191.9, rms=1.371 (2.708%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=85.9, 104 (45) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))]
%88 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.07-->6.39) (max @ vno 106323 --> 152152)
face area 0.34 +- 0.16 (0.00-->6.95)
mean absolute distance = 0.23 +- 0.35
4531 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1188095.6, rms=3.792
012: dt: 0.5000, sse=918986.5, rms=2.270 (40.154%)
013: dt: 0.5000, sse=907736.0, rms=2.196 (3.224%)
rms = 2.19, time step reduction 1 of 3 to 0.250...
014: dt: 0.5000, sse=900842.8, rms=2.189 (0.325%)
015: dt: 0.2500, sse=820975.2, rms=1.354 (38.142%)
016: dt: 0.2500, sse=809150.6, rms=1.217 (10.154%)
rms = 1.21, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=808378.4, rms=1.207 (0.803%)
rms = 1.17, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=805461.3, rms=1.168 (3.236%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=87.5, 110 (36) missing vertices, mean dist -0.1 [0.2 (%68.0)->0.2 (%32.0))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.09-->6.32) (max @ vno 106323 --> 152152)
face area 0.33 +- 0.16 (0.00-->6.88)
mean absolute distance = 0.21 +- 0.30
4062 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=912179.8, rms=2.386
019: dt: 0.5000, sse=852922.6, rms=1.887 (20.941%)
rms = 1.98, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=805822.6, rms=1.404 (25.601%)
021: dt: 0.2500, sse=789320.5, rms=1.168 (16.774%)
022: dt: 0.2500, sse=782370.5, rms=1.105 (5.387%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
rms = 1.09, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=780965.1, rms=1.089 (1.454%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.1, 115 (31) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))]
%92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=788040.1, rms=1.312
024: dt: 0.5000, sse=785306.8, rms=1.257 (4.129%)
rms = 1.65, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=764289.4, rms=0.962 (23.511%)
rms = 0.92, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=766876.1, rms=0.918 (4.592%)
027: dt: 0.1250, sse=761314.9, rms=0.863 (5.944%)
rms = 0.85, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=756585.7, rms=0.848 (1.781%)
positioning took 0.7 minutes
generating cortex label...
16 non-cortical segments detected
only using segment with 6801 vertices
erasing segment 0 (vno[0] = 42361)
erasing segment 1 (vno[0] = 42398)
erasing segment 2 (vno[0] = 46842)
erasing segment 4 (vno[0] = 69635)
erasing segment 5 (vno[0] = 93981)
erasing segment 6 (vno[0] = 108364)
erasing segment 7 (vno[0] = 109341)
erasing segment 8 (vno[0] = 109469)
erasing segment 9 (vno[0] = 109484)
erasing segment 10 (vno[0] = 111496)
erasing segment 11 (vno[0] = 111547)
erasing segment 12 (vno[0] = 113607)
erasing segment 13 (vno[0] = 115193)
erasing segment 14 (vno[0] = 152183)
erasing segment 15 (vno[0] = 152419)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.03-->6.19) (max @ vno 106323 --> 152152)
face area 0.33 +- 0.16 (0.00-->6.86)
refinement took 6.1 minutes
PIDs (1320 1323) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 00:56:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 00:56:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

Waiting for PID 1529 of (1529 1532) to complete...
Waiting for PID 1532 of (1529 1532) 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 (1529 1532) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 00:56:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 00:56:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 1576 of (1576 1579) to complete...
Waiting for PID 1579 of (1576 1579) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 48.7 mm, total surface area = 92052 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.093 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.045 (target=0.015)   
step 035: RMS=0.039 (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=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 1.2 minutes
mris_inflate utimesec    69.078498
mris_inflate stimesec    0.162975
mris_inflate ru_maxrss   223720
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32489
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11984
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2287
mris_inflate ru_nivcsw   7023

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.8 mm, total surface area = 91378 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.053 (target=0.015)   
step 030: RMS=0.045 (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=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 1.3 minutes
mris_inflate utimesec    86.152902
mris_inflate stimesec    0.286956
mris_inflate ru_maxrss   223560
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32451
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11960
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5328
mris_inflate ru_nivcsw   5282
PIDs (1576 1579) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 00:57:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 00:57:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 1782 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1785 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1788 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1791 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1794 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1797 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1800 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1803 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1806 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1809 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1813 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...
Waiting for PID 1816 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 0.707*4pi (8.888) --> 0 handles
ICI = 188.0, FI = 1974.2, variation=31086.455
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
204 vertices thresholded to be in k1 ~ [-0.20 0.45], k2 ~ [-0.09 0.06]
total integrated curvature = 0.537*4pi (6.745) --> 0 handles
ICI = 1.5, FI = 9.2, variation=159.135
120 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
140 vertices thresholded to be in [-0.11 0.16]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 2.385*4pi (29.966) --> -1 handles
ICI = 196.0, FI = 2254.9, variation=34871.325
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
203 vertices thresholded to be in k1 ~ [-0.26 0.35], k2 ~ [-0.10 0.06]
total integrated curvature = 0.493*4pi (6.195) --> 1 handles
ICI = 1.4, FI = 10.3, variation=169.243
134 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
156 vertices thresholded to be in [-0.14 0.16]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022
done.
PIDs (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 00:59:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050006 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      [ 0050006/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                      [ 325 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.051931
WARN:    S explicit min:                          0.000000	vertex = 249

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 00:59:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050006 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      [ 0050006/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                      [ 265 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.067015
WARN:    S explicit min:                          0.000000	vertex = 96
#--------------------------------------------
#@# Sphere lh Sun Oct  8 00:59:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 00:59:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 2016 of (2016 2020) to complete...
Waiting for PID 2020 of (2016 2020) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0.265...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.37
pass 1: epoch 2 of 3 starting distance error %20.23
unfolding complete - removing small folds...
starting distance error %20.17
removing remaining folds...
final distance error %20.19
MRISunfold() return, current seed 1234
-01: dt=0.0000, 154 negative triangles
159: dt=0.9900, 154 negative triangles
160: dt=0.9900, 84 negative triangles
161: dt=0.9900, 61 negative triangles
162: dt=0.9900, 55 negative triangles
163: dt=0.9900, 43 negative triangles
164: dt=0.9900, 40 negative triangles
165: dt=0.9900, 35 negative triangles
166: dt=0.9900, 37 negative triangles
167: dt=0.9900, 31 negative triangles
168: dt=0.9900, 29 negative triangles
169: dt=0.9900, 31 negative triangles
170: dt=0.9900, 24 negative triangles
171: dt=0.9900, 27 negative triangles
172: dt=0.9900, 20 negative triangles
173: dt=0.9900, 18 negative triangles
174: dt=0.9900, 20 negative triangles
175: dt=0.9900, 13 negative triangles
176: dt=0.9900, 12 negative triangles
177: dt=0.9900, 11 negative triangles
178: dt=0.9900, 12 negative triangles
179: dt=0.9900, 6 negative triangles
180: dt=0.9900, 8 negative triangles
181: dt=0.9900, 6 negative triangles
182: dt=0.9900, 4 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.13 hours
mris_sphere utimesec    4078.326000
mris_sphere stimesec    1.913709
mris_sphere ru_maxrss   311248
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   54496
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10808
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    134372
mris_sphere ru_nivcsw   336179
FSRUNTIME@ mris_sphere  1.1325 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0.267...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.87
pass 1: epoch 2 of 3 starting distance error %20.78
unfolding complete - removing small folds...
starting distance error %20.70
removing remaining folds...
final distance error %20.72
MRISunfold() return, current seed 1234
-01: dt=0.0000, 138 negative triangles
185: dt=0.9900, 138 negative triangles
186: dt=0.9900, 73 negative triangles
187: dt=0.9900, 56 negative triangles
188: dt=0.9900, 58 negative triangles
189: dt=0.9900, 58 negative triangles
190: dt=0.9900, 52 negative triangles
191: dt=0.9900, 57 negative triangles
192: dt=0.9900, 62 negative triangles
193: dt=0.9900, 60 negative triangles
194: dt=0.9900, 50 negative triangles
195: dt=0.9900, 52 negative triangles
196: dt=0.9900, 55 negative triangles
197: dt=0.9900, 50 negative triangles
198: dt=0.9900, 46 negative triangles
199: dt=0.9900, 46 negative triangles
200: dt=0.9900, 42 negative triangles
201: dt=0.9900, 32 negative triangles
202: dt=0.9900, 36 negative triangles
203: dt=0.9900, 32 negative triangles
204: dt=0.9900, 30 negative triangles
205: dt=0.9900, 33 negative triangles
206: dt=0.9900, 33 negative triangles
207: dt=0.9900, 29 negative triangles
208: dt=0.9900, 28 negative triangles
209: dt=0.9900, 33 negative triangles
210: dt=0.9900, 27 negative triangles
211: dt=0.9900, 24 negative triangles
212: dt=0.9900, 24 negative triangles
213: dt=0.9900, 23 negative triangles
214: dt=0.9900, 22 negative triangles
215: dt=0.9900, 26 negative triangles
216: dt=0.9900, 23 negative triangles
217: dt=0.9900, 19 negative triangles
218: dt=0.9900, 18 negative triangles
219: dt=0.9900, 18 negative triangles
220: dt=0.9900, 15 negative triangles
221: dt=0.9900, 15 negative triangles
222: dt=0.9900, 14 negative triangles
223: dt=0.9900, 17 negative triangles
224: dt=0.9900, 15 negative triangles
225: dt=0.9900, 15 negative triangles
226: dt=0.9900, 15 negative triangles
227: dt=0.9900, 12 negative triangles
228: dt=0.9900, 14 negative triangles
229: dt=0.9900, 13 negative triangles
230: dt=0.9900, 17 negative triangles
231: dt=0.9900, 17 negative triangles
232: dt=0.9900, 15 negative triangles
233: dt=0.9900, 13 negative triangles
234: dt=0.9900, 10 negative triangles
235: dt=0.9900, 11 negative triangles
236: dt=0.9900, 13 negative triangles
237: dt=0.9900, 11 negative triangles
238: dt=0.9900, 11 negative triangles
239: dt=0.9900, 11 negative triangles
240: dt=0.9900, 7 negative triangles
241: dt=0.9900, 11 negative triangles
242: dt=0.9900, 10 negative triangles
243: dt=0.9900, 8 negative triangles
244: dt=0.9900, 9 negative triangles
245: dt=0.9900, 8 negative triangles
246: dt=0.9900, 9 negative triangles
247: dt=0.9900, 8 negative triangles
248: dt=0.9900, 8 negative triangles
249: dt=0.9900, 3 negative triangles
250: dt=0.9900, 3 negative triangles
251: dt=0.9900, 2 negative triangles
252: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.17 hours
mris_sphere utimesec    4320.467189
mris_sphere stimesec    1.813724
mris_sphere ru_maxrss   314308
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55262
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10792
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    132392
mris_sphere ru_nivcsw   342765
FSRUNTIME@ mris_sphere  1.1689 hours 1 threads
PIDs (2016 2020) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 02:09:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 02:09:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 7879 of (7879 7882) to complete...
Waiting for PID 7882 of (7879 7882) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 5.608
curvature mean = 0.007, std = 0.816
curvature mean = 0.022, std = 0.853
Starting MRISrigidBodyAlignGlobal()
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 232989.9, tmin=3.5675
  d=8.00 min @ (-2.00, 0.00, 2.00) sse = 232185.1, tmin=4.7817
  d=4.00 min @ (1.00, 0.00, -1.00) sse = 227551.9, tmin=6.0289
  d=2.00 min @ (0.00, 0.50, 0.00) sse = 227404.2, tmin=7.2737
  d=1.00 min @ (0.25, 0.00, 0.00) sse = 227180.6, tmin=8.5104
  d=0.50 min @ (-0.12, -0.12, 0.12) sse = 227132.3, tmin=9.7379
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.74 min
curvature mean = -0.015, std = 0.825
curvature mean = 0.009, std = 0.940
curvature mean = -0.018, std = 0.834
curvature mean = 0.003, std = 0.975
curvature mean = -0.018, std = 0.836
curvature mean = 0.001, std = 0.990
2 Reading smoothwm
curvature mean = -0.030, std = 0.297
curvature mean = 0.035, std = 0.244
curvature mean = 0.074, std = 0.325
curvature mean = 0.033, std = 0.302
curvature mean = 0.039, std = 0.520
curvature mean = 0.033, std = 0.328
curvature mean = 0.021, std = 0.667
curvature mean = 0.033, std = 0.339
curvature mean = 0.008, std = 0.778
MRISregister() return, current seed 0
-01: dt=0.0000, 49 negative triangles
122: dt=0.9900, 49 negative triangles
expanding nbhd size to 1
123: dt=0.9900, 72 negative triangles
124: dt=0.9900, 53 negative triangles
125: dt=0.9900, 62 negative triangles
126: dt=0.9900, 59 negative triangles
127: dt=0.9900, 55 negative triangles
128: dt=0.9900, 53 negative triangles
129: dt=0.9900, 49 negative triangles
130: dt=0.9900, 42 negative triangles
131: dt=0.9900, 37 negative triangles
132: dt=0.9900, 38 negative triangles
133: dt=0.9900, 33 negative triangles
134: dt=0.9900, 32 negative triangles
135: dt=0.9900, 27 negative triangles
136: dt=0.9900, 23 negative triangles
137: dt=0.9900, 24 negative triangles
138: dt=0.9900, 22 negative triangles
139: dt=0.9900, 15 negative triangles
140: dt=0.9900, 19 negative triangles
141: dt=0.9900, 13 negative triangles
142: dt=0.9900, 13 negative triangles
143: dt=0.9900, 10 negative triangles
144: dt=0.9900, 13 negative triangles
145: dt=0.9900, 9 negative triangles
146: dt=0.9900, 9 negative triangles
147: dt=0.9900, 8 negative triangles
148: dt=0.9900, 8 negative triangles
149: dt=0.9900, 7 negative triangles
150: dt=0.9900, 12 negative triangles
151: dt=0.9900, 10 negative triangles
152: dt=0.9900, 6 negative triangles
153: dt=0.9900, 7 negative triangles
154: dt=0.9900, 5 negative triangles
155: dt=0.9900, 7 negative triangles
156: dt=0.9900, 5 negative triangles
157: dt=0.9900, 7 negative triangles
158: dt=0.9900, 6 negative triangles
159: dt=0.9900, 6 negative triangles
160: dt=0.9900, 6 negative triangles
161: dt=0.9900, 5 negative triangles
162: dt=0.9900, 4 negative triangles
163: dt=0.9900, 3 negative triangles
164: dt=0.9900, 3 negative triangles
165: dt=0.9900, 5 negative triangles
166: dt=0.9900, 3 negative triangles
167: dt=0.9900, 2 negative triangles
168: dt=0.9900, 4 negative triangles
169: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.73 hours
mris_register utimesec    6228.721090
mris_register stimesec    5.315191
mris_register ru_maxrss   277876
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39558
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10856
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    323678
mris_register ru_nivcsw   352562
FSRUNTIME@ mris_register  1.7308 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 5.627
curvature mean = 0.013, std = 0.801
curvature mean = 0.024, std = 0.853
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (8.00, 0.00, 8.00) sse = 280927.8, tmin=2.3841
  d=8.00 min @ (-2.00, -2.00, -2.00) sse = 268219.4, tmin=4.7867
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 267522.8, tmin=6.0133
  d=2.00 min @ (0.00, 0.50, 0.00) sse = 267054.6, tmin=7.2351
  d=1.00 min @ (-0.25, -0.25, 0.00) sse = 266968.7, tmin=8.4627
  d=0.50 min @ (0.00, 0.12, 0.12) sse = 266888.7, tmin=9.7011
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.70 min
curvature mean = -0.022, std = 0.804
curvature mean = 0.008, std = 0.939
curvature mean = -0.027, std = 0.811
curvature mean = 0.003, std = 0.975
curvature mean = -0.029, std = 0.812
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.031, std = 0.311
curvature mean = 0.028, std = 0.236
curvature mean = 0.068, std = 0.319
curvature mean = 0.026, std = 0.294
curvature mean = 0.040, std = 0.501
curvature mean = 0.026, std = 0.321
curvature mean = 0.022, std = 0.640
curvature mean = 0.026, std = 0.332
curvature mean = 0.009, std = 0.746
MRISregister() return, current seed 0
-01: dt=0.0000, 57 negative triangles
120: dt=0.9900, 57 negative triangles
expanding nbhd size to 1
121: dt=0.9900, 79 negative triangles
122: dt=0.9900, 54 negative triangles
123: dt=0.9900, 51 negative triangles
124: dt=0.9900, 57 negative triangles
125: dt=0.9900, 54 negative triangles
126: dt=0.9900, 49 negative triangles
127: dt=0.9900, 50 negative triangles
128: dt=0.9900, 52 negative triangles
129: dt=0.9900, 47 negative triangles
130: dt=0.9900, 45 negative triangles
131: dt=0.9900, 46 negative triangles
132: dt=0.9900, 38 negative triangles
133: dt=0.9900, 39 negative triangles
134: dt=0.9900, 34 negative triangles
135: dt=0.9900, 36 negative triangles
136: dt=0.9900, 29 negative triangles
137: dt=0.9900, 29 negative triangles
138: dt=0.9900, 27 negative triangles
139: dt=0.9900, 24 negative triangles
140: dt=0.9900, 29 negative triangles
141: dt=0.9900, 26 negative triangles
142: dt=0.9900, 23 negative triangles
143: dt=0.9900, 14 negative triangles
144: dt=0.9900, 11 negative triangles
145: dt=0.9900, 8 negative triangles
146: dt=0.9900, 8 negative triangles
147: dt=0.9900, 9 negative triangles
148: dt=0.9900, 5 negative triangles
149: dt=0.9900, 7 negative triangles
150: dt=0.9900, 4 negative triangles
151: dt=0.9900, 3 negative triangles
152: dt=0.9900, 4 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.91 hours
mris_register utimesec    7252.648429
mris_register stimesec    6.846959
mris_register ru_maxrss   278452
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   40659
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10832
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    395255
mris_register ru_nivcsw   336185
FSRUNTIME@ mris_register  1.9088 hours 1 threads
PIDs (7879 7882) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 04:04:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 04:04:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

Waiting for PID 14950 of (14950 14953) to complete...
Waiting for PID 14953 of (14950 14953) 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 (14950 14953) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 04:04:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

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

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 04:04:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 14997 of (14997 15000) to complete...
Waiting for PID 15000 of (14997 15000) 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 (14997 15000) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 04:04:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 04:04:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 15043 of (15043 15046) to complete...
Waiting for PID 15046 of (15043 15046) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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...
1571 labels changed using aseg
relabeling using gibbs priors...
000:   3405 changed, 153025 examined...
001:    845 changed, 14179 examined...
002:    197 changed, 4661 examined...
003:     74 changed, 1220 examined...
004:     26 changed, 448 examined...
005:     22 changed, 161 examined...
006:      4 changed, 133 examined...
007:      0 changed, 24 examined...
286 labels changed using aseg
000: 136 total segments, 93 labels (382 vertices) changed
001: 46 total segments, 3 labels (4 vertices) changed
002: 43 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...
2017 vertices marked for relabeling...
2017 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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...
1530 labels changed using aseg
relabeling using gibbs priors...
000:   2989 changed, 152724 examined...
001:    703 changed, 12779 examined...
002:    159 changed, 3945 examined...
003:     54 changed, 963 examined...
004:     19 changed, 350 examined...
005:      5 changed, 116 examined...
006:      2 changed, 38 examined...
007:      0 changed, 10 examined...
156 labels changed using aseg
000: 104 total segments, 66 labels (326 vertices) changed
001: 41 total segments, 3 labels (6 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1734 vertices marked for relabeling...
1734 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 16 seconds.
PIDs (15043 15046) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 04:04:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 04:04:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 rh 

Waiting for PID 15230 of (15230 15233) to complete...
Waiting for PID 15233 of (15230 15233) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
19474 bright wm thresholded.
3500 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.orig...
computing class statistics...
border white:    288670 voxels (1.72%)
border gray      347901 voxels (2.07%)
WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0]
GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70)
setting MAX_BORDER_WHITE to 110.9 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 52.8 (was 40)
setting MAX_GRAY to 95.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-5.2,    GM=71+-6.1
mean inside = 94.2, mean outside = 78.2
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.03-->7.07) (max @ vno 77459 --> 152075)
face area 0.33 +- 0.17 (0.00-->13.71)
mean absolute distance = 0.55 +- 0.79
4669 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 108 points - only 0.00% unknown
deleting segment 3 with 11 points - only 0.00% unknown
deleting segment 4 with 146 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 18 points - only 0.00% unknown
deleting segment 8 with 22 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 47 points - only 0.00% unknown
deleting segment 11 with 16 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
deleting segment 13 with 89 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
mean border=82.9, 194 (189) missing vertices, mean dist 0.4 [0.6 (%16.2)->0.5 (%83.8))]
%82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.07-->7.08) (max @ vno 77459 --> 152075)
face area 0.33 +- 0.17 (0.00-->12.59)
mean absolute distance = 0.32 +- 0.52
3271 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2075721.1, rms=6.765
001: dt: 0.5000, sse=1200676.5, rms=4.006 (40.783%)
002: dt: 0.5000, sse=968008.8, rms=2.881 (28.091%)
003: dt: 0.5000, sse=926051.4, rms=2.613 (9.297%)
004: dt: 0.5000, sse=899295.0, rms=2.466 (5.616%)
rms = 2.56, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=832619.7, rms=1.892 (23.271%)
006: dt: 0.2500, sse=806595.8, rms=1.608 (15.015%)
007: dt: 0.2500, sse=801238.6, rms=1.541 (4.169%)
rms = 1.51, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=798399.7, rms=1.506 (2.293%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=794388.6, rms=1.463 (2.821%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 127 points - only 0.00% unknown
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 55 points - only 0.00% unknown
deleting segment 4 with 8 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
deleting segment 8 with 23 points - only 0.00% unknown
deleting segment 9 with 13 points - only 0.00% unknown
deleting segment 10 with 17 points - only 0.00% unknown
deleting segment 11 with 33 points - only 0.00% unknown
deleting segment 12 with 12 points - only 0.00% unknown
deleting segment 13 with 78 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
mean border=85.8, 167 (70) missing vertices, mean dist -0.2 [0.3 (%78.2)->0.2 (%21.8))]
%89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.09-->7.05) (max @ vno 77459 --> 152075)
face area 0.35 +- 0.18 (0.00-->14.49)
mean absolute distance = 0.23 +- 0.38
3627 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1254533.9, rms=4.017
010: dt: 0.5000, sse=940914.5, rms=2.298 (42.789%)
011: dt: 0.5000, sse=917445.9, rms=2.137 (7.015%)
rms = 2.14, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=857901.1, rms=1.598 (25.216%)
013: dt: 0.2500, sse=835324.1, rms=1.280 (19.895%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=834137.2, rms=1.231 (3.875%)
rms = 1.19, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=824504.8, rms=1.195 (2.903%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 127 points - only 0.00% unknown
deleting segment 1 with 7 points - only 0.00% unknown
deleting segment 2 with 58 points - only 0.00% unknown
deleting segment 3 with 8 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 14 points - only 0.00% unknown
deleting segment 7 with 27 points - only 0.00% unknown
deleting segment 8 with 13 points - only 0.00% unknown
deleting segment 9 with 18 points - only 0.00% unknown
deleting segment 10 with 39 points - only 0.00% unknown
deleting segment 11 with 17 points - only 0.00% unknown
deleting segment 12 with 72 points - only 20.83% unknown
deleting segment 13 with 79 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
mean border=87.4, 167 (52) missing vertices, mean dist -0.1 [0.2 (%68.4)->0.2 (%31.6))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.06-->7.08) (max @ vno 77459 --> 152075)
face area 0.34 +- 0.18 (0.00-->14.44)
mean absolute distance = 0.21 +- 0.33
3435 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=919985.6, rms=2.386
016: dt: 0.5000, sse=861556.2, rms=1.875 (21.428%)
rms = 1.99, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=813718.8, rms=1.393 (25.690%)
018: dt: 0.2500, sse=796317.3, rms=1.157 (16.941%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=792110.2, rms=1.119 (3.288%)
rms = 1.10, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=791668.9, rms=1.103 (1.411%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 130 points - only 0.00% unknown
deleting segment 1 with 7 points - only 0.00% unknown
deleting segment 2 with 69 points - only 0.00% unknown
deleting segment 3 with 9 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 47 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
deleting segment 8 with 18 points - only 0.00% unknown
deleting segment 9 with 45 points - only 0.00% unknown
deleting segment 10 with 19 points - only 0.00% unknown
deleting segment 11 with 72 points - only 20.83% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 79 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
mean border=88.0, 184 (42) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))]
%93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=799669.9, rms=1.353
021: dt: 0.5000, sse=794534.5, rms=1.223 (9.597%)
rms = 1.57, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=777377.6, rms=0.984 (19.509%)
rms = 0.94, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=774450.8, rms=0.944 (4.087%)
rms = 0.93, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=772762.3, rms=0.934 (1.053%)
positioning took 0.5 minutes
generating cortex label...
23 non-cortical segments detected
only using segment with 7397 vertices
erasing segment 0 (vno[0] = 35908)
erasing segment 2 (vno[0] = 65028)
erasing segment 3 (vno[0] = 67491)
erasing segment 4 (vno[0] = 74662)
erasing segment 5 (vno[0] = 90456)
erasing segment 6 (vno[0] = 102824)
erasing segment 7 (vno[0] = 106432)
erasing segment 8 (vno[0] = 106567)
erasing segment 9 (vno[0] = 107694)
erasing segment 10 (vno[0] = 107726)
erasing segment 11 (vno[0] = 108911)
erasing segment 12 (vno[0] = 109903)
erasing segment 13 (vno[0] = 109987)
erasing segment 14 (vno[0] = 111828)
erasing segment 15 (vno[0] = 112678)
erasing segment 16 (vno[0] = 112774)
erasing segment 17 (vno[0] = 113616)
erasing segment 18 (vno[0] = 114550)
erasing segment 19 (vno[0] = 123498)
erasing segment 20 (vno[0] = 129161)
erasing segment 21 (vno[0] = 129216)
erasing segment 22 (vno[0] = 129270)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.area
vertex spacing 0.89 +- 0.26 (0.03-->6.98) (max @ vno 77459 --> 152075)
face area 0.33 +- 0.18 (0.00-->14.12)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 83 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 6 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=61.7, 163 (163) missing vertices, mean dist 1.2 [0.6 (%0.0)->3.6 (%100.0))]
%12 local maxima, %21 large gradients and %63 min vals, 283 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=22235186.0, rms=27.089
001: dt: 0.0500, sse=19704072.0, rms=25.445 (6.068%)
002: dt: 0.0500, sse=17905706.0, rms=24.209 (4.857%)
003: dt: 0.0500, sse=16534452.0, rms=23.223 (4.075%)
004: dt: 0.0500, sse=15428163.0, rms=22.395 (3.564%)
005: dt: 0.0500, sse=14500116.0, rms=21.676 (3.210%)
006: dt: 0.0500, sse=13698389.0, rms=21.035 (2.956%)
007: dt: 0.0500, sse=12990610.0, rms=20.453 (2.769%)
008: dt: 0.0500, sse=12356911.0, rms=19.917 (2.621%)
009: dt: 0.0500, sse=11781887.0, rms=19.418 (2.507%)
010: dt: 0.0500, sse=11255720.0, rms=18.949 (2.412%)
positioning took 1.1 minutes
mean border=61.4, 132 (71) missing vertices, mean dist 1.1 [0.6 (%0.0)->3.1 (%100.0))]
%13 local maxima, %21 large gradients and %62 min vals, 239 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=12173746.0, rms=19.758
011: dt: 0.0500, sse=11683745.0, rms=19.330 (2.166%)
012: dt: 0.0500, sse=11229690.0, rms=18.925 (2.097%)
013: dt: 0.0500, sse=10807222.0, rms=18.539 (2.035%)
014: dt: 0.0500, sse=10413641.0, rms=18.173 (1.975%)
015: dt: 0.0500, sse=10045978.0, rms=17.824 (1.920%)
016: dt: 0.0500, sse=9702392.0, rms=17.492 (1.865%)
017: dt: 0.0500, sse=9380718.0, rms=17.175 (1.814%)
018: dt: 0.0500, sse=9079002.0, rms=16.871 (1.764%)
019: dt: 0.0500, sse=8796039.0, rms=16.582 (1.715%)
020: dt: 0.0500, sse=8530628.0, rms=16.306 (1.665%)
positioning took 1.1 minutes
mean border=61.3, 175 (51) missing vertices, mean dist 1.0 [0.1 (%0.3)->2.8 (%99.7))]
%13 local maxima, %22 large gradients and %61 min vals, 255 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=8649533.0, rms=16.437
021: dt: 0.0500, sse=8397825.0, rms=16.173 (1.607%)
022: dt: 0.0500, sse=8161398.0, rms=15.920 (1.560%)
023: dt: 0.0500, sse=7938880.5, rms=15.679 (1.515%)
024: dt: 0.0500, sse=7729375.0, rms=15.448 (1.471%)
025: dt: 0.0500, sse=7532066.0, rms=15.228 (1.427%)
026: dt: 0.0500, sse=7345766.0, rms=15.017 (1.387%)
027: dt: 0.0500, sse=7169365.0, rms=14.814 (1.351%)
028: dt: 0.0500, sse=7002075.5, rms=14.619 (1.317%)
029: dt: 0.0500, sse=6843180.0, rms=14.431 (1.285%)
030: dt: 0.0500, sse=6691885.5, rms=14.249 (1.256%)
positioning took 1.1 minutes
mean border=61.2, 215 (37) missing vertices, mean dist 0.9 [0.1 (%2.6)->2.6 (%97.4))]
%13 local maxima, %22 large gradients and %61 min vals, 260 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=6782491.0, rms=14.360
031: dt: 0.5000, sse=5700381.0, rms=13.000 (9.474%)
032: dt: 0.5000, sse=4922298.5, rms=11.918 (8.317%)
033: dt: 0.5000, sse=4327131.5, rms=11.016 (7.567%)
034: dt: 0.5000, sse=3831588.2, rms=10.202 (7.395%)
035: dt: 0.5000, sse=3397759.0, rms=9.431 (7.553%)
036: dt: 0.5000, sse=2989004.0, rms=8.643 (8.357%)
037: dt: 0.5000, sse=2611181.0, rms=7.848 (9.196%)
038: dt: 0.5000, sse=2283338.8, rms=7.088 (9.692%)
039: dt: 0.5000, sse=2027349.8, rms=6.434 (9.230%)
040: dt: 0.5000, sse=1843114.9, rms=5.917 (8.031%)
041: dt: 0.5000, sse=1714173.6, rms=5.528 (6.573%)
042: dt: 0.5000, sse=1627641.5, rms=5.249 (5.052%)
043: dt: 0.5000, sse=1566138.0, rms=5.044 (3.907%)
044: dt: 0.5000, sse=1529266.4, rms=4.914 (2.577%)
045: dt: 0.5000, sse=1503782.6, rms=4.822 (1.860%)
046: dt: 0.5000, sse=1487359.1, rms=4.762 (1.255%)
047: dt: 0.5000, sse=1472893.0, rms=4.709 (1.098%)
rms = 4.67, time step reduction 1 of 3 to 0.250...
048: dt: 0.5000, sse=1463779.5, rms=4.673 (0.768%)
049: dt: 0.2500, sse=1399507.8, rms=4.389 (6.083%)
050: dt: 0.2500, sse=1378363.2, rms=4.305 (1.910%)
rms = 4.32, time step reduction 2 of 3 to 0.125...
rms = 4.28, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1371940.2, rms=4.276 (0.667%)
positioning took 3.4 minutes
mean border=60.9, 5064 (20) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.7 (%54.4))]
%19 local maxima, %18 large gradients and %55 min vals, 146 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=1577696.2, rms=4.297
052: dt: 0.5000, sse=1544609.1, rms=4.177 (2.797%)
053: dt: 0.5000, sse=1500392.4, rms=4.010 (3.992%)
rms = 4.17, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1439485.6, rms=3.700 (7.721%)
055: dt: 0.2500, sse=1431768.9, rms=3.649 (1.394%)
rms = 3.68, time step reduction 2 of 3 to 0.125...
rms = 3.62, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1425851.0, rms=3.617 (0.884%)
positioning took 1.2 minutes
mean border=60.7, 5769 (15) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.5 (%55.4))]
%24 local maxima, %14 large gradients and %54 min vals, 246 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=1441488.6, rms=3.704
rms = 4.04, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1423730.9, rms=3.614 (2.446%)
rms = 3.64, time step reduction 2 of 3 to 0.125...
rms = 3.60, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1421701.1, rms=3.602 (0.318%)
positioning took 0.7 minutes
mean border=60.4, 10871 (15) missing vertices, mean dist 0.1 [0.2 (%42.4)->0.4 (%57.6))]
%26 local maxima, %11 large gradients and %51 min vals, 263 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-6.0.0/0050006/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1436238.1, rms=3.677
rms = 3.64, time step reduction 1 of 3 to 0.250...
059: dt: 0.5000, sse=1417560.0, rms=3.643 (0.923%)
060: dt: 0.2500, sse=1374928.1, rms=3.423 (6.041%)
061: dt: 0.2500, sse=1350653.0, rms=3.309 (3.335%)
rms = 3.30, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1347627.8, rms=3.298 (0.329%)
063: dt: 0.1250, sse=1318916.4, rms=3.136 (4.915%)
rms = 3.10, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1312231.6, rms=3.103 (1.046%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.area.pial
vertex spacing 1.01 +- 0.46 (0.04-->8.60) (max @ vno 99895 --> 98711)
face area 0.40 +- 0.33 (0.00-->8.78)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 153025 vertices processed
25000 of 153025 vertices processed
50000 of 153025 vertices processed
75000 of 153025 vertices processed
100000 of 153025 vertices processed
125000 of 153025 vertices processed
150000 of 153025 vertices processed
0 of 153025 vertices processed
25000 of 153025 vertices processed
50000 of 153025 vertices processed
75000 of 153025 vertices processed
100000 of 153025 vertices processed
125000 of 153025 vertices processed
150000 of 153025 vertices processed
thickness calculation complete, 1100:2208 truncations.
28114 vertices at 0 distance
92828 vertices at 1 distance
93976 vertices at 2 distance
48520 vertices at 3 distance
19121 vertices at 4 distance
6669 vertices at 5 distance
2280 vertices at 6 distance
875 vertices at 7 distance
347 vertices at 8 distance
186 vertices at 9 distance
102 vertices at 10 distance
81 vertices at 11 distance
61 vertices at 12 distance
62 vertices at 13 distance
44 vertices at 14 distance
22 vertices at 15 distance
23 vertices at 16 distance
19 vertices at 17 distance
8 vertices at 18 distance
15 vertices at 19 distance
13 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.thickness
positioning took 17.4 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
19474 bright wm thresholded.
3500 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.orig...
computing class statistics...
border white:    288670 voxels (1.72%)
border gray      347901 voxels (2.07%)
WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0]
GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70)
setting MAX_BORDER_WHITE to 110.9 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 53.8 (was 40)
setting MAX_GRAY to 95.1 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-6.1,    GM=72+-5.2
mean inside = 94.0, mean outside = 78.1
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.03-->6.19) (max @ vno 106323 --> 152152)
face area 0.33 +- 0.16 (0.00-->6.80)
mean absolute distance = 0.54 +- 0.77
3722 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 0 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 40 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 100 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 11 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 39 points - only 0.00% unknown
deleting segment 14 with 7 points - only 0.00% unknown
deleting segment 15 with 32 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 16 with 2 points - only 0.00% unknown
deleting segment 17 with 7 points - only 0.00% unknown
deleting segment 18 with 9 points - only 0.00% unknown
mean border=83.0, 165 (165) missing vertices, mean dist 0.4 [0.6 (%15.8)->0.5 (%84.2))]
%79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.06-->5.94) (max @ vno 151609 --> 151552)
face area 0.33 +- 0.16 (0.00-->6.30)
mean absolute distance = 0.31 +- 0.49
3108 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2002834.9, rms=6.579
001: dt: 0.5000, sse=1168329.0, rms=3.866 (41.242%)
002: dt: 0.5000, sse=945729.2, rms=2.754 (28.760%)
003: dt: 0.5000, sse=912597.3, rms=2.543 (7.650%)
004: dt: 0.5000, sse=884369.5, rms=2.377 (6.541%)
rms = 2.50, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=816359.1, rms=1.760 (25.935%)
006: dt: 0.2500, sse=792347.1, rms=1.475 (16.202%)
007: dt: 0.2500, sse=787284.1, rms=1.409 (4.453%)
rms = 1.38, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=785247.1, rms=1.377 (2.338%)
rms = 1.35, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=782843.9, rms=1.347 (2.110%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 41 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 44 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 16 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 22 points - only 0.00% unknown
deleting segment 12 with 15 points - only 0.00% unknown
deleting segment 13 with 13 points - only 0.00% unknown
deleting segment 14 with 5 points - only 0.00% unknown
deleting segment 15 with 15 points - only 0.00% unknown
mean border=85.8, 133 (56) missing vertices, mean dist -0.2 [0.3 (%76.9)->0.2 (%23.1))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.06-->6.13) (max @ vno 151609 --> 151552)
face area 0.35 +- 0.17 (0.00-->7.08)
mean absolute distance = 0.23 +- 0.35
4626 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1210182.0, rms=3.837
010: dt: 0.5000, sse=926547.0, rms=2.220 (42.148%)
011: dt: 0.5000, sse=908255.2, rms=2.108 (5.048%)
rms = 2.12, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=847593.5, rms=1.533 (27.246%)
013: dt: 0.2500, sse=822406.8, rms=1.205 (21.433%)
rms = 1.16, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=819837.1, rms=1.158 (3.900%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=816615.6, rms=1.122 (3.098%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 0.00% unknown
deleting segment 1 with 37 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 44 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 16 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
deleting segment 10 with 38 points - only 0.00% unknown
deleting segment 11 with 14 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
deleting segment 13 with 15 points - only 0.00% unknown
mean border=87.5, 106 (36) missing vertices, mean dist -0.1 [0.2 (%68.4)->0.2 (%31.6))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.06-->6.16) (max @ vno 151609 --> 151552)
face area 0.34 +- 0.17 (0.00-->6.91)
mean absolute distance = 0.21 +- 0.30
4201 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=919439.4, rms=2.388
016: dt: 0.5000, sse=865029.1, rms=1.878 (21.327%)
rms = 1.96, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=812689.7, rms=1.385 (26.265%)
018: dt: 0.2500, sse=793599.2, rms=1.146 (17.281%)
019: dt: 0.2500, sse=788036.3, rms=1.072 (6.402%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
rms = 1.06, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=786417.6, rms=1.056 (1.545%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 0.00% unknown
deleting segment 1 with 30 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 46 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 11 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 21 points - only 0.00% unknown
deleting segment 8 with 58 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 44 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 15 points - only 0.00% unknown
mean border=88.0, 113 (30) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))]
%93 local maxima, % 4 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-6.0.0/0050006/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=793853.4, rms=1.305
rms = 1.26, time step reduction 1 of 3 to 0.250...
021: dt: 0.5000, sse=803175.3, rms=1.256 (3.782%)
022: dt: 0.2500, sse=779353.4, rms=0.978 (22.154%)
023: dt: 0.2500, sse=766539.1, rms=0.896 (8.406%)
rms = 0.92, time step reduction 2 of 3 to 0.125...
rms = 0.86, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=764261.8, rms=0.862 (3.724%)
positioning took 0.5 minutes
generating cortex label...
15 non-cortical segments detected
only using segment with 6826 vertices
erasing segment 0 (vno[0] = 41284)
erasing segment 1 (vno[0] = 45796)
erasing segment 3 (vno[0] = 69635)
erasing segment 4 (vno[0] = 93981)
erasing segment 5 (vno[0] = 108364)
erasing segment 6 (vno[0] = 109341)
erasing segment 7 (vno[0] = 109469)
erasing segment 8 (vno[0] = 109484)
erasing segment 9 (vno[0] = 111496)
erasing segment 10 (vno[0] = 111547)
erasing segment 11 (vno[0] = 112651)
erasing segment 12 (vno[0] = 113607)
erasing segment 13 (vno[0] = 152183)
erasing segment 14 (vno[0] = 152186)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.03-->6.16) (max @ vno 151552 --> 151609)
face area 0.33 +- 0.16 (0.00-->6.89)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 11 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.2, 148 (148) missing vertices, mean dist 1.3 [0.0 (%0.0)->3.4 (%100.0))]
%12 local maxima, %25 large gradients and %59 min vals, 515 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=21602798.0, rms=26.658
001: dt: 0.0500, sse=19110168.0, rms=25.016 (6.159%)
002: dt: 0.0500, sse=17349288.0, rms=23.788 (4.910%)
003: dt: 0.0500, sse=16009576.0, rms=22.809 (4.115%)
004: dt: 0.0500, sse=14930113.0, rms=21.988 (3.597%)
005: dt: 0.0500, sse=14025922.0, rms=21.276 (3.237%)
006: dt: 0.0500, sse=13246935.0, rms=20.644 (2.975%)
007: dt: 0.0500, sse=12561588.0, rms=20.070 (2.778%)
008: dt: 0.0500, sse=11948572.0, rms=19.543 (2.627%)
009: dt: 0.0500, sse=11393386.0, rms=19.053 (2.508%)
010: dt: 0.0500, sse=10885821.0, rms=18.593 (2.411%)
positioning took 1.1 minutes
mean border=61.9, 116 (80) missing vertices, mean dist 1.2 [0.1 (%0.0)->3.0 (%100.0))]
%13 local maxima, %26 large gradients and %58 min vals, 478 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=11778653.0, rms=19.394
011: dt: 0.0500, sse=11305979.0, rms=18.975 (2.164%)
012: dt: 0.0500, sse=10868231.0, rms=18.577 (2.093%)
013: dt: 0.0500, sse=10461578.0, rms=18.201 (2.028%)
014: dt: 0.0500, sse=10082463.0, rms=17.842 (1.970%)
015: dt: 0.0500, sse=9728547.0, rms=17.501 (1.913%)
016: dt: 0.0500, sse=9397624.0, rms=17.175 (1.860%)
017: dt: 0.0500, sse=9087727.0, rms=16.865 (1.808%)
018: dt: 0.0500, sse=8797181.0, rms=16.568 (1.758%)
019: dt: 0.0500, sse=8524659.0, rms=16.285 (1.709%)
020: dt: 0.0500, sse=8268469.0, rms=16.014 (1.663%)
positioning took 1.1 minutes
mean border=61.8, 127 (58) missing vertices, mean dist 1.1 [0.1 (%0.3)->2.7 (%99.7))]
%13 local maxima, %26 large gradients and %57 min vals, 467 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=8396921.0, rms=16.157
021: dt: 0.0500, sse=8152757.5, rms=15.897 (1.610%)
022: dt: 0.0500, sse=7923124.5, rms=15.648 (1.564%)
023: dt: 0.0500, sse=7706509.0, rms=15.410 (1.523%)
024: dt: 0.0500, sse=7502198.0, rms=15.181 (1.482%)
025: dt: 0.0500, sse=7309335.5, rms=14.963 (1.441%)
026: dt: 0.0500, sse=7126519.5, rms=14.752 (1.407%)
027: dt: 0.0500, sse=6952859.5, rms=14.549 (1.375%)
028: dt: 0.0500, sse=6787329.0, rms=14.353 (1.348%)
029: dt: 0.0500, sse=6629220.0, rms=14.163 (1.324%)
030: dt: 0.0500, sse=6477803.5, rms=13.979 (1.302%)
positioning took 1.1 minutes
mean border=61.7, 190 (47) missing vertices, mean dist 1.0 [0.1 (%3.3)->2.4 (%96.7))]
%13 local maxima, %26 large gradients and %57 min vals, 430 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=6552345.0, rms=14.071
031: dt: 0.5000, sse=5456689.5, rms=12.666 (9.988%)
032: dt: 0.5000, sse=4666664.0, rms=11.540 (8.892%)
033: dt: 0.5000, sse=4065347.5, rms=10.599 (8.148%)
034: dt: 0.5000, sse=3588981.2, rms=9.786 (7.673%)
035: dt: 0.5000, sse=3191605.2, rms=9.051 (7.508%)
036: dt: 0.5000, sse=2841333.0, rms=8.349 (7.755%)
037: dt: 0.5000, sse=2517725.0, rms=7.647 (8.415%)
038: dt: 0.5000, sse=2227771.8, rms=6.959 (9.001%)
039: dt: 0.5000, sse=1980247.0, rms=6.314 (9.257%)
040: dt: 0.5000, sse=1800302.6, rms=5.800 (8.141%)
041: dt: 0.5000, sse=1672457.8, rms=5.405 (6.816%)
042: dt: 0.5000, sse=1593637.1, rms=5.145 (4.807%)
043: dt: 0.5000, sse=1543909.0, rms=4.974 (3.324%)
044: dt: 0.5000, sse=1513202.6, rms=4.865 (2.195%)
045: dt: 0.5000, sse=1489349.1, rms=4.778 (1.787%)
046: dt: 0.5000, sse=1474945.1, rms=4.726 (1.094%)
rms = 4.68, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1463555.1, rms=4.682 (0.935%)
048: dt: 0.2500, sse=1407027.5, rms=4.429 (5.386%)
049: dt: 0.2500, sse=1386206.9, rms=4.348 (1.849%)
rms = 4.35, time step reduction 2 of 3 to 0.125...
rms = 4.32, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1379466.2, rms=4.318 (0.673%)
positioning took 3.1 minutes
mean border=61.4, 4348 (13) missing vertices, mean dist 0.1 [0.2 (%46.8)->0.7 (%53.2))]
%21 local maxima, %21 large gradients and %52 min vals, 209 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=1580453.6, rms=4.270
051: dt: 0.5000, sse=1536655.5, rms=4.101 (3.949%)
052: dt: 0.5000, sse=1497056.2, rms=3.950 (3.684%)
rms = 4.11, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1440530.8, rms=3.659 (7.380%)
rms = 3.61, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1434117.4, rms=3.614 (1.228%)
rms = 3.57, time step reduction 3 of 3 to 0.062...
055: dt: 0.1250, sse=1426453.2, rms=3.567 (1.293%)
positioning took 1.1 minutes
mean border=61.1, 4894 (10) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.5 (%55.4))]
%27 local maxima, %15 large gradients and %51 min vals, 260 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=1446334.0, rms=3.677
rms = 3.95, time step reduction 1 of 3 to 0.250...
056: dt: 0.2500, sse=1433671.5, rms=3.613 (1.749%)
rms = 3.66, time step reduction 2 of 3 to 0.125...
rms = 3.60, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1432282.1, rms=3.605 (0.222%)
positioning took 0.6 minutes
mean border=60.8, 10016 (10) missing vertices, mean dist 0.1 [0.2 (%42.6)->0.4 (%57.4))]
%29 local maxima, %12 large gradients and %48 min vals, 282 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-6.0.0/0050006/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1443737.0, rms=3.660
rms = 3.62, time step reduction 1 of 3 to 0.250...
058: dt: 0.5000, sse=1425259.9, rms=3.624 (0.999%)
059: dt: 0.2500, sse=1383500.9, rms=3.411 (5.874%)
060: dt: 0.2500, sse=1360999.9, rms=3.307 (3.042%)
rms = 3.30, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1357993.1, rms=3.296 (0.325%)
062: dt: 0.1250, sse=1331251.2, rms=3.147 (4.524%)
rms = 3.11, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1323619.4, rms=3.110 (1.195%)
positioning took 1.3 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.area.pial
vertex spacing 1.02 +- 0.46 (0.04-->7.47) (max @ vno 151522 --> 151599)
face area 0.40 +- 0.33 (0.00-->9.88)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 152724 vertices processed
25000 of 152724 vertices processed
50000 of 152724 vertices processed
75000 of 152724 vertices processed
100000 of 152724 vertices processed
125000 of 152724 vertices processed
150000 of 152724 vertices processed
0 of 152724 vertices processed
25000 of 152724 vertices processed
50000 of 152724 vertices processed
75000 of 152724 vertices processed
100000 of 152724 vertices processed
125000 of 152724 vertices processed
150000 of 152724 vertices processed
thickness calculation complete, 782:1838 truncations.
28502 vertices at 0 distance
95061 vertices at 1 distance
95383 vertices at 2 distance
47759 vertices at 3 distance
17844 vertices at 4 distance
5927 vertices at 5 distance
2002 vertices at 6 distance
679 vertices at 7 distance
308 vertices at 8 distance
146 vertices at 9 distance
71 vertices at 10 distance
58 vertices at 11 distance
55 vertices at 12 distance
42 vertices at 13 distance
38 vertices at 14 distance
36 vertices at 15 distance
36 vertices at 16 distance
11 vertices at 17 distance
22 vertices at 18 distance
15 vertices at 19 distance
19 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.thickness
positioning took 16.9 minutes
PIDs (15230 15233) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 04:21:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label
Total face volume 308565
Total vertex volume 305456 (mask=0)
#@# 0050006 lh 305456
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 04:21:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label
Total face volume 306687
Total vertex volume 303030 (mask=0)
#@# 0050006 rh 303030
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 04:22:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 

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 = 120
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/ribbon.mgz
mris_volmask took 17.74 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 04:39:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 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 0050006 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 04:39:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 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 0050006 rh pial 

Waiting for PID 17824 of (17824 17828 17831 17847) to complete...
Waiting for PID 17828 of (17824 17828 17831 17847) to complete...
Waiting for PID 17831 of (17824 17828 17831 17847) to complete...
Waiting for PID 17847 of (17824 17828 17831 17847) 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 0050006 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565
Total vertex volume 305456 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1454   1006   2706  2.788 0.459     0.112     0.021       13     1.1  bankssts
  920    613   1473  2.372 0.724     0.132     0.017       13     0.5  caudalanteriorcingulate
 3582   2249   7632  3.081 0.553     0.118     0.033       41     4.8  caudalmiddlefrontal
 2176   1436   2881  1.920 0.452     0.143     0.036       31     3.2  cuneus
  718    518   2163  3.578 0.709     0.108     0.016        6     0.4  entorhinal
 5367   3659  12584  2.876 0.599     0.137     0.036       85     8.2  fusiform
 7839   5147  16172  2.874 0.532     0.124     0.026       91     7.9  inferiorparietal
 5148   3496  13162  3.122 0.790     0.136     0.035       81     6.8  inferiortemporal
 1970   1288   3747  2.535 0.895     0.128     0.024       29     1.6  isthmuscingulate
 9590   5971  15819  2.438 0.634     0.132     0.033      126    12.8  lateraloccipital
 4395   3043  10377  3.207 0.829     0.144     0.040       64     7.2  lateralorbitofrontal
 4858   3332   8041  2.239 0.660     0.138     0.041       61     8.0  lingual
 3072   2183   6075  2.633 0.811     0.164     0.053       77     6.3  medialorbitofrontal
 4827   3185  12272  3.188 0.715     0.129     0.031       82     5.9  middletemporal
 1055    695   2459  3.110 0.887     0.100     0.023        7     0.9  parahippocampal
 2707   1696   5381  2.941 0.552     0.117     0.027       28     2.8  paracentral
 2525   1712   6395  3.149 0.580     0.120     0.026       28     2.4  parsopercularis
 1275    853   3948  3.336 0.741     0.135     0.031       21     1.5  parsorbitalis
 2283   1529   5183  3.131 0.610     0.122     0.031       27     2.5  parstriangularis
 2030   1444   2144  1.713 0.411     0.142     0.034       24     2.9  pericalcarine
 7937   5066  13300  2.396 0.693     0.116     0.026       84     8.2  postcentral
 1761   1210   3631  2.663 0.923     0.134     0.026       25     1.9  posteriorcingulate
 9023   5814  16761  2.709 0.622     0.113     0.025       84     9.4  precentral
 7345   5070  14551  2.688 0.548     0.132     0.028       99     8.9  precuneus
 1058    713   1984  2.559 0.845     0.136     0.038       18     1.4  rostralanteriorcingulate
10516   6969  22103  2.861 0.551     0.128     0.028      138    11.9  rostralmiddlefrontal
12975   8588  31883  3.177 0.600     0.130     0.034      168    17.6  superiorfrontal
 9630   6291  19214  2.675 0.561     0.126     0.026      113     9.6  superiorparietal
 5853   3805  15174  3.283 0.819     0.106     0.022       53     5.2  superiortemporal
 5800   3927  12767  2.985 0.558     0.131     0.029       81     6.5  supramarginal
  496    319   1690  3.355 0.624     0.168     0.060       12     1.1  frontalpole
  634    446   2892  3.935 0.810     0.158     0.060       15     1.5  temporalpole
  706    436   1360  2.764 0.648     0.143     0.038       11     0.9  transversetemporal
 3546   2409   7483  3.200 0.754     0.114     0.029       34     4.3  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 0050006 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565
Total vertex volume 305456 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1454    921   2706  2.788 0.459     0.116     0.031       21     2.0  bankssts
  920    616   1473  2.372 0.724     0.136     0.034       29     1.3  caudalanteriorcingulate
 3582   2658   7632  3.081 0.553     0.125     0.031       45     4.9  caudalmiddlefrontal
 2176   1684   2881  1.920 0.452     0.143     0.038       38     3.7  cuneus
  718    699   2163  3.578 0.709     0.141     0.029       15     0.9  entorhinal
 5367   5034  12584  2.876 0.599     0.164     0.039       89    10.0  fusiform
 7839   6032  16172  2.874 0.532     0.137     0.033      108    11.7  inferiorparietal
 5148   4680  13162  3.122 0.790     0.162     0.039       76     9.7  inferiortemporal
 1970   1626   3747  2.535 0.895     0.136     0.033       30     2.6  isthmuscingulate
 9590   7113  15819  2.438 0.634     0.124     0.029      126    12.4  lateraloccipital
 4395   3408  10377  3.207 0.829     0.149     0.041       78     8.2  lateralorbitofrontal
 4858   3992   8041  2.239 0.660     0.150     0.040       63     8.8  lingual
 3072   2526   6075  2.633 0.811     0.166     0.052       69     6.8  medialorbitofrontal
 4827   4376  12272  3.188 0.715     0.150     0.034       65     8.0  middletemporal
 1055    969   2459  3.110 0.887     0.186     0.055       24     2.7  parahippocampal
 2707   2017   5381  2.941 0.552     0.136     0.037       45     4.7  paracentral
 2525   2277   6395  3.149 0.580     0.155     0.034       46     4.2  parsopercularis
 1275   1405   3948  3.336 0.741     0.170     0.036       16     2.1  parsorbitalis
 2283   1818   5183  3.131 0.610     0.134     0.030       31     3.1  parstriangularis
 2030   1124   2144  1.713 0.411     0.113     0.031       43     2.6  pericalcarine
 7937   6135  13300  2.396 0.693     0.133     0.030       87    11.0  postcentral
 1761   1473   3631  2.663 0.923     0.154     0.039       30     3.2  posteriorcingulate
 9023   6551  16761  2.709 0.622     0.121     0.028      109    11.5  precentral
 7345   5707  14551  2.688 0.548     0.136     0.032      121    10.4  precuneus
 1058    854   1984  2.559 0.845     0.165     0.047       23     2.2  rostralanteriorcingulate
10516   8379  22103  2.861 0.551     0.139     0.055      286    16.6  rostralmiddlefrontal
12975  11226  31883  3.177 0.600     0.149     0.036      192    21.8  superiorfrontal
 9630   7830  19214  2.675 0.561     0.138     0.033      135    14.1  superiorparietal
 5853   5200  15174  3.283 0.819     0.156     0.037       81    10.7  superiortemporal
 5800   4656  12767  2.985 0.558     0.143     0.032       96     8.4  supramarginal
  496    677   1690  3.355 0.624     0.211     0.042        5     1.1  frontalpole
  634    980   2892  3.935 0.810     0.237     0.059       40     2.2  temporalpole
  706    596   1360  2.764 0.648     0.146     0.037        8     1.2  transversetemporal
 3546   2200   7483  3.200 0.754     0.137     0.045       64     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 0050006 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687
Total vertex volume 303030 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1318    928   2501  2.889 0.556     0.127     0.024       12     1.4  bankssts
 1443    971   2634  2.351 0.833     0.132     0.028       23     1.5  caudalanteriorcingulate
 3132   2061   7122  2.979 0.516     0.108     0.024       31     2.9  caudalmiddlefrontal
 2610   1683   3645  1.964 0.518     0.145     0.037       37     3.8  cuneus
  686    478   2209  3.526 0.763     0.130     0.033        8     0.9  entorhinal
 5428   3627  12050  2.891 0.716     0.126     0.031       75     6.6  fusiform
 9662   6328  22000  2.999 0.608     0.128     0.030      125    11.1  inferiorparietal
 6016   4085  15840  3.094 0.824     0.127     0.034       91     8.3  inferiortemporal
 1516    998   2866  2.305 0.899     0.132     0.031       26     1.8  isthmuscingulate
 9228   5735  15334  2.398 0.631     0.132     0.036      122    13.0  lateraloccipital
 4357   2985   9815  3.051 0.745     0.137     0.038       62     6.4  lateralorbitofrontal
 5002   3312   8038  2.250 0.604     0.149     0.048       72    10.4  lingual
 3376   2259   6821  2.676 0.749     0.127     0.041       50     5.3  medialorbitofrontal
 5320   3685  13994  3.083 0.709     0.125     0.026       65     5.8  middletemporal
 1071    707   2045  2.609 0.697     0.108     0.025       10     1.0  parahippocampal
 2915   1850   5580  2.757 0.509     0.117     0.026       28     3.1  paracentral
 2480   1646   5925  3.025 0.609     0.115     0.023       26     2.3  parsopercularis
 1629   1083   4369  3.306 0.636     0.143     0.032       25     2.1  parsorbitalis
 2337   1604   5218  2.891 0.568     0.120     0.026       30     2.4  parstriangularis
 2408   1629   2321  1.736 0.488     0.139     0.037       26     3.8  pericalcarine
 6526   4051  10279  2.282 0.623     0.110     0.028       68     7.2  postcentral
 2408   1651   4983  2.626 0.899     0.141     0.035       37     3.3  posteriorcingulate
 7409   4656  13810  2.747 0.588     0.110     0.025       65     7.3  precentral
 7797   5203  14618  2.658 0.562     0.133     0.031      106     9.2  precuneus
 1067    746   2201  2.577 0.765     0.155     0.042       22     2.1  rostralanteriorcingulate
10857   7266  23821  2.877 0.586     0.129     0.030      141    13.4  rostralmiddlefrontal
12067   7918  27923  3.073 0.647     0.128     0.034      155    16.1  superiorfrontal
 8917   5691  16760  2.555 0.586     0.128     0.028      112     9.7  superiorparietal
 5734   3809  14467  3.204 0.746     0.113     0.025       60     5.6  superiortemporal
 5625   3711  11457  2.873 0.509     0.133     0.028       79     6.4  supramarginal
  560    353   1681  2.995 0.856     0.156     0.050       10     1.1  frontalpole
  659    453   2651  3.771 0.837     0.127     0.037        9     1.1  temporalpole
  519    346   1015  2.731 0.677     0.149     0.034        8     0.6  transversetemporal
 3290   2267   7036  3.219 0.799     0.116     0.030       30     3.8  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050006 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687
Total vertex volume 303030 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1318    796   2501  2.889 0.556     0.130     0.037       19     2.2  bankssts
 1443   1213   2634  2.351 0.833     0.145     0.035       15     2.3  caudalanteriorcingulate
 3132   2605   7122  2.979 0.516     0.130     0.027       33     3.7  caudalmiddlefrontal
 2610   2118   3645  1.964 0.518     0.148     0.039       39     4.7  cuneus
  686    779   2209  3.526 0.763     0.173     0.042       13     1.3  entorhinal
 5428   4536  12050  2.891 0.716     0.171     0.186     1579    73.6  fusiform
 9662   8023  22000  2.999 0.608     0.143     0.034      133    14.9  inferiorparietal
 6016   5870  15840  3.094 0.824     0.164     0.039       96    11.1  inferiortemporal
 1516   1317   2866  2.305 0.899     0.144     0.032       31     2.0  isthmuscingulate
 9228   6900  15334  2.398 0.631     0.128     0.061      323    34.4  lateraloccipital
 4357   3518   9815  3.051 0.745     0.167     0.046       83     9.2  lateralorbitofrontal
 5002   3930   8038  2.250 0.604     0.155     0.061      117    16.8  lingual
 3376   2902   6821  2.676 0.749     0.166     0.047       64     7.3  medialorbitofrontal
 5320   5200  13994  3.083 0.709     0.162     0.037       76     9.5  middletemporal
 1071    892   2045  2.609 0.697     0.160     0.038       26     2.0  parahippocampal
 2915   2142   5580  2.757 0.509     0.128     0.037       39     4.3  paracentral
 2480   2283   5925  3.025 0.609     0.159     0.038       28     4.4  parsopercularis
 1629   1563   4369  3.306 0.636     0.159     0.036       32     2.5  parsorbitalis
 2337   2019   5218  2.891 0.568     0.157     0.035       38     4.1  parstriangularis
 2408   1281   2321  1.736 0.488     0.111     0.034       52     3.3  pericalcarine
 6526   5118  10279  2.282 0.623     0.132     0.031       67     9.7  postcentral
 2408   2046   4983  2.626 0.899     0.149     0.036       40     4.1  posteriorcingulate
 7409   5269  13810  2.747 0.588     0.119     0.028      132     9.0  precentral
 7797   5807  14618  2.658 0.562     0.140     0.036      150    12.3  precuneus
 1067    941   2201  2.577 0.765     0.162     0.042       14     1.9  rostralanteriorcingulate
10857   9047  23821  2.877 0.586     0.145     0.033      132    16.3  rostralmiddlefrontal
12067   9881  27923  3.073 0.647     0.148     0.039      211    21.3  superiorfrontal
 8917   7124  16760  2.555 0.586     0.140     0.033      120    13.0  superiorparietal
 5734   5283  14467  3.204 0.746     0.178     0.045       90    12.8  superiortemporal
 5625   4274  11457  2.873 0.509     0.142     0.036       89     9.2  supramarginal
  560    677   1681  2.995 0.856     0.196     0.039        6     1.2  frontalpole
  659    946   2651  3.771 0.837     0.230     0.048        8     1.7  temporalpole
  519    416   1015  2.731 0.677     0.161     0.051        7     1.2  transversetemporal
 3290   2135   7036  3.219 0.799     0.156     0.052       69     8.3  insula
PIDs (17824 17828 17831 17847) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 04:41:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 04:41:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 17957 of (17957 17960) to complete...
Waiting for PID 17960 of (17957 17960) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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...
228 labels changed using aseg
relabeling using gibbs priors...
000:  10087 changed, 153025 examined...
001:   2410 changed, 39255 examined...
002:    696 changed, 12466 examined...
003:    335 changed, 4014 examined...
004:    141 changed, 1897 examined...
005:     77 changed, 819 examined...
006:     43 changed, 432 examined...
007:     19 changed, 256 examined...
008:      7 changed, 110 examined...
009:      7 changed, 42 examined...
010:      0 changed, 36 examined...
7 labels changed using aseg
000: 294 total segments, 204 labels (2336 vertices) changed
001: 101 total segments, 13 labels (103 vertices) changed
002: 88 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 37 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1351 vertices marked for relabeling...
1351 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 0050006 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...
45 labels changed using aseg
relabeling using gibbs priors...
000:   9866 changed, 152724 examined...
001:   2265 changed, 38793 examined...
002:    658 changed, 11905 examined...
003:    286 changed, 3732 examined...
004:    134 changed, 1664 examined...
005:     66 changed, 751 examined...
006:     40 changed, 388 examined...
007:     20 changed, 229 examined...
008:     15 changed, 121 examined...
009:      7 changed, 84 examined...
010:      5 changed, 44 examined...
011:      1 changed, 29 examined...
012:      0 changed, 9 examined...
12 labels changed using aseg
000: 293 total segments, 205 labels (2677 vertices) changed
001: 103 total segments, 16 labels (56 vertices) changed
002: 87 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 39 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1098 vertices marked for relabeling...
1098 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (17957 17960) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 04:41:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 04:41:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh white 

Waiting for PID 18053 of (18053 18056) to complete...
Waiting for PID 18056 of (18053 18056) 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 0050006 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565
Total vertex volume 305456 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1663   1104   3745  2.952 0.731     0.138     0.036       23     2.4  G&S_frontomargin
 2203   1451   4556  2.787 0.521     0.136     0.031       33     2.8  G&S_occipital_inf
 2099   1266   3859  2.574 0.635     0.114     0.031       22     2.5  G&S_paracentral
 1755   1145   4019  3.178 0.588     0.127     0.028       22     1.7  G&S_subcentral
  941    615   2696  3.142 0.573     0.157     0.039       20     1.4  G&S_transv_frontopol
 2124   1498   4490  3.002 0.547     0.134     0.031       27     2.5  G&S_cingul-Ant
 1437   1044   2928  2.989 0.545     0.115     0.019       10     1.1  G&S_cingul-Mid-Ant
 1283    906   2916  3.186 0.611     0.122     0.025       10     1.3  G&S_cingul-Mid-Post
  788    526   2231  3.166 0.636     0.145     0.034       15     0.9  G_cingul-Post-dorsal
  347    216    849  2.963 0.809     0.154     0.032        7     0.3  G_cingul-Post-ventral
 2060   1329   2781  1.894 0.446     0.148     0.039       32     3.4  G_cuneus
 1504   1001   4107  3.031 0.634     0.125     0.032       23     1.8  G_front_inf-Opercular
  561    354   1763  3.252 0.747     0.161     0.047       14     0.8  G_front_inf-Orbital
 1464    949   3903  3.174 0.652     0.137     0.039       23     2.2  G_front_inf-Triangul
 5418   3385  13257  3.021 0.566     0.137     0.038       97     8.1  G_front_middle
 9502   6062  25496  3.248 0.636     0.139     0.040      150    15.4  G_front_sup
  601    425   1512  3.136 0.911     0.127     0.044        9     0.9  G_Ins_lg&S_cent_ins
  713    441   2106  3.480 0.996     0.113     0.028        9     0.8  G_insular_short
 2936   1733   6611  2.832 0.563     0.137     0.033       46     3.7  G_occipital_middle
 1827   1141   3113  2.323 0.616     0.148     0.035       28     2.4  G_occipital_sup
 2283   1505   5526  2.912 0.605     0.150     0.045       49     4.2  G_oc-temp_lat-fusifor
 3405   2249   5693  2.169 0.657     0.159     0.050       55     7.2  G_oc-temp_med-Lingual
 1700   1113   4741  3.389 0.773     0.120     0.030       21     1.7  G_oc-temp_med-Parahip
 2764   1823   7966  3.199 0.909     0.149     0.046       52     5.1  G_orbital
 2904   1836   7188  3.016 0.580     0.134     0.033       47     3.5  G_pariet_inf-Angular
 3013   2017   7340  2.950 0.633     0.148     0.037       59     4.7  G_pariet_inf-Supramar
 3768   2429   9113  2.861 0.580     0.139     0.033       59     4.5  G_parietal_sup
 3148   1878   5284  2.303 0.479     0.123     0.030       39     3.8  G_postcentral
 3403   2042   7017  2.788 0.676     0.120     0.031       41     4.6  G_precentral
 3514   2350   8693  2.851 0.570     0.139     0.033       63     4.8  G_precuneus
  991    717   2536  2.791 0.817     0.185     0.067       34     2.4  G_rectus
  875    602   1235  2.170 1.034     0.166     0.070       25     2.6  G_subcallosal
  529    303   1106  2.774 0.733     0.130     0.041        9     0.7  G_temp_sup-G_T_transv
 2003   1263   7404  3.603 0.815     0.130     0.027       30     2.2  G_temp_sup-Lateral
  656    455   1950  3.818 0.764     0.091     0.020        3     0.6  G_temp_sup-Plan_polar
  932    636   2070  2.845 0.785     0.092     0.016        7     0.4  G_temp_sup-Plan_tempo
 2628   1721   7403  3.145 0.875     0.148     0.044       55     4.4  G_temporal_inf
 2896   1868   8610  3.290 0.706     0.140     0.038       66     4.2  G_temporal_middle
  322    232    604  3.036 0.383     0.114     0.012        2     0.2  Lat_Fis-ant-Horizont
  235    159    379  2.714 0.545     0.092     0.018        1     0.1  Lat_Fis-ant-Vertical
 1220    830   1779  2.815 0.554     0.134     0.029       13     1.4  Lat_Fis-post
 2544   1476   3226  2.028 0.625     0.140     0.042       39     4.2  Pole_occipital
 1614   1152   6283  3.625 0.727     0.152     0.051       33     3.2  Pole_temporal
 2775   2031   3651  2.123 0.739     0.133     0.029       30     3.8  S_calcarine
 3248   2233   3965  2.032 0.564     0.109     0.019       22     2.6  S_central
 1197    836   1885  2.595 0.400     0.097     0.012        6     0.6  S_cingul-Marginalis
  642    443   1116  3.164 0.586     0.093     0.014        2     0.4  S_circular_insula_ant
 1517   1025   2755  3.298 0.614     0.093     0.018        8     1.2  S_circular_insula_inf
 1748   1228   3089  3.117 0.515     0.099     0.016        7     1.2  S_circular_insula_sup
 1269    897   2327  2.968 0.528     0.100     0.014        7     0.8  S_collat_transv_ant
  545    365    718  2.248 0.448     0.143     0.039        6     0.9  S_collat_transv_post
 2588   1769   4781  2.940 0.504     0.106     0.017       18     1.9  S_front_inf
 2320   1572   3831  2.642 0.507     0.115     0.022       20     2.3  S_front_middle
 2924   1987   5682  2.890 0.416     0.110     0.021       23     2.6  S_front_sup
   73     55    183  3.556 0.395     0.188     0.044        1     0.1  S_interm_prim-Jensen
 2758   1877   4478  2.630 0.393     0.104     0.017       18     1.8  S_intrapariet&P_trans
 1442    969   1956  2.365 0.449     0.115     0.024       10     1.5  S_oc_middle&Lunatus
 1545   1041   2293  2.356 0.453     0.112     0.019       12     1.2  S_oc_sup&transversal
  781    553   1574  2.852 0.462     0.122     0.024        8     0.8  S_occipital_ant
  818    591   1302  2.471 0.412     0.124     0.022        8     0.8  S_oc-temp_lat
 2007   1441   3798  2.640 0.711     0.107     0.021       13     1.7  S_oc-temp_med&Lingual
  569    385    937  2.920 0.515     0.083     0.011        2     0.2  S_orbital_lateral
  582    534   1223  2.695 0.761     0.167     0.030        7     0.8  S_orbital_med-olfact
 1789   1234   4003  3.410 0.643     0.133     0.033       20     2.3  S_orbital-H_Shaped
 2523   1725   4082  2.437 0.541     0.118     0.023       25     2.4  S_parieto_occipital
 1450    891   1086  1.557 0.474     0.131     0.020       27     0.8  S_pericallosal
 4406   2988   7717  2.738 0.506     0.105     0.020       31     3.3  S_postcentral
 1826   1225   3337  3.008 0.513     0.114     0.022       14     1.6  S_precentral-inf-part
 1939   1321   3416  2.836 0.440     0.106     0.018       14     1.3  S_precentral-sup-part
  751    513   1223  2.754 0.510     0.123     0.025        9     0.8  S_suborbital
 1783   1266   2809  2.508 0.455     0.127     0.023       16     1.8  S_subparietal
 1618   1160   3178  3.084 0.603     0.119     0.021       12     1.5  S_temporal_inf
 6723   4499  12376  2.884 0.553     0.110     0.020       52     5.5  S_temporal_sup
  354    236    602  2.994 0.613     0.110     0.016        2     0.3  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050006 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687
Total vertex volume 303030 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1186    791   2713  2.721 0.854     0.139     0.040       16     1.8  G&S_frontomargin
 1580   1044   2817  2.451 0.662     0.119     0.026       19     1.6  G&S_occipital_inf
 1858   1102   3397  2.577 0.607     0.118     0.036       22     2.6  G&S_paracentral
 1528   1002   3115  2.689 0.619     0.142     0.041       25     2.7  G&S_subcentral
 1328    889   3530  3.010 0.593     0.156     0.039       24     2.3  G&S_transv_frontopol
 3239   2265   6843  2.903 0.566     0.123     0.030       38     4.2  G&S_cingul-Ant
 1741   1191   3489  2.879 0.569     0.126     0.031       21     2.0  G&S_cingul-Mid-Ant
 1687   1171   3685  2.968 0.568     0.123     0.029       16     1.9  G&S_cingul-Mid-Post
  708    470   2150  3.049 0.693     0.161     0.053       16     1.7  G_cingul-Post-dorsal
  351    214    773  2.687 0.668     0.139     0.036        6     0.4  G_cingul-Post-ventral
 2437   1562   3475  1.941 0.579     0.146     0.038       36     4.0  G_cuneus
 1859   1215   4487  2.842 0.621     0.127     0.028       25     2.0  G_front_inf-Opercular
  479    307   1301  2.993 0.732     0.165     0.044       12     0.8  G_front_inf-Orbital
  931    638   2653  3.053 0.491     0.136     0.034       18     1.4  G_front_inf-Triangul
 4936   3093  13520  3.095 0.541     0.143     0.039       97     7.4  G_front_middle
 8102   5139  20966  3.149 0.717     0.139     0.040      134    13.1  G_front_sup
  634    426   1652  3.501 0.815     0.126     0.035        9     0.8  G_Ins_lg&S_cent_ins
  757    497   1923  3.317 1.017     0.121     0.039        9     1.1  G_insular_short
 3633   2210   8815  2.961 0.584     0.140     0.038       59     5.1  G_occipital_middle
 2096   1320   3832  2.339 0.716     0.149     0.034       32     3.1  G_occipital_sup
 2091   1361   5552  2.992 0.737     0.144     0.038       40     3.3  G_oc-temp_lat-fusifor
 3200   2025   5175  2.144 0.614     0.152     0.049       50     6.7  G_oc-temp_med-Lingual
 1679   1119   4442  3.131 0.827     0.137     0.044       26     2.9  G_oc-temp_med-Parahip
 3365   2265   9470  3.246 0.740     0.146     0.039       62     5.0  G_orbital
 3548   2236  10113  3.232 0.658     0.145     0.039       65     5.1  G_pariet_inf-Angular
 2859   1858   6802  3.031 0.523     0.138     0.032       48     3.6  G_pariet_inf-Supramar
 2916   1775   6680  2.742 0.595     0.138     0.035       49     3.8  G_parietal_sup
 2500   1369   4123  2.309 0.567     0.108     0.035       31     3.4  G_postcentral
 2571   1415   5648  2.908 0.558     0.105     0.029       27     2.8  G_precentral
 3160   2065   7359  2.763 0.579     0.148     0.038       60     4.7  G_precuneus
  864    588   2299  2.647 0.737     0.152     0.055       19     2.1  G_rectus
  574    358    714  2.184 0.841     0.133     0.063       12     1.2  G_subcallosal
  370    253    876  2.654 0.706     0.147     0.034        6     0.5  G_temp_sup-G_T_transv
 2128   1383   6899  3.437 0.733     0.139     0.034       35     2.9  G_temp_sup-Lateral
  848    563   2525  3.660 0.767     0.107     0.031        8     0.9  G_temp_sup-Plan_polar
  766    522   1651  2.724 0.692     0.107     0.024        8     0.6  G_temp_sup-Plan_tempo
 3287   2220  10301  3.292 0.851     0.144     0.041       63     5.7  G_temporal_inf
 3145   2143   9978  3.274 0.759     0.142     0.035       55     4.5  G_temporal_middle
  382    272    582  2.741 0.587     0.107     0.014        2     0.2  Lat_Fis-ant-Horizont
  261    181    454  2.752 0.402     0.091     0.022        1     0.2  Lat_Fis-ant-Vertical
 1172    854   1986  2.847 0.431     0.120     0.020        8     0.9  Lat_Fis-post
 4152   2419   5712  2.115 0.588     0.142     0.048       61     7.8  Pole_occipital
 1673   1127   5899  3.554 0.801     0.143     0.039       29     2.7  Pole_temporal
 2788   1962   3488  2.092 0.604     0.145     0.040       35     4.9  S_calcarine
 2768   1877   3208  1.989 0.505     0.094     0.016       12     1.8  S_central
 1500   1024   2685  2.649 0.555     0.126     0.024       15     1.6  S_cingul-Marginalis
  766    532   1258  3.093 0.619     0.107     0.019        4     0.7  S_circular_insula_ant
 1143    770   1988  2.964 0.694     0.082     0.012        4     0.6  S_circular_insula_inf
 1487   1022   2491  3.069 0.596     0.100     0.018        7     1.1  S_circular_insula_sup
 1623   1088   2756  2.718 0.525     0.091     0.019       12     1.2  S_collat_transv_ant
  429    293    631  2.296 0.422     0.137     0.033        4     0.6  S_collat_transv_post
 2665   1822   5390  2.885 0.577     0.105     0.019       18     2.0  S_front_inf
 2700   1893   4449  2.667 0.476     0.112     0.021       17     2.4  S_front_middle
 3286   2248   6365  2.889 0.450     0.108     0.023       22     3.0  S_front_sup
  437    301    651  2.733 0.360     0.131     0.020        4     0.4  S_interm_prim-Jensen
 3253   2181   5228  2.470 0.474     0.107     0.017       24     2.2  S_intrapariet&P_trans
 1098    781   1431  2.303 0.406     0.125     0.028        8     1.3  S_oc_middle&Lunatus
 1273    897   1954  2.425 0.384     0.113     0.018        9     0.9  S_oc_sup&transversal
  885    614   1672  2.725 0.447     0.105     0.016        6     0.6  S_occipital_ant
 1532   1070   2728  2.905 0.695     0.100     0.021       11     1.2  S_oc-temp_lat
 1939   1353   3198  2.574 0.636     0.112     0.021       14     1.6  S_oc-temp_med&Lingual
  445    317    698  2.709 0.479     0.113     0.015        3     0.3  S_orbital_lateral
  836    573   1289  2.535 0.776     0.130     0.034        9     1.1  S_orbital_med-olfact
 1703   1154   3624  3.106 0.635     0.124     0.031       16     2.1  S_orbital-H_Shaped
 2944   1990   4302  2.491 0.597     0.123     0.024       30     2.6  S_parieto_occipital
 1915   1222   1410  1.544 0.449     0.119     0.017       27     1.0  S_pericallosal
 3067   2047   4447  2.511 0.394     0.116     0.021       27     2.4  S_postcentral
 1447    998   2927  2.957 0.582     0.100     0.015        8     0.9  S_precentral-inf-part
 1639   1137   2872  2.844 0.470     0.105     0.018       10     1.2  S_precentral-sup-part
  465    318    800  2.769 0.634     0.109     0.022        3     0.4  S_suborbital
 1780   1215   2995  2.664 0.483     0.116     0.024       14     1.4  S_subparietal
 1482   1050   2508  2.514 0.547     0.105     0.016       10     1.1  S_temporal_inf
 7166   4883  12789  2.896 0.517     0.113     0.022       59     6.5  S_temporal_sup
  286    200    422  2.941 0.412     0.133     0.022        2     0.2  S_temporal_transverse
PIDs (18053 18056) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 04:42:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 04:42:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 18112 of (18112 18115) to complete...
Waiting for PID 18115 of (18112 18115) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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...
1759 labels changed using aseg
relabeling using gibbs priors...
000:   2116 changed, 153025 examined...
001:    496 changed, 9886 examined...
002:    143 changed, 2884 examined...
003:     52 changed, 855 examined...
004:     23 changed, 310 examined...
005:      8 changed, 124 examined...
006:      8 changed, 59 examined...
007:      7 changed, 43 examined...
008:      6 changed, 36 examined...
009:      4 changed, 33 examined...
010:      7 changed, 26 examined...
011:      5 changed, 34 examined...
012:      7 changed, 28 examined...
013:      3 changed, 34 examined...
014:      4 changed, 21 examined...
015:      3 changed, 17 examined...
016:      4 changed, 17 examined...
017:      6 changed, 28 examined...
018:      4 changed, 28 examined...
019:      4 changed, 23 examined...
020:      3 changed, 26 examined...
021:      3 changed, 18 examined...
022:      2 changed, 17 examined...
023:      4 changed, 13 examined...
024:      3 changed, 21 examined...
025:      4 changed, 21 examined...
026:      3 changed, 23 examined...
027:      2 changed, 22 examined...
028:      1 changed, 12 examined...
029:      1 changed, 7 examined...
030:      1 changed, 7 examined...
031:      2 changed, 7 examined...
032:      1 changed, 10 examined...
033:      1 changed, 7 examined...
034:      3 changed, 7 examined...
035:      5 changed, 13 examined...
036:      1 changed, 17 examined...
037:      3 changed, 8 examined...
038:      3 changed, 14 examined...
039:      0 changed, 14 examined...
291 labels changed using aseg
000: 63 total segments, 30 labels (320 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1041 vertices marked for relabeling...
1041 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 0050006 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...
1595 labels changed using aseg
relabeling using gibbs priors...
000:   2132 changed, 152724 examined...
001:    525 changed, 9901 examined...
002:    148 changed, 3016 examined...
003:     72 changed, 899 examined...
004:     37 changed, 419 examined...
005:     26 changed, 219 examined...
006:     25 changed, 142 examined...
007:     22 changed, 125 examined...
008:     12 changed, 102 examined...
009:      7 changed, 67 examined...
010:      5 changed, 42 examined...
011:      5 changed, 29 examined...
012:      2 changed, 29 examined...
013:      2 changed, 16 examined...
014:      1 changed, 11 examined...
015:      1 changed, 7 examined...
016:      1 changed, 7 examined...
017:      1 changed, 7 examined...
018:      1 changed, 7 examined...
019:      2 changed, 9 examined...
020:      1 changed, 14 examined...
021:      0 changed, 7 examined...
245 labels changed using aseg
000: 58 total segments, 25 labels (212 vertices) changed
001: 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...
987 vertices marked for relabeling...
987 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (18112 18115) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 04:42:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 04:42:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh white 

Waiting for PID 18177 of (18177 18180) to complete...
Waiting for PID 18180 of (18177 18180) 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 0050006 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565
Total vertex volume 305456 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1847   1270   3891  2.762 0.749     0.132     0.022       25     1.5  caudalanteriorcingulate
 3894   2466   8232  3.063 0.543     0.119     0.033       45     5.1  caudalmiddlefrontal
 3079   2025   4282  2.004 0.475     0.133     0.033       41     4.1  cuneus
  690    483   2064  3.570 0.685     0.111     0.023        8     0.6  entorhinal
 4965   3384  11141  2.839 0.588     0.134     0.032       75     7.0  fusiform
 7673   5021  15958  2.873 0.538     0.124     0.026       89     7.8  inferiorparietal
 5230   3550  13403  3.096 0.791     0.137     0.037       84     7.5  inferiortemporal
 1911   1253   3699  2.580 0.890     0.129     0.024       28     1.6  isthmuscingulate
 9593   5967  15829  2.438 0.631     0.132     0.032      126    12.4  lateraloccipital
 5009   3463  11972  3.105 0.946     0.152     0.046       83     9.7  lateralorbitofrontal
 5046   3447   8243  2.224 0.656     0.140     0.041       64     8.5  lingual
 2303   1669   5142  2.707 0.783     0.164     0.056       64     4.7  medialorbitofrontal
 6414   4298  15772  3.154 0.671     0.128     0.030      100     7.5  middletemporal
 1084    711   2487  3.124 0.894     0.098     0.022        7     0.8  parahippocampal
 3297   2070   6843  3.015 0.551     0.118     0.029       34     3.6  paracentral
 2281   1530   5707  3.146 0.603     0.123     0.028       27     2.3  parsopercularis
 1297    873   3415  3.110 0.684     0.135     0.028       20     1.3  parsorbitalis
 2890   1950   6199  3.072 0.573     0.117     0.027       30     3.0  parstriangularis
 1972   1409   2087  1.711 0.408     0.143     0.034       23     2.9  pericalcarine
 9055   5804  15247  2.437 0.688     0.116     0.026       94     9.3  postcentral
 1955   1347   3855  2.669 0.898     0.130     0.026       25     2.0  posteriorcingulate
 8743   5625  16312  2.721 0.625     0.113     0.025       80     8.9  precentral
 7305   5023  14742  2.714 0.541     0.135     0.029      103     9.0  precuneus
 1498   1043   2696  2.708 0.719     0.134     0.032       21     1.7  rostralanteriorcingulate
 7675   5033  16912  2.947 0.561     0.127     0.028      102     8.6  rostralmiddlefrontal
14128   9318  33795  3.092 0.625     0.132     0.034      192    19.6  superiorfrontal
 7674   5029  15658  2.713 0.554     0.126     0.026       90     7.6  superiorparietal
 7462   4934  20065  3.273 0.832     0.111     0.025       77     7.6  superiortemporal
 5448   3697  11953  2.980 0.565     0.132     0.029       78     6.1  supramarginal
  721    449   1368  2.744 0.633     0.146     0.038       12     1.0  transversetemporal
 2944   1990   6490  3.267 0.735     0.107     0.026       26     2.9  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 0050006 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687
Total vertex volume 303030 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1578   1058   2805  2.338 0.829     0.131     0.028       24     1.7  caudalanteriorcingulate
 3395   2230   7527  2.975 0.506     0.110     0.024       34     3.1  caudalmiddlefrontal
 3332   2125   4701  2.028 0.535     0.141     0.035       46     4.8  cuneus
  620    439   2096  3.610 0.778     0.127     0.033        7     0.7  entorhinal
 4984   3348  10648  2.840 0.685     0.126     0.031       68     6.1  fusiform
 9550   6244  21562  2.989 0.609     0.129     0.030      125    11.0  inferiorparietal
 6455   4371  17078  3.106 0.830     0.125     0.033       94     8.5  inferiortemporal
 1454    960   2792  2.344 0.888     0.134     0.031       25     1.7  isthmuscingulate
 9194   5706  15241  2.396 0.629     0.133     0.036      122    13.1  lateraloccipital
 4948   3371  11685  3.029 0.788     0.137     0.039       72     7.4  lateralorbitofrontal
 4888   3237   7870  2.243 0.602     0.149     0.047       70    10.0  lingual
 2425   1632   5224  2.652 0.769     0.138     0.047       42     4.5  medialorbitofrontal
 6540   4512  16526  3.049 0.683     0.126     0.026       80     7.1  middletemporal
 1131    757   2215  2.650 0.708     0.108     0.024       11     1.0  parahippocampal
 3007   1920   5860  2.764 0.517     0.116     0.026       27     3.1  paracentral
 2802   1863   6771  3.045 0.607     0.115     0.024       29     2.6  parsopercularis
 1459    972   3505  3.080 0.739     0.135     0.031       20     1.7  parsorbitalis
 2325   1586   5083  2.914 0.562     0.123     0.026       30     2.5  parstriangularis
 2356   1604   2301  1.741 0.491     0.138     0.036       24     3.7  pericalcarine
 7293   4545  11654  2.307 0.634     0.111     0.029       78     8.3  postcentral
 2453   1680   5033  2.637 0.892     0.140     0.035       37     3.3  posteriorcingulate
 7171   4467  13519  2.751 0.596     0.111     0.026       65     7.3  precentral
 7887   5271  14959  2.668 0.565     0.135     0.032      110     9.5  precuneus
 1388    952   2655  2.537 0.743     0.142     0.040       25     2.4  rostralanteriorcingulate
 7494   5033  16261  2.892 0.584     0.128     0.029       94     8.9  rostralmiddlefrontal
15822  10417  36372  3.037 0.627     0.130     0.033      209    21.2  superiorfrontal
 7288   4644  13768  2.561 0.570     0.127     0.027       92     7.6  superiorparietal
 7339   4931  18947  3.231 0.762     0.119     0.028       82     8.5  superiortemporal
 5300   3497  10954  2.888 0.513     0.132     0.028       74     5.9  supramarginal
  506    342   1025  2.722 0.663     0.146     0.033        8     0.6  transversetemporal
 2944   2031   6393  3.229 0.823     0.110     0.025       25     2.8  insula
PIDs (18177 18180) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 04:43:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 pctsurfcon --s 0050006 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 04:43:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts

 pctsurfcon --s 0050006 --rh-only 

Waiting for PID 18235 of (18235 18246) to complete...
Waiting for PID 18246 of (18235 18246) to complete...

 pctsurfcon --s 0050006 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts/pctsurfcon.log
Sun Oct  8 04:43:22 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-6.0.0/0050006/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-573 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-6.0.0/0050006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.wm.mgh --regheader 0050006 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000  -0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 76909
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.wm.mgh
Dim: 153025 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.gm.mgh --projfrac 0.3 --regheader 0050006 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000  -0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 92775
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.gm.mgh
Dim: 153025 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.w-g.pct.mgh --annot 0050006 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/lh.w-g.pct.mgh --annot 0050006 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/lh.w-g.pct.mgh
Vertex Area is 0.66309 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 0050006 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts/pctsurfcon.log
Sun Oct  8 04:43:22 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-6.0.0/0050006/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-573 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-6.0.0/0050006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.wm.mgh --regheader 0050006 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000  -0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 76245
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.wm.mgh
Dim: 152724 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.gm.mgh --projfrac 0.3 --regheader 0050006 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00003;
 0.00000  -1.00000   0.00000  -0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 92814
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.gm.mgh
Dim: 152724 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.w-g.pct.mgh --annot 0050006 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.w-g.pct.mgh --annot 0050006 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.w-g.pct.mgh
Vertex Area is 0.659549 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 (18235 18246) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 04:43:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2112 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2058 voxels changed to hypointensity...
4100 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 04:43:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006

 mri_aparc2aseg --s 0050006 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 04:43:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006

 mri_aparc2aseg --s 0050006 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 04:43:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006

 mri_aparc2aseg --s 0050006 --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 18468 of (18468 18471 18474) to complete...
Waiting for PID 18471 of (18468 18471 18474) to complete...
Waiting for PID 18474 of (18468 18471 18474) to complete...

 mri_aparc2aseg --s 0050006 --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 0050006
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.11
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 65
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 35
rescaling Left_Cerebellum_White_Matter from 86 --> 93
rescaling Left_Cerebellum_Cortex from 60 --> 61
rescaling Left_Thalamus from 94 --> 100
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 70
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 68
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 64
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 18
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 92
rescaling Right_Cerebellum_Cortex from 59 --> 59
rescaling Right_Thalamus_Proper from 85 --> 86
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 79
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 63
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 76
  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 = 602800
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 230 changed.
pass 2: 40 changed.
pass 3: 18 changed.
pass 4: 11 changed.
pass 5: 7 changed.
pass 6: 1 changed.
pass 7: 1 changed.
pass 8: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050006 --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 0050006
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.11
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 65
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 35
rescaling Left_Cerebellum_White_Matter from 86 --> 93
rescaling Left_Cerebellum_Cortex from 60 --> 61
rescaling Left_Thalamus from 94 --> 100
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 70
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 68
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 64
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 18
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 92
rescaling Right_Cerebellum_Cortex from 59 --> 59
rescaling Right_Thalamus_Proper from 85 --> 86
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 79
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 63
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 76
  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 = 602783
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 230 changed.
pass 2: 40 changed.
pass 3: 18 changed.
pass 4: 11 changed.
pass 5: 7 changed.
pass 6: 1 changed.
pass 7: 1 changed.
pass 8: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050006 --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 0050006
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.11
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 65
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 35
rescaling Left_Cerebellum_White_Matter from 86 --> 93
rescaling Left_Cerebellum_Cortex from 60 --> 61
rescaling Left_Thalamus from 94 --> 100
rescaling Left_Thalamus_Proper from 84 --> 86
rescaling Left_Caudate from 75 --> 70
rescaling Left_Putamen from 80 --> 85
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 68
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 64
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 18
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 92
rescaling Right_Cerebellum_Cortex from 59 --> 59
rescaling Right_Thalamus_Proper from 85 --> 86
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 79
rescaling Right_Pallidum from 97 --> 91
rescaling Right_Hippocampus from 53 --> 63
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 76
  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 = 602783
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 230 changed.
pass 2: 40 changed.
pass 3: 18 changed.
pass 4: 11 changed.
pass 5: 7 changed.
pass 6: 1 changed.
pass 7: 1 changed.
pass 8: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (18468 18471 18474) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 04:53:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri

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

Sun Oct  8 04:53:45 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-6.0.0/0050006/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-573 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-6.0.0/0050006/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-573
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 04:53:45 CEST 2017 
Ended   at Sun Oct  8 04:53:51 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 04:53:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006

 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 0050006 


$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 0050006 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1616394 mm^3    (det: 1.205217 )
Computing euler number
orig.nofix lheno = -108, rheno = -92
orig.nofix lhholes =   55, rhholes = 47
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 04:55:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006

 mri_aparc2aseg --s 0050006 --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 0050006
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-6.0.0/0050006/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7954 vertices from left hemi
Ripped 7355 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-6.0.0/0050006/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 1071593
Used brute-force search on 111 voxels
Fixing Parahip LH WM
  Found 12 clusters
     0 k 48.000000
     1 k 1.000000
     2 k 4.000000
     3 k 1.000000
     4 k 3.000000
     5 k 2.000000
     6 k 1.000000
     7 k 1616.000000
     8 k 1.000000
     9 k 1.000000
     10 k 3.000000
     11 k 1.000000
Fixing Parahip RH WM
  Found 6 clusters
     0 k 2.000000
     1 k 1524.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1.000000
     5 k 40.000000
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 0050006 --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 0050006 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-573
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1616394 mm^3    (det: 1.205217 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
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-6.0.0/0050006/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 05:05:12 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 19709 of (19709 19715 19721 19727 19732) to complete...
Waiting for PID 19715 of (19709 19715 19721 19727 19732) to complete...
Waiting for PID 19721 of (19709 19715 19721 19727 19732) to complete...
Waiting for PID 19727 of (19709 19715 19721 19727 19732) to complete...
Waiting for PID 19732 of (19709 19715 19721 19727 19732) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 704
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4833
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 1460
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9369
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 191
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4268
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 527
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6510
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 1028
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6812
mri_label2label: Done

PIDs (19709 19715 19721 19727 19732) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 19788 of (19788 19794 19800 19806) to complete...
Waiting for PID 19794 of (19788 19794 19800 19806) to complete...
Waiting for PID 19800 of (19788 19794 19800 19806) to complete...
Waiting for PID 19806 of (19788 19794 19800 19806) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 347
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4417
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 2733
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16322
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 403
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4584
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 1198
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4620
mri_label2label: Done

PIDs (19788 19794 19800 19806) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 19853 of (19853 19859 19865 19870 19877) to complete...
Waiting for PID 19859 of (19853 19859 19865 19870 19877) to complete...
Waiting for PID 19865 of (19853 19859 19865 19870 19877) to complete...
Waiting for PID 19870 of (19853 19859 19865 19870 19877) to complete...
Waiting for PID 19877 of (19853 19859 19865 19870 19877) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 1467
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6108
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 3588
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11702
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 775
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2793
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 203
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1493
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 239
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1438
mri_label2label: Done

PIDs (19853 19859 19865 19870 19877) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 19939 of (19939 19945 19951 19957 19962) to complete...
Waiting for PID 19945 of (19939 19945 19951 19957 19962) to complete...
Waiting for PID 19951 of (19939 19945 19951 19957 19962) to complete...
Waiting for PID 19957 of (19939 19945 19951 19957 19962) to complete...
Waiting for PID 19962 of (19939 19945 19951 19957 19962) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 221
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1235
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 556
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2648
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 77
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1581
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 143
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2139
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 413
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2732
mri_label2label: Done

PIDs (19939 19945 19951 19957 19962) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 20135 of (20135 20141 20147 20152) to complete...
Waiting for PID 20141 of (20135 20141 20147 20152) to complete...
Waiting for PID 20147 of (20135 20141 20147 20152) to complete...
Waiting for PID 20152 of (20135 20141 20147 20152) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1620
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 1432
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8467
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2045
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 434
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1585
mri_label2label: Done

PIDs (20135 20141 20147 20152) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 20198 of (20198 20204 20210 20215 20220) to complete...
Waiting for PID 20204 of (20198 20204 20210 20215 20220) to complete...
Waiting for PID 20210 of (20198 20204 20210 20215 20220) to complete...
Waiting for PID 20215 of (20198 20204 20210 20215 20220) to complete...
Waiting for PID 20220 of (20198 20204 20210 20215 20220) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 918
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4323
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 1704
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5038
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 185
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 698
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 61
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 531
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025
Number of reverse mapping hits = 126
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 576
mri_label2label: Done

PIDs (20198 20204 20210 20215 20220) completed and logs appended.

 mris_label2annot --s 0050006 --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-6.0.0/0050006/label
cmdline mris_label2annot --s 0050006 --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-573
machine  x86_64
user     ntraut

subject 0050006
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-6.0.0/0050006/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 103255 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050006 --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-6.0.0/0050006/label
cmdline mris_label2annot --s 0050006 --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-573
machine  x86_64
user     ntraut

subject 0050006
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-6.0.0/0050006/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 123872 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 308565
Total vertex volume 305456 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1525    844   2689  2.421 0.426     0.117     0.033       18     1.9  BA1_exvivo
 5656   3767  10294  2.686 0.514     0.110     0.022       49     4.6  BA2_exvivo
 1147    764   1109  1.904 0.473     0.139     0.027       11     1.3  BA3a_exvivo
 2552   1712   4158  2.152 0.854     0.119     0.026       27     2.6  BA3b_exvivo
 2183   1296   4188  2.792 0.532     0.113     0.030       21     2.8  BA4a_exvivo
 1321    935   2101  2.354 0.546     0.103     0.022        6     1.2  BA4p_exvivo
12206   7771  27084  3.030 0.620     0.123     0.033      158    16.6  BA6_exvivo
 2354   1592   5385  3.113 0.531     0.115     0.026       24     2.4  BA44_exvivo
 3756   2516   8391  3.023 0.642     0.121     0.027       42     3.8  BA45_exvivo
 3539   2474   4047  1.684 0.436     0.139     0.036       42     5.3  V1_exvivo
 9429   5993  13981  2.223 0.589     0.147     0.041      139    16.1  V2_exvivo
 2530   1653   5387  2.947 0.483     0.129     0.027       33     2.7  MT_exvivo
  656    463   1925  3.696 0.671     0.098     0.014        4     0.4  perirhinal_exvivo
  916    612   3060  3.499 0.682     0.131     0.031       15     1.3  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 0050006 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 308565
Total vertex volume 305456 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1005    533   1760  2.399 0.454     0.125     0.037       14     1.3  BA1_exvivo
 2335   1570   4114  2.502 0.440     0.115     0.025       22     2.3  BA2_exvivo
  997    662    898  1.839 0.413     0.142     0.030       10     1.2  BA3a_exvivo
 1538   1035   1888  1.743 0.456     0.109     0.021       14     1.3  BA3b_exvivo
 2076   1273   3792  2.669 0.566     0.113     0.031       19     2.7  BA4a_exvivo
 1098    762   1694  2.411 0.526     0.100     0.020        5     1.0  BA4p_exvivo
 7153   4494  15395  2.978 0.595     0.122     0.033       95    10.0  BA6_exvivo
 1448    983   3502  3.084 0.552     0.123     0.029       18     1.6  BA44_exvivo
 1455    945   4021  3.245 0.621     0.134     0.032       21     1.8  BA45_exvivo
 3751   2616   4464  1.720 0.481     0.138     0.037       45     5.5  V1_exvivo
 4767   2959   6654  2.134 0.563     0.152     0.045       77     9.1  V2_exvivo
  655    434   1365  2.951 0.433     0.130     0.024        7     0.6  MT_exvivo
  348    255    914  3.696 0.657     0.095     0.011        2     0.2  perirhinal_exvivo
  527    336   1552  3.545 0.720     0.122     0.031        9     0.6  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 05:08:46 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 20355 of (20355 20361 20367 20373 20377) to complete...
Waiting for PID 20361 of (20355 20361 20367 20373 20377) to complete...
Waiting for PID 20367 of (20355 20361 20367 20373 20377) to complete...
Waiting for PID 20373 of (20355 20361 20367 20373 20377) to complete...
Waiting for PID 20377 of (20355 20361 20367 20373 20377) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 431
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4393
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 640
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7327
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 86
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4066
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 255
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4777
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 600
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6347
mri_label2label: Done

PIDs (20355 20361 20367 20373 20377) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 20428 of (20428 20434 20440 20444) to complete...
Waiting for PID 20434 of (20428 20434 20440 20444) to complete...
Waiting for PID 20440 of (20428 20434 20440 20444) to complete...
Waiting for PID 20444 of (20428 20434 20440 20444) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 235
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4708
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 1353
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13609
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 1102
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8014
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 1516
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6871
mri_label2label: Done

PIDs (20428 20434 20440 20444) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 20502 of (20502 20508 20514 20519 20524) to complete...
Waiting for PID 20508 of (20502 20508 20514 20519 20524) to complete...
Waiting for PID 20514 of (20502 20508 20514 20519 20524) to complete...
Waiting for PID 20519 of (20502 20508 20514 20519 20524) to complete...
Waiting for PID 20524 of (20502 20508 20514 20519 20524) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 2029
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6756
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 3717
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11733
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 870
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2802
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 207
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1245
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 161
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 913
mri_label2label: Done

PIDs (20502 20508 20514 20519 20524) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 20635 of (20635 20641 20647 20652 20658) to complete...
Waiting for PID 20641 of (20635 20641 20647 20652 20658) to complete...
Waiting for PID 20647 of (20635 20641 20647 20652 20658) to complete...
Waiting for PID 20652 of (20635 20641 20647 20652 20658) to complete...
Waiting for PID 20658 of (20635 20641 20647 20652 20658) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 155
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1031
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 198
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2886
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 29
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1727
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2254
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 213
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1601
mri_label2label: Done

PIDs (20635 20641 20647 20652 20658) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 20719 of (20719 20725 20731 20737) to complete...
Waiting for PID 20725 of (20719 20725 20731 20737) to complete...
Waiting for PID 20731 of (20719 20725 20731 20737) to complete...
Waiting for PID 20737 of (20719 20725 20731 20737) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 52
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1541
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 704
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7663
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 300
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1312
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1362
mri_label2label: Done

PIDs (20719 20725 20731 20737) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 20777 of (20777 20783 20789 20794 20800) to complete...
Waiting for PID 20783 of (20777 20783 20789 20794 20800) to complete...
Waiting for PID 20789 of (20777 20783 20789 20794 20800) to complete...
Waiting for PID 20794 of (20777 20783 20789 20794 20800) to complete...
Waiting for PID 20800 of (20777 20783 20789 20794 20800) 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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 1279
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4511
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 1676
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5113
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 150
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 418
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 139
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 833
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 0050006 --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 = 0050006
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-6.0.0/0050006/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724
Number of reverse mapping hits = 59
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 350
mri_label2label: Done

PIDs (20777 20783 20789 20794 20800) completed and logs appended.

 mris_label2annot --s 0050006 --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-6.0.0/0050006/label
cmdline mris_label2annot --s 0050006 --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-573
machine  x86_64
user     ntraut

subject 0050006
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-6.0.0/0050006/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 106878 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050006 --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-6.0.0/0050006/label
cmdline mris_label2annot --s 0050006 --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-573
machine  x86_64
user     ntraut

subject 0050006
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-6.0.0/0050006/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 127337 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 306687
Total vertex volume 303030 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
 1111    571   1987  2.437 0.582     0.126     0.039       18     1.5  BA1_exvivo
 3661   2337   5774  2.492 0.465     0.113     0.026       36     3.8  BA2_exvivo
 1039    693   1016  1.902 0.454     0.127     0.025        9     1.0  BA3a_exvivo
 1840   1190   2629  1.936 0.592     0.094     0.023       14     1.8  BA3b_exvivo
 1868   1093   3570  2.772 0.468     0.106     0.025       15     1.9  BA4a_exvivo
 1168    774   1813  2.395 0.482     0.090     0.018        5     0.8  BA4p_exvivo
 8745   5506  19425  3.022 0.628     0.119     0.032      105    11.5  BA6_exvivo
 4082   2720   8966  2.925 0.599     0.118     0.025       41     4.1  BA44_exvivo
 4779   3224  11370  2.987 0.620     0.126     0.026       60     5.0  BA45_exvivo
 4367   2785   5288  1.905 0.560     0.136     0.045       53     8.1  V1_exvivo
 9320   5891  13554  2.152 0.584     0.148     0.042      139    16.2  V2_exvivo
 2696   1785   5263  2.736 0.535     0.118     0.025       27     2.5  MT_exvivo
  718    480   2171  3.403 0.724     0.133     0.035       10     1.0  perirhinal_exvivo
  452    319   1360  3.254 0.852     0.114     0.025        6     0.4  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 0050006 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 306687
Total vertex volume 303030 (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) = 1616394 mm^3    (det: 1.205217 )
lhCtxGM: 303019.103 302203.000  diff=  816.1  pctdiff= 0.269
rhCtxGM: 300790.957 300235.000  diff=  556.0  pctdiff= 0.185
lhCtxWM: 237481.483 238242.000  diff= -760.5  pctdiff=-0.320
rhCtxWM: 233553.125 234089.000  diff= -535.9  pctdiff=-0.229
SubCortGMVol  63577.000
SupraTentVol  1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305
SupraTentVolNotVent  1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308
BrainSegVol  1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108
BrainSegVolNotVent  1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001
BrainSegVolNotVent  1305905.000
CerebellumVol 167490.000
VentChorVol    9084.000
3rd4th5thCSF   2575.000
CSFVol  1148.000, OptChiasmVol    69.000
MaskVol 1699011.000
  771    381   1287  2.315 0.599     0.134     0.054       15     1.6  BA1_exvivo
 2004   1255   3290  2.466 0.434     0.098     0.019       16     1.5  BA2_exvivo
  914    613    785  1.838 0.361     0.134     0.025        8     0.9  BA3a_exvivo
 1415    951   1679  1.720 0.373     0.075     0.014        5     0.8  BA3b_exvivo
 1238    712   2394  2.796 0.454     0.112     0.031       13     1.5  BA4a_exvivo
  977    649   1403  2.327 0.454     0.088     0.018        3     0.7  BA4p_exvivo
 5637   3529  12484  3.041 0.549     0.115     0.029       61     6.0  BA6_exvivo
 1189    799   3119  3.007 0.634     0.118     0.025       14     1.1  BA44_exvivo
 1112    754   3000  3.008 0.476     0.122     0.030       15     1.4  BA45_exvivo
 4169   2686   4904  1.869 0.539     0.137     0.044       50     7.7  V1_exvivo
 4804   3001   6563  2.043 0.517     0.154     0.047       79     9.3  V2_exvivo
  408    248    975  3.037 0.547     0.120     0.028        4     0.4  MT_exvivo
  432    290   1218  3.324 0.712     0.124     0.031        5     0.6  perirhinal_exvivo
  317    236    844  3.389 0.756     0.101     0.018        2     0.2  entorhinal_exvivo

Started at Sat Oct 7 18:13:09 CEST 2017 
Ended   at Sun Oct 8 05:12:19 CEST 2017
#@#%# recon-all-run-time-hours 10.986
recon-all -s 0050006 finished without error at Sun Oct  8 05:12:19 CEST 2017